Talks and seminars

Presentations

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, 29-30 September 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, 29-30 September 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, 29-30 September 2021.

L. Pu and R. Shamir. "A 3-way classifier for metagenomic sequences". Poster presentation, Edmond J. Safra Center Retreat 2021, Maagan-Eden, Sea of Galilee, 29-30 September 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, 29-30 September 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, 29-30 September 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, 29-30 September 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, 29-30 September 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 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

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

 

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".
UC San Diego, February 12, 2019.

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".
Tsinghua University, Beijing, China, January 17, 2019.

R. Shamir. "Integrated analysis of cancer data and precision medicine''. Keynote speaker, APBC 2019, Wuhan, China, January 14-16, 2019.