Towards Regulatory-Confirmed Adaptive Clinical Trials: Machine Learning Opportunities and Solutions
O. Noy Klein, A. Hüyük, R. Shamir, U. Shalit, M. van der Schaar
arXiv doi: https://doi.org/10.48550/arXiv.2503.09226 (2025).
Integrating gene expression, mutation and copy number data to identify driver genes of recurrent chromosome-arm losses
R. Saad, R. Shamir*, U. Ben-David*.
BioRxiv doi: https://doi.org/10.1101/2025.02.22.639659 (2025).
Predicting appropriateness of antibiotic treatment among ICU patients with hospital acquired infection
E. Rannon, E. Goldschmidt, D. Bernstein, A. Wasserman, M. Roimi, A. Shrot, D. Coster, R. Shamir.
npj Digit. Med. 8, 87 https://doi.org/10.1038/s41746-024-01426-9 (2025).
The cGAS–STING, p38 MAPK, and p53 pathways link genome instability to accelerated cellular senescence in ATM-deficient murine lung fibroblasts
M. Haj, Y. Frey, A. Levon, A. Maliah, T. Ben-Yishay, R. Slutsky, R. Smoom, Y. Tzfati, U. Ben-David, C. Levy, R. Elkon, Y. Ziv, Y. Shiloh
PNAS 122 (2) e2419196122, https://doi.org/10.1073/pnas.2419196122 (2025).
A p62-dependent rheostat dictates micronuclei catastrophe and chromosome rearrangements
S. Martin, S. Scorzoni, S. Cordone, A. Mazzagatti, G. V. Beznoussenko, A. L. Gunn, M. Di Bona, Y. Eliezer, G. Leor, T. Ben-Yishay, A. Loffreda, V. Cancila, M. C. Rainone, M. R. Ippolito, V. Martis, F. Bedin, M. Garré, L. P. Vaites, P. Vasapolli, S. Polo, D. Parazzoli, C. Tripodi, A. A. Mironov, A. Cuomo, U. Ben-David, S. F. Bakhoum, E. M. Hatch, P. Ly, S. Santaguida.
Science adj7446, https://doi.org/10.1126/science.adj7446 (2024).
Increased RNA and Protein Degradation Is Required for Counteracting Transcriptional Burden and Proteotoxic Stress in Human Aneuploid Cells
M. R. Ippolito, J. Zerbib, Y. Eliezer, E. Reuveni, S. Viganò, G. De Feudis, E. D. Shulman, A. S. Kadmon, R. Slutsky, T. Chang, E. M. Campagnolo, S. Taglietti, S. Scorzoni, S. Gianotti, S. Martin, J. Muenzner, M. Mülleder, N. Rozenblum, C. Rubolino, T. Ben-Yishay, K. Laue, Y. Cohen-Sharir, I. Vigorito, F. Nicassio, E. Ruppin, M. Ralser, F. Vazquez, S. Santaguida, U. Ben-David
Cancer Discovery CD-23-0309 https://doi.org/10.1158/2159-8290.CD-23-0309 (2024).
Aneuploidy as a driver of human cancer
E. Sdeor, H. Okada, R. Saad, T. Ben-Yishay, U. Ben-David.
Nature Genetics s41588-024-01916-2, https://doi.org/10.1038/s41588-024-01916-2 (2024).
4CAC: 4-class classifier of metagenomic assemblies using machine learning and assembly graphs
L. Pu, R. Shamir.
Nucleic Acids Research gkae799, https://doi.org/10.1093/nar/gkae799 (2024).Race-dependent variability in the human tumor mycobiome
D. Coster, T. Margalit, B. Bursi*, R. Shamir*.
BioRxiv doi: https://doi.org/10.1101/2024.06.01.596924 (2024).
Drugst.One -- A plug-and-play solution for online systems medicine and network-based drug repurposing
A. Maier, M. Hartung, M. Abovsky, K. Adamowicz, G. D. Bader, S. Baier, D. B. Blumenthal, J. Chen, M. L. Elkjaer, C. Garcia-Hernandez, M. Hoffmann, I. Jurisica, M. Kotlyar, O. Lazareva, H. Levi, M. List, S. Lobentanzer, J. Loscalzo, N. Malod-Dognin, Q. Manz, J. Matschinske, M. Oubounyt, A. R. Pico, R. T. Pillich, J. M. Poschenrieder, D. Pratt, N. Pržulj, S. Sadegh, J. Saez-Rodriguez, S. Sakar, G. Shaked, R. Shamir, N. Trummer, U. Turhan, R. Wang, O. Zolotareva, J. Baumbach.
Nucleic Acids Research gkae388 (2024).
Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases
A. Zorea, D. Pellow, L. Levin, S. Pilosof, J. Friedman, R. Shamir, I. Mizrahi.
Nature Communications 15, Article number: 3147, https://doi.org/10.1038/s41467-024-47272-x (2024).
The predictive capacity of polygenic risk scores for disease risk is only moderately influenced by imputation panels tailored to the target population
H. Levi, R. Elkon*, R. Shamir*.
Bioinformatics, btae036, https://doi.org/10.1093/bioinformatics/btae036 (2024).
Clustering the cortical laminae: in vivo parcellation
I. Shamir, Y. Assaf, R. Shamir.
Brain Structure and Function, https://doi.org/10.1007/s00429-023-02748-2 (2024).
A feature ranking algorithm for clustering medical data
E. Shpigelman, R. Shamir.
MedRxiv doi: 10.1101/2023.09.30.23296349 (2023).
Inferring transcriptional activation and repression activity maps in single-nucleotide resolution using deep-learning
T. Hait, R. Elkon, R. Shamir.
Research Square https://doi.org/10.21203/rs.3.rs-3270775/v1 (2023).
Efficient minimizer orders for large values of $k$ using minimum decycling sets
D. Pellow, L. Pu, B. Ekim, L. Kotlar, B. Berger, R. Shamir, Y. Orenstein
Genome Research DOI: 10.1101/gr.277644.123 (2023).
Evaluation of European-based polygenic risk score for breast cancer on Ashkenazi Jewish women
H. Levi, S. Carmi, S. Rosset, R. Yerushalmi, A. Zick, T. Yablonski-Peretz, .... (127 members of the BCAC Consortium)..., S. Ben-Shachar, N. Elefant*, R. Shamir* and R. Elkon*.
Journal of Medical Genetics doi:10.1136/jmg-2023-109185 (2023).Integration of gene expression and DNA methylation data across different experiments
Y. Itai, N. Rappoport, R. Shamir.
Nucleic Acids Research, gkad566, https://doi.org/10.1093/nar/gkad566 (2023).Single cell Hi-C identifies plastic chromosome conformations underlying the gastrulation enhancer landscape
N. Rappaport, E. Chomsky, T. Nagano, C. Seibert, Y. Lubling, Y. Baran, A. Lifshitz, W. Leung, Z. Mukamel, R. Shamir, P. Fraser, A. Tanay.
Nature Communications 14(1):3844. doi: 10.1038/s41467-023-39549-4 (2023).
Clustering of clinical-echocardiographic phenotypes of covid-19 disease using machine-learning techniques
E. Shpigelman*, A. Hochstadt*, D. Coster, I. Merdler, E. Ghantous, Y. Szekely, Y, Lichter, P. Taieb, A. Banai, O. Sapir, Y. Granot, L. Lupu, A. Borohovitz, S. Sadon, S. Banai, R. Rubinshtein, Y. Topilsky, R. Shamir.
Scientific Reports 13:8832 doi: 10.1038/s41598-023-35449-1 (2023).
The Effect of Body Mass Index Reduction on Intraocular Pressure in a Large, Prospective Population-based Cohort Study in Israel
D. Coster, A. Rafie, N. Savion, R. Rachmiel, S. Kurtz, S. Berliner, I. Shapira, D. Zeltser, O. Rogowski, S. Shenhar-Tsarfaty, M. Waisbourd
PLoS One, https://doi.org/10.1371/journal.pone.0285759 (2023).Time-dependent Iterative Imputation for Multivariate Longitudinal Clinical Data
Omer Noy, Ron Shamir
arXiv https://doi.org/10.48550/arXiv.2304.07821 (2023).
Parameterized syncmer schemes improve long-read mapping
A. Dutta, D. Pellow, R. Shamir.
PLOS Comp Bio, https://doi.org/10.1371/journal.pcbi.1010638 (2022).
The DOMINO web-server for active module identification analysis.
H. Levi, N. Rahmanian, R. Elkon, R. Shamir.
Bioinformatics, btac067, https://doi.org/10.1093/bioinformatics/btac067 (2022).
Whole-genome duplication shapes the aneuploidy landscape of human cancers.
Prasad, M. Bloomfield, H. Levi, K. Keuper, S. V. Bernhard, N. C. Baudoin, G. Leor, Y. Eliezer, M. Giam, C. Kit Wong, G. Rancati, Z. Storchová, D. Cimini, U. Ben-David.
Cancer Res, https://doi.org/10.1158/0008-5472.CAN-21-2065 (2022).
Relationship Between Pemphigus Vulgaris Severity and PCR-positive Herpes Simplex Virus
Baum, I. Atar, D. Coster, S. Dovrat, M. Solomon, E. Sprecher, T. Zeeli and A. Barzilai.
ActaDV, Vol. 102 (2022), DOI: https://doi.org/10.2340/actadv.v102.917 (2022).
Data Set-Adaptive Minimizer Order Reduces Memory Usage in k-Mer Counting
D. Flomin, D. Pellow and R. Shamir.
Journal of Computational Biology, Vol. 29, Pp. 1–14 DOI: 10.1089/cmb.2021.0599 (2022).
3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs
L. Pu and R. Shamir.
Bioinformatics, Volume 38, Issue Supplement 2, September 2022, Pages ii56–ii61, https://doi.org/10.1093/bioinformatics/btac468 (2022).A machine learning model for predicting deterioration of COVID-19 inpatients
O. Noy*, D. Coster*, M. Metzger, I. Attar, S. Shenhar-Tsafraty, S. Berliner, G. Rahav, O.Rogowski, R. Shamir.
Nature Scientific Reports Article 2630 DOI 10.1038/s41598-022-05822-7 (2022).
CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps.
T.A. Hait, R. Elkon, R. Shamir.
Nucleic Acids Research gkac048, https://doi.org/10.1093/nar/gkac048 (2022).
DOMINO: a novel network-based module detection algorithm with reduced rate of false calls
H. Levi, R. Elkon, R. Shamir.
Molecular Systems Biology 17:e9593 (2021).
Improving the efficiency of de Bruijn graph construction using compact universal hitting sets
Y. Ben-Ari, D. Flomin, L. Pu, Y. Orenstein, R. Shamir.
Proc. ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), August 2021, Article No.: 4, pp 1–9, https://dl.acm.org/doi/10.1145/3459930.3469520 (2021).
Early detection of prostate gland and breast cancer risk based on routine check-up data using survival analysis trees for left-truncated and right-censored data
D. Coster, E. Fischer, S. Shenhar-Tsarfaty, T. Menes, S. Berliner, O. Rogowski, D. Zeltser, I. Shapira, E. Halperin, S. Rosset, M. Gorfine, R. Shamir.
MedRxiv, doi: https://doi.org/10.1101/2021.01.11.21249491 (2021).
SCAPP: An algorithm for improved plasmid assembly in metagenomes
D. Pellow, M. Probst, O. Furman, A. Zorea, A. Segal, I. Mizrahi, R. Shamir.
Microbiome 9, 144 (2021), https://doi.org/10.1186/s40168-021-01068-z (2021).
Contribution of clinical breast exam to cancer detection in women participating in a modern screening program.
T.S. Menes, D. Coster and S. Shenhar-Tsarfaty.
BMC Women's Health, 21(1) 368, pp.1-8., https://doi.org/10.1186/s12905-021-01507-x (2021).
C-reactive protein velocity discriminates between acute viral and bacterial infections in patients who present with relatively low CRP concentrations
D. Bernstein, D. Coster, S. Berliner, I. Shapira, D. Zeltser, O. Rogowski, A. Adler, O. Halutz, T. Levinson, O. Ritter, S. Shenhar-Tsarfaty & A. Wasserman.
BMC Infect Dis 21, 1210 (2021). https://doi.org/10.1186/s12879-021-06878-y (2021).
Classification of node-positive melanomas into prognostic subgroups using keratin, immune and melanogenesis expression patterns
D. Netanely, S. Leibou, R. Parikh, N. Stern, H. Vaknine, R. Brenner, S. Amar, R. Haiat Factor, T. Perluk, J. Frand, E Nizri, D. Hershkovitz, V. Zemser-Werner, C. Levy, R. Shamir.
Oncogene https://doi.org/10.1038/s41388-021-01665-0 (2021).
Using the kinetics of C-reactive protein response to improve the differential diagnosis between acute bacterial and viral infections
D. Coster, A. Wasserman, E. Fisher, O. Rogowski, D. Zeltser, I. Shapira, D. Bernstein, Ahuva Meilik, E. Raykhshtat, P. Halpern, S. Berliner, S. Shenhar-Tsarfaty, R. Shamir.
Infection, https://doi.org/10.1007/s15010-019-01383-6 (2020).
PlasClass improves plasmid sequence classification
D. Pellow, I. Mizrahi, R. Shamir.
PLoS Comput Biol, 16(4): e1007781. https://doi.org/10.1371/journal.pcbi.1007781 (2020).MONET: Multi-omic patient module detection by omic selection
N. Rappoport, R. Safra, R. Shamir.
PLoS Computational Biology 16 (9) e1008182 (2020).
Melanoma-secreted lysosomes trigger monocyte-derived dendritic cell apoptosis and limit cancer immunotherapy
N. S. Magal , L. Farhat-Younis , D. Rasoulouniriana , A. Glieberman , A. Gutwillig , L. Tal , D. Netanely, R. Shamir , R. Blau , H. Gutman ,P. Rider, Y. Carmi.
Cancer Research, doi: 10.1158/0008-5472.CAN-19-2944 (2020).
CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps
T. Hait, R. Elkon, R. Shamir.
BioRxiv, https://www.biorxiv.org/content/10.1101/707158v3 (2019).Personalized prediction of adverse heart and kidney events using baseline and longitudinal data from SPRINT and ACCORD
G. Dinstag, D. Amar, E. Ingelsson, E. Ashley and R. Shamir.
PLOS ONE, https://doi.org/10.1371/journal.pone.0219728 (2019).
Inaccuracy of the log‐rank approximation in cancer data analysis
N. Rappoport and R. Shamir.
Molecular Systems Biology (2019) 15:e8754https://doi.org/10.15252/msb.20188754 (2019).
Prodigy: personalized prioritization of driver genes
G. Dinstag, R. Shamir.
Bioinformatics btz815, https://doi.org/10.1093/bioinformatics/btz815 (2019).PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets
D. Netanely, N. Stern, I. Laufer, R. Shamir.
BMC Bioinformatics 20:732, https://doi.org/10.1186/s12859-019-3142-5 (2019).
Unravelling plasmidome distribution and interaction with its hosting microbiome
A. Kav Brown, R. Rozov, D. Bogmil, S. J. Sorensen, I. Benhar, E. Halperin, R. Shamir, I. Mizrahi.
Environmental Microbiology, https://doi.org/10.1111/1462-2920.14813 (2019).
The EXPANDER integrated platform for transcriptome analysis
T. A. Hait, A.Maron-Katz., D. Sagir, D. Amar, I. Ulitsky, C. Linhart, A. Tanay, R. Sharan, Y. Shiloh, R. Elkon, R.Shamir.
Journal of Molecular Biology, https://doi.org/10.1016/j.jmb.2019.05.013 (2019).
Genome Rearrangement Problems with Single and Multiple Gene Copies: A Review
R. Zeira and R. Shamir.
Bioinformatics and Phylogenetics: Seminal contributions of Bernard Moret, T. Warnow, Editor, pp. 205--242, Springer Nature Switzerland AG (2019).