Publications


2007

CellFrame: a data structure for abstraction of cell biology experiments and construction of perturbation networks

2007. Annals of the New York Academy of Sciences, Accepted
Gong Y and Zhang Z

Alternative pathway approach for automating analysis and validation of cell perturbation networks and design of perturbation experiments

2007. Annals of the New York Academy of Sciences, Accepted
Gong Y and Zhang Z

A high-resolution atlas of nucleosome occupancy in yeast

2007. Nature Genetics [Epub ahead of print]
Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR and Nislow C

Experimental and computational procedures for the assessment of protein complexes in a genome-wide scale

2007. Chemical Reviews 107:3585-3600.
Musso G, Zhang Z, and Emili A

Structural and biochemical characterization of a novel Mn2+-dependent phosphodiesterase encoded by the yfcE gene

2007. Protein Science 16(7):1338-1348
Miller DJ, Shuvalova L, Evdokimova E, Savchenko A, Yakunin AF and Anderson WF

RankMotif++: a motif-search that accounts for relative ranks of K-mers in binding transcription factors.

2007. Bioinformatics 23:i72-i79.
Chen X, Hughes TR, and Morris Q

Retention of protein complex membership by ancient duplicated gene products in budding yeast

2007. Trends in Genetics 23(6):266-269
Musso G, Zhang Z and Emili A

2006

Genome-wide analysis of substrate specificities of the Escherichia coli haloacid dehalogenase-like phosphatase family.

2006. Journal of Biological Chemistry 281(47):36149-36161.
Kuznetsova E, Proudfoot M, Gonzalez GF, Brown G, Omelchenko MV, Borozan I, Carmel L, Wolf YI, Mori H, Savchenko AV, Arrowsmith CH, Koonin EV, Edwards AM, and Yakunin, AF

A survey of essential gene function in the yeast cell division cycle.

Molecular Biology of the Cell 17:4736-4747.
Yu L, Castillo LP, Mnaimneh S, Hughes TR, and Brown GW (2006) A survey of essential gene function in the yeast cell division cycle.

Experimental approaches to identify genetic networks

2006. Current Opinion In Biotechnology 17:472-480.
Costanzo M, Giaever G, Nislow C, and Andrews B

Identifying transcription factor functions and targets by phenotypic activation.

2006. Proceedings of the National Academy of Sciences 103:12045-12050
Chua G, Morris QD, Sopko R, Robinson MD, Ryan O, Chan ET, Frey BJ, Andrews BJ, Boone C, and Hughes TR

Molecular basis of formaldehyde detoxification: characterization of two S-formylglutathione hydrolases from Escherichia coli, FrmB and YeiG. Journal of Biological Chemistry

(2006) 281(20):14514-14522.
Gonzalez CF, Proudfoot M, Brown G, Korniyenko Y, Mori H, Savchenko AV, and Yakunin AF

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling.

2006. Cell 125:173-186.
Kislinger T, Cox B, Kannan A, Chung C, Hu P, Ignatchenko A, Scott MS, Gramolini AO, Morris Q, Hallett MT, Rossant J, Hughes TR, Frey J, and Emili AE

Global landscape of protein complexes in the yeast Saccharomyces cerevisiae.

2006. Nature 440:637-643.
Krogan NJ, Cagney G, Yu H, Zhong G, Guo X, Ignatchenko A, Li J, Pu S, Datta N, Tikuisis AP, Punna T, Peregrin-Alvarez JM, Shales M, Zhang X, Davey M, Robinson MD, Paccanaro A, Bray JE, Sheung A, Beattie B, Richards DP, Canadien V, Lalev A, Mena F, Wong P, Starostine A, Canete MM, Vlasblom J, Wu S, Orsi C, Collins SR, Chandran S, Haw R, Rilestone J, Gandi K, Thompson NJ, Musso G, St. Onge P, Ghanny S, Lam MHY, Butland G, Altaf A, Kanaya S, Shilatifard A, O’Shea E, Weissman JS, Ingles CJ, Hughes TR, Parkinson J, Gerstein M, Wodak SJ, Emili A, and Greenblatt JF

Genetic characterization of the yeast amphiphysins RVS161 and RVS167 reveals roles for the Rvs heterodimer in vivo.

2006. Molecular Biology of the Cell 17:1306-1321
Friesen H, Humphries C, Schub O, Collwill K, and Andrews B

Mapping pathways and phenotypes by systematic gene overexpression.

2006. Molecular Cell 21:319-30.
Sopko R, Huang D, Preston N, Chua G, Papp B, Kafadar K, Snyder, M., Oliver, S., Cyert, M., Hughes, T., Boone, C., and Andrews, B.

A phosphatase complex that dephosphorylates γH2A.X regulates DNA damage checkpoint recovery.

(2006) Nature 439:497-501.
Keogh MC, Kim JA, Downey M, Fillingham J, Chowdhury D, Harrison JC, Onishi M, Galicia S, Emili A, Lieberman J, Shen X, Buratowski S, Haber JE, Durocher D, Greenblatt JF, and Krogan NJ

Identification of a bacterial type III effector family with G-protein mimicry functions.

2006. Cell 124:133-145.
Alto NM, Shao F, Lazar CS, Brost RL, Chua G, Mattoo S, McMahon SA, Ghosh P, Hughes TR, Boone C, and Dixon JE


2007

A yeast split-ubiquitin based cytosolic screening system (cytoY2H) to detect interactions between transcriptionally active proteins

2007. Biotechniques 42(6):725-730
Mockli N, Deplazes A, Hassa PO, Zhang Z, Peter M, Hottiger MO, Stagljar I and Auerbach D

NetMatch: a Cytoscape plugin for searching biological networks.

2007. Bioinformatics 23(7):910-912.
Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, and Shasha D

Toward a comprehensive atlas of the physical interactome of Saccharomyces cerevisiae.

2007. Molecular and Cellular Proteomics 6(3):439-450.
Collins SR, Kemmeren P, Zhao X-C, Greenblatt J, Spencer F, Holstege FCP, Weissman JS, and Krogan NJ

Identifying functional modules in the physical interactome of Saccharomyces cerevisiae.

2007. Proteomics 7(6):944-960.
Pu S, Vlasblom J, Emili A, Greenblatt J, and Wodak S

2006

cPath: open source software for collecting, storing, and querying biological pathways.

BMC Bioinformatics 7: 497-505.
E. Cerami, G.D. Bader, B.E. Gross and C. Sander.

PIPE: a protein-protein interaction prediction engine based on the re-occurring short polypeptide sequences between known interacting protein pairs.

2006. BMC Bioinformatics 7:365.
Pitre S, Dehne F, Chan A, Cheetham J, Duong A, Emili A, Gebbia M, Greenblatt J, Jessulat M, Krogan NJ, Luo X, and Golshani A

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae.

2006. Journal of Biology 5:11.
Reguly T, Breitkreutz A, Boucher L, Breitkreutz B-J, Hon G, Myers C, Parsons A, Friesen H, Oughtred R, Tong A, Ho Y, Botstein D, Andrews B, Boone C, Troyanskya O, Ideker T, Dolinksi K, Batada N, and Tyers M

Enhancing the Prediction of Transcription Factor Binding Sites by Incorporating Structural Properties and Nucleotide Covariations.

2006. J. Comp. Biol. 13(4): 929-945.
S. Gunewardena, P. Jeavons and Z. Zhang.

A genome wide screen identifies the evolutionarily conserved KEOPS complex as a telomere regulator.

2006. Cell 124:1155-1168.
Downey MS, Houlsworth R, Rollie A, Brehme M, Galicia S, Guillard S, Zubko MK, Krogan NJ, Emili A, Greenblatt JF, Harrington L, Lydall D, and Durocher D

Systems-level analyses identify extensive coupling among gene expression machines.

2006. Molecular Systems Biology 2:2006-0003.
Maciag K, Altschuler SJ, Slack MD, Krogan NJ, Emili A, Greenblatt JF, Maniatis T, and Wu LF