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
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.
Faucet: streaming de novo assembly graph construction
R. Rozov, G. Goldshlager, E. Halperin, R. Shamir.
Bioinformatics, doi.org/10.1093/bioinformatics/btx471.
Complexity and algorithms for copy-number evolution problems
M. El-Kebir, B. J. Raphael, R. Shamir, R. Sharan, S. Zaccaria, M. Zehavi and R. Zeira
Algorithms for Molecular Biology, 12(1), 13, 2017.
Improving the performance of minimizers and winnowing schemes
G. Marcais, D. Pellow, D. Bork, Y. Orenstein, R. Shamir, C. Kingsford.
Bioinformatics, special issue of ISMB/ECCB 2017, Vol. 33, i110–i117 doi: 10.1093/bioinformatics/btx235, 2017.
Reconstructing cancer karyotypes from short read data: the half full and half empty glass
R. Eitan, R. Shamir.
bioRxiv 152447; doi: https://doi.org/10.1101/152447
Tired and misconnected: A breakdown of brain modularity following sleep deprivation.
E. Ben Simon, A. Maron-Katz, N. Lahav, R. Shamir and T. Hendler.
Human Brain Mapping, 38(6):3300-3314. doi: 10.1002/hbm.23596.
Reduced changes in protein compared to mRNA levels across non-proliferating tissues
K. Perl, K. Ushakov, Y. Pozniak, O. Yizhar-Barnea, Y. Bhonker, S. Shivatzki, T. Geiger, K.B. Avraham and R. Shamir
BMC Genomics, 18:305, DOI 10.1186/s12864-017-3683-9, 2017.
Faucet: streaming de novo assembly graph construction
R. Rozov, G. Goldshlager, E. Halperin, R. Shamir
BioRxiv, doi: http://dx.doi.org/10.1101/125658, 2017
Transcription factor family-specific DNA shape readout revealed by quantitative specificity models
L. Yang, Y. Orenstein, A. Jolma, Y. Yin, J. Taipale, R. Shamir and R. Rohs.
Molecular Systems Biology, 13, 910, DOI 10.15252/msb.20167238, 2017.
Improving the performance of minimizers and winnowing schemes
G. Marcais, D. Pellow, D. Bork, Y. Orenstein, R. Shamir, C. Kingsford.
BioarXiv, https://doi.org/10.1101/104075(2017).