4CAC: 4-class classification of metagenomic assemblies using machine learning and assembly graphs
L. Pu, R. Shamir.
BioRxiv 2023.01.20.524935 doi: https://doi.org/10.1101/2023.01.20.524935 (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).
Clustering multilayered cytoarchitectonic surface-based data in the brain.
I. Shamir, Y. Assaf, R. Shamir.
BioRxiv doi: doi: https://doi.org/10.1101/2022.10.29.514347 (2022).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.
BioRxiv doi: https://www.biorxiv.org/content/10.1101/2022.10.18.512682v1 (2022).
Integration of gene expression and DNA methylation data across different experiments
Y. Itai, N. Rappoport, R. Shamir.
BioRxiv 2022.09.21.508920 https://doi.org/10.1101/2022.09.21.508920 (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).
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).
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).
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).
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).
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).
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).
Using syncmers improves long-read mapping
A. Dutta, D. Pellow, R. Shamir.
BioRxiv 2022.01.10.475696 (2022).
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).
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).
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).
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).
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).
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).
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).MONET: Multi-omic patient module detection by omic selection
N. Rappoport, R. Safra, R. Shamir.
PLoS Computational Biology 16 (9) e1008182 (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).
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).
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).
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).
Prodigy: personalized prioritization of driver genes
G. Dinstag, R. Shamir.
Bioinformatics btz815, https://doi.org/10.1093/bioinformatics/btz815 (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).
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).
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).
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).
NEMO: cancer subtyping by integration of partial multi-omic data
N. Rappoport and R. Shamir.
Bioinformatics, https://doi.org/10.1093/bioinformatics/btz058 (2018).
GePMI: A statistical model for personal intestinal microbiome identification
Z. Wang, H. Lou, R. Shamir, R. Jiang, T. Chen.
npj Biofilm and Microbiome} 4: 20, https://doi.org/10.1038/s41522-018-0065-2 (2018).
Genomic meta-analysis of the interplay between 3D chromatin organization and gene expression programs under basal and stress conditions
I. Nurick, R. Shamir and R. Elkon.
Epigenetics & Chromatin (2018) 11:49 https://doi.org/10.1186/s13072-018-0220-2 (2018).
Multi-omic and multi-view clustering algorithms: review and cancer benchmark
N. Rappoport & R. Shamir
Nucleic Acids Research, 46 (20) pp. 10546–-10562 (2018).
Computational analysis of mRNA expression profiling in the inner ear reveals candidate transcription factors associated with proliferation, differentiation, and deafness
K. Perl, R. Shamir and K. B. Avraham
Human Genomics, 12:30, https://doi.org/10.1186/s40246-018-0161-7 (2018).
Sorting cancer karyotypes using double-cut-and-joins, duplications and deletions
R. Zeira and R. Shamir.
Bioinformatics, bty381, https://doi.org/10.1093/bioinformatics/bty381 (2018).
FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map
T. A. Hait, D. Amar, R. Shamir, R. Elkon.
Genome Biology, 19:56, https://doi.org/10.1186/s13059-018-1432-2 (2018).
MorphDB: Prioritizing Genes for Specialized Metabolism Pathways and Gene Ontology Categories in Plants
A. Zwaenepoel, T. Diels, D. Amar, T. Van Parys, R. Shamir, Y. Van de Peer and O. Tzfadia.
Front. Plant Sci., https://doi.org/10.3389/fpls.2018.0035 (2018).
ADEPTUS: A discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases
D. Amar, A. Vizel, C. Levy & R. Shamir.
Bioinformatics, bty027, https://doi.org/10.1093/bioinformatics/bty027 (2018).
Faucet: streaming de novo assembly graph construction
R. Rozov, G. Goldshlager, E. Halperin, R. Shamir.
Bioinformatics, 34 (1) 147–154 (2018).
Tracing the neural carryover effects of interpersonal anger on resting-state fMRI and their relation to traumatic stress symptoms in a subsample of soldiers
G. Gilam, A. Maron-Katz, E. Kliper, T. Lin, E. Fruchter, R. Shamir, T. Hendler.
Frontiers in Behavioral Neuroscience, doi: 10.3389/fnbeh.2017.00252 (2017).
Reconstructing cancer karyotypes from short read data: the half full and half empty glass
R. Eitan, R. Shamir.
BMC Bioinformatics, 18:488, 2017. Preliminary version: bioRxiv 152447; doi: https://doi.org/10.1101/152447 (2017).
Analysis of blood-based gene expression in idiopathic Parkinson disease
R. Shamir, C. Klein, D. Amar, E. J. Vollstedt, M. Bonin, M. Usenovic, Y. C. Wong, A. Maver, A. Troiano, S. Poths, H. Safer, J.-C. Corvol, S. Lesage, O. Lavi, G. Deuschl, G. Kuhlenbaeumer, H. Pawlack, I. Ulitsky, M. Kasten, O. Riess, A. Brice, B. Peterlin, D. Krainc.
Neurology, 89(16):1676-1683 (2017).
Designing small universal k-mer hitting sets for improved analysis of high throughput sequencing
Y. Orenstein, D. Pellow, G. Marcais, R. Shamir, C. Kingsford.
PLoS Computational Biology, 13(10): e1005777 (2017).
A Linear-Time Algorithm for the Copy Number Transformation Problem
R. Zeira, M. Zehavi and R. Shamir
Journal of Computational Biology, DOI: 10.1089/cmb.2017.0060 (2017).
An extensive enhancer-promoter map generated by genome-scale analysis of enhancer and gene activity patterns
T. A. Hait, D. Amar, R. Shamir and R. Elkon.
BioRxiv, doi: https://doi.org/10.1101/190231 (2017).
Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate
D. Amar, R. Shamir, D. Yekutieli.
PLoS Computational Biology 13(8): e1005700 (2017).