CT-FOCS: a novel method for inferring cell type-specific enhancer-promoter maps
T. Hait, R. Elkon, R. Shamir.
BioRxiv, https://doi.org/10.1101/707158 (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).
PROMO: An interactive tool for analyzing clinically-labeled multi-omic cancer datasets
D. Netanely, N. Stern, I. Laufer and R. Shamir
bioRxiv: http://biorxiv.org/cgi/content/short/629584v1, 2019
PRODIGY: personalized prioritization of driver genes
G. Dinstag and R. Shamir
bioRxiv , doi: https://doi.org/10.1101/456723, 2018.
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
Multi-omic and multi-view clustering algorithms: review and cancer benchmark
N. Rappoport & R. Shamir
Nucleic Acids Research, 46 (20) pp. 10546–-10562, (2018).
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.
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
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.