Research Areas (all)	Publication Type	Years
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:	CHR	DATA	DYN	EVOL	EXP	FUN	GI	MET	NS	P2P	REC	REG	REV	SIG	TRANS
2006
J   Jensen, Lars J., Jensen, Thomas S., de Lichtenberg, Ulrik, Brunak, S., and Bork, Peer (2006). "Co-evolution of transcriptional and post-translational cell-cycle regulation." Nature. PDF bib
topics:			DYN	EVOL						P2P				SIG	TRANS
J   Chua, G., Morris, Q. D., Sopko, R., Robinson, M. D., Ryan, O., Chan, E. T., Frey, B. J., Andrews, B. J., Boone, C., and Hughes, T. R. (2006). "Identifying transcription factor functions and targets by phenotypic activation.." Proc Natl Acad Sci U S A, 103, 12045-12050. PDF bib
topics:		DATA			EXP						REC				TRANS
J   Beyer, A., Workman, C., Hollunder, J., Radke, D., Mauller, U., Wilhelm, T., and Ideker, T. (2006). "Integrated assessment and prediction of transcription factor binding.." PLoS Comput Biol, 2. PDF bib
topics:											REC				TRANS
J   Ho, Su-Wen W., Jona, Ghil, Chen, Christina T L T., Johnston, Mark, and Snyder, Michael (2006). "Linking DNA-binding proteins to their recognition sequences by using protein microarrays.." Proc Natl Acad Sci U S A. PDF bib
topics:		DATA													TRANS
J   Balaji, S., Iyer, L. M., Aravind, L., and Babu, M. M. (2006). "Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks.." J Mol Biol, 360, 204-212. PDF bib
topics:									NS						TRANS
J   Tanay, Amos (2006). "Extensive low-affinity transcriptional interactions in the yeast genome.." Genome Res. PDF bib
topics:											REC				TRANS
J   Workman, Christopher T., Mak, Craig H., Mccuine, Scott, Tagne, Jean-Bosco, Agarwal, Maya, Ozier, Owen, Begley, Thomas J., Samson, Leona D., and Ideker, Trey (2006). "A Systems Approach to Mapping DNA Damage Response Pathways." Science, 312, 1054-1059. PDF bib
topics:						FUN					REC				TRANS
J   Nguyen, Dat H. and D'Haeseleer, Patrik (2006). "Deciphering principles of transcription regulation in eukaryotic genomes." Mol Syst Biol, 2, msb4100054-E1-msb4100054-E10. PDF bib
topics:				EVOL											TRANS
J   Borneman, A. R., Leigh-Bell, J. A., Yu, H., Bertone, P., Gerstein, M., and Snyder, M. (2006). "Target hub proteins serve as master regulators of development in yeast.." Genes Dev, 20, 435-448. PDF bib
topics:									NS						TRANS
J   Blanchette, M., Bataille, A.R., Chen, X., Poitras, C., Laganiere, J., Lefebvre, C., Deblois, G., Giguere, V., Ferretti, V., Bergeron, D., and others (2006). "Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression." Genome Research, 16, 656. PDF bib
topics:				EVOL							REC				TRANS
J   Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C.A.M., Taylor, M.S., Engström, P.G., Frith, M.C., and others (2006). "Genome-wide analysis of mammalian promoter architecture and evolution." . PDF bib
topics:				EVOL											TRANS
J   Davidson, E.H. and Erwin, D.H. (2006). "Gene Regulatory Networks and the Evolution of Animal Body Plans." Science, 311, 796. PDF bib
topics:				EVOL											TRANS
J   Odom, D.T., Dowell, R.D., Jacobsen, E.S., Nekludova, L., Rolfe, P.A., Danford, T.W., Gifford, D.K., Fraenkel, E., Bell, G.I., and Young, R.A. (2006). "Core transcriptional regulatory circuitry in human hepatocytes." Nature. PDF bib
topics:									NS						TRANS
J   Yeang, C.H. and Jaakkola, T. (2006). "Modeling the Combinatorial Functions of Multiple Transcription Factors." JOURNAL OF COMPUTATIONAL BIOLOGY, 13, 463. PDF bib
topics:											REC				TRANS
J   Kim, Seon-Young and Kim, YongSung (2006). "Genome-wide prediction of transcriptional regulatory elements of human promoters using gene expression and promoter analysis data." BMC Bioinformatics, 7(1), 330. PDF bib
topics:											REC				TRANS
J   Bar-Even, A., Paulsson, J., Maheshri, N., Carmi, M., O'Shea, E., Pilpel, Y., and Barkai, N. (2006). "Noise in protein expression scales with natural protein abundance." Nature Genetics, 38, 636-643. PDF bib
topics:					EXP										TRANS
2005
J   Boyer, L. A., Lee, T. I., Cole, M. F., Johnstone, S. E., Levine, S. S., Zucker, J. P., Guenther, M. G., Kumar, R. M., Murray, H. L., Jenner, R. G., Gifford, D. K., Melton, D. A., Jaenisch, R., and Young, R. A. (2005). "Core transcriptional regulatory circuitry in human embryonic stem cells.." Cell, 122, 947-956. PDF bib
topics:									NS						TRANS
J   Siggia, E. D. (2005). "Computational methods for transcriptional regulation.." Curr Opin Genet Dev, 15, 214-221. PDF bib
topics:											REC		REV		TRANS
J   Ihmels, J., Bergmann, S., Gerami-Nejad, M., Yanai, I., McClellan, M., Berman, J., and Barkai, N. (2005). "Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage." Science, 309, 938-940. PDF bib
topics:				EVOL											TRANS
J   Kafri, R., Bar-Even, A., and Pilpel, Y. (2005). "Transcription control reprogramming in genetic backup circuits." Nature Genetics, 37(3), 295-299. PDF bib
topics:						FUN	GI								TRANS
J   Kim, TH, Barrera, LO, Zheng, M., Qu, C., Singer, MA, Richmond, TA, Wu, Y., Green, RD, and Ren, B. (2005). "A high-resolution map of active promoters in the human genome.." Nature, 436(7052), 876-80. PDF bib
topics:	CHR	DATA													TRANS
J   Tanay, A., Regev, A., and Shamir, R. (2005). "Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast." Proceedings of the National Academy of Sciences, 102, 7203-7208. PDF bib
topics:				EVOL											TRANS
J   Balazsi, G., Barabasi, A.L., and Oltvai, ZN (2005). "Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli." Proceedings of the National Academy of Sciences, 102(22), 7841-7846. PDF bib
topics:									NS						TRANS
J   Wang, W., Cherry, J.M., Nochomovitz, Y., Jolly, E., Botstein, D., and Li, H. (2005). "Inference of combinatorial regulation in yeast transcriptional networks: A case study of sporulation." Proceedings of the National Academy of Sciences, 102(6), 1998-2003. PDF bib
topics:											REC				TRANS
J   Zhang, L. V., King, O. D., Wong, S. L., Goldberg, D. S., Tong, A. H., Lesage, G., Andrews, B., Bussey, H., Boone, C., and Roth, F. P. (2005). "Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network.." J Biol, 4. PDF bib
topics:						FUN			NS	P2P					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   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   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   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   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   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   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   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   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   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   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
2003
J   Bar-Joseph, Z., Gerber, G. K., Lee, T. I., Rinaldi, N. J., Yoo, J. Y., Robert, F., Gordon, D. B., Fraenkel, E., Jaakkola, T. S., Young, R. A., and Gifford, D. K. (2003). "Computational discovery of gene modules and regulatory networks.." Nat Biotechnol, 21, 1337-1342. PDF bib
topics:											REC				TRANS
J   Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S., and O'Shea, E. K. (2003). "Global analysis of protein localization in budding yeast.." Nature, 425, 686-691. PDF bib
topics:										P2P					TRANS
J   Qian, J., Lin, J., Luscombe, N. M., Yu, H., and Gerstein, M. (2003). "Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data.." Bioinformatics, 19, 1917-1926. PDF bib
topics:					EXP						REC				TRANS
2002
J   Lee, T. I., Rinaldi, N. J., Robert, F., Odom, D. T., Bar-Joseph, Z., Gerber, G. K., Hannett, N. M., Harbison, C. T., Thompson, C. M., Simon, I., Zeitlinger, J., Jennings, E. G., Murray, H. L., Gordon, D. B., Ren, B., Wyrick, J. J., Tagne, J. B., Volkert, T. L., Fraenkel, E., Gifford, D. K., and Young, R. A. (2002). "Transcriptional regulatory networks in Saccharomyces cerevisiae.." Science, 298, 799-804. PDF bib
topics:		DATA							NS						TRANS
J   Rajewsky, N., Vergassola, M., Gaul, U., and Siggia, E. D. (2002). "Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo.." BMC Bioinformatics, 3. PDF bib
topics:											REC				TRANS
J   Covert, M. W. and Palsson, B. Ø. (2002). "Transcriptional regulation in constraints-based metabolic models of Escherichia coli.." J Biol Chem, 277, 28058-28064. PDF bib
topics:						FUN		MET							TRANS
J   Guelzim, N., Bottani, S., Bourgine, P., and Képès, F. (2002). "Topological and causal structure of the yeast transcriptional regulatory network." Nature Genetics, 31, 60-63. PDF bib
topics:									NS						TRANS
C   Segal, E., Barash, Y., Simon, I., Friedman, N., and Koller, D. (2002). "From promoter sequence to expression: a probabilistic framework." (pp. 263-272). PDF bib
topics:					EXP						REC				TRANS
2001
J   Covert, M. W., Schilling, C. H., and Palsson, B. (2001). "Regulation of gene expression in flux balance models of metabolism.." J Theor Biol, 213, 73-88. PDF bib
topics:						FUN		MET							TRANS
J   Pilpel, Y., Sudarsanam, P., and Church, G. M. (2001). "Identifying regulatory networks by combinatorial analysis of promoter elements.." Nat Genet, 29, 153-159. PDF bib
topics:					EXP						REC				TRANS
J   Herrg\aard, M.J., Covert, M.W., and Palsson, B.\O. (). "Reconciling Gene Expression Data With Known Genome-Scale Regulatory Network Structures." Genome Research, 13, 2423-2434. PDF bib
topics:					EXP										TRANS
J   Kolbe, D., Taylor, J., Elnitski, L., Eswara, P., Li, J., Miller, W., Hardison, R., and Chiaromonte, F. (). "Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat." Genome Research, 14, 700-707. PDF bib
topics:				EVOL											TRANS
J   Yu, H., Luscombe, N.M., Qian, J., and Gerstein, M. (). "Genome-wide analysis of gene expression relationships in transcriptional regulatory networks." Trend in Genetics, 19, 422-427. PDF bib
topics:					EXP				NS						TRANS