2025
T. Wertheimer, O. Noy Klein, D. Bielopolski, B. Rosen-Zvi and R.Shamir. “Using time-dependent matching to assess the effect of nephrological intervention on CKD progression”. Annual retreat of the Edmond J. Safra Center for Bioinformatics. Kiryat Yearim, May 26-27, 2025.
T. Margalit, H. Levi, R. Elkon and R. Shamir. “Robust performance of deep learning in identifying functional non-coding GWAS variants”. Annual retreat of the Edmond J. Safra Center for Bioinformatics. Kiryat Yearim, May 26-27, 2025.
O. Shapira and R. Shamir. “Algorithms for multi-omic integration”. Annual retreat of the Edmond J. Safra Center for Bioinformatics. Kiryat Yearim, May 26-27, 2025.
N. Teomim, C. Levy and R. Shamir. “Predicting response to immunotherapy: A retrospective, EMR-based, machine learning strategy”. Annual retreat of the Edmond J. Safra Center for Bioinformatics. Kiryat Yearim, May 26-27, 2025.
H. Levi, R.Elkon and R. Shamir. “Improving the accuracy of polygenic risk scores for Non-European populations using deep learning”. Annual retreat of the Edmond J. Safra Center for Bioinformatics. Kiryat Yearim, May 26-27, 2025.
T. Ben-Yishay, G. Leor, U. Ben-David and R. Shamir. “A novel HMM-based approach for detecting chromothripsis from copy number data”. Annual retreat of the Edmond J. Safra Center for Bioinformatics. Kiryat Yearim, May 26-27, 2025.
R. Shamir. "Computational vignettes in genomics and medicine''. Annual retreat of the Edmond J. Safra Center for Bioinformatics. Kiryat Yearim, May 27, 2025.
R. Shamir. "Algorithmic analysis in cancer and Parkinson’s disease''. Bar Ilan University, Department of Computer Science, May 22, 2025.
T. Wertheimer, O. Noy Klein, D. Bielopolski, B. Rosen-Zvi and R. Shamir. “Using time-dependent matching to assess the effect of nephrological intervention on CKD progression”. Poster presentation. 23rd Israeli Bioinformatics Symposium, Reichman University, Herzliya, Israel, April 23, 2025.
T. Margalit, H. Levi, R. Elkon and R. Shamir. “Robust performance of deep learning in identifying functional non-coding GWAS variants”. Poster presentation. 23rd Israeli Bioinformatics Symposium, Reichman University, Herzliya, Israel, April 23, 2025.
H. Levi, R. Elkon and R. Shamir. “Improving the accuracy of polygenic risk scores for Non-European populations using deep learning”. Poster presentation. 23rd Israeli Bioinformatics Symposium, Reichman University, Herzliya, Israel, April 23, 2025.
O. Peleg, M. Metzger, and E. Borenstein. “BLINCHESS: A novel league-based approach for studying differential abundance in microbiome data”. Poster presentation. 23rd Israeli Bioinformatics Symposium, Reichman University, Herzliya, Israel, April 23, 2025.
R. Shamir and A. Benesh. "Simplifying and improving the MDS-UPDRS scale for Parkinson's Disease progression''. Sourasky Medical Center, Department of Neurology, Tel Aviv, Israel, April 8, 2025.
R. Shamir. "Multi-omics and EMRs in cancer analysis''. Invited speaker. The Fourth Israeli Data Science and AI Initiative Conference (IDSAI). Maale Hachamisha, Israel, January 2025.
2024
G. Leor, T. Ben-Yishay, Y. Eliezer, M. Getz, E. Reuveni, L. Raz, R. Shamir and U. Ben-David. "Characterizing the Landscape of Chromothripsis in Human Cancer Cell Lines". Poster presentation. FASEB: Consequences of Aneuploidy. Melbourne, Florida. September 15-19, 2024.
R. Shamir. "Multi-omics and EMRs in disease analysis''. Invited speaker, Advances in Computational Biology, CRG, Barcelona. September 15-18, 2024.
R. Shamir. "Headways in disease research using omic and EMR data''. Invited speaker, Computational Genomics Summer Institute (CGSI) 2024, UCLA, Los Angeles, CA. July 30 2024.
R. Saad, U. Ben-David and R. Shamir. “Analysis of cancer-type specific aneuploidy patterns”. Poster presentation. Workshop on cancer genome structure and dynamics. Weizmann Institute of Science, Rehovot, Israel. July 18, 2024.
G. Leor, T. Ben-Yishay, Y. Eliezer, M. Getz, E. Reuveni, L. Raz, R. Shamir and U. Ben-David. "Characterizing the Landscape of Chromothripsis in Human Cancer Cell Lines". Poster presentation. Workshop on cancer genome structure and dynamics. Weizmann Institute of Science, Rehovot, Israel. July 18, 2024.
G. Leor, T. Ben-Yishay, Y. Eliezer, M. Getz, E. Reuveni, L. Raz, R. Shamir and U. Ben-David. "Characterizing the Landscape of Chromothripsis in Human Cancer Cell Lines". Short talk. Edmond J. Safra center retreat 2024. Hotel Ye'arim, Ma'ale Ha'chamisha, Israel. May 22-23, 2024.
T. Ben-Yishay, G. Leor, U. Ben-David and R. Shamir. “A novel HMM-based approach for detecting chromothripsis from copy number data”. Poster presentation. Edmond J. Safra center retreat 2024. Hotel Ye'arim, Ma'ale Ha'chamisha, Israel. May 22-23, 2024.
M. Metzger, O. Peleg, and E. Borenstein. “BLINCHESS - A novel league-based approach for studying differential abundance in microbiome data”. Poster presentation. Edmond J. Safra center retreat 2024. Hotel Ye'arim, Ma'ale Ha'chamisha, Israel. May 22-23, 2024.
R. Saad, U. Ben-David and R. Shamir. “Analysis of cancer-type specific aneuploidy patterns”. Poster presentation. Edmond J. Safra center retreat 2024. Hotel Ye'arim, Ma'ale Ha'chamisha, Israel. May 22-23, 2024.
T. Wertheimer, O. Noy, D. Beilopolsky, B. Rosen-Zvi and R. Shamir. “Using electronic health records to understand, predict, and manage kidney disease”. Poster presentation. Edmond J. Safra center retreat 2024. Hotel Ye'arim, Ma'ale Ha'chamisha, Israel. May 22-23, 2024.
H. Levi, R. Elkon and R. Shamir. “The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population”. Poster presentation. Edmond J. Safra center retreat 2024. Hotel Ye'arim, Ma'ale Ha'chamisha, Israel. May 22-23, 2024.
D. Coster, T. Margalit, B. Boursi and R. Shamir. “Fungi populations differ across races in many tumor types”. Poster presentation. Edmond J. Safra center retreat 2024. Hotel Ye'arim, Ma'ale Ha'chamisha, Israel. May 22-23, 2024.
O. Shapira and R. Shamir. “Algorithms for multi-omic integration”. Poster presentation. Edmond J. Safra center retreat 2024. Hotel Ye'arim, Ma'ale Ha'chamisha, Israel. May 22-23, 2024.
R. Shamir. "Early prediction of cancer risk via genetics and routine EHRs". Joint TAU-Clalit MOONSHOT-MED kickoff symposium, Tel Aviv University, May 9 2024.
H. Levi, R. Elkon and R. Shamir. “The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population”. Poster presentation. 22nd Israeli Bioinformatics Symposium, Ben-Gurion University of the Negev, Be'er Sheva, Israel, May 7, 2024.
G. Leor, T. Ben-Yishay, Y. Eliezer, M. Getz, E. Reuveni, L. Raz, R. Shamir and U. Ben-David. "Characterizing the Landscape of Chromothripsis in Human Cancer Cell Lines". Flash talk & poster presentation. 22nd Israeli Bioinformatics Symposium, Ben-Gurion University of the Negev, Be'er Sheva, Israel, May 7, 2024.
E. Rannon, E. Goldschmidt, D. Bernstein, A. Wasserman, D. Coster, R. Shamir . "Predicting appropriateness of antibiotic treatment in ICU patients with hospital-acquired infection". Poster presentation and Short-Talk, ESCMID, Barcelona, April 27-30, 2024.
2023
D. Coster, E. Fischer, S. Shenhar-Tsarfaty, T. Menes, S. Berliner, O. Rogowski, D. Zeltser, I. Shapira, E. Halperin, S. Rosset and M. Gorfine, R. Shamir. “Risk Modeling of Time-Varying Covariates Using an Ensemble of Survival Trees: Predicting Future Cancer Events". Oral Presentation, 2023 AAAI Fall Symposium on Survival Prediction Algorithms, Challenges & Applications, Arlington, Virginia, October 25-27 2023.
D. Coster, T. Margalit, B. Boursi, R. Shamir. "The human intratumor mycobiome is significantly influenced by an individual's race". Poster presentation, European Society for Medical Oncology (ESMO) Congress 2023, Madrid, 20-24 October 2023.
R. Shamir. "Algorithms for multiomic disease data''. Zoom talk, SorinFest: Phase Transitions in Computer Science and Computational Biology, Brown University, October 7, 2023.
R. Shamir. "Using modularity, multi-omics and networks to understand disease''. Invited speaker, QBI - University of California San Francisco, CA, Aug 23, 2023.
R. Shamir. "Methods for disease analysis using multiomic data''. Invited speaker, Computational Genomics Summer Institute (CGSI) 2023, UCLA, Los Angeles, CA July 31, 2023.
T. Aharon Hait, R. Elkon and R. Shamir. “Constructing genomic activation and repression maps at base resolution using deep learning”. Poster presentation. Edmond J. Safra center retreat 2023. Nof-Ginosar. Sea of Galilee. June 6-7, 2023.
T. Ben Yishay*, G. Leor*, Y. Eliezer, M. Getz, E. Reuveni, L. Raz, U. Ben-David and R. Shamir. “A novel tool for chromothripsis detection based on copy number data”. Poster presentation. Edmond J. Safra center retreat 2023. Nof-Ginosar. Sea of Galilee. June 6-7, 2023.
E. Shpigelman and R. Shamir. “A feature ranking algorithm for clustering medical data”. Poster presentation. Edmond J. Safra center retreat 2023. Nof-Ginosar. Sea of Galilee. June 6-7, 2023.
N. Rappoport*, N.Saar-Furer*, N. Zioni, N. Dusaj, D. A. Landau, R. Shamir, L. Shlush and A. Tanay. “Natural and age-related variation in circulating human hematopoietic stem cells”. Poster presentation. Edmond J. Safra center retreat 2023. Nof-Ginosar. Sea of Galilee. June 6-7, 2023.
O. Noy and R. Shamir. “Time-dependent iterative imputation for multivariate longitudinal clinical data”. Poster presentation. Edmond J. Safra center retreat 2023. Nof-Ginosar. Sea of Galilee. June 6-7, 2023.
H. Levi, S. Carmi, S. Rosset, R. Yerushalmi, A. Zick, T. Yablonski-Peretz, S. Ben-Sachar, N. Elefant, R. Shamir and R. Elkon. “Using polygenic prediction models for early breast cancer detection on diverse ethnic groups in Israel”. Poster presentation. Edmond J. Safra center retreat 2023. Nof-Ginosar. Sea of Galilee. June 6-7, 2023.
R. Saad, U. Ben-David and R. Shamir. “Analysis of cancer-type specific aneuploidy patterns”. Poster presentation. Edmond J. Safra center retreat 2023. Nof-Ginosar. Sea of Galilee. June 6-7, 2023.
D. Coster, D. Bernstein, A. Kodesh, S. Berliner, L. Sheena, I. Krause, B. Boursi, E. Maor, E. Lev, S. Segev, R. Shamir "Decline in platelet counts in apparently healthy individuals between 2006 and 2014". Oral presentation, 70th Annual Conference of the Israel Heart Society in association with the Israel Society of Cardiothoracic Surgery, Expo, Tel-Aviv, 5-6 June 2023.
R. Shamir. "Analysis of disease using multiomic data''. UCSF-TAU Symposium in Computational Biology and Drug Discovery, University of California, San Francisco (UCSF), May 16-17, 2023.
H. Levi, S. Carmi, S. Rosset, R. Yerushalmi, A. Zick, T. Yablonski-Peretz, S. Ben-Sachar, N. Elefant, R. Shamir and R. Elkon. “Using polygenic prediction models for early breast cancer detection on diverse ethnic groups in Israel”. Flash-talk, CBRC, Yesod Hama'ala, Israel, May 10-12, 2023.
R. Shamir. "Improving cancer analysis by integrating heterogeneous ‘omic’ data''. Colloquium, School of Computer Science, Tel Aviv University, May 7, 2023.
O. Noy, R. Shamir. "Time-Dependent Iterative Imputation for Multivariate Longitudinal Clinical Data''. International Conference on Learning Representation (ICLR) workshop on Time Series Representation Learning for Health. Kigali, Rwanda, May 1-5, 2023.
E. Shpigelman and R. Shamir. “A feature ranking algorithm for clustering medical data”. Poster presentation. 21st Israeli bioinformatics symposium. The Hebrew University of Jerusalem. Israel. April 27, 2023.
O. Noy and R. Shamir. “Time-dependent iterative imputation for multivariate longitudinal clinical data”. Poster presentation. 21st Israeli bioinformatics symposium. The Hebrew University of Jerusalem. Israel. April 27, 2023.
H. Levi, S. Carmi, S. Rosset, R. Yerushalmi, A. Zick, T. Yablonski-Peretz, S. Ben-Sachar, N. Elefant, R. Shamir and R. Elkon. “Using polygenic prediction models for early breast cancer detection on diverse ethnic groups in Israel”. Poster presentation. 21st Israeli bioinformatics symposium. The Hebrew University of Jerusalem. Israel. April 27, 2023.
R. Shamir. "Analysis of early embryonic lineages using single-cell HiC". Minerva-Gentner Symposium on Single Cell Analysis: from Development to Disease. Tel Aviv University, April 23-24, 2023.
R. Shamir. "Improving the handling of missing data in Multivariate Longitudinal Clinical Data''. Center for AI and Data Science Annual Conference, Tel Aviv University, March 20, 2023.
N. Saar-Furer*, N. Rappoport*, N. Zioni, N. Dusaj, D.A. Landau, R. Shamir, A. Tanay and L. Shlush. “Natural and age-related variation in circulating human hematopoietic stem cells”. Poster presentation & Lighting talk. Spring School on Algorithmic Cancer Biology, National Cancer Institute, NIH Bethesda, Maryland, March 13-19, 2023.
T. Ben-Yishay*, G. Leor*, Y. Eliezer, M. Getz, E. Reuveni, L. Raz, U. Ben-David and R. Shamir. “A novel tool for chromothripsis detection based on copy number data”. Poster presentation. Spring School on Algorithmic Cancer Biology, National Cancer Institute, NIH Bethesda, Maryland, March 13-19, 2023.
R. Shamir. "Integrated analysis of multi-omic data in cancer''. Invited speaker, Spring School on Algorithmic Cancer Biology, National Cancer Institute, NIH Bethesda, Maryland, March 13-19, 2023.
G. Leor*, T. Ben-Yishay*, Y. Eliezer, M. Getz, E. Reuveni, L. Raz, R. Shamir and U. Ben-David. "Characterizing the Landscape of Chromothripsis in Human Cancer Cell Lines". Poster presentation, ILANIT-FISEB, Eilat, Israel, February 20-23, 2023.
L. Pu, R. Shamir. "Classification of contigs in the assembly graph of metagenomic sequences using machine learning". Poster presentation, ILANIT-FISEB, Eilat, Israel, February 20-23, 2023.
T.A Hait, R. Elkon and R. Shamir. "Identification and annotation of functional silencers". Poster presentation, ILANIT-FISEB, Eilat, Israel, February 20-23, 2023.
O. Noy and R. Shamir. "Time-Dependent Iterative Imputation for Multivariate Longitudinal Clinical Data". Poster presentation, ILANIT-FISEB, Eilat, Israel, February 20-23, 2023.
H. Levi, N. Elefant, S. Rosset, R. Yerushalmi, S. Ben-Sachar, A. Zik, T. Yablonski-Peretz, S. Carmi, R. Shamir and R. Elkon. "European Polygenic Risk Scores identify Ashkenazi Jewish women with markedly elevated risk for Breast Cancer". Flash-talk, ILANIT-FISEB, Eilat, Israel, February 20-23, 2023.
D. Coster, O. Noy, M. Metzger, I. Atar, S. Shenhar-Tsarfaty, S. Berliner, G. Rahav, O. Rogowsky, A. Mayo, R. Shamir. "A large multicenter model for predicting deterioration of Covid-19 inpatients". Poster presentation, ILANIT-FISEB, Eilat, Israel, February 20-23, 2023.
Shpigelman* E, Hochstadt* A, Coster D, Merdler I, Ghantous E, Szekely Y, Lichter Y, Taieb P, Banai A, Sapir O, Granot Y, Lupu L, Borohovitz A, Sadon S, Banai S, Rubinshtein R, Topilsky Y, Shamir R. “Clustering of Clinical-Echocardiographic Phenotypes of COVID-19 Disease Using Machine-Learning Techniques”. Flash talk, ILANIT-FISEB, Eilat, Israel, February 20-23, 2023.
R. Shamir. "Multiomic analysis". Computational Modeing of Complex Systems,
Workshop in honor of Prof. Ron Pinter's retirement. The Technion, January 11, 2023.
2022
R. Shamir. "Computational analysis of large scale cancer multi-omic data''.
Computational Cancer Genomics Conference, The Technion, Haifa, December 14-15, 2022.
Shpigelman* E, Hochstadt* A, Coster D, Merdler I, Ghantous E, Szekely Y, Lichter Y, Taieb P, Banai A, Sapir O, Granot Y, Lupu L, Borohovitz A, Sadon S, Banai S, Rubinshtein R, Topilsky Y, Shamir R. “Clustering of Clinical-Echocardiographic Phenotypes of COVID-19 Disease Using Machine-Learning Techniques”, poster presentation, COVID and Beyond: Novel Approaches to Global Infectious Diseases, Marriott Brussels Grand Place, Bruxelles, Belgium, October 26-29, 2022.
L. Pu, R. Shamir. "3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs". Paper presentation, The 21st European Conference on Computational Biology (ECCB), Sitges, Barcelona, September 12-21, 2022.
R. Shamir. "Integration, modularity and network analysis for understanding disease''. MIT Bioinformatics Seminar Series, MIT, Boston MA. Online talk,
September 12, 2022.
N. Rappoport. "Multi-Omic cancer subtyping". Talk at the Youdim Family prize award ceremony, Rambam Health Care Campus, Haifa, July 26 2022.
L. Pu, R. Shamir. "3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs". Poster presentation, Computational Challenges in Very Large-Scale 'Omics, UC Berkeley, USA, July 18-21, 2022.
D. Coster, I. Krause, L. Sheena, S. Shenhar-Tsarfaty, S. Berliner, B. Boursi, E. Maor, R. Shamir. "Predicting personal risk of developing cancer based on data from routine check-ups from multi-center cohort". Poster presentation, Computational Challenges in Very Large-Scale 'Omics, UC Berkeley, USA, July 18-21, 2022.
Dutta*, D. Pellow*, R. Shamir. "Parameterized syncmer schemes improve long read mapping". Poster presentation, Computational Challenges in Very Large-Scale 'Omics, UC Berkeley, USA, July 18-21, 2022.
R. Shamir. "Integration, modularity and network analysis for understanding disease''. ISCB Accomplishments by a Senior Scientist Award Keynote talk,
ISMB 2022, Madison, Wisconsin, July 13, 2022.
O. Noy, R. Shamir. "Time-Dependent Iterative Imputation for Multivariate Longitudinal Clinical Data". Poster presentation, AI and Big Data in Medical and Public Health Sciences Conference, Ben Gurion University, Beer Sheva, 20 June 2022.
N. Rappoport*, N. Saar-Furer*, A. Tanay, L. Shlush, R. Shamir. "Hematopoietic stem cell gene expression in peripheral blood across individuals at single-cell resolution". Poster presentation, Gordon Research Conference for Systems Aging, Grand Summit Hotel at Sunday River, Maine, USA, 29 May - 3 June 2022.
H. Levi, R. Elkon, R. Shamir. "Genotype imputation strategy for improving disease risk prediction on diverse ethnic groups ". Poster presentation, The Israeli Society for Cancer Research Annual Meeting 2022 , Bar-Ilan University, Ramat Gan, 31 May 2022.
O. Noy, R. Shamir. "Time-Dependent Iterative Imputation for Multivariate Longitudinal Clinical Data". Poster presentation, The 25th Human Genome Meeting 2022, Dan Tel-Aviv Hotel, Tel-Aviv, 23-25 May 2022.
L. Pu, R. Shamir. "3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs". Poster presentation, The 25th Human Genome Meeting 2022, Dan Tel-Aviv Hotel, Tel-Aviv, 23-25 May 2022.
H. Levi, R. Elkon, R. Shamir. "Genotype imputation strategy for improving disease risk prediction on diverse ethnic groups". Poster presentation, The 25th Human Genome Meeting 2022, Dan Tel-Aviv Hotel, Tel-Aviv, 23-25 May 2022.
H. Amira-Haham, G. Shanel, T.-H. S. Hsieh, X. Darzacq, R. Shamir, R. Elkon. "Genomic analysis of the spatial organization of the genome and its effect on cell-type specific p53 transcriptional responses". Poster presentation, The 25th Human Genome Meeting 2022, Dan Tel-Aviv Hotel, Tel-Aviv, 23-25 May 2022.
E. Shpigelman, A. Hochstadt, D. Coster, I. Merdler, Y. Topilsky, R. Shamir. "Clustering of clinical-echocardiographic phenotypes of COVID-19 disease using machine-learning techniques". Poster presentation, The 25th Human Genome Meeting 2022, Dan Tel-Aviv Hotel, Tel-Aviv, 23-25 May 2022.
R. Shamir. "Employing multi-omics, biological networks and medical records to understand cancer''. Keynote talk, USC Computational Biology symposium, celebrating Prof. Michael S. Waterman's 80th birthday University of Southern California, Los Angeles, May 19-21, 2022.
H. Levi, R. Elkon, R. Shamir. "Reducing false GO term calls in network-based active module identification: methodology and a new algorithm ". Poster presentation, Faculty of Medicine Research Fair 2022, Tel-Aviv university, Tel-Aviv, 13 April 2022.
A. Hochstadt, E. Shpigelman, D. Coster, I. Merdler, Y. Topilsky, R. Shamir. "Clustering of Clinical-Echocardiographic Phenotypes of Covid-19 Disease Using Machine-Learning Techniques", ePoster presentation, American College of Cardiology Annual Scientific Session & Expo, Washington, DC, April 2-4, 2022.
R. Shamir. "Early prediction of deterioration in covid-19 inpatients''.
Invited speaker, Annual conference of Tel Aviv University Center for Combatting Pandemics, Tel Aviv University, March 30, 2022.
H. Levi, R. Elkon and R. Shamir. "Adapting Breast Cancer Polygenic Risk Scores to Diverse Ethnic Groups in Israel". Oral presentation, Israel Data Science Initiative 2022, Ein-Gedi hotel, Ein-Gedi, 3-6 January 2022.
O. Noy*, D. Coster*, M. Metzger, I. Attar, S. Shenhar-Tsafraty, S. Berliner, G. Rahav, O.Rogowski, R. Shamir. "A Model for Predicting Deterioration Of COVID-19 Inpatients". Oral presentation, Israel Data Science Initiative 2022, Ein-Gedi hotel, Ein-Gedi, 3-6 January 2022.
2021
N. Kadosh and R. Shamir. "Personalized phylogeny-guided detection of cancer driver genes". Poster presentation, Edmond J. Safra Center Retreat 2021, Maagan-Eden, Sea of Galilee, 24-25 November 2021.
Nili Saar-Furer*, Nimrod Rappoport*, Amos Tanay, Liran Shlush, Ron Shamir. "Hematopoietic stem cell gene expression in peripheral blood across individuals at single-cell resolution". Poster presentation, Edmond J. Safra Center Retreat 2021, Maagan-Eden, Sea of Galilee, 24-25 November 2021.
E. Shpigelman, A. Hochstadt, D. Coster, Y. Toplisky and R. Shamir. "Characterizing Covid-19 patients using heart echo measurements". Poster presentation, Edmond J. Safra Center Retreat 2021, Maagan-Eden, Sea of Galilee, 24-25 November 2021.
H. Levi, R. Elkon and R. Shamir. "Reducing false GO term calls in network-based active module identification: methodology and a new algorithm". Poster presentation, Edmond J. Safra Center Retreat 2021, Maagan-Eden, Sea of Galilee, 24-25 November 2021.
D. Coster, I. Krause, L. Sheena, S. Shenhar-Tsarfaty, S. Berliner, B. Boursi and R. Shamir. "Predicting personal risk of developing cancer based on routine check-up data: a multi-center study". Poster presentation, Edmond J. Safra Center Retreat 2021, Maagan-Eden, Sea of Galilee, 24-25 November 2021.
O. Noy, D. Coster, M. Metzger, I. Attar, S. Shenhar-Tsafraty, S. Berliner, G. Rahav, O. Rogowski and R. Shamir. "A Machine learning model for predicting deterioration of COVID-19 inpatients". Poster presentation, Edmond J. Safra Center Retreat 2021, Maagan-Eden, Sea of Galilee, 24-25 November 2021.
H. Amira-Haham, G. Shanel, T-H. S. Hsieh, X. Darzacq, R. Shamir and R. Elkon. "Spatial structure of the genome and its effect on cell type-specific response to stress using multiple omics data". Poster presentation, Edmond J. Safra Center Retreat 2021, Maagan-Eden, Sea of Galilee, 24-25 November 2021.
D. Flomin, D. Pellow and R. Shamir. "AdaOrder: Tailoring the order of a minimizer scheme to the dataset can improve binning applications". Poster presentation, Edmond J. Safra Center Retreat 2021, Maagan-Eden, Sea of Galilee, 24-25 November 2021.
R. Shamir. "Computational integration in cancer analysis: from multi-omic to personalized drivers''. India-Israel Digital Health Forum, November 10, 2021.
O. Noy*, D. Coster*, M. Metzger, I. Attar, S. Shenhar-Tsafraty, S. Berliner, G. Rahav, O.Rogowski, R. Shamir. "A machine learning model for predicting deterioration of COVID-19 inpatients''. Talk accepted to ISMB/ECCB 2021 COVID-19 Track, July 25-30, 2021.
N. Rappoport, R. Safra, R. Shamir. "MONET: Multi-omic patient module detection by omic selection". Talk accepted to Translational Medicine Track, ISMB/ECCB 2021, July 25-30, 2021.
H. Levi, R. Elkon, R. Shamir. "Reducing false GO term calls in network-based active module identification: methodology and a new algorithm". Talk accepted to Network Biology Track, ISMB/ECCB 2021, July 25-30, 2021.
D. Pellow, M. Probst, O. Furman, A. Zorea, Arik Segal, I. Mizrahi, R. Shamir. "SCAPP: An algorithm for improved plasmid assembly in metagenomes''. Talk
accepted to Microbiome Track, ISMB/ECCB 2021, July 25-30, 2021.
D. Coster, E. Fisher, S. Shenhar-Tsarfaty, T. Menes, S. Berliner, E. Halperin, S. Rosset, M. Gorfine, R. Shamir. "Early detection of breast and prostate cancer risk based on routine check-up data using machine learning and survival analysis". Poster presentation, Machine Learning in Computational and Systems Biology Track, ISMB/ECCB 2021, July 25-30, 2021.
R. Shamir. "Cancer risk prediction and subtyping using medical records and omic data''. Invited talk, Anthem Israel and Edmond J. Safra Center for Bioinformatics Digital Medicine Conference, 29 June 2021.
R. Shamir. "Utilizing multi-omics and medical records to understand cancer''. Invited speaker, Belgrade Bioinformatics Conference, online, 21-25 June 2021.
O. Noy*, D. Coster*, M. Metzger, I. Attar, S. Shenhar-Tsafraty, S. Berliner, G. Rahav, O.Rogowski, R. Shamir. "A machine learning model for predicting deterioration of COVID-19 inpatients". International Conference on Learning Representations (ICLR) 2021 Workshop: Machine Learning for Preventing and Combating Pandemics (online), May 8, 2021.
R. Shamir. "Methods for computational analysis of multiple 'omics' to understand cancer''. Guest lecture, Multi-omics and machine learning workshop, Haifa University, February 16, 2021.
2020
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R. Shamir. "Computational integration in cancer analysis: from multi-omic to personalized drivers". Invited talk, Cancer Data Science Laboratory Seminar, NIH, Online, December 7, 2020. N. Rappoport, R. Safra and R. Shamir. "Multi-omic module discovery in cancer by omic selection". Student talk, 4th virtual seminar of the Cancer Biology Research Center at Tel Aviv University (CBRC) on "AI and Big Data: now its cancers' turn", Online, December 2, 2020. R. Shamir. "Integrated computational analysis in cancer". Invited talk, 4th virtual seminar of the Cancer Biology Research Center at Tel Aviv University (CBRC) on "AI and Big Data: now its cancers' turn", Online, December 2, 2020. D. Coster, E. Fisher, S. Shenhar, S. Berliner, E. Halperin, S. Rosset, M. Gorfine and R. Shamir. "Early detection of cancer based on EMR data - a modern screening approach". Invited short talk, the 3rd virtual seminar of Cancer Biology Research Center (CBRC), TAU, November 18 2020. H. Levi, R. Elkon and R. Shamir. "DOMINO: a novel algorithm for network-based discovery of active modules with reduced rate of false calls". Talk in the Human Genetics Dept. Seminar, Medicine Faculty, Tel Aviv University, November 9, 2020. D. Coster, E. Fisher, S. Shenhar, S. Berliner, E. Halperin, S. Rosset, M. Gorfine and R. Shamir. "Early detection of cancer based on EMR data - a modern screening approach". A student talk, Edmond J. Safra Retreat, Online, October 14, 2020. N. Kadosh and R. Shamir. "Personalized cancer driver genes affected by large scale genomic alterations". Poster presentation, Edmond J. Safra Retreat, Online, October 14, 2020. D. Coster*, O. Noy*, S. Shenhar-Tsafraty, O. Rogowski and R. Shamir. "A predictive model for deterioration of Covid-19 patients". Poster presentation, Edmond J. Safra Retreat 2020, online, October 14, 2020 L. Pu and R. Shamir. "A 3-way classifier for metagenomic sequences". Poster presentation, Edmond J. Safra Retreat 2020, online, October 14, 2020. T. A. Hait, R. Elkon and R. Shamir. "Identification of silencers that repress gene expression". Poster presentation, Edmond J. Safra Retreat 2020, online, October 14, 2020. Y. Ben-Ari, L. Pu, Y. Orenstein and R. Shamir. "Improving the efficiency of de Bruijn graph construction using compact universal hitting sets". Poster presentation, Edmond J. Safra Retreat 2020, online, October 14, 2020. D. Pellow, A. Zorea, M. Probst, O. Furman, A. Segal, I. Mizrahi and R. Shamir. "SCAPP: An algorithm for improved plasmid assembly in metagenomes". Poster presentation, Edmond J. Safra Retreat 2020, online, October 14, 2020. H. Amira-Haham, G. Shanel, T.-H. S. Hsieh, X. Darzacq, R. Shamir and R. Elkon. "Spatial structure of the genome and its effect on cell type-specific response to stress using multiple omics data". Poster presentation, Edmond J. Safra Retreat 2020, online, October 14, 2020. N. Saar-Furer*, N. Rappoport*, A. Tanay, L. Shlush and R. Shamir. "Hematopoietic stem cell gene expression during aging at single-cell resolution". Poster presentation, Edmond J. Safra Retreat 2020, online, October 14, 2020. H. Levi, R. Elkon and R. Shamir. "DOMINO: a novel network based module detection algorithm with reduced rate of false calls". Poster presentation, Edmond J. Safra Retreat 2020, online, October 14, 2020. Y. Ben-Ari, L. Pu, Y. Orenstein, R. Shamir. "Improving the efficiency of de Bruijn graph construction using compact universal hitting sets". Poster presentation and flash talk, Hit-seq track, ISMB 2020 (online), July 2020. D. Pellow, M. Probst, O. Furman, A. Zorea, A. Segal, I. Mizrahi and R. Shamir. "SCAPP: An algorithm for improved plasmid assembly in metagenomes". Research talk, RECOMB-SEQ 2020 (online), June 27 2020. N. Rappoport, R. Safra, R. Shamir. "MONET: Multi-omic patient module detection by omic selection". Research talk, RECOMB-CCB 2020 (online), June 18-19 2020. R. Shamir,"Proliferation and differentiation in early embryonic lineages''. Minerva-Gentner symposium: Single Cell Analysis: From Development to Disease. Tel Aviv University, May 31-June 1 2020. R. Shamir, "Expression-based classification in Parkinson's disease". Bar Ilan University, April 27, 2020. N. Rappoport, E. Chomsky, T. Nagano, C. Seibert, Y. Lubling, A. Lifshitz, Z. Mukamel, R. Shamir, P. Fraser, A. Tanay, "Single cell Hi-C and dissection of replication landscapes and chromosomal organization in mouse embryonic lineages". Poster presentation. ILANIT-FISEB, Eilat, Israel, February 17-20, 2020. D. Pellow, I. Mizrahi, R. Shamir, "Improved complete plasmid reconstruction from metagenomic samples". Poster presentation. ILANIT-FISEB, Eilat, Israel, February 17-20, 2020. L. Pu, A. Mikheenko, Yu Lin, P. Pevzner, "Comparative analysis of segmental duplications in human and great ape genomes". Poster presentation. ILANIT-FISEB, Eilat, Israel, February 17-20, 2020. T.A. Hait, R. Elkon and R. Shamir "CT-FOCS: a novel method for genome-wide inference of cell type-specific enhancer-promoter maps". Poster presentation. ILANIT-FISEB, Eilat, Israel, February 17-20, 2020. T.A. Hait, R. Elkon and R. Shamir "CT-FOCS: a novel method for genome-wide inference of cell type-specific enhancer-promoter maps". Poster presentation, Gene Regulation: From Mechanisms to Disease, Keystone Resort, Keystone CO, USA, January 26-30, 2020. |
2019
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D. Netanely, N. Stern, R. Parikh, S. Leibo, S. Amar, R. Brenner, C. Levy, R. Shamir, "Improving the classification of cutaneous melanoma tumors using PROMO". Poster presentation, The 8th Graduate conference in Genetics, Genomics and Evolution, Tel Aviv university, Israel, Sep 24, 2019. R. Shamir , "Integrated computational analysis in cancer and precision medicine". Invited speaker, Inaugural Blavatnik US-Israel Scientific Forum, Israel Academy of Sciences and Humanities, Jerusalem, Israel, September 16-18, 2019. R. Shamir and G. Dinstag, "Personalized prioritization of cancer driver genes". A talk in the annual workshop of the Koret-Berkeley-TAU Initiative in Computational Biology and Bioinformatics, Tel Aviv University, July 28-29, 2019. D. Netanely, N. Stern, C. Levy, R. Shamir, "Improving the classification of cutaneous melanoma tumors using PROMO". Poster presentation, Cancer Genomics 2019, Cambridge, UK, June 23-26, 2019. R. Shamir. "On the power of integrated analysis in cancer and precision medicine''. Invited speaker, I-CORE symposium on Chromatin and RNA in gene regulation, Zichron Yaakov, Israel, June 10-12, 2019. T.A. Hait, R. Elkon and R. Shamir "CT-FOCS: a novel method for genome-wide inference of cell type-specific enhancer-promoter maps". Poster presentation, I-CORE Chromatin and RNA in Gene Regulation, Zichron Yaakov, June 10-12, 2019. T.A. Hait, R. Elkon and R. Shamir "CT-FOCS: a novel method for genome-wide inference of cell type-specific enhancer-promoter maps". Poster presentation, Edmond J. Safra Center Annual Retreat 2019, Maagan, May 26-27, 2019. N. Rappoport, E. Chomsky, T. Nagano, C. Seibert, Y. Lubling, A. Lifshitz, Z. Mukamel, R. Shamir, P. Fraser and A. Tanay. "Chromosomal organization in the mouse embryo at single cell resolution". Poster presentation, Edmond J. Safra Center Annual Retreat 2019, Maagan, May 26-27, 2019. D. Pellow, I. Mizrahi and R. Shamir "Improving assembly of plasmid sequences in metagenomic samples". Poster presentation, Edmond J. Safra Center Annual Retreat 2019, Maagan, May 26-27, 2019. D. Netanely, N. Stern, C. Levy and R. Shamir. "Improving the classification of cutaneous melanoma tumors using PROMO". Poster presentation, Edmond J. Safra Center Annual Retreat 2019, Maagan, May 26-27, 2019. L. Pu and R. Shamir. "Efficient algorithm to design small universal k-mer hitting sets". Poster presentation, Edmond J. Safra Center Annual Retreat 2019, Maagan, May 26-27, 2019. D. Coster, E. Fisher, S. Shenhar, S. Berliner, E. Halperin, S. Rosset and R. Shamir. "A model for early detection of cancer risk based on routine check-up data using random forest of survival analysis trees for left-truncated and right-censored data". Poster presentation, Edmond J. Safra Center Annual Retreat 2019, Maagan, May 26-27, 2019. Y. Ben-Ari and R. Shamir. "Memory efficient de Bruijn graph construction - DOCKS Implementation on MSP". Poster presentation, Edmond J. Safra Center Annual Retreat 2019, Maagan, May 26-27, 2019. H. Levi, R. Elkon and R. Shamir. "Network-based functional analysis: Bias correction and evaluation". Poster presentation, Edmond J. Safra Center Annual Retreat 2019, Maagan, May 26-27, 2019. N. Rappoport, R. Safra and R. Shamir. "Methods for multi-omic data visualization". Poster presentation, Edmond J. Safra Center Annual Retreat 2019, Maagan, May 26-27, 2019. T. A. Hait, D. Amar, R. Shamir and R. Elkon."FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map". Seminar talk, Ronna Hertzano Laboratory, Maryland University, Baltimore, Maryland, USA, 9 May 2019. T. A. Hait, D. Amar, R. Shamir and R. Elkon."FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map". Highlight talk, RECOMB 2019, Washington DC, USA, 5-8 May 2019. T. A. Hait, R. Elkon and R. Shamir: "CT-FOCS: a novel method for genome-wide inference of cell type-specific enhancer-promoter maps". Symposium talk. Epigenetics, genome regulation and the impact on medicine, The Tel-Aviv University, Tel-Aviv, Israel, April 10 2019. R. Shamir. "On the power of integrated analysis in cancer and precision medicine". Invited speaker, Advances in Precision Medicine: Big Data conference, Columbia University, April 8, 2019. R. Shamir. "Integrated analysis of cancer data: multi-omic clustering and personalized ranking of driver genes". UC Berkeley, February 14, 2019. R. Shamir. "Integrated analysis of cancer data and precision medicine". D. Pellow, I. Mizrahi, R. Shamir. "Improving assembly of plasmid sequences in metagenomic samples". Poster presentation, Frontiers in genetics symposium, Tel Aviv University, January 30, 2019. T.A. Hait , D. Amar, R. Shamir and R. Elkon. "Cell type specific enhancer-promoter network inference based on single omic data". Poster presentation, Frontiers in genetics symposium, Tel Aviv University, January 30, 2019. D. Netanely , N. Stern, I. Laufer and R. Shamir. "Integrative analysis of multi-omic cancer data using PROMO". Poster presentation, Frontiers in genetics symposium, Tel Aviv University, January 30, 2019. D. Coster, E. Fisher, S. Shenhar, S. Berliner, E. Halperin, S. Rosset, M. Gorfine, R. Shamir. "Early Detection of Cancer Risk Based on Routine Check-up Data". A short talk, Digital Health: From Science to Application, Keystone, January 24, 2019. D. Coster, E. Fisher, S. Shenhar, S. Berliner, E. Halperin, S. Rosset, M. Gorfine, R. Shamir. "Early Detection of Cancer Risk Based on Routine Check-up Data". Poster presentation, Digital Health: From Science to Application, Keystone, January 22, 2019. R. Shamir. "Integrated analysis of cancer data and precision medicine". R. Shamir. "Integrated analysis of cancer data and precision medicine''. Keynote speaker, APBC 2019, Wuhan, China, January 14-16, 2019. |
2018
R. Shamir. "Universal hitting sets and minimizers''. Bar Ilan University, November 8 2018.
D. Netanely, N. Stern, I. Laufer and R. Shamir. "PROMO: Integrative analysis of multi-omic cancer data". Poster presentation, EACR-AACR-ISCR Conference 2018, The Cutting Edge of Contemporary Cancer Research, 9-11 October 2018, ICC Jerusalem, Israel.
N. Rappoport and R. Shamir. "NEMO: Cancer Subtyping by Multi-Omics Integration". Poster presentation, EACR-AACR-ISCR Conference 2018, The Cutting Edge of Contemporary Cancer Research, 9-11 October 2018, ICC Jerusalem, Israel.
A. Avraham, N. Rappoport, S. Feldman, E. Nahmias, L. Heller, T. Karni, A. Sella, R. Shamir and E. Evron . "RNA-Seq Reveals Deregulation of G2/M and p53-p21-DREA- CDE/CHR Pathways in HMEC BRCA1+/- Upon DNA Damage". Poster presentation, EACR-AACR-ISCR Conference 2018, The Cutting Edge of Contemporary Cancer Research, 9-11 October 2018, ICC Jerusalem, Israel.
G. Dinstag and R. Shamir. "Personalized prioritization of cancer driver mutations". Poster presentation, EACR-AACR-ISCR Conference 2018, The Cutting Edge of Contemporary Cancer Research, 9-11 October 2018, ICC Jerusalem, Israel.
R. Shamir. Computational genomics for medicine: some examples. Kickoff meeting of the Koret - UC Berkeley - Tel Aviv University Initiative in Computational Biology and Bioinformatics, UC Bekreley, October 9 2018.
G. Dinsdag and R. Shamir. "Prodigy: personalized prioritization of cancer driver genes". Poster presentation, The 20th Israeli Bioinformatics Symposium (IBS 2018), Rappaport Faculty of Medicine, Technion, Haifa, Israel, October 7, 2018.
D. Coster E. Fisher, S. Rosset, S. Shenhar-Tsarfaty, S. Berliner, E. Halperin and R. Shamir. "Early detection of cancer risk based on routine check-up data". Poster presentation, The 20th Israeli Bioinformatics Symposium (IBS 2018), Rappaport Faculty of Medicine, Technion, Haifa, Israel, October 7, 2018.
D. Netanely , N. Stern, I. Laufer and R. Shamir. "Integrative analysis of multi-omic cancer data using PROMO". Poster presentation, The 20th Israeli Bioinformatics Symposium (IBS 2018), Rappaport Faculty of Medicine, Technion, Haifa, Israel, October 7, 2018.
D. Pellow , I. Mizrahi and R. Shamir. "Exploring sequence properties in plasmid assemblies". Poster presentation, The 20th Israeli Bioinformatics Symposium (IBS 2018), Rappaport Faculty of Medicine, Technion, Haifa, Israel, October 7, 2018.
N. Rappoport and R. Shamir. "NEMO: Cancer Subtyping by Multi-Omics Integration". Poster presentation, The 20th Israeli Bioinformatics Symposium (IBS 2018), Rappaport Faculty of Medicine, Technion, Haifa, Israel, October 7, 2018.
T. A. Hait, D. Amar, R. Shamir and R. Elkon "Cell type specific enhancer-promoter network inference based on single omic data". Poster presentation, The 20th Israeli Bioinformatics Symposium (IBS 2018), Rappaport Faculty of Medicine, Technion, Haifa, Israel, October 7, 2018.
T. A. Hait, D. Amar, R. Shamir and R. Elkon "Cell type specific enhancer-promoter network inference based on single omic data". Poster presentation, Genome Informatics, Wellcome Genome Campus, Hinxton, Cambridge, UK, September 17-20, 2018.
T. A. Hait, D. Amar, R. Shamir and R. Elkon "Cell type specific enhancer-promoter network inference based on single omic data". A talk in the 7th Graduate conference in Genetics, Genomics and Evolution, The Hebrew University of Jerusalem, Givat Ram, Jerusalem, September 4, 2018.
D. Netanely, N. Stern and R. Shamir. "Integrative analysis of multi-omic cancer data using PROMO". Poster presentation, The 3rd graduate student symposium on cancer, DJERASSI-ELIAS Institute of Oncology, Sackler faculty of Medicine, Tel Aviv University, July 3, 2018.
T. A. Hait, D. Amar, R. Shamir and R. Elkon "Experimental FOCS: a new method for enhancer-promoter mapping". Poster presentation, Edmond J. Safra Center Annual Retreat 2018, Maagan, May 27-28, 2018.
G. Dinstag and R. Shamir. "Personalized prioritization of cancer driver genes". Poster presentation, Edmond J. Safra Center Annual Retreat 2018, Maagan, May 27-28, 2018.
D. Netanely, Z. Yakhini and R. Shamir. "Multi-omic correlation graph for analyzing cancer genomic data". Poster presentation, Edmond J. Safra Center Annual Retreat 2018, Maagan, May 27-28, 2018.
R. Zeira and R. Shamir. "Sorting cancer genomes using DCJs, duplications and deletions". Poster presentation, Edmond J. Safra Center Annual Retreat 2018, Maagan, May 27-28, 2018.
D. Coster, S. Shenhar-Tsarfaty, S. Berliner and R. Shamir. "Distinguishing between acute bacterial and viral infections based on EMR data". Poster presentation, Edmond J. Safra Center Annual Retreat 2018, Maagan, May 27-28, 2018.
H. Levi, C. Levy and R. Shamir. "Using metabolic gene families for understanding melanoma". Poster presentation, Edmond J. Safra Center Annual Retreat 2018, Maagan, May 27-28, 2018.
D. Pellow, I. Mizrahi and R. Shamir. "Exploring sequence properties in plasmid assemblies". Poster presentation, Edmond J. Safra Center Annual Retreat 2018, Maagan, May 27-28, 2018.
N. Rappoport and R. Shamir. "MOCCASIN: Cancer subtyping by multi-omics integration". Poster presentation, Edmond J. Safra Center Annual Retreat 2018, Maagan, May 27-28, 2018.
D. Netanely, N. Stern, I. Laufer and R. Shamir. "PROMO: An interactive tool for integrative analysis of multi-omic cancer data". Poster presentation, Edmond J. Safra Center Annual Retreat 2018, Maagan, May 27-28, 2018.
R. Shamir. "Computational tools for analysis of big cancer data: the power of integration". Cancer Research Club seminar, Weizmann Institute of Science, May 17, 2018.
R. Shamir. "Disease bioinformatics: the good, the bad and the ugly". Keynote speaker, RECOMB 2018, Paris, France, April 21-24, 2018.
N. Rappoport, R. Shamir. "MOCCASIN: Cancer Subtyping by Multi-Omics Integration". Poster presentation. RECOMB-Computational Cancer Biology. Paris, France, April 19-20, 2018.
R. Zeira, R. Shamir. "Sorting cancer genomes using double-cut-and-joins, duplications and deletions". Oral presentation. RECOMB-Computational Cancer Biology. Paris, France, April 19-20, 2018.
R. Zeira, R. Shamir "Sorting cancer genomes using double-cut-and-joins, duplications and deletions". Poster presentation, The annual meeting of the Genetic Society of Israel, FRONTIERS IN GENETICS XI, Tel Aviv University, February 7, 2018.
T.A. Hait, D. Amar, R. Shamir, R. Elkon "FOCS: A new method for enhancer-promoter mapping" Poster presentation, The annual meeting of the Genetic Society of Israel, FRONTIERS IN GENETICS XI, Tel Aviv University, February 7, 2018.
D. Pellow, Y. Orenstein, G. Marçais, D. Bork, C. Kingsford, R. Shamir "Compact covering of sequences with universal hitting k-mer sets". Poster presentation, The annual meeting of the Genetic Society of Israel, FRONTIERS IN GENETICS XI, Tel Aviv University, February 7, 2018.
N. Rappoport, R. Shamir "MOCCASIN: Cancer Subtyping by Multi-Omics Integration". Poster presentation, The annual meeting of the Genetic Society of Israel, FRONTIERS IN GENETICS XI, Tel Aviv University, February 7, 2018.
D. Netanely, N. Stern, I. Laufer, R. Shamir "PROMO: An interactive tool for analyzing large high-throughput genomic datasets". Poster presentation, The annual meeting of the Genetic Society of Israel, FRONTIERS IN GENETICS XI, Tel Aviv University, February 7, 2018.
D. Coster, E. Fisher, S. Shenhar-Tsarfaty, S. Berliner, E. Halperin, S. Rosset, R. Shamir "Early detection of cancer risk based on routine check-up data". Poster presentation, The annual meeting of the Genetic Society of Israel, FRONTIERS IN GENETICS XI, Tel Aviv University, February 7, 2018.
G. Dinstag, D. Amar, R. Shamir "Multivariate analysis enables personalized prediction of adverse heart and kidney events". Poster presentation, The annual meeting of the Genetic Society of Israel, FRONTIERS IN GENETICS XI, Tel Aviv University, February 7, 2018.
R. Shamir, "A blood-based gene signature characterizing idiopathic Parkinson's disease". Invited speaker, Brainstorming Parkinson's Disease conference, Haifa, Israel, January 11-13, 2018.
2017
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D. Netanely, N. Stern, I. Laufer, R. Shamir "PROMO: An interactive tool for analyzing large high-throughput genomic datasets". Poster presentation, Biomedical Big Data Science: Vision, Promises and Challenges, Technion, Israel, December 13-14, 2017. D. Coster, Fisher, S. Shenhar-Tsarfaty, S. Berliner, E. Halperin, S. Rosset and R. Shamir. "A model for early detection of cancer risk based on routine check-up data". Poster presentation, Biomedical Big Data Science: Vision, Promises and Challenges, Technion, Israel, December 13-14, 2017. T. Hait, D. Amar, R. Elkon, R. Shamir. "Large-scale analysis of genome-wide enhancer and gene activity reveals a novel enhancer-promoter map". Oral presentation, Cold Spring Harlbor Laboratory meeting on Genome Informatics, Cold Spring Harbor, New York, November, 1-4 2017. R. Zeira and R. Shamir. "Sorting cancer genomes using double-cut-and-joins, duplications and deletions". Poster presentation, 15th RECOMB Comparative Genomics satellite workshop, Barcelona, Spain, October 4-6, 2017. R. Shamir. "Universal hitting sets and minimizers". Invited speaker, UCLA Computational Genomics Summer Institute, Los Angeles, California, July 11, 2017. |
| Dvir Netanely, Ayelet Avraham, Adit Ben-Baruch, Ella Evron, Ron Shamir. "Identification of breast cancer subtypes using multi-omic high-throughput genomic data". 2nd Graduate Student Symposium on Cancer, Djerassi-Elias Institute of Oncology, Sackler School of Medicine, Tel-Aviv University, July 9, 2017. |
| R. Shamir. "Bioinformatic tools for genomic analysis in human and plants". Volcani Institute, June 14, 2017. |
| D. Netanely, N. Stern, I. Laufer and R. Shamir. "PROMO: An interactive tool for analyzing large high-throughput genomic datasets". Poster presentation, Edmond J. Safra Center Annual Retreat 2017, Ginosar, May 22-23, 2017. |
| N. Rappoport, and R. Shamir. "Multi-Omics integration". Poster presentation, Edmond J. Safra Center Annual Retreat 2017, Ginosar, May 22-23, 2017. |
| A. Vizel, D. Amar and R. Shamir. "Disease biomarkers: discovery and analysis tools". Poster presentation, Edmond J. Safra Center Annual Retreat 2017, Ginosar, May 22-23, 2017. |
| E. Nurick, R. Elkon and R. Shamir. "3-D genomic interactions and their relation to gene expression". Poster presentation, Edmond J. Safra Center Annual Retreat 2017, Ginosar, May 22-23, 2017. |
| R. Zeira and R. Shamir. "Sorting cancer genomes using inversions, tandem duplications and deletions". Poster presentation, Edmond J. Safra Center Annual Retreat 2017, Ginosar, May 22-23, 2017. |
| D. Pellow, Y. Orenstein, G. Marçais, D. Bork, C. Kingsford and R. Shamir. "Compact covering of sequences with universal hitting k-mer sets". Poster presentation, Edmond J. Safra Center Annual Retreat 2017, Ginosar, May 22-23, 2017. |
| G. Dinstag, D. Amar and R. Shamir. "Multivariate analysis enables personalized prediction of adverse heart and kidney outcomes- lessons from the SPRINT challenge". Poster presentation, Edmond J. Safra Center Annual Retreat 2017, Ginosar, May 22-23, 2017. |
| R. Shamir. "Modularity, classification and networks in analysis of big biomedical data". Tsinghua University, Beijing, May 8, 2017. |
| D. Amar, S. Izraeli, R. Shamir. "Utilizing somatic mutation data from numerous studies for cancer research: proof of concept and applications".Highlight talk, RECOMB 2017, Hong Kong, May 3-7, 2017. |
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R. Shamir. "Modularity, classification and networks in analysis of big biomedical data". Faculty of Computer Science, Technion, April 4, 2017. R. Shamir. "Analysis of heterogeneous big data in cancer - challenges and opportunities". Hadassah Hospital, Hebrew University, Jerusalem, March 26, 2017. |
| R. Shamir. "Modularity, classification and networks in analysis of big biomedical data". Invited talk, University of Sydney, March 2, 2017. |
| D. Chen, Y. Orenstein, R. Golodnitsky, M. Pellach, D. Avrahami, C. Wachtel, A. Ovadia-Shochat, H. Shir-Shapira, A. Kedmi, T. Juven-Gershon, R. Shamir, D. Gerber. "SELMAP - SELEX Affinity Landscape Mapping of Transcription Factor Binding Sites Using Integrated Microfluidics". Ilanit/FISEB - Federation of all the Israel Societies for Experimental Biology, Eilat, Israel, February 20-23, 2017. |
| K. B. Avraham, K. Perl, K. Ushakov, Y. Pozniak, O. Yizhar-Barnea, Y. Bhonker, S. Shivatzki, T. Geiger, R. Shamir. "Transcriptomic and proteomic expression profiles of non-proliferating tissues reveal changes in protein levels are reduced relative to MRNA". Human Genome Meeting, From Genomics to therapy, Barcelo Sants hotel, Barcelona, Spain, February 5-7, 2017. |
2016
| R. Shamir. "Utilizing diverse omic data from many cancer studies: proof of concept and applications". TAU-University of Toronto joint workshop on Big-data and Health, Tel Aviv University, Tel Aviv, Israel, November 1-2, 2016. |
| R. Shamir. "Modularity and classification through the network lens". Invited speaker, QNetS Workshop: What’s new in networks? – Building bridges between computational, mathematical and statistical network analysis, Ludwig-Maximilian Universitaet Munich, October 5-7, 2016. |
| D. Amar. "Novel methods for integrative analysis of heterogeneous large scale biomedical data". Guest talk, Biocomp seminar, Ghent University,September 27, 2016. |
| R. Shamir. "Chips, pains and computers". Guest talk, Gentle Introduction to Programming, Tel Aviv University, September 11, 2016. |
| R. Zeira, M. El-Kebir, B.J. Raphael, R. Shamir, R. Sharan, S. Zaccaria, M. Zehavi. "Copy-Number Evolution Problems: Complexity and Algorithms".Oral presentation, The 16th Workshop on Algorithms in Bioinformatics, Aarhus, Denmark, August 22-24, 2016. |
| Y. Orenstein, Lin Yang, Arttu Jolma, Jussi Taipale, Remo Rohs, Ron Shamir. "DNA Shape Readout Specificities of Different TF Families". Oral presentation, RegGen ISMB SIG meeting, Orlando, Florida, USA, July 8-9, 2016. |
| Y. Orenstein, D. Pellow, G. Marcais, R. Shamir, C. Kingsford. "Compact universal k-mer hitting sets". Poster presentation, HiTseq16 conference, Orlando, Florida, July 8-9, 2016. |
| R. Zeira, M. Zehavi and and R. Shamir. "A Linear-Time Algorithm for the Copy Number Transformation Problem". Oral presentation, The 27th Annual Symposium on Combinatorial Pattern Matching, Tel Aviv, Israel, June 27-29, 2016. |
| D. Pellow and R. Shamir. "Clustering optical map intensity profiles for metagenomics applications". Poster presentation, The eleventh Retreat of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Maagan, See of Galilee, Israel, May 29-30, 2016. |
| T. A. Hait, R. Elkon and R. Shamir. "Enhancer RNAs as markers of active enhancers". Poster presentation, The eleventh Retreat of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Maagan, See of Galilee, Israel, May 29-30, 2016. |
| R. Rozov, A. Brown Kav, D. Bogumil, E. Halperin, I. Mizrahi and R. Shamir. "Recycler : an algorithm for detecting plasmids from de novo assembly graphs". Poster presentation, The eleventh Retreat of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Maagan, See of Galilee, Israel, May 29-30, 2016. |
| K. Perl, K. Ushakov, Y. Pozniak, O. Yizhar-Barnea, Y. Bhonker, S. Shivatzki, T. Geiger, K. B. Avraham and R. Shamir. "Changes in transcription levels across non-proliferating tissues are buffered on the protein level". Poster presentation, The eleventh Retreat of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Maagan, See of Galilee, Israel, May 29-30, 2016. |
| R. Zeira, M. Zehavi and R. Shamir. "On copy number transformation problems". Poster presentation, The eleventh Retreat of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Maagan, See of Galilee, Israel, May 29-30, 2016. |
| I. Nurick, M. Ozery-Flato, L. Ein-Dor and R. Shamir. "3-D chromosomal domains and their relation to genomic function". Poster presentation, The eleventh Retreat of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Maagan, See of Galilee, Israel, May 29-30, 2016. |
| D. Netanely, A. Avraham, A. Ben-Baruch, E. Evron and R. Shamir. "Identification of breast cancer subtypes using high-throughput genomic data".Poster presentation, The eleventh Retreat of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Maagan, See of Galilee, Israel, May 29-30, 2016. |
| D. Amar, S. Izraeli and R. Shamir. "Cancer subtype classification using somatic mutation data alone and its applications". Poster presentation, The eleventh Retreat of the Edmond J. Safra Center for Bioinformatics at Tel Aviv University, Maagan, See of Galilee, Israel, May 29-30, 2016. Dvir |
| D. Netanely , I. Laufer and R. Shamir "PROMO: A new tool for analyzing large high-throughput genomic datasets". Poster presentation, The 18th Israeli Symposium on Bioinformatics (IBS 2016), May 18, 2016, Haifa University, Israel, May 18, 2016. |
| R. Rozov , A. Brown Kav, D. Bogumil, E. Halperin, I. Mizrahi and R. Shamir "Recycler: an algorithm for detecting plasmids from de novo assembly graphs". Poster presentation, The 18th Israeli Symposium on Bioinformatics (IBS 2016), May 18, 2016, Haifa University, Israel, May 18, 2016. |
| A. Sloutskin , Y. M. Danino, Y. Zehavi, Y. Orenstein, T. Doniger, R. Shamir, T. Juven-Gershon. "ElemeNT: A computational tool for detecting core promoter elements". Poster presentation, The 18th Israeli Symposium on Bioinformatics (IBS 2016), May 18, 2016, Haifa University, Israel, May 18, 2016. |
| R. Shamir . "Network querying and copy number triplet problems - ILP to the rescue". Simons workshop on Iinteger Linear Programming in Computational Biology, Simons Institute for the Theory of Computing, Berkeley, CA, USA, May 9, 2016. |
| R. Shamir . "Supple algorithms for better dissection of cancer and brain data". Invited talk, Stanford University, USA, April 28, 2016. |
| D. Amar , S. Izraeli, R. Shamir. "Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets". Highlights presentation, RECOMB satellite conference on Computational Cancer Biology, Los Angeles, CA, USA, April 16, 2016. |
| R. Shamir , D. Amar, A. Maron-Katz, D. Yekutieli, T. Hendler. "Module discovery in 3-way data" Workshop on Biological Networks, Simons Institute for Theoretical Computer Science, UC Berkeley, Berkeley, CA, USA, April 11-15, 2016. |
| K. Perl , K. Ushakov, Y. Pozniak, O. Yizhar-Barnea, Y. Bhonker, S. Shivatzki, T. Geiger, Karen B. Avraham and R. Shamir. "Changes in transcription levels across non-proliferating tissues are buffered on the protein level". Workshop on Proteomics, Genomics and High Throughput Screening in Health and Disease, The Nancy & Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Israel, April 4, 2016. |
| R. Shamir, Y. Orenstein . "Utilizing de Bruijn Graphs in Universal Sequence Design for Discovery of Regulatory Elements". Workshop on Reguatory Genomics and Epigenomics, Simons Institute for Theoretical Computer Science, UC Berkeley, Berkeley, CA, USA, March 10, 2016. |
| M. Zehavi , R. Zeira, R. Shamir. "The Copy Number Transformation Problem". Workshop on Computational Cancer Biology, Simons Institute for Theoretical Computer Science, UC Berkeley, CA, USA, February 2, 2016. |
| R. Shamir , D. Amar. "Joint Analysis of Multiple Cancer Types for Revealing Disease-Specific Genomic Events". Workshop on Computational Cancer Biology, Simons Institute for Theoretical Computer Science, UC Berkeley, CA, USA, February 1, 2016. |
| I. Nurick , M. Ozery-Flato, L. Ein-Dor, R. Shamir. "3-D chromosomal domains and their relation to genomic function". Poster presentation, FRONTIERS IN GENETICS X, The Hebrew University of Jerusalem, Givat Ram, January 25, 2016. |
| D. Netanely , A. Avraham, A. Ben-Baruch, E. Evron, R. Shamir. "Unsupervised analysis of high-throughput genomic data for the identification of breast cancer subtypes". A seminar talk, Efi Arazi School of Computer Science, IDC, January 14, 2016. |
2015
| D. Amar, T. Hait, S. Izraeli and R. Shamir "Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets". Poster Presentation, CSBio, Bangkok, Thailand, November 22-25, 2015. |
| R. Shamir. "Some Current Computational Challenges in Bioinformatics" Invited speaker, KarpFest 80: A special conference celebrating Dick Karp's 80th birthday, Berkeley, CA, USA, October 17 2015. |
| D. Amar. "Extracting reliable information from Big Expression Data" A lecture, Conference on Computational Modeling of Gene Expression and its Evolution, Tel Aviv University, October 13-16 2015. |
| R. Shamir. "Using gene expression to understand and distinguish diseases" Invited talk, Conference on Computational Modeling of Gene Expression and its Evolution, Tel Aviv University, October 13-16 2015. |
| A. Sloutskin Y. M. Danino, Y. Zehavi, Y. Orenstein, T. Doniger, R. Shamir, T. Juven-Gershon. "ElemeNT: A computational tool for detecting core promoter elements" Poster presentation, 24th European Drosophila Research Conference, Heidelberg, Germany, September 9, 2015. |
| R. Shamir D. Amar, T. Hait, A. Maron-Katz, D. Yekutieli (Tel Aviv University), S. Izraeli (Sheba Hospital), and T. Hendler (Sourasky Medical Center)."Supple algorithms and data integration for understanding diseases" Keynote speaker, Genomic Medicine conference, Ho Chi Minh City, Vietnam, July 22, 2015. |
| R. Shamir. "Do networks help in making sense of the omics data deluge?" Invited talk, Network Biology SIG meeting, ISMB Dublin, Ireland, July 10-14, 2015. |
| R. Zeira, R. Shamir. "Sorting by cuts, joins and whole chromosome duplications" Oral presentation, The 26th Annual Symposium on Combinatorial Pattern Matching, Ischia Island, Italy, June 29- July 1, 2015. |
| Y. Orenstein, R. Shamir. "Computational inference of binding site models from high-throughput SELEX data" Oral presentation, BIRS meeting on Rules of Protein-DNA Recognition: Computational and Experimental Advances Oaxaca, Mexico, June 22-26, 2015. |
| R. Zeira, R. Shamir. "Sorting by cuts, joins and whole chromosome duplications" Oral presentation, the 15th Haifa Workshop on Interdisciplinary Applications of Graph Theory, Combinatorics, and Algorithms,Haifa, Israel, June 22-25, 2015. |
| O. Tzfadia, A. Maron-Katz, T. Hait, D. Amar, C. Linhart, R. Elkon, I. Ulitsky, A. Tanay, R. Sharan, Y. Shiloh, R. Shamir. "EXPANDER (EXpression Analyzer and DisplayER), a tool for the analysis of gene expression and NGS data". Invited talk, Workshop on "Machine Learning and Systems Biosciences", Jozef Stefan International postgraduate School, Ljubljana, Slovenia, June 22, 2015. |
| O. Tzfadia, D. Amar, L.M.T. Bradbury, E.T. Wurtzel, and R. Shamir. "MORPH, an algorithm for revealing missing genes in biological pathways" Invited talk, Workshop on "Machine Learning and Systems Biosciences", Jozef Stefan International postgraduate School, Ljubljana, Slovenia, June 22, 2015. |
| R. Shamir. "Supple algorithms and data integration for understanding diseases" A talk, meeting of ACGT, Ron Shamir's research group, The School of Computer Science, Tel Aviv University, June 17, 2015. |
| R. Rozov, Gil Goldshlager, Ron Shamir, Eran Halperin. "Bloom filter methods in compression and de novo assembly" A lecture, BCB 2015, Bertinoro Computational Biology, Bertinoro, Italy, June 14-18, 2015. |
| A. Domingo, A. Westenberger, D. Amar, L. Lee, R. Rosales, R. D. Jamora, E. dela Paz, K. Lohmann, R. Shamir, C. Klein. "Genome-wide expression profiling identifies potential molecular pathways involved in X-linked dystonia-parkinsonism (XDP, DYT3)" Late breaking abstract presentation, 19th International Parkinsons Disease and Movement Disorders Conference, San Diego, CA, USA, June 14-18, 2015. |
| R. Shamir. "Inference of binding site models from HT-Selex data" Invited talk, Workshop: "Beyond Position weight matrices - towards next generation tools for predicting protein-DNA interactions", Basel, Switzerland, June 8, 2015. |
| R. Shamir, D. Amar, T. Hait, A. Maron-Katz, D. Yekutieli, S. Izraeli, and T. Hendler. "Supple algorithms and data integration for understanding diseases" Keynote speaker, [BC]2 Computational Biology Conference, Basel, Switzerland, June 7-10, 2015. |
| R. Zeira and R. Shamir. "Models for sorting complex genomes with simple operations" Poster presentation, The 10th Annual Retreat of the Edmond J. Safra Center for Bioinformatics, Maagan, Sea of Galilee, Israel, May 31 - June 1, 2015. |
| T. Hait, D. Amar, S. Izraeli and R. Shamir. "Harnessing the power of myriad heterogeneous expression profiles to classify diseases and propose drug targets" Poster presentation, The 10th Annual Retreat of the Edmond J. Safra Center for Bioinformatics, Maagan, Sea of Galilee, Israel, May 31 - June 1, 2015. |
| D. Amar, D. Yekutieli, A. Maron-Katz, T. Hendler and R. Shamir. "A hierarchical Bayesian model for flexible module discovery in three-way time series data" Poster presentation, The 10th Annual Retreat of the Edmond J. Safra Center for Bioinformatics, Maagan, Sea of Galilee, Israel, May 31 - June 1, 2015. |
| D. Netanely, A. Avraham, E. Evron and R. Shamir. "Identification of breast cancer subtypes using high-throughput genomic data" Poster presentation, The 10th Annual Retreat of the Edmond J. Safra Center for Bioinformatics, Maagan, Sea of Galilee, Israel, May 31 - June 1, 2015. |
| M. Dan, Y. Orenstein and R. Shamir. "Discovery of RNA regulatory elements by multiple sequence and structure alignment" Poster presentation, The 10th Annual Retreat of the Edmond J. Safra Center for Bioinformatics, Maagan, Sea of Galilee, Israel, May 31 - June 1, 2015. |
| K. Perl, Y. Bhonker, O. Yizhar-Barnea, S. Shivatzki, K. Ushakov, Y. Pozniak, O. Yaron, N. Shomron, T. Geiger, K.B. Avraham and R. Shamir. "Gene expression shows higher diversity than protein expression in mammalian tissues: observations and hypotheses" Poster presentation, The 10th Annual Retreat of the Edmond J. Safra Center for Bioinformatics, Maagan, Sea of Galilee, Israel, May 31 - June 1, 2015. |
| R. Shamir. "Some Current Computational Challenges in Bioinformatics" Plenary talk, Annual meeting of the Israeli Mathematical Union, the Dead Sea, Israel, May 29, 2015. |
| D. Netanely A. Avraham, E. Evron and R. Shamir "Identification of breast cancer subtypes using high-throughput genomic data". Poster presentation, The 17th Israeli Bioinformatics Symposium - IBS 2015, Tel Aviv University, May 26, 2015. |
| T. Hait, D. Amar, S. Izraeli and R. Shamir "Harnessing the power of myriad heterogeneous expression profiles to classify diseases and propose drug targets" Poster presentation, The 17th Israeli Bioinformatics Symposium - IBS 2015, Tel Aviv University, May 26, 2015. |
| D. Amar, D. Yekutieli, A. Maron-Katz, T. Hendler and R. Shamir. "A hierarchical Bayesian model for flexible module discovery in three-way time series data" Poster presentation, The 17th Israeli Bioinformatics Symposium - IBS 2015, Tel Aviv University, May 26, 2015. |
| R. Shamir. "Understanding the signals of gene regulation" Bioinformatics undergraduate seminar, Tel Aviv University, May 12, 2015. |
| A. Maron-Katz, S. Vaisvaser, T. Lin, T. Hendler and R. Shamir. "Stress induced dynamics in resting state networks revealed by anatomic enrichment".Presentation, The Restless Brain - Practice and Perspectives of Resting State fMRI, The Sourasky medical center, Ichilov Hospital, Tel Aviv, March 31, 2015. |
| D. Netanely, A. Avraham, E. Evron, R. Shamir. "Identification of breast cancer subtypes using high-throughput genomic data". Poster presentation, Frontiers in Genetics IX, The Genetic Society of Israel, Weizmann Institute of Science, Rehovot, Israel, February 23, 2015. |
| R. Eitan, and R. Shamir. "Reconstructing cancer karyotypes". Poster presentation, Frontiers in Genetics IX, The Genetic Society of Israel, Weizmann Institute of Science, Rehovot, Israel, February 23, 2015. |
| D. Amar, T. Hait, S. Izraeli, and R. Shamir. "Integrated analysis of expression data across many diseases produces specific, robust biomarkers and suggests treatments". Poster presentation, Frontiers in Genetics IX, The Genetic Society of Israel, Weizmann Institute of Science, Rehovot, Israel,February 23, 2015. |
| R. Rozov, R. Shamir, E. Halperin. "Fast lossless compression via cascading Bloom Filters". Poster presentation, Frontiers in Genetics IX, The Genetic Society of Israel, Weizmann Institute of Science, Rehovot, Israel, February 23, 2015. |
| A. Maron-Katz, T. Hait, R. Elkon, D. Netanely, R. Sharan, I. Ulitsky, C. Linhart, D. Sagir, H. Safer, D. Amar, Y. Shiloh, R. Shamir. "EXPANDER: A platform for dissecting networks and functions using RNA-Seq and microarray expression profiles". Poster presentation, Frontiers in Genetics IX, The Genetic Society of Israel, Weizmann Institute of Science, Rehovot, Israel, February 23, 2015. |
| A. Maron-Katz, D. Amar, T. Hendler and R. Shamir. "RichMind: a tool for statistically rigorous interpretation of large-scale neuroimaging results".Poster presentation, 2nd International Israel Brain Technology Conference (IBT), Hangar 11, Tel-Aviv, Israel, March 11-12, 2015. |
| D. Netanely, A. Avraham, E. Evron and R. Shamir. "Identification of breast cancer subtypes using high-throughput genomic data". Poster presentation, 7th German-Israeli Cancer Research School, Grainau, Germany, February 8-12, 2015. |
| D. Amar, T. Hait, S. Izraeli, and R. Shamir. "Harnessing the power of large-scale heterogeneous expression profile collections to diagnose disease and propose treatment". Poster presentation, The first TAU-AGAUR Biomed Symposium on Gene Regulation, Genomics and Stem Cells in Disease, Tel Aviv University, January 18, 2015. |
| R. Rozov, R. Shamir, E. Halperin. "Fast lossless compression via cascading Bloom Filters". Poster presentation, The first TAU-AGAUR Biomed Symposium on Gene Regulation, Genomics and Stem Cells in Disease, Tel Aviv University, January 18, 2015. |
| R. Shamir, T. Hait, S. Izraeli, D. Amar. "Improved disease classification using Big Expression Data". Invited talk, The first TAU-AGAUR Biomed Symposium on Gene Regulation, Genomics and Stem Cells in Disease, Tel Aviv University, January 18, 2015. |
| R. Shamir, Y. Orenstein. "Shortest double-stranded DNA sequences covering all k-mers". Invited talk, Stringology 2015, the Dead Sea, Israel,January 4, 2015. |
2014
| R. Shamir, Y. Orenstein, C. Linhart, E. Mick. "Understanding gene regulation using high throughput in vitro methods". Invited talk, Department of Molecular and Computational Biology, University of Southern California, November 10, 2014. |
| R. Shamir, T. Hait, D. Amar. "Pathway-based biomarkers specifically and robustly classify diverse multiple diseases". Oral presentation, 2014 RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges and Cytoscape Workshops, San Diego, California,November 9-14, 2014. |
| R. Shamir. "Computations can help in understanding cancer: some examples". Advancing Cell Biology and Cancer Research, a conference honoring Prof. Yoel Kloog, Tel Aviv University, October 7, 2014. |
| R. Shamir. "Understanding gene regulation using high throughput in vitro methods". I-CORE Meeting: Cancer, Tel Aviv University, October 6, 2014. |
| Y. Orenstein , R. Shamir. "The use of HT-SELEX to infer TF binding models: comparison to PBM and an improved algorithm". Oral presentation, RegGen SIG meeting, ISMB 2014, Boston, July 12, 2014. |
| D. Amar , T. Hait and R. Shamir. "Pathways as robust biomarkers for cancer classification: the power of big expression data". Oral presentation, Network Biology SIG meeting, Boston, MA, July 11, 2014. |
| D. Netanely, and R. Shamir. "Identification of breast cancer subtypes using RNA-Seq data". Poster presentation, The 16th Israeli Bioinformatics Symposium, IBS 14, Bar Ilan University, June 24, 2014. |
| R. Eitan, and R. Shamir. "Reconstructing cancer karyotypes". Poster presentation, The 16th Israeli Bioinformatics Symposium, IBS 14, Bar Ilan University, June 24, 2014. |
| Y. Orenstein, and R. Shamir. "Inferring binding site motifs from HT-SELEX data". Poster presentation, The 16th Israeli Bioinformatics Symposium, IBS 14, Bar Ilan University, June 24, 2014. |
| K. Perl , Y. Bhonker, O. Yizhar-Barnea, S. Shivatzki, K. Ushakov, Y. Pozniak, O. Yaron, N. Shomron, T. Geiger, K. B. Avraham and R. Shamir."Understanding the connection between transcriptome and proteome in non-proliferating tissues through the example of the auditory system". Poster presentation, The 16th Israeli Bioinformatics Symposium, IBS 14, Bar Ilan University, June 24, 2014. |
| D. Amar , T. Hait and R. Shamir. "Pathways as robust biomarkers for cancer classification: the power of big expression data". Poster presentation, The 16th Israeli Bioinformatics Symposium, IBS 14, Bar Ilan University, June 24, 2014. |
| T. Hait , A. Maron-Katz, R. Elkon, I. Ulitsky, C. Linhart , D. Amar, A. Tanay, R. Sharan, E. David, D. Sagir, H. Safer, Y. Shiloh and R. Shamir."EXPANDER: A platform for dissecting networks and functions using NGS and microarray expression profiles". Poster presentation, The 16th Israeli Bioinformatics Symposium, IBS 14, Bar Ilan University, June 24, 2014. |
| R. Shamir . "Bioinformatic Methods of Functional Analysis". Invited talk, XDP Workshop, Luebeck, Germany, June 13-15, 2014. |
| D. Amar . "Computational Analysis of Genomewide Expression Data in XDP". Invited talk, XDP Workshop, Luebeck, Germany, June 13-15, 2014. |
| A. Maron-Katz , S. Vaisvaser, T. Lin, R. Shamir and T. Hendler. "Depicting network dynamic patterns related to prior affective state using a data driven approach". Poster presentation, 20th Annual Meeting of the Organization for Human Brain Mapping (OHBM) 2014, Hamburg, June 8-12, 2014. |
| Y. Orenstein, R. Shamir. "Inferring binding site motifs from HT-SELEX data". Poster presentation, The ninth retreat of the Edmond J. Safra Center for bioinformatics at Tel Aviv University, Ohalo-Kinneret, May 26-27, 2014. |
| D. Netanely, R. Shamir. "Identification of breast cancer subtypes using RNA-Seq data". Poster presentation, The ninth retreat of the Edmond J. Safra Center for bioinformatics at Tel Aviv University, Ohalo-Kinneret, May 26-27, 2014. |
| R. Eitan, R. Shamir. "Reconstructing Cancer Karyotypes". Poster presentation, The ninth retreat of the Edmond J. Safra Center for bioinformatics at Tel Aviv University, Ohalo-Kinneret, May 26-27, 2014. |
| R. Herzig, O. Zuqert, Y. Orenstein, R. Shamir, Y. Ebenstein. "Beyond sequencing: optical mapping of DNA". Poster presentation, The ninth retreat of the Edmond J. Safra Center for bioinformatics at Tel Aviv University, Ohalo-Kinneret, May 26-27, 2014. |
| D. Amar, T. Hait and R. Shamir. "Pathway as robust biomarkers for cancer classification: the power of big expression data". Poster presentation, The ninth retreat of the Edmond J. Safra Center for bioinformatics at Tel Aviv University, Ohalo-Kinneret, May 26-27, 2014. |
| K. Perl, Y. Bhonker, O. Yizhar-Barnea, S. Shivatzki, K. Ushakov, Y. Pozniak, O. Yaron, N. Shomron, T. Geiger, K. B. Avraham and R. Shamir."Understanding the connection between transcriptome and proteome in non-proliferating tissues through the example of the auditory system". Poster presentation, The ninth retreat of the Edmond J. Safra Center for bioinformatics at Tel Aviv University, Ohalo-Kinneret, May 26-27, 2014. |
| R. Rozov, R. Shamir, E. Halperin. "Fast lossless compression via cascading Bloom Filters". Poster presentation, The ninth retreat of the Edmond J. Safra Center for bioinformatics at Tel Aviv University, Ohalo-Kinneret, May 26-27, 2014. |
| Y. Orenstein, R. Shamir. "Inferring binding site motifs from high-throughput in vitro data". Oral presentation, The ninth retreat of the Edmond J. Safra Center for bioinformatics at Tel Aviv University, Ohalo-Kinneret, May 26-27, 2014. |
| T. Hait, D. Amar and R. Shamir. "Pathway as robust biomarkers for cancer classification: the power of big expression data". Poster presentation, Sixth Annual meeting of the Israeli Society for Cancer Research, ISCR 14, Faculty of Medicine, Technion, May 22, 2014. |
| R. Shamir, D. Amar. "Joint analysis of two biological networks using module maps". Computer Science Colloquium, The Technion, April 29, 2014. |
| R. Rozov, R. Shamir, E. Halperin. "Fast Lossless Compression via Cascading Bloom Filters". Poster presentation, RECOMB 2014 confenrece, Pittsburgh, PA, April 2-5 , 2014. |
| A. Maron-Katz. "Basic tools for computational genomics". A tutorial, TAU bioinformatics workshops series 2013-2014, Sherman building, room 09,March 18, 2014. |
| R. Shamir. "Joint analysis of two different networks using module maps". IBM meets Sagol School of Neuroscience – The 2nd Joint Cognitive Computing Symposium, Tel Aviv University, Sackler Faculty of Medicine, Room 201, March 6, 2014. |
| D. Netanely, R. Shamir. "Identification of breast cancer sub-types using rna-seq data". Poster Presentation, the 7th Congress of the Federation of the Israel Societies for Experimental Biology, Eilat, February 10-13, 2014. |
| R.E. Bell , M. Khaled, D. Netanely, S. Schubert, T. Golan, A. Buxbaum, M.M. Janas Maja, B.Postolsky, R. Shamir, C. Levy. "Transcription Factor/microRNA Axis Blocks Melanoma Invasion Program by miR-211 Targeting NUAK1". Poster Presentation, the 7th Congress of the Federation of the Israel Societies for Experimental Biology, Eilat, February 10-13, 2014. |
| D. Amar, C. Klein, D. Krainc, B. Peterlin, A. Brice, O. Reiss and R. Shamir. "The GenePark project: predicting Parkinson's disease using blood expression profiles". Poster Presentation, the 7th Congress of the Federation of the Israel Societies for Experimental Biology, Eilat, February 10-13, 2014. |
| K. Perl, Y. Bhonker, O. Yizhar-Barnea, S. Shivatzki, K. Ushakov, Y. Pozniak, O. Yaron, R. Shamir, N. Shomron, T. Geiger and K.B. Avraham ."Understanding the developmental and physiological conditions of the inner ear using transcriptome and proteome analysis". Poster Presentation, the 7th Congress of the Federation of the Israel Societies for Experimental Biology, Eilat, February 10-13, 2014. |
| R. Shamir. "Chromosome organization and gene function in normal and tumor cells". Oral Presentation, the 7th Congress of the Federation of the Israel Societies for Experimental Biology, Eilat, February 10-13, 2014. |
| R. Rozov, R. Shamir, E. Halperin. "Fast lossless compression via cascading bloom filters". Oral Presentation, IBM, Ramat Ha'hayal, Tel-Aviv, January 15, 2014. |
2013
| R. Shamir, L. Ein-Dor, M. Ozery-Flato, A. Thevenin. "Chromosome organization and gene function in normal and tumor cells". Seminar of the Faculty of Life Sciences, Bar Ilan University, December 18, 2013. |
| A. Maron-Katz, S. Vaisvaser, T. Lin, Y. Bar-Haim, R. Shamir and T. Hendler. "A data-driven approach for characterizing human brain networks that are involved in response to stress". Oral Presentation, The 22nd Israel Society for Neuroscience (ISFN) Annual Meeting, Eilat, December 15-17, 2013. |
| Y. Orenstein, R. Shamir. "Design of shortest double-stranded DNA sequence covering all k-mers". Invited talk, A special workshop: Bioinformatics, Optimization and Graphs, Celebrating Ron Shamir's 60th Birthday, Beit Hatfutsot, Tel-Aviv University, December 12, 2013. |
| Y. Orenstein, R. Shamir. "A comparative analysis of TF binding models learned from PBM, HT-SELEX and ChIP data". Poster presentation, RECOMB/ISCB Conference on Regulatory and System Genomics, Toronto, November 8-12, 2013. |
| A. Thevenin, L. Ein-Dor, M. Ozery-Flato, and R. Shamir. "Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome". Poster presentation, Recomb-CG, Lyon, France, October 17-19, 2013. |
| Y. Orenstein, R. Shamir. "Inferring binding sits motifs from high-throughput in vitro data". Poster presentation, EMS Autumn School on Computational Aspects of Gene Regulation, Bedlewo, Poland, October 13-19, 2013. |
| R. Shamir. "chromosome organization and gene function in normal and tumor cells". Invited talk, Computational Cancer Genomics meeting, Bertinoro, Italy, September 8-13, 2013. |
| A. Thevenin, L. Ein-Dor, M. Ozery-Flato, R. Shamir. "Organization of functional gene groups". Poster presentation, Workshop on Algorithms in Bioinformatics (WABI), Sophia Antipolis, France, September 2-4, 2013. |
| A. Thevenin, L. Ein-Dor, M. Ozery-Flato, R. Shamir. "Organization of functional gene groups". Poster presentation, Conference on Models and Algorithms for Genome Evolution, Montreal, Canada, August 23-26, 2013. |
| R. Shamir. "David Sankoff and other rearrangements". Invited talk, Conference on Models and Algorithms for Genome Evolution, Montreal, Canada,August 23-26, 2013. |
| R. Shamir. "Revealing Structure in Disease Regulation and Networks". Short course, International Summer School on Trends in Computing (SSTC 2013), Tarragona, Spain, July 22-26, 2013. |
| D. Amar, R. Shamir. "Algorithms for mapping modules in pairs of biological networks". Oral presentation, Network Biology SIG meeting, Berlin, Germany, July 19, 2013. |
| R. Shamir. "The little Dutch boy and the Genomics tsunami". Invited talk, The 15th Israeli Bioinformatics Symposium, Ben-Gurion University of the Negev, June 27, 2013. |
| R. Rozov, E. Halperin, R. Shamir. "Graph based reference-free encoding and compression of sequencing reads". Poster presentation, The 15th Israeli Bioinformatics Symposium, Ben-Gurion University of the Negev, June 27, 2013. |
| D. Netanely, R. Shamir. "Identification of Breast Cancer Subtypes Based on RNA-Seq Data". Poster presentation, The 15th Israeli Bioinformatics Symposium, Ben-Gurion University of the Negev, June 27, 2013. |
| D. Amar, R. Shamir. "Algorithms for mapping modules in pairs of biological networks". Poster presentation, The 15th Israeli Bioinformatics Symposium, Ben-Gurion University of the Negev, June 27, 2013. |
| Y. Orenstein, R. Shamir. "Inferring binding site motifs from high-throughput in vitro data". Poster presentation, The 15th Israeli Bioinformatics Symposium, Ben-Gurion University of the Negev, June 27, 2013. |
| A. Maron-Katz, R. Elkon, I. Ulitsky, C. Linhart , D. Amar, A. Tanay, R. Sharan, E. David, T. Hait, D. Sagir, H. Safer, Y. Shiloh, R. Shamir. "EXPANDER: A platform for dissecting networks and functions using expression profiles". Poster presentation, The 15th Israeli Bioinformatics Symposium, Ben-Gurion University of the Negev, June 27, 2013. |
| D. Amar, and R. Shamir. "Algorithms for mapping modules in pairs of biological networks". Poster presentation, First Annual Broad-Israel Cell Circuits Symposium, Jerusalem, Israel, June 10 - 12, 2013. |
| Y. Orenstein, E. Mick, C. Linhart and R. Shamir. "Inferring binding site motifs from high-throughput technologies". Poster presentation, DNA @ 60: The 60th Anniversary of the Discovery of the DNA Double Helix, The Technion, Haifa, May 26 - 29, 2013. |
| D. Amar, R. Shamir. "Discovery of structure in pairs of biological networks: application to disease dysregulation and genetic interactions". Poster presentation, DNA @ 60: The 60th Anniversary of the Discovery of the DNA Double Helix,The Technion, Haifa, May 26 - 29, 2013. |
| A. Maron-Katz, Y. Orenstein, D. Sagir. "Expander and Related Tools". Hands-on workshop, Tel Aviv University, May 19, 2013. |
| Y. Orenstein, R. Shamir "Design of Shortest Double-Stranded DNA Sequence Covering All K-mers". 13th Haifa Workshop on Interdisciplinary Applications of Graph Theory, Combinatorics and Algorithms Haifa University, May 16-17 2013. |
| R. Zeira, R. Shamir "Finding Maximum Cohesion Subgraphs". 13th Haifa Workshop on Interdisciplinary Applications of Graph Theory, Combinatorics and Algorithms Haifa University, May 16-17 2013. |
| R. Rozov, Eran Halperin, Ron Shamir. "Graph based reference-free encoding and compression of sequencing reads". Poster presentation, The Eighth Retreat of the Edmond J. Safra Center for Bioinformatics, Kfar Giladi, May 1 - 2, 2013. |
| T. Hait, Adi Maron-Katz, Ran Elkon, Igor Ulitsky, Chaim Linhart , David Amar, Amos Tanay, Roded Sharan, Eyal David, Dorit Sagir, Hershel Safer, Yosef Shiloh, Ron Shamir. "EXPANDER: A platform for dissecting networks and functions using expression profiles". Poster presentation, The Eighth Retreat of the Edmond J. Safra Center for Bioinformatics, Kfar Giladi, May 1 - 2, 2013. |
| D. Amar, Adi Maron-Katz, Sharon Visvaser, Talma Hendler, Ron Shamir. "A machine learning approach for characterizing human brain networks that are involved in response to stress". Poster presentation, The Eighth Retreat of the Edmond J. Safra Center for Bioinformatics, Kfar Giladi, May 1 - 2, 2013. |
| D. Amar, Ron Shamir. "Algorithms for mapping modules in pairs of biological networks". Poster presentation, The Eighth Retreat of the Edmond J. Safra Center for Bioinformatics, Kfar Giladi, May 1 - 2, 2013. |
| Y. Orenstein, Eran Mick, Chaim Linhart, Ron Shamir. "Inferring binding site motifs from high-throughput technologies". Poster presentation, The Eighth Retreat of the Edmond J. Safra Center for Bioinformatics, Kfar Giladi, May 1 - 2, 2013. |
| R. Shamir. "On the relation of gene function and organization in normal and cancer cells". National University of Singapore, April 12, 2013. |
| L. Ein-Dor, M. Ozery-Flato, A. Thevenin, R. Shamir. "On the association of chromosomal aneuploidy in cancer and the functional linkage between chromosomes". Poster presentation, Genome Stability Meeting, Hadassah Medical Center, Jerusalem, March 21, 2013. |
| A. Maron-Katz, D. Amar, S. Visvaser, T. Hendler, R. Shamir. "A machine learning approach for characterizing human brain networks that are involved in response to stress". Emotional, All Too Emotional. Conference on Neuroscience Views of Affect and Regulation. Tel Aviv University, March 19-21, 2013. |
| D. Amar, H. Safer, R. Shamir. "Algorithms for bi-module discovery in pairs of biological networks - Application to disease-specific differential co-expression analysis". Poster presentation,Cold Spring Harbor meeting on Systems Biology - Networks. Cold Spring Harbor Laboratory, NY, USA,March 13-16, 2013. |
| R. Shamir. "Cancer, chromosomes and computing". Weekly seminar, Dept. of Cell Research and Immunology, Faculty of Life Sciences, Tel Aviv University, March 5, 2013. |
| Y. Orenstein, C. Linhart, Y. Halperin, I. Ulitsky, R. Shamir. "Accurate and user-friendly tools for discovering transcription factor and microRNA binding sites". Poster Presentation, The Annual Meeting of the Genetic Society of Israel, FRONTIERS IN GENETICS VIII, The Technion, Haifa, January 28, 2013. |
| A. Maron-Katz, R. Elkon, I. Ulitsky, C. Linhart , D. Amar, A. Tanay, R. Sharan, E. David, T. Hait,D. Sagir, H. Safer, Y. Shiloh, R. Shamir. "EXPANDER: A platform for dissecting networks and functions using expression profiles". Poster Presentation, The Annual Meeting of the Genetic Society of Israel, FRONTIERS IN GENETICS VIII, The Technion, Haifa, January 28, 2013. |
| D. Amar, H. Safer, C. Klein, D. Krainc, B. Peterlin, A. Brice, O. Reiss, R. Shamir. "The GENEPARK project: predicting Parkinson's disease using blood expression profiles". Poster Presentation, The Annual Meeting of the Genetic Society of Israel, FRONTIERS IN GENETICS VIII, The Technion, Haifa,January 28, 2013. |
2012
| R. Shamir. "Cancer, chromosomes and computing". Department of Genetics, Hebrew University, December 12, 2012. |
| D. Amar, O. Lavi, G. Dror, R. Shamir. "Improving cancer classification and interpretation using advanced gene expression analysis". Poster presentation, International Society of Oncology and Biomarker (ISOBM) 2012 Congress, Jerusalem, Israel, October, 13-17, 2012. |
| R. Shamir. "Dissecting dysregulated pathways and chromosomal aberrations in cancer". Invited talk, I-CORE Fellows Meeting, Bar-Ilan University,October 11, 2012. |
| A. Maron-Katz, R. Elkon, I. Ulitsky, C. Linhart, D. Amar, A. Tanay, R. Sharan, E. David, T. Hait. D. Sagir, H. Safer, Y. Shiloh and R. Shamir."EXPANDER: A Platform for Dissecting Networks and Functions Using Expression Profiles". Poster presentation, The 2012 Annual Meeting of The Israel Society for Biochemistry & Molecular Biology (ISBMB), School of Medicine, Tel Aviv University, October 10, 2012. |
| Y. Orenstein, E. Mick, C. Linhart and R. Shamir. "Inferring binding site motifs from protein binding microarray data". Poster presentation, The 2012 Annual Meeting of The Israel Society for Biochemistry & Molecular Biology (ISBMB), School of Medicine, Tel Aviv University, October 10, 2012. |
| R. Rozov, E. Halperin and R. Shamir. "MGMR: leveraging RNA-Seq Population Data to Optimize Expression Estimation". Poster presentation, The 2012 Annual Meeting of The Israel Society for Biochemistry & Molecular Biology (ISBMB), School of Medicine, Tel Aviv University, October 10, 2012. |
| R. Shamir. "Dissecting inner structure in disease regulatory networks using differential co-expression". From Phenotypes to Pathways 2012, Inferring genetic architecture from perturbation maps, Lucy Cavendish College, Cambridge, UK, Aug 30 - Sept 01, 2012. |
| R. Shamir (joint with D. Amar, H. Safer). "Dissecting inner structure in disease regulatory networks using differential co-expression". Invited speaker, RECOMB Satellite Conference on Open Problems in Algorithmic Biology (RECOMB-AB), St. Petersburg, Russia, August 27-29, 2012. |
| R. Shamir. "Gene Regulation, Protein Networks and Disease - a Computational Perspective". Keynote speaker, 23rd Annual Symposium on Combinatorial Pattern Matching, Helsinki, Finland, July 3-5, 2012. |
| R. Shamir. "Transcriptomics: Does it contribute to our understanding of Parkinson's disease?". 16th International Congress of Parkinson’s Disease and Movement Disorders, Dublin, Ireland, June 18, 2012. |
| R. Shamir. "Functional genomics and networks". Epigenetics meets System Biology, A course and a symposium, Lopati Center, Weizmann Institute of Science, Rehovot, Israel, June 3, 2012. |
| Y. Orenstein. "Tools for discovery of transcription factor and microRNA binding sites: Amadeus and Allegro". TAU Bioinformatics Worksop, 03 Sherman building, Tel Aviv University, May 13, 2012. |
| D. Amar, D. Netanely, O. Lavi, G. Dror, R. Shamir. "Classifying Disease Expression Profiles Using Networks". Poster presentation, The Fourth Annual Meeting of the Israeli Society for Cancer Research (ISCR), Bar Ilan University , May 8, 2012. |
| H. Safer, A. Maron-Katz, D. Amar , R. Elkon , I. Ulitsky , C. Linhart, A. Tanay, R. Sharan, E. David, D. Sagir, Y. Shiloh, R. Shamir. "The EXPANDER suite for accessible analysis of microarray dataworks". Poster presentation, The Seventh Annual Edmond J. Safra Center for Bioinformatics Retreat, Kibbutz Ginosar, Sea of Galilee, May 6-7, 2012. |
| R. Zeira, D. Korchemny, R. Shamir. "Using Computational Biology Methods to Improve Post-silicon Microprocessor Testing". Poster presentation, The Seventh Annual Edmond J. Safra Center for Bioinformatics Retreat, Kibbutz Ginosar, Sea of Galilee, May 6-7, 2012. |
| Y. Orenstein, E. Mick, R. Shamir. "RAP: accurate prediction of cis regulatory motifs from protein binding microarrays". Poster presentation, The Seventh Annual Edmond J. Safra Center for Bioinformatics Retreat, Kibbutz Ginosar, Sea of Galilee, May 6-7, 2012. |
| R. Rozov, E. Halperin, R. Shamir. "MGMR: leveraging RNA-Seq population data to optimize expression estimation". Poster presentation, The Seventh Annual Edmond J. Safra Center for Bioinformatics Retreat, Kibbutz Ginosar, Sea of Galilee, May 6-7, 2012. |
| A. Maron Katz and D. Sagir. "Expander & Spike". Worksops Expander and SPIKE, 03 Sherman building, Tel Aviv University, April 22, 2012. |
| R. Rozov, E. Halperin, R. Shamir. "MGMR: leveraging RNA-Seq population data to optimize expression estimation". The second annual RECOMB satellite workshop on massively parallel sequencing (RECOMB-seq), April 21-24, 2012. |
| R. Shamir. "Some Computational Challenges in Cancer Genomics". Keynote speaker. Symposium on 30 Years of Computational Biology at USC, University of Southern California, March 30 - April 1, 2012. |
| Y. Orenstein. "Algorithms and software tools for understanding gene regulation". I-CORE Meeting, Gene Regulation in Complex Human Disease, Sackler School of Medicine, Tel Aviv University, April 3, 2012. |
| R. Shamir. "Computational methods in analysis of gene regulation and protein interactions". in Houry, W.A. (ed.)Protein Homeostasis: The Biomedical & Life Sciences Collection, Henry Stewart Talks Ltd, London, February, 2012. |
| Y.Orenstein,C. Linhart, Y. Halperin, I. Ulitsky, R. Shamir. "Accurate and user-friendly tools for discovering transcription factor and microrna binding sites". Poster presentation, Annual Meeting FRONTIERS IN GENETICS VII, The Genetic Society of Israel, Faculty of Agriculture Hebrew University of Jerusalem, Rehovot, Israel, February 20, 2012. |
| R. Shamir. "Computational Analysis of Gene Regulation, Disease Classification and Protein Networks". Distinguished lecture series, Bioinformatics center,Saarbrucken University, Germany, February 8, 2012. |
2011
| R. Zeira, D. Korchemny, R. Shamir. "Using Computational Biology Methods to Improve Post-silicon Microprocessor Testing". Poster presentation, IBM Haifa Verification Conference, Haifa, Israel, Dec 4-6 2011. |
| R. Shamir. "Gene regulation, protein interaction and disease - a computational perspective". X CRG Annual Symposium "Computational Biology of Molecular Sequences",Barcelona, November 10-11, 2011. |
| D. Amar. "Using differentially correlated gene pairs for classification and regulatory analysis of expression profiles from multiple disease phenotypes".IBM - TAU OCR joint event, Tel Aviv University , November 3, 2011. |
| L. Ein-Dor and A. Thevenin. "Relation between chromosomal organization of genes and their function". IBM - TAU OCR joint event, Tel Aviv University , November 3, 2011. |
| R. Shamir, M. Ozery-Flato, C. Linhart, L. Trakhtenbrot, S. Izraeli, A. Thevenin and L. Ein-Dor. "Large-scale analysis of chromosomal aberrations in cancer karyotypes: towards understanding the role of aneuploidy". Workshop on Cancer Genomics,Institute of Pure and Applied Mathematics,University of California, Los Angeles, USA, October 31 - Nov 1, 2011. |
| D. Amar, R.Shamir. "Using differentially correlated gene pairs for classification and regulatory analysis of expression profiles from multiple disease phenotypes". oral presentation, systems biology track, 4th RECOMB Satellite Conference on Regulatory Genomics, Systems Biology, and DREAM Challenges Barcelona, Spain, October 14-19 2011. |
| R. Shamir. "Algorithmic methods for analyzing regulatory networks and complex disease". Boehringer Ingelheim Fonds 104th International Titisee Conference on Genomic Regulation,Titisse, Germany, Oct 12-16 2011. |
| R. Shamir. M. Ozery-Flato,C. Linhart, L. Trakhtenbrot, S. Izraeli . "Large-scale analysis of chromosomal aberrations in cancer karyotypes reveals two distinct paths to aneuploidy". Oral presentation, Meeting in celebration of 30 years since the establishment of the Cancer Biology Research Center, Safed, Israel. September 14-17, 2011. |
| A. Maron-Katz . D. Amar, E. Ben Simon, Y. Jacob, K. Rosenberg, R. M. Karp, T. Hendler, R. Shamir. "Using Contiguous Bi-Clustering for data driven temporal analysis of fMRI based functional connectivity". Poster presentation, INCF Neuro Informatics 2011,Boston, USA, 4-6 Sept 2011. |
| A. Maron-Katz, E. David, Y. Oresntein. "Advanced tools for analyzing microarrays, cis-regulation, and signaling pathways". Microarray Workshop, Bar Ilan University, July 4, 2011. |
| R. Shamir. "Graph-theoretic methods in genomics and disease". Invited talk, Paris-6 University, Paris, June 17 2011. |
| R. Shamir. "Computational Analysis of Gene Regulation, Disease Classification, and Protein Networks". Clinical Genomic Analysis Workshop 2011,IBM Haifa Research Lab, Israel, June 2 2011. |
| G. Banay, M. Bansal, T. J. Harlow1, J. P. Gogarten1, and R. Shamir. "Systematic Detection of Highways of Horizontal Gene Transfer". Sixth E.J.Safra Bioinformatics Retreat,Ha'goshrim,Israel, May 18-19 2011. |
| G. Karlebach, and R. Shamir. "Reconstructing logical models for gene regulatory networks: an entropy based approach". Sixth E.J.Safra Bioinformatics Retreat,Ha'goshrim,Israel, May 18-19 2011. |
| R. Zeira, D. Korchemny and R. Shamir. "Using expression microarray algorithms to improve microprocessor testing". Poster presentation, Sixth E.J.Safra Bioinformatics Retreat,Ha'goshrim,Israel, May 18-19 2011. |
| R. Rozov, E. Halperin and R. Shamir. "MGMR: Multiple Genome expression estimation incorporating MultiReads". Poster presentation, Sixth E.J.Safra Bioinformatics Retreat,Ha'goshrim,Israel, May 18-19 2011. |
| E. David, A. Paz, D. Sagir, R. Elkon, I. Ulitksy, Y. Ber, S. Bialik, Z. Brownstein, K. B. Avraham, A. Kimchi, Y. Shiloh and R. Shamir. "SPIKE 2.0: A WEB-BASED database and visualization tool of signaling pathways and protein interactions". Poster presentation, Sixth E.J.Safra Bioinformatics Retreat,Ha'goshrim, Israel, May 18-19 2011. |
| D. Amar, O. Tzfadia, E. Wurtzel and R. Shamir. "Pathway Extension: A case study on carotenoid biosynthesis in plants". Poster presentation, Sixth E.J.Safra Bioinformatics Retreat,Ha'goshrim, Israel, May 18-19 2011. |
| Y. Orenstein C. Linhart and R. Shamir. "Discovering transcription factor binding site motifs from protein binding microarray data". Poster presentation, Sixth E.J.Safra Bioinformatics Retreat,Ha'goshrim, Israel, May 18-19 2011. |
| R. Shamir, I. Ulitsky, M. Ozery-Flato, C. Linhart, R.M. Karp, A.Krishnamurthy, L. Laurent, J. Loring, F.-J. Mueller, Y. Orenstein, Y. Halperin."Dissecting regulatory networks and complex disease". 11th Haifa Workshop on Interdisciplinary Applications of Graph Theory, Combinatorics and Algorithms,Haifa, Israel, May 17-19 2011. |
| H. Safer and A. Maron-Katz. "Microarray and network analysis: From Expander to Matisse". Oral presentation, Bioinformatics Approaches in Molecular Networks, Technion, April 28 2011. |
| R. Shamir, Michal Ozery-Flato, Chaim Linhart, Luba Trachtenbrot and Shai Izraeli. "A systematic assessment of associations among chromosomal aberrations in cancer karyotypes ". Oral presentation, the RECOMB-CCB satellite workshop, March 26-27 2011. |
| R. Shamir, Igor Ulitsky, Chaim Linhart, Yonit Halperin, Ofer Lavi, Richard M Karp, Akshay Krishnamurthy, Louise Laurent, Jean Loring, and Franz-Joseph Mueller. "Computational Analysis of Gene Regulation, Disease Classification and Protein Networks". Simon Fraser University, March 25 2011. |
| R. Shamir. "Computational tools for dissecting regulatory networks and complex disease". Department of Biological Chemistry Weizmann Institute of Science, March 1 2011. |
| Zippora Brownstein, Arnon Paz, Ran Elkon, Yosef Shiloh, Ron Shamir and Karen B. Avraham. "HEarSpike: A Biological Pathways Resource for the Auditory System". Association for Research in Otolaryngology (ARO) MidWinter Meeting, Baltimore, MD, USA, Feb 19-23, 2011. |
| O. Tzfadia, A. Ma'ayan, L. Bradbury, R. Shamir, E. Wurtzel. "A systems biology approach for revealing the provitamin A carotenoid biosynthesis transcriptional regulation network". Poster presentation,6th FISEB (Ilanit) meeting,Eilat, Israel, Feb 7-10, 2011. |
| Y. Orenstein, C. Linhart, Y. Halperin, I. Ulitsky, R. Shamir. "Accurate and user-friendly tools for discovering transcription factor and microRNA binding sites". Poster presentation,6th FISEB (Ilanit) meeting,Eilat, Israel, Feb 7-10, 2011. |
| A. Paz, E. David, Y. Ber, S. Bialik, Z. Brownstein,D. Sagir, R. Elkon, I. Ulitksy, K. B. Avraham, A Kimchi, Y. Shiloh, R. Shamir. "SPIKE: A signaling pathways resource for DNA damage, apoptosis and the auditory system". Poster presentation,6th FISEB (Ilanit) meeting,Eilat, Israel, Feb 7-10, 2011. |
2010
| G. Karlebach, R. Shamir. "Modeling the mouse embryonic stem cell gene regulatory network". Poster presentation, 3rd annual RECOMB satellite on system biology, regulatory genomics, and DREAM,New York, NY, Nov. 16-20, 2010. |
| Y. Orenstein, C. Linhart, R. Shamir. "Analyzing protein binding microarray data to find binding site motifs and predict TF binding intensities". Poster presentation, 3rd annual RECOMB satellite on system biology, regulatory genomics, and DREAM,New York, NY, Nov. 16-20, 2010. |
| R. Shamir, Igor Ulitsky, Michal Ozery-Flato, Chaim Linhart, Richard M Karp, Akshay Krishnamurthy, Louise Laurent, Jean Loring, Fanz-Joseph Mueller, Shai Izraeli, Luba Trachtenbrot . "Computational tools for dissecting complex disease". COLD SPRING HARBOR ASIA CONFERENCES, Computational Biology, Suzhou Dushu Lake Conference Center, China, September 27 - October 1, 2010. |
| R. Shamir, Igor Ulitsky, Michal Ozery-Flato, Chaim Linhart, Richard M Karp, Akshay Krishnamurthy, Louise Laurent, Jean Loring, Fanz-Joseph Mueller, Shai Izraeli, Luba Trachtenbrot . "Algorithms for dissecting regulatory networks and complex disease: a graph theoretic approach". Tsinghua University, Beijing, Sept. 25, 2010. |
| Sharon Rashi-Elkeles, Hans-Jörg Warnatz, Ana Kupershtein, Daniela Balzereit, Aydah Sabah, Roye Rozov, Jeannine Wilde, Vyacheslav Amstislavskiy, Tatiana Borodina, Ran Elkon, Wilfried Nietfeld, Hans Lehrach, Marie-Laure Yaspo, Ron Shamir and Y. Shiloh. "Dissection of the transcriptional response to DNA damage using an integrated experimental and computational approach". 3rd SFB TR5 SYMPOSIUM 2010 - Chromatin, München, Germany, October 6-8, 2010. |
| G. Karlebach, R. Shamir. "Finding Minimal Perturbations in Gene Regulatory Networks". Poster presentation, 2010 Haifa Verification Conference, Haifa, Israel, October 5-7, 2010. |
| Y. Shiloh, Y. Ziv, R. Elkon, S. Rashi-Elkeles, A. Kuperstein, A. Ben-Simon, A. Schmidt, R. Aebersold, R. Shamir. "The ATM-mediated DNA damage response: the system and the pathways" 21st meeting of the European Association of Cancer Research, Oslo, Norway, June 26-29, 2010. |
| I. Ulitsky, R. Shamir. "Towards Computational Prediction of MicroRNA Function and Activity" Poster presentation, RNA 2010: 15th Annual meeting of the RNA society, Seattle, Washington, June 22-26, 2010. |
| R. Shamir. "Integrated analysis of biomedical data - from connectivity to cancer". Computer Science Department, University of Minnesota, Minneapolis, May 25, 2010. |
| R. Shamir. "From DNA chips to cancer treatment" 2nd RECOMB satellite workshop on bioinformatics education, San Diego, CA, May 22-23, 2010. |
| G. Karlebach. R "Gene regulatory networks: modeling and perturbation analysis", Oral presentation, Fifth Safra Bioinformatics retreat,Neve Ilan, May 16-17, 2010. |
| M. Ozery-Flato, C. Linhart, L. Trakhtenbrot, S. Izraeli, R. Shamir. "Analysis of Chromosomal Alterations in Cancer" Poster presentation, Israel Society for Cancer Research annual meeting, Weizmann Institute, Rehovot, May 5, 2010. |
| M. Bansal, P. Gogarten, R. Shamir. "Detecting Highways of Horizontal Gene Transfer" Stringology 2010 - ISF reserach workshop, Tel Aviv , May 2-6, 2010. |
| R. Shamir, Y. Halperin, C. Linhart, I. Ulitsky. "Allegro: Analyzing expression and sequence in concert to discover regulatory programs" Accepted for highlights track presentation in RECOMB 2010 conference, Lisbon, Portugal, April 25-29, 2010. |
| A. Maron-Katz, E. David. "Advanced genomic analysis tools: Expander and beyond" Training workshop,Tel Aviv University, March 24, 2010. |
| Z. Brownstein, A. Paz, R. Elkon, Y. Shiloh, R. Shamir, K. B. Avraham. "HEarSpike: A Biological Pathways Resource for the Auditory System" Poster presentation,Frontiers in Genetics VI annual meeting,Weizmann Institute of Sciences, Rehovot, February 18, 2010. |
| G.H. Romano, Y. Gurevich, O. Lavi, I. Ulitsky, R. Shamir, M. Kupiec. "Different sets of QTLs influence fitness variation in yeast" Poster presentation,Frontiers in Genetics VI annual meeting,Weizmann Institute of Sciences, Rehovot, February 18, 2010. |
| R. Meller, I. Gat-Viks, M. Kupiec, R. Shamir. "Understanding gene sequence variation in the context of transcription regulation in yeast" Poster presentation,Frontiers in Genetics VI annual meeting, Weizmann Institute of Sciences, Rehovot, February 18, 2010. |
| R. Shamir. "Computationally dissecting cis-regulation", Max Planck Institute for Molecular Genetics, Berlin, Germany, February 2, 2010. |
| T. Elkan, R. Hertzano, I. Ulitsky, R. Elkon, M. Irmler, R. Shamir,J. Beckers, K. B. Avraham. "Identification of microRNA Targets in the Inner Ear Using an Integrative Approach" 33rd MidWinter Meeting of the Association for Research in Otolaryngology, Anaheim, California, USA, February 6-10, 2010. |
| R. Shamir. "Computational tools for dissecting microRNA networks" The 2nd Annual Tel Aviv University microRNA Consortium Conference, Green House, Tel Aviv University, January 14, 2010. |
| R. Shamir. "Integrated computational analysis of biological data: from connectivity to cancer" Systems-X seminar,ETH Zurich, January 11, 2010. |
2009
| R. Shamir. "Computational dissection of gene regulation" Department of Life Sciences,Ben Gurion University, December 28, 2009. |
| R. Shamir, I. Ulitsky, D. Sagir, E. David, Y. Ber, A. Paz, Z. Brownstein, G.Karlebach, R. Elkon, K. B. Avraham, A. Kimchi, Y. Shiloh. "SPIKE - Signaling Pathways Knowledge-base and Analysis Tool" RECOMB satellite on Systems Biology,Boston,MA, December 2-6, 2009. |
| I. Ulitsky, Laurent, R. Shamir. "Towards Computational Prediction of MicroRNA Function and Activity" RECOMB Satellite conference on Regulatory Genomics,Boston,MA, December 2-6, 2009. |
| R. Shamir, "From Amadeus to Allegro: A melodious computational approach dissecting gene regulation" Department of Computer Science seminar,Weizmann Institute of Science, November 23, 2009. |
| G. Karlebach, D. Sagir, E. David, Y. Azaria, A. Paz, J. Assa, I. Ulitsky, R. Elkon, A. Kimchi, Y. Shiloh, R. Shamir. "SPIKE: A Cellular Signaling Pathways Resource for the DNA Damage and Apoptosis communities" The 17th ECDO Euroconference on apoptosis, Paris, September 23-26, 2009. |
| S. Böcker, F. Hüffner, A. Truss, and M. Wahlström. "A faster fixed-parameter approach to drawing binary tanglegrams" Lecture Notes in Computer Science, Springer, In Proceedings of the 4th International Workshop on Parameterized and Exact Computation(IWPEC '09),Copenhagen,Denmark,September 10-11, 2009. |
| Z. Brownstein, A. Paz, R. Elkon, Y. Shiloh, R. Shamir, K. B. Avraham. "HEarSpike: A Biological Pathways Resource for the Auditory System" Poster presentation,The Mediterranean Medical Genetics 2009 Meeting, Ankara, Turkey, June 28 - July 1, 2009. |
| Guy Karlebach and R.Shamir. "Logical Modeling of Gene Regulatory Networks" Poster presentation,ISMB/ECCB 2009 Conference, Stockholm, Sweden,June 27 - July 2, 2009. |
| F.J. Mueller, D. Kostka, L. Laurent,I. Ulitsky, R. Williams, C. Lu, M.S. Rao, R.Shamir, P.H. Schwartz, N.O. Schmidt and J.F. Loring. "Regulatory networks define phenotypic classes of human stem cell lines" Oral presentation, highlights track. ISMB/ECCB 2009 Conference, Stockholm, Sweden,June 27 - July 2, 2009. |
| Z. Brownstein, A. Paz, R. Elkon, Y. Shiloh, R. Shamir, K. B. Avraham. "HEarSpike: A Biological Pathways Resource for the Auditory System" Poster presentation, The 7th Molecular Biology of Hearing & Deafness Conference, Boston, USA, June 20-23 2009. |
| R. Shamir, I, Ulitsky, R. M. Karp, A. Maron-Katz, Y. Halperin, C. Linhart, R. Elkon, Y. Shiloh. "Matrices, Modules and Motifs for Understanding Gene Regulation" Invited speaker,Israeli Statistical Society meeting, Ben Gurion University, Beer Sheva, June 17, 2009. |
| F.J. Mueller, D. Kostka, L. Laurent,I. Ulitsky, R. Williams, C. Lu, M.S. Rao, R. Shamir, P.H. Schwartz, N.O. Schmidt and J.F. Loring. "Regulatory networks define phenotypic classes of human stem cell lines" 3rd International Stem Cell Meeting, Tel Aviv, Israel, June 15-17, 2009. |
| R. Shamir "Computational tools for dissecting biological networks ." Faculty of Life Sciences, Bar Ilan University. May 6, 2009 |
| A. Paz, I. Zohar, R. Vesterman, D. Sagir, E. David, G. Karlebach, J. Assa, I. Ulitsky, R. Elkon, Y. Shiloh and R. Shamir. "SPIKE – a signaling pathways integrated knowledge resource for the DNA damage and apoptosis communities ." Poster presentation, The Edmond J.Safra Bioinformatics Program at TAU, Retreat 09, Ohalo, Sea of Galilee. May 3-4, 2009 |
| I. Gat-Viks, R. Meller, M. Kupiec and R. Shamir. "Understanding gene sequence variation in the context of transcription regulation in yeast ." Poster presentation, The Edmond J.Safra Bioinformatics Program at TAU, Retreat 09, Ohalo, Sea of Galilee. May 3-4, 2009 |
| O. Lavi, M. Gutkin, G. Dror and R. Shamir. "Selecting Gene Expression Markers for Cancer Prognosis and Treatment." Poster presentation, The Edmond J.Safra Bioinformatics Program at TAU, Retreat 09, Ohalo, Sea of Galilee. May 3-4, 2009 |
| L. Mechlovich, M. Ozery-Flato, F. Swidan and R. Shamir. "Computational Models of Tumor Development." Poster presentation, The Edmond J.Safra Bioinformatics Program at TAU, Retreat 09, Ohalo, Sea of Galilee. May 3-4, 2009 |
| M. Ozery-Flato, C. Linhart, L. Mechlovich and R. Shamir. "Analysis of Chromosomal Alterations in Cancer." Poster presentation, The Edmond J.Safra Bioinformatics Program at TAU, Retreat 09, Ohalo, Sea of Galilee. May 3-4, 2009 |
| I.Ulitsky, L.C. Laurent, F.J. Mueller, J.F. Loring and R. Shamir. "Computational Methods for Dissection of MicroRNA Function." Poster presentation, The Edmond J.Safra Bioinformatics Program at TAU, Retreat 09, Ohalo, Sea of Galilee. May 3-4, 2009 |
| S. Bruckner,F. Hueffner, R. M. Karp, R. Shamir and R. Sharan . "Topology-free querying of protein interaction networks" Poster presentation, The Edmond J.Safra Bioinformatics Program at TAU, Retreat 09, Ohalo, Sea of Galilee . May 3-4, 2009 |
| Y. Shiloh,S. Rashi-Elkeles, A. Ben-Simon, A. Schmidt, R. Aebersold, R. Shamir. "The ATM-mediated DNA damage response: the system and the pathways" US-EU Workshop on Systems Level understanding of DNA damage Responses, Egmond aan Zee, the Netherlands, March 30, 2009 |
| R. Shamir. "Computational tools for dissecting biological networks" US-EU Workshop on Systems Level understanding of DNA damage Responses, Egmond aan Zee, the Netherlands, March 30, 2009 |
| S. Bruckner,F. Hueffner, R. M. Karp, R. Shamir and R. Sharan . "Topology-free querying in protein interaction networks" Stringology 2009, Bar Ilan University . March 29 - April 2, 2009 |
| I.Ulitsky, D. Sagir, A. Maron Katz, S. Shavit and R. Shamir. "Advanced genomic analysis tools: Expander and beyond." Bioinformatics unit Weizmann Institute. March 25, 2009 |
| L. Laurent,I. Ulitsky, S. Peterson, I. Garitaonandia, R. Shamir, J. F. Loring. "Integrated analysis of recurrent regions of copy number variation and gene coexpression in human embryonic stem cells" Cold Spring Harbor meeting on Systems Biology: Networks. March 18-22, 2009 |
| R. Shamir,I. Ulitsky, R. M. Karp, L. Laurent, J. Loring. "Integrated analysis of biomedical data: the power of connectivity" Cold Spring Harbor meeting on Systems Biology: Networks. March 18-22, 2009 |
| G. Karlebach, I. Zohar, I. Gat-Viks, R. Vesterman, D. Sagir, A. Paz, J. Assa, I. Ulitsky, R. Elkon, Y. Shiloh, R. Shamir. "Computational Tools for System-level Analysis of Signalling Networks." Poster presentation,3rd FEBS Advanced Lecture Course on Systems Biology: From Molecules to Function,Alpbach, Austria. March 7-13, 2009 |
| G-H. Romano, Y. Gurevich, O. Lavi, I. Ulitsky, R. Shamir, M. Kupiec. "Genetic Dissection of Several Independent Genetic Networks Affect Alkali Stress Resistance." Poster presentation,Frontiers in Genetics V, The Hebrew University, Jerusalem. February 23, 2009 |
| I.Ulitsky, L.C. Laurent, F.J. Mueller, J.F. Loring and R. Shamir. "Computational Methods for Dissecting MicroRNA Function." Poster presentation,Frontiers in Genetics V, The Hebrew University, Jerusalem. February 23, 2009 |
| T. Elkan, R. Herzano, I. Ulitsky, R. Elkon, M. Irmler, R. Shamir, J. Beckers, K. B. Avraham. "Integration of Approaches for the Study of Biological Networks in the Inner Ear." Poster presentation,Frontiers in Genetics V, The Hebrew University, Jerusalem. February 23, 2009 |
| O.Lavi, I.Ulitsky and R. Shamir. "Identification of Cancer Biomarkers Using Gene Expression and Signaling Networks." Poster presentation, Meeting of the Israeli Society for Cancer Research, Tel Aviv University. February 17, 2009 |
| M.Ozery-Flato , C. Linhart , L. Mechlovich , and R. Shamir. "Large-scale Computational Analysis of Chromosomal Aberrations in Cancer." Poster presentation, Meeting of the Israeli Society for Cancer Research, Tel Aviv University. February 17, 2009 |
| Rashi-Elkeles S. , Y.Lerenthal , A.Kupershtein , R.Elkon , S.Shavit , C.Linhart , N.Amariglio , G.Rechavi , R.Shamir and Y.Shiloh. "Dissection of the p53-Mediated Transcriptional Response to DNA Damage." Poster presentation, Meeting of the Israeli Society for Cancer Research, Tel Aviv University.February 17, 2009 |
| I.Ulitsky , R.M.Karp and R.Shamir. " Meta-Analysis of Breast Cancer-Specific Dysregulated Pathways via Analysis of Expression Profiles in Multiple Case-Control Studies." Poster presentation, Meeting of the Israeli Society for Cancer Research, Tel Aviv University. February 17, 2009 |
| A. Maron-Katz, I. Ulitsky, C. Linhart, D. Sagir. "Advanced genomic analysis tools: Expander and beyond" TAU Bioinformatics Worskhop Series, Tel Aviv University. January 27, 2009 |
| I.Ulitsky, L.C. Laurent, F.J. Mueller, J.F. Loring and R. Shamir. "Computational Methods for Dissecting MicroRNA Function." Poster presentation, TAU miRNA consortium conference. Tel Aviv University. January 14, 2009 |
| R. Shamir,C. Linhart, Y. Halperin and I. Ulitsky. "Dissecting regulatory signals of transcription factors and microRNAs" Computational Biology Seminar, the Hebrew University, Jerusalem. 11 January 2009 |
2008
| R. Shamir. ``Network analysis tools in systems biology'' Lawrence Berkeley National Laboratory, November 26, 2008. |
| R. Shamir. ``Motifs, modules and evolution in transcription regulation''. PAIL seminar, Stanford University, November 11, 2008. |
| Y. Halperin, C. Linhart, I. Ulitsky, R. Shamir. "Discovering transcriptional modules by combined analysis of expression profiles and regulatory sequences" Talk, the RECOMB Satellite conference on Regulatory Genomics and Systems Biology, Boston, MA, Oct. 29-Nov. 2, 2008. |
| R. Shamir `` Integrated analysis of biomedical data: from connectivity to cancer''. UC Davis Distinguished Lecturer Series, UC Davis, October 16, 2008. |
| R. Shamir ``Computational challenges in understanding gene regulatory networks'', MacKay Lecture , Electrical Engineering and Computer Science Colloquium, UC Berkeley, October 1, 2008. |
| M. Ozery-Flato, L. Mechlovich, R. Shamir. "Analysis of chromosomal alterations in cancer". Poster presentation, Workshop on genome stability in health and disease, The Hebrew University, Jerusalem September 21--25 2008. |
| A. Paz, I. Zohar, R. Vesterman, D. Sagir, G. Karlebach, J. Assa, I. Ulitksy, R. Elkon, Y. Shiloh, R. Shamir. "SPIKE . A Signaling Pathways Resource for the DNA Damage and Apoptosis communities". Workshop on genome stability in health and disease, The Hebrew University, Jerusalem September 21-25 2008. |
| R. Shamir. "Integrated analysis of biomedical data - from connectivity to cancer" IEOR seminar, Univeristy of California, Berkeley September 8, 2008. |
| I. Zohar, R. Vesterman, D. Sagir, A. Paz, G. Karlebach, J. Assa, I. Ulitksy, R. Elkon, Y. Shiloh, R. Shamir. "SPIKE . A Signaling Pathways Resource for the DNA Damage and Apoptosis communities". 16th Euroconference on Apoptosis, Bern, Switzerland, 6-9 September 2008. |
| I. Ulitsky and R. Shamir "Detecting pathways transcriptionally correlated with clinical parameters" 7th Annual International Conference on Computational Systems Bioinformatics, Stanford, California. August 27 2008. |
| E-K. Suk, N. Potoczna, T. Kroslak, W. Terhalle, S. Dahm, A. Bauerfeind, K. Rohde, S. Schreiber, H. Lehrach, O. Davidovich, R. Shamir, F.F. Horber and M.R. Hoehes. "A Case-Control Study with 83 Candidate Genes in Severe Obesity" late-breaker poster presentation, The International Conference of Genetics, Berlin, July 12 - 17 2008. |
| M. Ozery-Flato, R. Shamir. "Sorting cancer karyotypes by elementary operations", The 8th Haifa Workshop in Interdisciplinary Applications of Graph Theory,Combinatorics, and Algorithm, Haifa University, May 2008. |
| C. Linhart and R. Shamir, "Matching with don't-cares and a small number of mismatches", 8th Haifa Workshop on Interdisciplinary Applications of Graph Theory, Combinatorics, and Algorithms, May 2008. |
| R. Shamir, C. Linhart, Y. Halperin, I. Ulitsky "Analysis of regulatory microRNAs using sequence and interaction networks", Invited speaker,European Science Foundation workshop on Non-coding RNAs: Computational Challenges and Applications. Antalia, Turkey, April 28--30, 2008. |
| R. Elkon, R. Vesterman, N. Amit, I. Ulitsky, G. Mass, I. Zohar, D. Sagir, J. Assa, Y. Shiloh, R. Shamir. "SPIKE - Signaling Pathways Integrated Knowledge Engine" Poster presentation, The 11th Israeli Bioinformatics Symposium, Tel Aviv University, April 27, 2008. |
| I. Ulitsky, R.M. Karp and R. Shamir Identification of biologically and clinically relevant functional modules through integration of network and expression data. Poster presentation, The 11th Israeli Bioinformatics Symposium, Tel Aviv University, April 27, 2008. |
| A. Maron-Katz, R. Elkon, S. Shavit, I. Ulitsky, C. Linhart, A. Tanay, R. Sharan, I. Steinfeld , Y. Shiloh, R. Shamir. "Expander 4.0 - a comprehensive platform for expression profile analysis". Poster presentation, The 11th Israeli Bioinformatics Symposium, Tel Aviv University, April 27, 2008. |
| M. Ozery-Flato, L. Mechlovich, R. Shamir. "Analysis of chromosomal alterations in cancer". Poster presentation, The 11th Israeli Bioinformatics Symposium, Tel Aviv University, April 27, 2008. |
| Y. Halperin, C. Linhart and R. Shamir. "Amadeus: an advanced platform for diverse motif discovery tasks". Poster presentation, The 11th Israeli Bioinformatics Symposium, Tel Aviv University, April 27, 2008. |
| A. Maron-Katz, S. Shavit "EXPANDER - an integrative program suite for microarray data analysis", Workshop, Weizmann Institute of Science, April 9 2008. |
| R. Elkon, R. Vesterman, N. Amit, I. Ulitsky, G. Mass, I. Zohar, D. Sagir, J. Assa, Y. Shiloh, R. Shamir. "SPIKE - Signaling Pathways Integrated Knowledge Engine" poster presentation, RECOMB 2008, Singapore March 30 - April 2 2008. |
| I. Ulitsky, R.M. Karp, R. Shamir Detecting disease-specific disregulated pathways via analysis of clinical expression profiles. Oral presentation,RECOMB 2008, Singapore March 30 - April 2 2008. |
| R. Shamir,I. Ulitsky, M. Ozery-Flato, L. Mechlovich Computational analysis in cancer and Huntington disease: genome rearrangements and dysregulated pathways. Clinical Systems Biology Symposium, Weizmann Institute, March 23-24 2008. |
| M. Ziv-Ukelson, I. Gat-Viks, R. Shamir. "A non-heuristic speedup of the Sankoff-85 algorithm". London Stringology Days and London Algorithmic Workshop 2008, King's College London, 7-8 February 2008. |
| S. Rashi-Elkeles, R. Elkon, S. Shavit, Y. Lerenthal, C. Linhart, N. Amariglio, G. Rechavi, R. Shamir, Y. Shiloh "A functional genomics approach to the dissection of the p53-mediated transcriptional response to DNA damage". Poster presentation, the Fifth Congress of the Federation of the Israel Societies for Experimental Biology (Ilanit), Eilat, Israel, 28-31 January 2008. |
| C. Linhart, S. Kidron, Y. Halperin, R. Shamir, L. Broday "Motif pairs in the promoters of C. elegans" Worm meeting, Tel Aviv University, January 2, 2008. |
| C. Linhart, Y. Halperin, D. Raijman, A. Tanay, R. Shamir Transcriptional regulatory elements: their evolution, selection and detection Invited talk, 5th Congress of the Federation of the Israel Societies for Experimental Biology (Ilanit) Eilat, January 2008 |
2007
| Ron Shamir, I. Gat-Viks, I. Ulitsky, D. Raijman and A. Tanay "Modeling and improving models of biological networks". Invited speaker, Meeting on Mathematics of Biological Networks, Institute Henri Poincare, Paris December 17-18 2007. |
| R. Shamir,Michal Ozery-Flato, Lior Mechlovich, Igor Ulitsky (Tel Aviv University) and Richakd Karp (Berkeley) "Computational studies of rearrangements and dysregulated pathways in cancer". Conference on Cancer Genome and EpiGenome: new technologies and new challenges December 13-14 2007/ Institut Mutualiste Montsouris, Paris |
| R. Shamir, I. Gat-Viks, I. Ulitsky, M. Kupiec, D. Raijman, I. Steinfeld, A. Tanay, and R.M. Karp "Models, modules and modes in biological networks". Keynote speaker, 2nd DREAM conference (Dialogue on Reverse Engineering Assessment and Methods) , New York Academy of Science, New York, December 3-4 2007. |
| D. Raijman, A. Tanay, R. Shamir "Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites" Oral presentation, RECOMB Satellite on Regulatory Genomics 2007, Boston, MA Oct 11-13 2007. |
| M. Ozery-Flato, R. Shamir. "On the frequency of genome rearrangement events in cancer karyotypes". Oral presentation, RECOMB satellite on Computational Cancer Biology, UCSD, September 16-18 2007. |
| M. Ozery-Flato, R. Shamir. "On the frequency of genome rearrangement events in cancer karyotypes". Poster presentation, Fifth Annual RECOMB Satellite Workshop on Comparative Genomics, San Diego, California Sept. 16-18, 2007. (Best Poster Award) |
| I. Ulitsky, L. Laurent, F.J. Mueller, J.F. Loring and R. Shamir Integrated analysis of concurrent microRNA and gene expression in the context of protein interactions. 3rd Cold Spring Harbor Laboratory/Wellcome Trust conference on "Interactome Networks" August 29 - September 1, 2008 |
| C. Linhart, Y. Halperin, R. Shamir. "The Amadeus motif dicovery platform", Gilad lab, University of Chicago, July 31 2007. |
| I. Steinfeld, R. Shamir, M. Kupiec. "A genome-wide analysis in Saccharomyces cerevisiae demonstrates the influence of chromatin modifiers on transcription" Oral presentation, highlights track. ISMB/ECCB 2007 Conference, Vienna, Austria, July 21-25 2007. |
| R. Shamir, D. Raijman, A. Tanay. "Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites" BigRoc and The Kahn Family Research Center for Systems Biology of the Human Cell joint seminar. Weizmann Institute of Science, Rehovot, Israel, May 28, 2007. |
| R. Elkon,C. Linhart,I. Ulitsky,A. Maron-Katz,S. Shavit,R. Verterman,N. Amit . "Advanced Computational Tools for the Analysis of Functional Genomic Data" Workshop organized by the Bioinformatics Unit, Tel Aviv University, May 2007. |
| O. Davidovich, G. Kimmel, E. Halperin, R. Shamir "Tag SNPs Selected According to Prediction Accuracy Provide Higher Power to Association Studies", oral presentation, Human Genome Meeting 2007, Montreal, Canada, 21-24 May 2007. |
| M. Ozery-Flato, R. Shamir. "Sorting genomes with centromeres by translocations" Seventh Haifa Workshop on Interdisciplinary Applications of Graph Theory, Combinatorics, and Algorithms May 14-16 2007. |
| G. Kimmel, M. Jordan, E. Halperin, R. Shamir, R. Karp. "Evaluating disease significance in genome wide association studies". poster presentation,CSHL meeting on the biology of genomes , Cold Spring Harbour, NY, USA, May 8-12, 2007. |
| E. Halperin, O. Davidovich, G. Kimmel, R. Shamir. "Maximizing SNP Prediction Accuracy Increases the Power in Association Studies". poster presentation,, CSHL meeting on the biology of genomes , Cold Spring Harbour, NY, USA, May 8-12, 2007. |
| I. Ulitsky, R. Shamir "Joint analysis of genetic and physical interaction networks in S. cerevisiae" Second Safra Bioinformatics Retreat, Ohalo, Sea of Galilee, May 1 2007. |
| R. Elkon. "Functional genomics dissections of transcriptional networks" Second Safra Bioinformatics Retreat, Ohalo, Sea of Galilee, May 1 2007. |
| I. Ulitsky, R. Shamir "Joint analysis of genetic and physical interactions in yeast reveals pathway redundancy and protein essentiality". poster presentation, Conference in Research in Computational Molecular Biology (RECOMB 2007), San Francisco Bay, April 21-25 2007. |
| I. Ulitsky, R. Shamir "Identification of Functional Modules using Network Topology and High-throughput Data". poster presentation, Conference in Research in Computational Molecular Biology (RECOMB 2007), San Francisco Bay, April 21-25 2007. |
| O. Davidovich, G. Kimmel, E. Halperin, R. Shamir "Maximizing SNP Prediction Accuracy Increases the Power in Association Studies" poster presentation, Conference in Research in Computational Molecular Biology (RECOMB 2007), San Francisco Bay, April 21-25 2007. |
| M. Ozery-Flato and R. Shamir "Rearrangements in Genomes with Centromeres — Part I: Translocations" Oral presentation, Conference in Research in Computational Molecular Biology (RECOMB 2007), San Francisco Bay, April 21-25 2007. |
| I. Gat-Viks and Ron Shamir "The Metareg modeling enviroment", Course on Systems Level Modeling, Max Planck Institute for Molecular Genetics, Berlin, Germany. April 25-27, 2007. |
| G. Kimmel, M. Jordan, E. Halperin, R. Shamir, R. Karp. "Evaluating disease significance in genome wide association studies". Invited oral presentation, Third RECOMB Satellite Workshop on: Computational Methods for SNPs and Haplotypes, University of Southern California, Los Angeles, Califronia, USA, January 27-28, 2007. |
| I. Gat-Viks "Refinement and Expansion of Signaling Pathways: The Osmotic Response Network in Yeast" contributed talk, European Conference on Computational Biology (ECCB 2006) Eilat, Israel January 21-24 2007. |
| I. Steinfeld, R. Shamir, M. Kupiec. "A genome-wide analysis in S. cerevisiae reveals the nfluence of chromatin modifiers on transcription", Poster presentation. European Conference on Computational Biology (ECCB 2006) Eilat, Israel January 21-24 2007. |
| Y. Halperin, C. Linhart , G. Weber, R. Shamir "The AMADEUS Motif Discovery Tool" Poster presentation, European Conference on Computational Biology (ECCB 2006) Eilat, Israel January 21-24 2007. |
| O. Davidovich, G. Kimmel, R. Shamir "GEVALT - An integrated software tool for genotype analysis" Poster presentation, European Conference on Computational Biology (ECCB 2006) Eilat, Israel January 21-24 2007. |
| I. Ulitsky, A. Maron-Katz, R. Elkon, A. Tanay, C. Linhart, I. Steinfeld, R. Sharan, Y. Shiloh, R. Shamir "EXPANDER - an integrative program suite for microarray data analysis". Poster presentation, European Conference on Computational Biology (ECCB 2006) Eilat, Israel January 21-24 2007. |
| R. Elkon, R. Vesterman, N. Amit, I. Ulitsky, M. Weisz, G. Sternberg, R. Blekhman, J. Assa, Y. Shiloh, R. Shamir. "SPIKE - A Database, Visualization and Analysis Tool for Signaling Pathways", Poster presentation, European Conference on Computational Biology (ECCB 2006) Eilat, Israel January 21-24 2007. |
2006
| I. Ulitsky, R. Shamir "Pathway Redundancy and Protein Essentiality Revealed in the S. cerevisiae Interaction Networks" Oral presentation, RECOMB satellite meeting on Systems Biology, San Diego, December 2 2006. |
| R. Shamir, I. Gat-Viks ``Modeling and expansion of signaling pathways'' Keynote speaker, RECOMB satellite meeting on Systems Biology, San Diego, December 1 2006. |
| R. Elkon, R. Vesterman, N. Amit, I. Ulitsky, M. Weisz, G. Sternberg, R. Blekhman, J. Assa, Y. Shiloh, R. Shamir. "SPIKE - A Database, Visualization and Analysis Tool for Signaling Pathways", poster presentation, RECOMB satellite meeting on Systems Biology, San Diego, December 1 2006. |
| R. Shamir, ``Some current computational challenges in biology and medicine''. Invited speaker, Algorithmic Biology 2006, UC San Diego, November 30 2006. |
| I. Ulitsky, I. Gat-Viks, A. Tanay, R. Shamir "MetaReg application: a graphical interface for modeling and evaluation of biological systems", poster presentation, Algorithmic Biology 2006, UC San Diego, November 30 2006. |
| Y. Halperin, C. Linhart , G. Weber, R. Shamir "The AMADEUS Motif Discovery Tool" Poster presentation, 9th Israeli Bioinformatics Symposium, Bar Ilan University, Israel, 16 October 2006. |
| O. Davidovich, G. Kimmel, R. Shamir "GEVALT - An integrated software tool for genotype analysis" Poster presentation, 9th Israeli Bioinformatics Symposium, Bar Ilan University, Israel, 16 October 2006. |
| A. Maron-Katz, R. Elkon, A. Tanay, C. Linhart, I. Steinfeld, R. Sharan, Y. Shiloh, R. Shamir "EXPANDER - an integrative program suite for microarray data analysis". Poster presentation, 9th Israeli Bioinformatics Symposium, Bar Ilan University, Israel, 16 October 2006. |
| R. Elkon, R. Vesterman, N. Amit, I. Ulitsky, M. Weisz, G. Sternberg, R. Blekhman, J. Assa, Y. Shiloh, R. Shamir. "SPIKE - A Database, Visualization and Analysis Tool for Signaling Pathways" poster presentation, 9th Israeli Bioinformatics Symposium, Bar Ilan University, Israel, 16 October 2006. |
| I. Steinfeld, R. Shamir, M. Kupiec. "The influence of chromatic modifiers on transcription: a genome-wide analysis". Poster presentation, 9th Israeli Bioinformatics Symposium, Bar Ilan University, Israel, 16 October 2006. |
| G. Dror, R. Sorek, R. Shamir. "Maximum likelihood estimation of the number of functional ancestral alternatively spliced exons in the human genome". Poster presentation, 9th Israeli Bioinformatics Symposium, Bar Ilan University, Israel, 16 October 2006. |
| R. Shamir "Representation and expansion of regulatory pathways" Invited speaker, Genomics and Cancer: Integrating Genomics with Clinical Research and Therapy Heidelberg, Germany September 14 2006. |
| M. Ozery-Flato, R. Shamir "Sorting by translocations via reversals theory" RECOMB Satellite on Comparative Genomics, Montreal, Canada, September 24 - 26, 2006 . |
| R. Shamir "Some computational challenges in today's bio-medicine" Keynote speaker,European Symposium on Algorithms, Zurich, Switzerland, September 11-14 2006. |
| D. Raijman, A. Tanay, R. Shamir "A model for the evloution of promoters". Otto Warburg International Summer School and Workshop, Berlin, Germany Aug. 29 - Sept. 8 2006. |
| I. Ulitsky, R. Shamir "Integrated identification of coherent interaction subnetworks" 2nd Cold Spring Harbor Laboratory/Wellcome Trust conference on "Interactome Networks" August 30 - September 3, 2006 |
| R. Shamir, Amos Tanay , Irit Gat-Viks, Chaim Linhart, Yonit Halperin, Daniela Raijman, and Aviv Regev "On the evolution of transcription regulation networks". The Third Annual RECOMB Satellite Workshop on Regulatory Genomics Singapore, July 17-18 2006. |
| R. Shamir, I. Gat-Viks. "Computational methods for refinement and expansion of signaling pathways" Workshop on Bioalgorithmics, Institute for Mathematical Sciences, National University of Singapore, Singapore, 14 July 2006. |
| R. Shamir "Computational tools for analysis of microarray data". Wellcome Trust course Functional Genomics and Systems Biology, Hinxton, UK, 21-22 June 2006 |
| C. Linhart and R. Shamir. "Pattern matching with character classes", The Third Haifa Annual International Stringology Research Workshop, Haifa, Israel, May 7-12, 2006. |
| M. Ozery-Flato and R. Shamir. An O(n3/2√log(n)) algorithm for sorting by reciprocal translocations, Proc. CPM 06, Barcelona, July 5-7 2006. |
| M. Ozery-Flato and R. Shamir. "Faster and generalized sorting by translocations". 6th Haifa Workshop on Interdisciplinary Applications of Graph Theory, Combinatorics and Computing, Haifa, Israel May 28-31, 2006. |
| G. Kimmel, R. Shamir. "Rapid and accurate significance evaluation in disease association tests for of SNPs and haplotypes". Cold Spring Harbor Biology of Genomes conference, 10-14 May 2006. |
| O. Davidovich, G. Kimmel, R. Shamir. "An integrated software tool for genotype analysis", poster presentation, RECOMB 2006, Venice, Italy April 2-5, 2006. |
| I. Ulitsky, I. Gat-Viks, A. Tanay, R. Shamir "MetaReg application: a graphical interface for modeling and evaluation of biological systems", poster presentation, RECOMB 2006, Venice, Italy April 2-5, 2006. |
| Y. Halperin, C. Linhart, G. Weber, R. Shamir "The AMADEUS Motif Discovery Tool", poster presentation, RECOMB 2006, Venice, Italy April 2-5, 2006. |
| R. Elkon, A. Maron-Katz, R. Vesterman. Introduction to EXPANDER and SHARP", Workshop on Microarrays: From Expression to Function Weizmann Institute of Science, March 23 2003. |
| I. Gat-Viks, R. Shamir. "A Computational Methodology for Improving the Knowledge on Biological Networks", poster presentation, Cold Spring Harbor meeting on Systems Biology: Global Regulation of Gene Expression Cold Spring Harbor, New York, March 23-26, 2006. |
| R. Elkon. "Reverse-Engineering of Transcriptional Networks". Lecture in a course on microarray analysis organized by Dr. Jesper Troelsen. Department of Medical Biochemistry and Genetics. Panum Institute. Copenhagen, Denmark. March 6, 2006. |
| R. Elkon, A. Maron-Katz and R. Vesterman Analysis of Microarray Data Using the EXPANDER and SHARP Tools, January 19th 2006, Bioinformatics workshop, TAU. |
2005
| R. Elkon "Analysis of gene expression microarray data using EXPANDER and SHARP" Workshop on Advances in the microarray technology and analysis. 12 December 2005, Rappoport Faculty of Medicine, Technion, Haifa. |
| R. Shamir "Modeling and analyzing regulatory networks", Department of Biological Chemistry, Weizmann Institute of Science, November 29 2005. |
| R. Shamir, G. Sternberg, R. Blekhman, A. Pavtulov, R. Vesterman, J. Assa, I. Ulitsky, R. Elkon, Y. Shiloh. "SHARP - A platform for recording, visualising and anlayzing signaling pathways" Invited talk, International Symposium on Signal Transduction in Health and Disease (STADY IV) October 26-28, 2005 Tel Aviv, Israel |
| M. Ozery-Flato,R. Shamir. "Sorting Signed Multi-Chromosomal Genomes by Generalized Translocations". Poster presentation, The 3rd RECOMB Comparative Genomics Satellite Workshop, Dublin, Ireland, 18-20 September 2005. |
| R. Elkon, S. Rashi-Elkeles, C. Linhart, G. Sternberg, R. Shamir, Y. Shiloh. "Global Dissection of Transcriptional Networks" Conference on Systems level understanding of DNA damage responses, Stowe, Vermont, USA September 30-October 4, 2005. |
| R. Shamir, A. Tanay, I. Gat-Viks, A. Regev, I. Steinfeld, M. Kupiec. "Modularity, evolution and regulation in bionetworks". Invited speaker, The German Society for Biochemistry and Molecular Biology (GBM), Berlin, Germany, September 18-21, 2005. |
| R. Shamir "Genetic Networks: Modeling, Inference and Expansion" International Workshop: Complex biomolecular networks: structure, evolution, and function Montauk Yacht Club, Long Island, New York September 6-9, 2005 |
| R. Shamir "Modeling, inference and evolution in bionetworks" Invited speaker, International Workshop on Complex biomolecular networks: structure, evolution, and function Montauk Yacht Club, Long Island, New York September 6-9, 2005. |
| E. Halperin, G. Kimmel, R. Shamir. "Tag SNP Selection in Genotype Data for Maximizing SNP Prediction Accuracy" ISMB 2005,Detroit, Michigan, June 25-29 2005 |
| Ronen Shemsh, Amit Novik, Sarit Edelheit and Rotem Sorek "Identification of novel human splice variants using 'genomic fossils'" Short Talk ,ISMB 2005,Detroit, Michigan, June 25-29 2005. |
| R. Shalgi, A. Bar-Even, R. Shamir, T. Pilpel. "Catalogs of sequence elements associated with transcript stability and sub-cellular localization derived from 3~R UTRs of yeast mRNAs" Poster presentation,ISMB 2005,Detroit, Michigan, June 25-29 2005. |
| G. Kimmel Introduction to the Computational Problems of SNPs and Haplotypes. Invited speaker, International School of Advanced BioMedicine and BioInformatics, Pantelleria, Italy, June 18-25, 2005. |
| G. Kimmel E. Halperin, R. Shamir. "Improved Algorithms and Models for Large-Scale Genotype Phasing, Block Partition, and Tag SNP Selection: GERBIL, STAMPA and HINT". Invited speaker, International School of Advanced BioMedicine and BioInformatics, Pantelleria, Italy, June 18-25, 2005. |
| C. Linhart "Identifying transcription factor binding sites: Transcriptional regulation of the human cell cycle", Third Bertinoro Computational Biology Meeting, Bertinoro, Italy, June 11-17 2005. |
| R. Shamir "Evolution of cis-regulation" Third Bertinoro Computational Biology Meeting, Bertinoro, Italy, June 11-17 2005. |
| S. Rashi-Elkeles, R. Elkon, N. Weizman, C. Linhart, N. Amariglio, N. Orlev, G. Sternberg, G. Rechavi, A. Barzilai, R. Shamir, Y. Shiloh "Reflection of the A-T Phenotype in Transcriptional Responses to Ionizing Radiation in Atm-Deficient Murine Tissues". Poster presentation, the 2005 international workshop on Ataxia-Telangiectasia, ATM and the DNA damage response. Belgirate, Lake Maggoiore, Italy. 8-11 June 2005. |
| G. Sternberg R. Blekhman, Y. Assa, I. Ulitsky, R. Elkon, R. Shamir, Y. Shiloh. "SHARP: A bioinformatic knowledge base for ATM-related singaling pathways", poster presentation, The 2005 International Workshop on Ataxia-Telangiectasia, ATM and the DNA Damage Response, Belgirate, Lake Maggiore, Italy, June 8-11 2005. |
| G. Kimmel E. Halperin, R. Shamir. "Improved Algorithms for Large-Scale Genotype Phasing, Block Partition, and Tag SNP Selection" oral presentation, Mutation Detection 2005, Santorini, Greece, 31 May - 4 June 2005. |
| I. Steinfeld, A. Tanay, M. Kupiec, R. Shamir. "Organization of the Yeast Molecular Network by Integrated Analysis of Genome-wide Data", Poster presentation, the 8th Israeli Symposium on Bioinformatics, Ben Gurion University, Be'er Sheva May 22, 2005. |
| I. Gat-Viks, A. Tanay, D. Raijman, R. Shamir "Factor graph network models for biological systems" RECOMB '05, Boston, May 15 2005 |
| R. Shamir , Amos Tanay, Irit Gat-Viks, Chaim Linhart, Rani Elkon, Aviv Regev "Glimpses on the evolution of transcription regulation networksd" DIMACS Workshop on Biomolecular Networks: Topological Properties and Evolution", DIMACS Center, Rutgers University, New Jersey May 13 2005. |
| C. Linhart, R. Elkon, Y. Shiloh, R. Shamir, "Conservation and Evolution of Promoter Sequences: A Comparative Analysis of Metazoan Genomes", poster presentation, Complexity Science meeting, Tel Aviv University, April 19, 2005. |
| A. Tany "Evolutionary Mechanisms Underlying Conservation and Evolvability in Regulatory Networks", Complexity Science meeting, Tel Aviv University, April 19, 2005. |
| R. Elkon "Integrative analysis of heterogeneous functional genomics data" European Science Foundation workshop: Microarray meets Diagnostics: Chip-Technology as an innovative technique to study complex and heterogeneous diseases, Tubingen, April 15-17 2005. |
| R. Shamir "Computational challenges in molecular biology" The First Tel-Hai Bioinformatics and Genome Research Conference, Tel-Hai Academic College, Israel April 14, 2005 |
| R. Shamir A. Tanay, I. Gat-Viks, R. Elkon, C. Linhart, A. Regeve "Tracing the evolution of regulatory signals in DNA" Stringology reserach workshop of the Israeli Science Foundation, Haifa Univeristy, April 4-8, 2005 |
| R. Shamir, G. Kimmel, M. Hoehe, E. Friedman "High resolution haplotypes, the HAPMAP project and disease gene discovery" Department of Deveolpmental and Cellular Biology, School of Medicine, Tel Aviv University, March 23 2005. |
| R. Sorek "Advanced Topics in Alternative Splicing" Biological Data Analysis Workshop Series 2004-2005 Weizmann Institute, March 3 2005. |
| T. Hartman R. Shamir "A simpler and faster 1.5-approximation algorithm for sorting by transpositions" Poster presentation, The fourth Congress of the Federation of the Israel Societies for Experimental Biology (Ilanit), Eilat, Israel, February 7-10 2005. |
| R. Elkon S. Rashi-Elkeles, Y. Lerenthal, C. Linhart, T. Tenne, N. Amariglio, G. Rechavi, R. Shamir, Y. Shiloh "Transcriptional network dissection using a combination of microarrays, RNAi and computational promoter analysis". Poster presentation,The fourth Congress of the Federation of the Israel Societies for Experimental Biology(Ilanit), Eilat, Israel, February 7-10 2005. |
| R. Shamir A. Tanay, I. Gat-Viks, A. Regev "Stability and change in transcription regulation: lessons from comparative and microarray analysis in yeast" The fourth Congress of the Federation of the Israel Societies for Experimental Biology (Ilanit), Eilat, Israel, February 7-10 2005. |
2004
| R. Shamir "Revealing the dynamics of cis-regulation" 2005 Jerusalem Winter School on Biological networks and evolution, Hebrew University, Jerusalem, Israel December 30 2004. |
| A. Tanay R. Shamir "Evolution of transcription regulation" Networking Systems Biology meeting, Weizmann Institute, Rehovot, Israel, December 13 2004. |
| R. Shamir "A computational approach to the understanding of trascription factor regulation" Annual meeting of the Israel Endcorine Society, Tel Aviv, Israel, December 21, 2004. |
| R. Shamir "Revealing the structure and dynamics of cis-regulation using heterogeneous, genome-wide, multi-species data" Keynote speaker, 15th Internaltional Conference on Genome Informatics, Yokohama, Japan, December 13-15 2004 |
| R. Sorek, R. Shemesh, Y. Cohen, O. Basechess, G. Ast and R. Shamir "The "promoters" of splicing-Intronic sequences that regulate alternative splicing" CSHL genomic workshop, Cold Spring Harbor, NY, 11-13 November 2004. |
| R. Sorek, R. Shemesh, Y. Cohen, O. Basechess, G. Ast and R. Shamir "Uncovering the hidden alternative splicing in the human genome" Gene Annotation and Alternative Splicing workshop, Berlin, Germany, 13-14 December 2004. |
| R. Shamir, "A computational approach to the understanding of trascription factor regulation", Annual meeting of the Israel Endcorine Society, Tel Aviv, December 21, 2004 |
| R. Sorek, R. Shemesh, Y. Cohen, O. Basechess, G. Ast and R. Shamir. "Uncovering the hidden alternative splicing in the human genome" Lyon's International Multidisciplinary Meeting on Post-Genomics 2004(IPG '04), La Doua, LYON, 13-15 October 2004 |
| R. Elkon. "Dissection of a DNA damage-induced transcriptional network using a combination of microarrays RNAi and computational promoter analysis". A special seminar on Whole Genome Studies And The Power of MicroArrays, Weizmann institute of science, Rehovot, October 11 2004. |
| R. Sorek, R. Shamir and G. Ast. "Assessing funcitonality of predicted splice variants". Genome Informatics meeting, Hinxton, UK, 22-26 September 2004. |
| R. Sorek, R. Shemesh, Y. Cohen, O. Basechess, G. Ast and R. Shamir. "The "promoters" of splicing: Intronic sequences that regulate alternative splicing", Genome Informatics meeting, Hinxton, UK, 22-26 September 2004. |
| C. Linhart, R. Elkon, Y. Shiloh, R. Shamir. "Conservation and Evolution of Promoter Sequences: A Comparative Analysis of Metazoan Genomes", poster presentation, The 4th Cold Spring Harbor Laboratory / Wellcome Trust conference on Genome Informatics, Hinxton, UK, September 2004. |
| R. Elkon, S. Rashi-Elkeles, Y. Lerenthal, C. Linhart, T. Tenne, N. Amariglio, G. Rechavi, R. Shamir and Y. Shiloh. "Dissection of DNA damage-induced transcriptional networks using a combination of microarrays, RNAi and computational promoter analysis" The 4th Cold Spring Harbor Laboratory / Wellcome Trust conference on Genome Informatics, Hinxton, UK, 22-26 September 2004. |
| T. Hartman, R. Sharan. "A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals" Fourth Workshop on Algorithms in Bioinformatics (WABI'04), September 14-17 2004. |
| R. Elkon. "SHARP - A Knowledgebase for Signalling Pathways". Cytoscape 2nd Annual Retreat, New York City, 8-9 September 2004. |
| R. Shamir"Computational dissection of regulatory networks using diverse high-throughput data" Keynote speaker, Computational Systems Bioinformatics conference (CSB2004) Stanford, California, August 16-19 2004. |
| T. Barzuza. J. S. Beckmann, R. Shamir, I. Pe'er, "Computational Problems in Perfect Phylogeny Haplotyping: XOR-Genotypes and Tag SNPs". Fifteenth Annual Combinatorial Pattern Matching Symposium (CPM '04), Istanbul, Turkey. July 5-7, 2004. |
| A. Tanay, I. Gat-Viks, R. Shamir "Transcription factor binding sites: selection forces caught in the action". Computer Science seminar, the Technion, June 24, 2004. |
| I. Gat-Viks, A. Tanay, R. Shamir "Modeling and Analysis of Heterogeneous Regulation in Biological Networks". Weizmann bioinformatics workshop on Computational Analysis of Biological Networks, June 24 2004. |
| R. Shamir "Transcription factor binding sites: selection forces caught in the action" BigRock and Systems Biology seminar, Weizmann Institute, June 14, 2004. |
| R. Shamir "Adventures in haplotyping" Computer Science colloquium, Tel Aviv University, June 6 2004. |
| I. Gat-Viks, A. Tanay, R. Shamir "A Global View of the Selection Forces in the Evolution of Yeast Cis-Regulation". Poster presentation, the Seventh Annual Israeli Bioinformatics Symposium, May 31 2004. |
| A. Tanay, I. Gat-Viks, R. Shamir "Modeling and analysis of heterogeneous regulation in biological networks". Poster presentation, the Seventh Annual Israeli Bioinformatics Symposium, May 31 2004. |
| G. Kimmel, R. Shamir "GERBIL: A New Algorithm for Resolving and Block Partitioning of Genotypes Using Maximum Likelihood". Poster presentation, the Seventh Annual Israeli Bioinformatics Symposium, May 31 2004. |
| M. R. Hoehe, R. Shamir, G. Kimmel, T. Kroslak, J. Ott, G. M. Church, H. Lehrach "High resolution haplotypes, the hapmap and the analysis of genotype-phenotype relationships" Cold Spring Harbor meeting on Biology of Genomes, May 12 - 16, 2004 |
| T. Hartman, R. Sharan. "A 1.5-Approximation Algorithm for Sorting by Transpositions and Transreversals" Fourth Haifa Workshop on Interdisciplinary Applications of Graph Theory, Combinatorics and Computing Haifa University, May 3-5 2004. |
| R. Sorek, R. Shamir, G. Ast. "The "promoters" of splicing: Intronic sequences that regulate alternative splicing" The first RECOMB satellite meeting on regulatory genomics, University of California, San Diego, March 26-27, 2004 |
| A. Tanay, I. Gat-Viks, R. Shamir. "Global patterns of evolutionary selection forces reveal multi-functionality in yeast transcription regulation". Cold Spring Harbor Laboratory Meeting on Systems Biology: Genomic Approaches to Transcriptional Regulation Cold Spring Harbor, NY March 4 - 7, 2004. |
| A. Tanay, I. Gat-Viks, R. Shamir "A global view of the selection forces in the evolution of yeast cis-regulation" Keystone Symposium on Biological Discovery Using Diverse High-Throughput Data, Colorado, April 2004. |
| R. Shamir"Revealing selection patterns in the evolution of yeast transcription regulation" The first RECOMB satellite meeting on regulatory genomics, University of California, San Diego, March 26-27, 2004 |
| R. Shamir "Algorithmic approaches to genetic networks analysis" University of California, San Diego March 25 2004. |
| R. Shamir"Maximum Likelihood Resolution of Multi-block Genotypes" Second RECOMB Satellite Workshop on Computational Methods for SNPs and Haplotypes, Carnegie Mellon University, 21 February 2004 |
| R. Shamir"Reverse engineering of genetic networks" Merck distinguished seminar series, Carnegie Mellon University 19 February 2004 |
| R. Shamir "Analysis of genetic networks: clsutering, biclustering and reverse engineering" Institute Curie, Paris January 26, 2004. |
| R. Shamir "Biological inference from high throughput heterogeneous data" Genopole, Evry, France, January 23, 2004. |
| T. Hartman. "A Simpler 1.5-Approximation Algorithm for Sorting by Transpositions" Bioinformatics Forum, Technion, January 22 2004. |
| T. Hartman, R. Shamir"A Simpler 1.5-Approximation Algorithm for Sorting by Transpositions" Bioinformatics Seminar, Ben-Gurion University, January 14, 2004. |
| R. Shamir"computational adventures in biology" Computer Science Department, the Weizmann Institute of Science, January 11 2004. |
2003
| R. Elkon, C. Linhart, G. Sternberg, R. Shamir, "DNA Microarray Analysis Workshop". Tel-Aviv University, Dec 31, 2003 |
| R. Shamir "Reverse engineering of biological systems" Distinguished Colloquium series, the Department of Electrical Systems, Tel Aviv University. December 28 2003. |
| R. Shamir"Inference in genetic networks" the First Viterbi Computational Biology Conference, University of Southern California, 16 December 2003 |
| R. Shamir"Bioinformatics in Israel" the First Viterbi Computational Biology Conference, University of Southern California, 15 December 2003 |
| R. Elkon, R. Sharan, C. Linhart, A. Tanay, A. Maron, N. Orlev, G. Sternberg, M. Kupiec, S. Rashi-Elkeles, Y. Shiloh, R. Shamir "Computational dissection of regulatory networks using gene expression and other high throughput data: case studies in mouse and yeast" Workshop on Bioinformatics for the management, analysis and interpretation of microarray data November 27 - 28, 2003, Bologna, Italy. |
| I. Gat-Viks, A. Tanay, R. Shamir. " Computational reconstruction of gene networks and regulatory signals" Tel Aviv University Bioinformatics Symposium 2003, 30 Sept. 2003. |
| G. Kimmel, M. Hoehe, R. Shamir. "GERBIL: A New Algorithm for Resolving and Block Partitioning of Genotypes Using Maximum Likelihood" 6th International Meeting On Single Nucleotide Polymorphism and Complex Genome Analysis, Virginia, November 2003. |
| R. Shamir"Computational dissection of regulatory networks using gene expression and other high throughput data" ESP exploratory workshop on "DNA microarray data analysis" National Center for Oncology Research (CNIO), Madrid, Spain, 30-31 October, 2003. |
| R. Shamir"Refined regulatory models and network inference via high level data integration" Bat Sheva Interdisciplinary Workshop on Global Information in Biological Systems: he Emergence of Functional Organization 19-21 October 2003, Hyatt Dead Sea, Israel |
| T. Hartman, R. Shamir."A Simpler 1.5-Approximation Algorithm for Sorting by Transpositions" Poster Presentation, IMA/RECOMB Satelite Workshop on Comparative Genomics, October 20-24 2003. |
| R. Elkon, S. Rashi-Elkeles, N. Weizman, C. Linhart, N. Amariglio, N. Orlev, G. Sternberg, A. Maron, G. Rechavi, A. Barzilai, R. Shamir, Y. Shiloh "Functional genomic dissection of ATM-dependent transcriptional response to ionizing radiation in the murine thymus". Poster presentation, International Workshop on Ataxia-Telangiectasia 2003, Fraser Island, Queensland, Australia, September 10 -14, 2003. |
| R. Elkon, S. Rashi-Elkeles, C. Linhart, N. Amariglio, N. Weizman, N. Orlev, G. Sternberg, A. Maron, G. Rechavi, A. Barzilai, R. Shamir, Y. Shiloh. "Dissection of ATM-dependent DNA damage response using a functional genomics approach" International Workshop on Ataxia-Telangiectasia 2003, Fraser Island, Queensland, Australia, September 10 -14, 2003. |
| I. Gat-Viks, R. Shamir. "Inference of genetic regulatory networks: problems and algorithms" Invited talk, ESF workshop on "Microarray data: untapped powers and hidden weaknesses", Leuven, Belguim, September 8-9 2003. |
| R. Shamir"Reconstructing Genetic Networks", Plenary speaker, 11th International Conference on Intelligent Systems for Molecular Biology (ISMB '03), Brisbane, Australia, 29 June - 3 July 2003. |
| T. Hartman. "A Simpler 1.5-Approximation Algorithm for Sorting by Transpositions". The fourteenth Annual Symposium on Combinatorial Pattern Matching (CPM'03), June 25-27 2003. |
| R. Shamir"Computational challenges in molecular biology" International Conference on Formal Power Series and Algebraic Combinatorics (FPSAC'03), Linkoping University (Sweden) June 23 - 27, 2003. |
| M. Ozery-Flato, R. Shamir. "Transforming Men into Mice Revisited" Poster presentation, Conference on Mathematics of Evolution and Phylogeny, Paris, 16-19 June 2003. |
| T. Hartman, R. Shamir."A Simpler 1.5-Approximation Algorithm for Sorting by Transpositions". Complexity and Cryptography Seminar, Weizmann Institute, June 8 2003. |
| T. Hartman, R. Shamir. "A Simpler 1.5-Approximation Algorithm for Sorting by Transposition" Third Haifa Workshop on Interdisciplinary Applications of Graph Theory, Combinatorics and Computing Haifa University, May 29 2003. |
| M. Ozery-Flato, R. Shamir. "Transforming men into mice revisited (a correction to the theory of sorting by reversals and translocations)" Third Haifa Workshop on Interdisciplinary Applications of Graph Theory, Combinatorics and Computing Haifa University, May 29 2003. |
| R. Shamir"Computational analysis of diverse genome-wide experimental data" Invited speaker, Conference on Genomics and Cancer: Integrating Genomics with Clinical Research and Therapy, The German Cancer Research Centre (DKFZ) Heidelberg, Germany, May 27, 2003. |
| I. Gat-Viks, A. Tanay, R. Sharan, R. Elkon, C. Linhart, M. Kupiec, Y. Shiloh, R. Shamir "Reverse Engineering of gene regulatory networks" Invited talk, Fourteenth Seminar on Algorithmics and Combinatorics in Biology, April 2-4, 2003, Lyon, France |
| A. Tanay, R. Sharan, M. Kupiec, R. Shamir "SAMBA: A framework for the integrated analysis of highly heterogenous genomic data" Invited talk, Cold Spring Harbor Meeting on Systems Biology: Genomic Approaches to Transcriptional Regulation March 6 2003. |
| R. Shamir "Degenerate primers and transcription modules" Israel Institute of Biological Research March 27 2003. |
| R. Shamir "Analysis Tools for Gene Expression and Gene Networks", Bioinformatics Workshop Series, the Weizmann Institute of Science, February 6, 2003. |
| R. Elkon, C. Linhart, R. Sharan, R. Shamir, and Y. Shiloh "Genome-wide In-silico Identification of Transcriptional Regulators Controlling Cell Cycle in Human Cells" Annual meeting of the Israeli Society for Genetics, Tel Aviv University, January 29 2003 |
2002
| R. Shamir "DNA Chips and their Applications in the Post-Genome Era" Felsenstein Medical Research Center, Beilinson campus, Rabin Medical Center, December 9, 2002. |
| R. Shamir "Analysis of Genetic Networks" Dagstuhl seminar on Computational Biology, Schloss Dagstuhl, Germany, 18 November 2002. |
| R. Shamir"Computational reconstruction of gene networks and regulatory signals" Cell Systems Biology. A European Research Training Conference. Berlin, Germany, November 2002. |
| R. Shamir "Spectrum Alignment: Basic Technology and Enhancements", Perlegen, Palo Alto, 22 October 2002. |
| I. Pe'er , N. Arbili, Y. Liu , C. Enck, C. Gelfand, R. Shamir "Genotyping with Partial and Universal Arrays" SNP 2002 meeting, Reykjavik, Iceland, October 2002. |
| R. Shamir "Resequencing with SBH". Callida Genomics, Sunnyvale, California 17 October 2002. |
| R. Shamir "Spectrum Alignment and Genetic Networks". Agilent Laboratories, Palo Alto, California 15 October 2002. |
| R. Shamir"Reverse engineering of gene networks and regulatory signals" Bat Sheva Interdisciplinary Workshop on Global Information in Biological Systems: The Emergence of Functional Organization, The Dead Sea, Israel, October 2002 |
| R. Shamir"Analysis of Microarry Gene Expression Data" Plenary speaker, Third Spanish Symposium on Bioinformatics and Computational Biology, Salamanca, Spain, September 18th-20th 2002 |
| C. Linhart, R. Shamir "Designing Degenerate Primers: Theory and Practice" National Center for Biotechnology, Madrid. September 17th 2002. |
| C. Linhart, R. Shamir. "The Degenerate Primer Design Problem". The 10th International Conference on Intelligent Systems for Molecular Biology (ISMB '02), Edmonton, Canada. August 3-7, 2002. |
| R. Shamir"Unraveling tight functional modules via microarry data" Invited talk, German Israeli Fund (GIF) meeting on Challenges in Genomic Research, Neurodegenerative Diseases, Stem-Cells and Bioethics. Heidelberg, July 8-10 2002. |
| C. Linhart, R. Shamir "The Degenerate Primer Design Problem". Poster presentation German Israeli Fund (GIF) meeting on Challenges in Genomic Research, Neurodegenerative Diseases, Stem-Cells and Bioethics. Heidelberg, July 8-10 2002. |
| R. Elkon, C. Linhart, R. Sharan, R. Shamir, Y. Shiloh "Genome-wide in-silico determination of transcriptional regulation modules controlling cell cycle in human cells". Poster presentation, German Israeli Fund (GIF) meeting on Challenges in Genomic Research, Neurodegenerative Diseases, Stem-Cells and Bioethics. Heidelberg, July 8-10 2002. |
| T. Fuchs, B. Malecova, C. Linhart, R. Sharan, M. Khen, R. Herwig, D. Shmulevich, R. Elkon, M. Steinfath, J. K. O'Brien, U.Radelof, H. Lehrach, D. Lancet and R. Shamir "DEFOG: A Practical Scheme for Deciphering Families of Genes" Invited talk, German Israeli Fund (GIF) meeting on Challenges in Genomic Research, Neurodegenerative Diseases, Stem-Cells and Bioethics. Heidelberg, July 8-10 2002. |
| R. Shamir R. Shamir, A. Maron. "Expander: A clustering and visualization tool for gene expression analysis" Special seminar, Faculty of Medicine, Tel Aviv University, June 2002. |
| A. Akavia, H. Aronowitz, A. Lerner, S. Safra, H.Senderowitz, R. Shamir "Algorithm and complexity for designing multi route mix and split libraries". Poster presentation, Annual Israeli Bioinformatics Symposium, Weizmann Institute, Rehovot, May 14 2002 |
| R. Shamir"Computational challenges in molecular biology in the post-genome era" Invited speaker, 2002 Annual Meeting of the Israeli Mathematical Union, Mitspe Ramon, May 9-10 2002. |
| E. Halperin, S. Halperin, T. Hartman, R. Shamir. Handling Long Targets and Errors in Sequencing by Hybridization. Computational Biology Seminar, McGill University, Montreal, Canada, April 2002. |
| A. Bergeron, C. Chauve, T. Hartman, K. St-Onge. Enumerating optimal sequences of reversals: tools and experiments. Poster Presentation, The Sixth International Conference on Computational Molecular Biology (RECOMB'02), April 18-21 2002. |
| E. Halperin, S. Halperin, T. Hartman, R. Shamir. Handling Long Targets and Errors in Sequencing by Hybridization. The Sixth Annual International Conference on Computational Molecular Biology (RECOMB'02), April 18-21 2002. |
| R. Elkon, R. Shamir and Y. Shiloh "Genome-wide in-silico identification of target genes of transcription factors". The third Medical School Research Fair, Tel Aviv University Faculty of Medicine, March 25 2002 |
| R. Shamir"The Restriction Scaffold Problem" Invited speaker, 2002 Annual Meeting of ISTMB - The Israeli Society for Theoretical and Mathematical Biology, Bar Ilan University, March 2002. |
| R. Shamir"Novel Computational Tools for Functional Genomics" Invited speaker, Bio-Tech Israel 2002, Israel National Biotechnology week, Tel Aviv March 20-21 2002. |
| R. Shamir"Computational Techniques for DNA Arrays: Gene Networks Expansion and Resequencing" Invited speaker, MGED Satellite Meeting to the 2002 AAAS Annual Meeting and Science Innovation Exposition, Boston, Mass, February 13-16 2002. |
| R. Shamir"Computational Analyses of Gene Expression Data" Invited speaker, FISEB 2002, The 3rd Federation of Israel Societies for Experimental Biology Congress, February 4th - 7th 2002, Eilat |
| R. Elkon, R. Shamir, Y. Shiloh "Genome-wide in silico identification of target human genes of transcription factors" poster, FISEB 2002, The 3rd Federation of Israel Societies for Experimental Biology Congress, February 4th - 7th 2002, Eilat |
| N. Orlev, R. Shamir, Y. Shiloh "PIVOT - A bioinformatic tool for visualization of protein-protein interactions" poster, FISEB 2002, The 3rd Federation of Israel Societies for Experimental Biology Congress, February 4th - 7th 2002, Eilat |
| R. Shamir "What is bioinformatics: A personal perspective" Bioinformatics program, the Weizmann Institute January 27 2002 |
| R. Shamir A. Ben-Dor, R. M. Karp, B. Schwikowsky, R. Shamir "The Restriction Scaffold Problem". Computer Science Colloquium, the Heberw University, Jerusalem, January 14 2002 |
| E. Halperin, S. Halperin, T. Hartman, R. Shamir. Handling Long Targets and Errors in Sequencing by Hybridization. Computational Biology Seminar, Hebrew University, 2002. |
| E. Halperin, S. Halperin, T. Hartman, R. Shamir. Handling Long Targets and Errors in Sequencing by Hybridization. Complexity and Cryptography Seminar, Weizmann Institute, 2002. |
2001
| R. Sharan, R. Elkon, R. Shamir "Analysis of Gene Expression Data Via Clustering" NIPS 2001 Workshop on Machine Learning Techniques for Bioinformatics, Whistler/Blackcomb resort, British Columbia, Canada December 9 2001 |
| R. Sharan, R. Elkon, R. Shamir "Analysis of Gene Expression Data Via Clustering" Fifth Annual Conference of Computational Genomics, November 28 2001 Baltimore, Maryland. |
| A. Akavia, H. Aronowitz, S. Safra, H.Senderowitz, R. Shamir "Algorithm and complexity for designing multi route mix and split libraries" First Israeli CombiTech Symposium, Weizmann Institute, 14 October 2001. |
| I. Pe'er, N. Arbili, R. Shamir "Computational Resequencing by Universal Microarrays" Single Nucleotide Polymorphism and Complex Genome Analysis, Stockholm, Sweden, 10th-13th October, 2001 |
| R. Shamir "Analysis of DNA Chips and Expression data" Department of Medical Informatics, Stanford University, September 5 2001 |
| R. Shamir "Analysis of DNA Chips and Expression data" Agilent Technologies, Palo Alto, September 5 2001 |
| R. Shamir "Computational approaches to the analysis of microarray data: From clusters to networks" GeneExpress seminar, Sheba Hospital, Tel Hashomer, Israel July 17 2001 |
| R. Shamir"Resurrecting SBH" Invited speaker, 12th Annual Symposium on Combinatorial Pattern Matching Jerusalem, Israel 1-4 July, 2001. |
| R. Shamir"Analysis of Gene Expression Data" Invited speaker, Ernst Schering Research Foundation Workshop on Bioinformatics and Genome Analysis, Berlin, June 17th-19th 2001. |
| R. Sharan, R. Elkon, R. Shamir, "Cluster Analysis and its Applications to Gene Expression Data" Annual Israel Bioinformatics Symposium, Tel Aviv University, June 17 2001 |
| R. Shamir "Algorithmic Challenges in the Human Genome Project - and beyond", Faculty of Computer Science, the Technion, Haifa, May 15 2001. |
| T. Pupko, R. Sharan, R. Shamir., D. Graur "A Test for Positive Darwinian Selection", Currents in Computational Molecular Biology 2001, N. El-Mabrouk, T. Lengauer, D. Sankoff (eds.), Les Publications CRM, Montreal 2001, pp. 213-214. |
| C. Linhart, R. Shamir. "The Degenerate Primer Selection Problem", Currents in Computational Molecular Biology 2001, N. El-Mabrouk, T. Lengauer, D. Sankoff (eds.), Les Publications CRM, Montreal 2001, pp. 5-6. |
| D. Tsur, R. Shamir. "Improved clustering algorithms for the random cluster graph model" Workshop on Interdisciplinary Applications of Graphs and Algorithms Haifa University April 17 2001. |
| R. Sharan, R. Shamir, D. Tsur, "Cluster Graph Modification Problems" Workshop on Interdisciplinary Applications of Graphs and Algorithms Haifa University April 17 2001. |
| S. Rashi-Elkeles, A. Regev, R. Elkon, R. Sharan, N. Zak, L. Brodsky, A. Kamsler, A. Leontovitch, N. Weisman, D. Leshkovitz, O. Mor, A. Barzilai, E. Feinstein, R. Shamir, Y. Shiloh, A. Bar-Shira `Constitutive Response to Genotoxic Stress in a Mouse Model of Ataxia-Telangiectasia", Research fair, Sackler Faculty of Medicine, Tel Aviv University, April 2001 |
| N. Orlev, R. Shamir, Y. Shiloh. "A bioinformatic tool for visualization of protein-protein interactions" Research fair, Sackler Faculty of Medicine, Tel Aviv University, April 2001 |
| R. Shamir"Algorithmic problems in the Human Genome Project - and beyond" Invited plenary speaker, Workshop on Interdisciplinary Applications of Graphs and Algorithms Haifa University April 17 2001. |
| I. Pe'er, R. Shamir "Spectrum alignment: Efficient resequencing by hybridization" 3rd Meeting on SNPs and Complex Genome Analysis, Taos, NM. September 2000. Human Mutation 17(4) pp. 338, April 2001. |
| R. Shamir "Bioinformatics challenges in high-throughput genomics and proteomics: from clusters to pathways" The Volcani Institute of Agriculture March 21 2001. |
| R. Shamir"Computational problems in DNA microarrays: from gene expression analysis to pathways" Bioinformatics 2001 Invited plenary talk, Skövde, Sweden, March 2001 |
| R. Shamir"Algorithmic tools for expression analysis and novel utilizations of DNA Chips" CHI Third Annual Conference on Integrated BioinformaticsInvited presentation, Zurich, Switzerland, January 2001. |
2000
| R. Sharan and R. Shamir. "CLICK: A Clustering Algorithm for Gene Expression Analysis", Currents in Computational Molecular Biology, S. Miyano, R. Shamir, T. Takagi, eds. Universal Academy Press, 2000. |
| R. Shamir "Bioinformatics challenges in high-throughput genomics and proteomics technologies: from clusters to pathways" Dept of Plant Genetics, Tel Aviv University, 21 December 2000. |
| R. Shamir "Bioinformatics challenges in analysis of DNA microarray data: from clusters to pathways" The Gilman International Conference on Current Trends in Science Research and High-Technlogy, Free University, Brusseles, Belgium 28 November 2000. |
| R. Shamir"Algorithmic tools for gene expression analysis and novel utilizations of DNA Chips", Symposium on Human Genetics in the Post-Genomic Age, Maagan, Israel November 2000. |
| C. Linhart, T. Fuchs, R. Sharan, M. Khen, G. Glusman, B. Malecova, U. Radelof, D. Shmulevich, J. O'Brien, T. Pilpel, H. Lehrach, D. Lancet, R. Shamir "Deciphering the Human olfactory subgenome", poster presentation, Symposuim on Human Genetics in the Post-Genomic Age, Maagan, Israel November 2000. |
| R. Shamir "Bioinformatics of DNA Chips and gene expression data", Israel Institute of Biological Research, October 26, 2000. |
| R. Shamir"DNA Chips and Algorithms: a Spectrum of Opportunities" invited speaker, Workshop on Expression Array Technologies and Methods of Analysis, Institute of Pure and Applied Mathematics, UCLA, October 12-15 2000. |
| R. Shamir"Novel algorithms for gene expression analysis and DNA Chips" ESABIO Conference on Bioinformatics, Paris, France, October 10 2000. |
| R. Shamir "Computational Methods in Gene Expression and Gene Networks" Proteome, Beverly MA, Sept. 21, 2000. |
| R. Shamir "CLICK and BPM: Utilizing Gene Expression data" Millennium Pharaceuticals, MA, Sept. 20, 2000. |
| R. Shamir "DNA Chips and Algorithms: a Spectrum of Opportunities" Incyte Pharmaceuticals, Palo Alto, CA, August 24, 2000. |
| T. Fuchs, Khen, M., Glusman, G., Malecova, B., Radelof,U., Linhart,C., Sharan,R., Shmulevich,D., O'Brien,J.K., Shamir,R., Lehrach,H., Lancet,D. "Deciphering the Human Olfactory Subgenome". Poster presented at: 13th International Symposium on Olfaction and Taste Meeting (ISOT XIII) and 14th European Chemoreception Research Organization Congress (ECRO XIV), Brighton, UK, July 2000. |
| P. Hell, R. Shamir, R. Sharan. "A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs", Workshop on Dynamic Graph Problems Victoria, Canada, June 2000. |
| A. Natanzon, R. Shamir, R. Sharan. "Complexity Classification of Some Edge Modification Problems ", Tenth SIAM conference on Discrete Mathematics, Minneapolis, June 2000. |
| P. Hell, R. Shamir, R. Sharan. "A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs", Tenth SIAM conference on Discrete Mathematics, Minneapolis, June 2000. |
| C. Linhart, R. Shamir. "The Degenerate Primer Design Problem" The Israel Bioinformatics Symposium 2001, June 17 2001, Tel-Aviv, Israel. |
| R. Shamir"Incomplete Directed Phylogeny: Graph characterizations, Sandwich formulations and an efficient algorithm", keynote speaker, Workshop on Structured Families of Graphs, Fields Institute, Toronto, May 2000. |
| P. Hell, R. Shamir, R. Sharan. "A Fully Dynamic Algorithm for Recognizing and Representing Proper Interval Graphs", Workshop on Structured Families of Graphs, Fields Institute, Toronto, May 2000. |
| R. Shamir, "Cluster Analysis of Gene Expression Data", invited speaker, workshop on Exploring the Genome with DNA Microarrays, Boehringer Ingelheim Vienna Biocenter, Vienna, March 2000. |
| R. Shamir, "Gene-Clustering Algorithm with Visualization Tools" CHI Second Annual Conference on Integrated Bioinformatics: High-Throughput Interpretation of Genes and Proteins", Invited presentation, Zurich, Switzerland, 19-21 January 2000. |