Nir Yosef

 
 

Postdoc in the Regev lab at the Broad institute of MIT and Harvard, and in the Kuchroo lab at the Brigham and Women's Hospital, Harvard Medical School. Previously I was a PhD student at the School of Computer Science, Tel Aviv University, working at the Ruppin and  Sharan labs.
















contact




Broad Institute 7 Cambridge Center, Room 6035 Cambridge, MA 02142




 

About

Impulse control: Temporal dynamics in gene transcription/ N. Yosef, A. Regev. Cell. ;144(6):886-96, 2011

Cover image (artwork by S. Hart).

 


Systematic identification of gene annotation errors in the widely used yeast mutation collections/ T. Ben-Shitrit1*, N. Yosef*, K. Shemesh, R. Sharan, E. Ruppin and M. Kupiec. Nature Methods (accepted)


 

ANAT – A Software Tool for Reconstructing and Analyzing Functional Networks of Proteins/ N. Yosef, E. Zalckvar, N. Atias, AD. Rubinstein, M. Homilius,  L. Vardi, H. Zur, A. Kimchi, E. Ruppin, and R. Sharan. Science signaling; 4, pl1, 2011.


 

 






Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. O. Ram, A. Goren, I. Amit, N. Shoresh, N. Yosef, J. Ernst, M. Kellis, M. Gymrek, R. Issner, M.

Coyne, T. Durham, X. Zhang, J. Donaghey, CB. Epstein, A. Regev, and BE. Bernstein. (2011). Cell (in press).



Systematic Discovery of Signaling Components Identifies New Branches in Viral-Sensing Pathways/ N. Chevrier P. Mertins, MN Artyomov, AK Shalek, M Iannacone, MF Ciaccio, I Gat-Viks, E Tonti, MM

DeGrace , KR Clauser, M Garber, TM Eisenhaure, N Yosef, JT Robinson, A Sutton, MS Andersen, DE Root, U von Andrian, RB Jones, H Park, SA Carr, A Regev , I Amit, N Hacohen . (2011). Cell (in press).



Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis/ N.Novershtern, A. Subramanian, L. Lawton, RH. Mak, W. Haining, ME. McConkey, N. Habib, N. Yosef, CY. Chang, T. Shay, GM. Frampton, ACB. Drake, I. Leskov, B. Nilsson, F. Preffer, D. Dombkowski, JW. Evans, T. Liefeld, JS. Smutko, J. Chen, N. Friedman, R. Young, T. Golub, A. Regev, BL. Ebert.  Cell. 21;144(2):296-309, 2011

 

 

Network-free inference of knockout effects in yeast/ T. Peleg*, N. Yosef*, E. Ruppin, and R. Sharan.  PLoS Computational Biology, 6(1): e1000635, 2010  

 

 

Prediction of Phenotype Information from Genotype Data/ N.Yosef, J. Gramm, Q. Wang, W.S. Noble, R. Karp, and R. Sharan. Communications in Information and Systems, 2010 ; 10(2), pp. 99-114.

 

 

A Systems Level Strategy for Analyzing the Cell Death Network: implications in exploring the apoptosis/ autophagy connection / E. Zalckvar, N. Yosef, S. Reef, R. Sharan, E. Ruppin, and A. Kimchi. Cell Death and Differentiation, 2010; doi: 10.1038/cdd.2010.7

 

 

Transcription Regulation by CHIP/LDB Complexes/ R. Bronstein, L. Levkovitz, N. Yosef, E. Ruppin, R. Sharan, He. Westphal, B. Oliver, D. Segal. PLoS Genetics, 2010

 

 

A novel HMM-based method for detecting enriched transcription factor binding sites reveals RUNX3 as a potential target in pancreatic cancer biology/ L. Levkovitz, N. Yosef,  MC.  Gershengorn, E. Ruppin, R. Sharan and Y. Oron. PLoS ONE, 2010

 

 

Toward Accurate Reconstruction of Functional Protein Networks / N.Yosef*, L. ungar*, E. Zalckvar, A.Kimchi, M.Kupeic, E. Ruppin and R. Sharan.  Mol Syst Biol, 2009;5;248.

 

 

A Complex-Centric View of Protein Network Evolution/ N.Yosef, M.Kupeic, E. Ruppin and R. Sharan. Nucleic Acids Res., doi:10.1093/nar/gkp414 2009.

 

 

A genome-wide screen for essential yeast genes that affect telomere length maintenance/ L. Ungar*, N.Yosef*, Y. Sela, R. Sharan, E. Ruppin, M. Kupiec. Nucleic Acids Res., doi:10.1093/nar/gkp259, 2009.

 

 

Metabolic environmental modeling predicts ecological strategies for bacterial growth/ S. Freilich, A. Kreimer, E. Borenstein, N.Yosef, R. Sharan, U. Gophna, E. Ruppin. Genome Biology , doi:10.1186/gb-2009-10-6-r61, 2009

 

 

Cross-species Analysis of Protein-protein Interaction Networks/ N.Yosef, E. Ruppin and R. Sharan.  In Protein-protein interactions and networks: identification analysis and prediction, Panchenko& Przytycka (ed) pp 163-186. Springer, 2008.

 

 

Improved Network-based Identification of Protein Orthologs/ N.Yosef, R. Sharan and W. S. Noble. Bioinformatics 24 (ECCB 2008), pp i200-6, 2008

 

 

From sequence to structure to networks/ N. Yosef, L. Käll. Genome Biology, 9(11):3022-7, 2008

 

 

A Supervised Approach for Identifying Discriminating Genotype Patterns and its Application to Breast Cancer Data/ N.Yosef, Z.Yakhini, A.Tsalenko, E.Ruppin and R.Sharan, Bioinformatics 23 (ECCB 2006), pp. e91-e98, 2007


 

Medical sequencing at the extremes of human body mass/ with N. Ahituv et al. American Journal of Human Genetics 80, pp. 779-791, 2007

 

 

Inferring Functional Pathways from Multi-Perturbation Data/ N. Yosef,  A. Kaufman and E. Ruppin Bioinformatics (ISMB 2006), 22(14), e539-e546, 2006.



 


 [*equal authorship]

 

 

Publications

Try ANAT at: http://www.cs.tau.ac.il/~bnet/ANAT/