Research Areas	Publication Type	Years (all)
ASSOC Association    CHR Chromatin DATA Data    DYN Dynamics EVOL Evolution    EXP Expression FUN Function    GI Genetic-Interaction MET Metabolic    NS Network-Structure P2P P2P    REC Reconstruction REG Regulatory    REV Review SIG Signaling    TRANS Transcription	J Journal Article C Conference Paper B Book Ch Book Chapter T Technical Report PhD PhD Disseration	2000 - 2000 2001 - 2001 2002 - 2002 2003 - 2003 2004 - 2004 2005 - 2005 2006 - 2006

Type Reference Download
topics:	ASSOC	CHR	DATA	DYN	EVOL	EXP	FUN	GI	MET	NS	P2P	REC	REG	REV	SIG	TRANS
2004
J   Chua, G., Robinson, M. D., Morris, Q., and Hughes, T. R. (2004). "Transcriptional networks: reverse-engineering gene regulation on a global scale.." Curr Opin Microbiol, 7, 638-646. PDF bib
topics:												REC		REV		TRANS
J   Segre, Daniel, Deluna, Alexander, Church, George M., and Kishony, Roy (2004). "Modular epistasis in yeast metabolism." Nature Genetics, 37, 77+. PDF bib
topics:							FUN	GI	MET
J   Luscombe, N. M., Babu, M. M., Yu, H., Snyder, M., Teichmann, S. A., and Gerstein, M. (2004). "Genomic analysis of regulatory network dynamics reveals large topological changes.." Nature, 431, 308-312. PDF bib
topics:				DYN		EXP				NS						TRANS
J   Han, Jing-Dong J., Bertin, Nicolas, Hao, Tong, Goldberg, Debra S., Berriz, Gabriel F., Zhang, Lan V., Dupuy, Denis, Walhout, Albertha J. M., Cusick, Michael E., Roth, Frederick P., and Vidal, Marc (2004). "Evidence for dynamically organized modularity in the yeast protein-protein interaction network." Nature, 430, 88-93. PDF bib
topics:				DYN							P2P
J   Kelley, B. P., Yuan, B., Lewitter, F., Sharan, R., Stockwell, B. R., and Ideker, T. (2004). "PathBLAST: a tool for alignment of protein interaction networks.." Nucleic Acids Res, 32. PDF bib
topics:					EVOL						P2P	REC
J   Wuchty, S. (2004). "Evolution and topology in the yeast protein interaction network.." Genome Res, 14, 1310-1314. PDF bib
topics:					EVOL					NS	P2P
J   Bork, P., Jensen, L. J., von Mering, C., Ramani, A. K., Lee, I., and Marcotte, E. M. (2004). "Protein interaction networks from yeast to human.." Curr Opin Struct Biol, 14, 292-299. PDF bib
topics:					EVOL						P2P			REV
J   Segre, D. (2004). "The regulatory software of cellular metabolism.." Trends Biotechnol, 22, 261-265. PDF bib
topics:									MET				REG
J   Babu, M. M., Luscombe, N. M., Aravind, L., Gerstein, M., and Teichmann, S. A. (2004). "Structure and evolution of transcriptional regulatory networks.." Curr Opin Struct Biol, 14, 283-291. PDF bib
topics:					EVOL											TRANS
J   Tanay, A., Gat-Viks, I., and Shamir, R. (2004). "A global view of the selection forces in the evolution of yeast cis-regulation.." Genome Res, 14, 829-834. PDF bib
topics:					EVOL											TRANS
J   Beer, M. A. and Tavazoie, S. (2004). "Predicting gene expression from sequence.." Cell, 117, 185-198. PDF bib
topics:						EXP						REC				TRANS
J   Yeger-Lotem, E., Sattath, S., Kashtan, N., Itzkovitz, S., Milo, R., Pinter, R. Y., Alon, U., and Margalit, H. (2004). "Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction.." Proc Natl Acad Sci U S A, 101, 5934-5939. PDF bib
topics:										NS	P2P					TRANS
J   Aloy, P., Böttcher, B., Ceulemans, H., Leutwein, C., Mellwig, C., Fischer, S., Gavin, A. C., Bork, P., Superti-Furga, G., Serrano, L., and Russell, R. B. (2004). "Structure-based assembly of protein complexes in yeast.." Science, 303, 2026-2029. PDF bib
topics:			DATA								P2P
J   Gao, F., Foat, B. C., and Bussemaker, H. J. (2004). "Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.." BMC Bioinformatics, 5. PDF bib
topics:						EXP						REC				TRANS
J   Burgard, Anthony P., Nikolaev, Evgeni V., Schilling, Christophe H., and Maranas, Costas D. (2004). "Flux Coupling Analysis of Genome-Scale Metabolic Network Reconstructions." Genome Res., 14, 301-312. PDF bib
topics:									MET			REC
J   Friedman, N. (2004). "Inferring cellular networks using probabilistic graphical models.." Science, 303, 799-805. PDF bib
topics:												REC	REG	REV
J   Tong, Amy H. Y., Lesage, Guillaume, Bader, Gary D., Ding, Huiming, Xu, Hong, Xin, Xiaofeng, Young, James, Berriz, Gabriel F., Brost, Renee L., Chang, Michael, Chen, Yiqun, Cheng, Xin, Chua, Gordon, Friesen, Helena, Goldberg, Debra S., Haynes, Jennifer, Humphries, Christine, He, Grace, Hussein, Shamiza, Ke, Lizhu, Krogan, Nevan, Li, Zhijian, Levinson, Joshua N., Lu, Hong, Menard, Patrice, Munyana, Christella, Parsons, Ainslie B., Ryan, Owen, Tonikian, Raffi, Roberts, Tania, Sdicu, Anne-Marie, Shapiro, Jesse, Sheikh, Bilal, Suter, Bernhard, Wong, Sharyl L., Zhang, Lan V., Zhu, Hongwei, Burd, Christopher G., Munro, Sean, Sander, Chris, Rine, Jasper, Greenblatt, Jack, Peter, Matthias, Bretscher, Anthony, Bell, Graham, Roth, Frederick P., Brown, Grant W., Andrews, Brenda, Bussey, Howard, and Boone, Charles (2004). "Global Mapping of the Yeast Genetic Interaction Network." Science, 303, 808-813. PDF bib
topics:			DATA				FUN	GI
J   Lahav, G., Rosenfeld, N., Sigal, A., Geva-Zatorsky, N., Levine, A. J., Elowitz, M. B., and Alon, U. (2004). "Dynamics of the p53-Mdm2 feedback loop in individual cells.." Nat Genet, 36, 147-150. PDF bib
topics:										NS					SIG	TRANS
J   Bergmann, S., Ihmels, J., and Barkai, N. (2004). "Similarities and differences in genome-wide expression data of six organisms.." PLoS Biol, 2. PDF bib
topics:					EVOL	EXP
J   Ihmels, J., Levy, R., and Barkai, N. (2004). "Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae.." Nat Biotechnol, 22, 86-92. PDF bib
topics:						EXP			MET							TRANS
J   Parsons, A. B., Brost, R. L., Ding, H., Li, Z., Zhang, C., Sheikh, B., Brown, G. W., Kane, P. M., Hughes, T. R., and Boone, C. (2004). "Integration of chemical-genetic and genetic interaction data links bioactive compounds to cellular target pathways.." Nat Biotechnol, 22, 62-69. PDF bib
topics:							FUN	GI
J   Pritsker, Moshe, Liu, Yir-Chung, Beer, Michael A., and Tavazoie, Saeed (2004). "Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation." Genome Res., 14, 99-108. PDF bib
topics:					EVOL							REC				TRANS
J   Zaslaver, A., Mayo, A.E., Rosenberg, R., Bashkin,P., Sberro, H., Tsalyuk, M., Surette, M.G., and Alon, U. (2004). "Just-in-time transcription program in metabolic pathways." Nature Genetics, 36, 486-491. PDF bib
topics:									MET
J   Fong, S.S. and Palsson, B.O. (2004). "Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes." Nature Genetics, 36(10), 1056-1058. PDF bib
topics:									MET
J   Duarte, NC, Herrgard, MJ, and Palsson, BO (2004). "Reconstruction and validation of Saccharomyces cerevisiaeiND750, a fully compartmentalized genome-scale metabolic model.." Genome Res, 14(7), 1298-309. PDF bib
topics:									MET
J   Lee, I., Date, S.V., Adai, A.T., and Marcotte, E.M. (2004). "A Probabilistic Functional Network of Yeast Genes." Science, 306(5701), 1555-1558. PDF bib
topics:
J   Almaas, E., Kovács, B., Vicsek, T., and Oltvai, ZN (2004). "Global organization of metabolic fluxes in the bacterium Escherichia coli." Nature, 427, 839-843. PDF bib
topics:									MET	NS
J   Gasch, A.P., Moses, A.M., Chiang, D.Y., Fraser, H.B., Berardini, M., and Eisen, M.B. (2004). "Conservation and evolution of cis-regulatory systems in ascomycete fungi." PLoS Biol, 2, e398. PDF bib
topics:					EVOL											TRANS
J   Haugen, A. C., Kelley, R., Collins, J. B., Tucker, C. J., Deng, C., Afshari, C. A., Brown, J. M., Ideker, T., and Van Houten, B. (2004). "Integrating phenotypic and expression profiles to map arsenic-response networks.." Genome Biol, 5. PDF bib
topics:						EXP	FUN					REC
J   Kurdistani, S.K., Tavazoie, S., and Grunstein, M. (2004). "Mapping Global Histone Acetylation Patterns to Gene Expression." Cell, 117, 721-733. PDF bib
topics:		CHR	DATA
J   Morley, M., Molony, C.M., Weber, T.M., Devlin, J.L., Ewens, K.G., Spielman, R.S., and Cheung, V.G. (2004). "Genetic analysis of genome-wide variation in human gene expression." Nature, 430, 743-747. PDF bib
topics:	ASSOC		DATA									REC	REG
J   Teichmann, S.A. and Babu, M.M. (2004). "Gene regulatory network growth by duplication." Nature Genetics, 36, 492-496. PDF bib
topics:					EVOL											TRANS
J   Wong, S.L., Zhang, L.V., Tong, A.H.Y., Li, Z., Goldberg, D.S., King, O.D., Lesage, G., Vidal, M., Andrews, B., Bussey, H., and others (2004). "Combining biological networks to predict genetic interactions." Proceedings of the National Academy of Sciences, 101(44), 15682-15687. PDF bib
topics:								GI				REC
J   Berg, J., Lässig, M., and Wagner, A. (2004). "Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications." BMC Evolutionary Biology, 4(1), 51-51. PDF bib
topics:					EVOL					NS	P2P
J   Covert, M.W., Knight, E.M., Reed, J.L., Herrgard, M.J., and Palsson, B.O. (2004). "Integrating high-throughput and computational data elucidates bacterial networks." Nature, 429(6987), 92-96. PDF bib
topics:									MET			REC				TRANS
J   Hall, D.A., Zhu, H., Zhu, X., Royce, T., Gerstein, M., Snyder, M., and Duty, D.D. (2004). "Regulation of Gene Expression by a Metabolic Enzyme." Science, 306(5695), 482-484. PDF bib
topics:													REG			TRANS
J   Harbison, Christopher T., Gordon, Benjamin D., Lee, Tong I., Rinaldi, Nicola J., Macisaac, Kenzie D., Danford, Timothy W., Hannett, Nancy M., Tagne, Jean-Bosco, Reynolds, David B., Yoo, Jane, Jennings, Ezra G., Zeitlinger, Julia, Pokholok, Dmitry K., Kellis, Manolis, Rolfe, Alex P., Takusagawa, Ken T., Lander, Eric S., Gifford, David K., Fraenkel, Ernest, and Young, Richard A. (2004). "Transcriptional regulatory code of a eukaryotic genome." Nature, 431, 99-104. PDF bib
topics:			DATA													TRANS
J   Herrgard, MJ, Covert, MW, and Palsson, BO (2004). "Reconstruction of microbial transcriptional regulatory networks.." Curr Opin Biotechnol, 15(1), 70-7. PDF bib
topics:												REC				TRANS
J   Howard, ML and Davidson, EH (2004). "cis-Regulatory control circuits in development.." Dev Biol, 271(1), 109-18. PDF bib
topics:										NS				REV		TRANS
J   Tanay, A. and Shamir, R. (2004). "Multilevel modeling and inference of transcription regulation.." J Comput Biol, 11, 357-375. PDF bib
topics:												REC				TRANS
J   Yeang, C. H., Ideker, T., and Jaakkola, T. (2004). "Physical network models.." J Comput Biol, 11, 243-262. PDF bib
topics:											P2P	REC				TRANS
J   Zhu, J., Lum, PY, Lamb, J., GuhaThakurta, D., Edwards, SW, Thieringer, R., Berger, JP, Wu, MS, Thompson, J., Sachs, AB, and others (2004). "An integrative genomics approach to the reconstruction of gene networks in segregating populations." Cytogenetic and Genome Research, 105(2-4), 363-374. PDF bib
topics:	ASSOC											REC	REG
J   Scholtens, D. and Gentleman, R. (2004). "Making sense of high-throughput protein-protein interaction data." Statistical Aplications in Genetics and Molecular Biology, 3. PDF bib
topics:											P2P	REC
J   Ihmels, J., Levy, R., and Barkai, N. (2004). "Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae." Nature Biotechnology, 22(1), 86-92. PDF bib
topics:						EXP			MET							TRANS
J   John, B., Enright, A.J., Aravin, A., Tuschl, T., Sander, C., and Marks, D.S. (2004). "Human microRNA targets." PLoS Biol, 2(11), 1373. PDF bib
topics: