Research Areas	Publication Type	Years
ASSOC Association CHR Chromatin    DATA Data DB Database    DYN Dynamics EVOL Evolution    EXP Expression FUN Function    GI Genetic-Interaction MET Metabolic    METHY Methylation MICRO MicroRNA    NS Network-Structure P2P P2P    DEG RNA-Degradation 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	DB	DYN	EVOL	EXP	FUN	GI	MET	METHY	MICRO	NS	P2P	DEG	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   Lamb, J., Crawford, E. D., Peck, D., Modell, J. W., Blat, I. C., Wrobel, M. J., Lerner, J., Brunet, J. P., Subramanian, A., Ross, K. N., Reich, M., Hieronymus, H., Wei, G., Armstrong, S. A., Haggarty, S. J., Clemons, P. A., Wei, R., Carr, S. A., Lander, E. S., and Golub, T. R. (2006). "The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.." Science, 313, 1929-1935. PDF bib
topics:								EXP	FUN
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   Haynes, C., Oldfield, C. J., Ji, F., Klitgord, N., Cusick, M. E., Radivojac, P., Uversky, V. N., Vidal, M., and Iakoucheva, L. M. (2006). "Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes.." PLoS Comput Biol, 2. PDF bib
topics:														NS	P2P
J   Ptacek, Jason and Snyder, Michael (2006). "Charging it up: global analysis of protein phosphorylation.." Trends Genet(52). PDF bib
topics:				DATA					FUN	GI					P2P					SIG
J   Deutscher, David, Meilijson, Isaac, Kupiec, Martin, and Ruppin, Eytan (2006). "Multiple knockout analysis of genetic robustness in the yeast metabolic network." Nature Genetics, 38, 993-998. PDF bib
topics:									FUN	GI	MET
J   . "Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states." PLoS Computational Biology. PDF bib
topics:											MET
J   Collins, Sean R., Schuldiner, Maya, Krogan, Nevan J., and Weissman, Jonathan S. (2006). "A strategy for extracting and analyzing large-scale quantitative epistatic interaction data." Genome Biology, 7, R63+. PDF bib
topics:										GI							REC
J   Herrgard, Markus J., Fong, Stephen S., and Palsson, Bernhard (2006). "Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles." PLoS Computational Biology, 2, e72+. PDF bib
topics:											MET						REC
J   Kafri, Ran, Levy, Melissa, and Pilpel, Yitzhak (2006). "The regulatory utilization of genetic redundancy through responsive backup circuits.." Proc Natl Acad Sci U S A. PDF bib
topics:									FUN	GI	MET
J   Lehner, Ben, Crombie, Catriona, Tischler, Julia, Fortunato, Angelo, and Fraser, Andrew G. (2006). "Systematic mapping of genetic interactions in Caenorhabditis elegans identifies common modifiers of diverse signaling pathways." Nature Genetics, 38, 896-903. PDF bib
topics:				DATA					FUN	GI
J   Yu, Haiyuan, Xia, Yu, Trifonov, Valery, and Gerstein, Mark (2006). "Design principles of molecular networks revealed by global comparisons and composite motifs." Genome Biology, 7, R55+. PDF bib
topics:											MET			NS	P2P			REG
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   Reguly, Teresa, Breitkreutz, Ashton, Boucher, Lorrie, Breitkreutz, Bobby-Joe, Hon, Gary C., Myers, Chad L., Parsons, Ainslie, Friesen, Helena, Oughtred, Rose, Tong, Amy, Stark, Chris, Ho, Yuen, Botstein, David, Andrews, Brenda, Boone, Charles, Troyanskya, Olga G., Ideker, Trey, Dolinski, Kara, Batada, Nizar N., and Tyers, Mike (2006). "Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae." Journal of Biology, 5, 11+. PDF bib
topics:					DB										P2P		REC
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   Herrgård, M. J., Lee, B. S., Portnoy, V., and Palsson, B. Ø. (2006). "Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.." Genome Res, 16, 627-635. PDF bib
topics:								EXP	FUN		MET							REG
J   Spirin, Victor, Gelfand, Mikhail S S., Mironov, Andrey A A., and Mirny, Leonid A A. (2006). "A metabolic network in the evolutionary context: Multiscale structure and modularity.." Proc Natl Acad Sci U S A. PDF bib
topics:							EVOL				MET
J   Sharan, Roded and Ideker, Trey (2006). "Modeling cellular machinery through biological network comparison." Nature Biotechnology, 24, 427-433. PDF bib
topics:							EVOL								P2P				REV
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   Jaimovich, A., Elidan, G., Margalit, H., and Friedman, N. (2006). "Towards an integrated protein-protein interaction network: a relational markov network approach.." J Comput Biol, 13, 145-164. PDF bib
topics:															P2P		REC
J   Scott, J., Ideker, T., Karp, R. M., and Sharan, R. (2006). "Efficient algorithms for detecting signaling pathways in protein interaction networks.." J Comput Biol, 13, 133-144. PDF bib
topics:															P2P		REC			SIG
J   Bhattacharyya, Roby P P., Reményi, Attila, Yeh, Brian J J., and Lim, Wendell A A. (2006). "Domains, Motifs, and Scaffolds: The Role of Modular Interactions in the Evolution and Wiring of Cell Signaling Circuits.." Annu Rev Biochem. PDF bib
topics:																			REV	SIG
J   Krogan, Nevan J., Cagney, Gerard, Yu, Haiyuan, Zhong, Gouqing, Guo, Xinghua, Ignatchenko, Alexandr, Li, Joyce, Pu, Shuye, Datta, Nira, Tikuisis, Aaron P., Punna, Thanuja, Peregrã­n-Alvarez, Josã© M., Shales, Michael, Zhang, Xin, Davey, Michael, Robinson, Mark D., Paccanaro, Alberto, Bray, James E., Sheung, Anthony, Beattie, Bryan, Richards, Dawn P., Canadien, Veronica, Lalev, Atanas, Mena, Frank, Wong, Peter, Starostine, Andrei, Canete, Myra M., Vlasblom, James, Wu, Samuel, Orsi, Chris, Collins, Sean R., Chandran, Shamanta, Haw, Robin, Rilstone, Jennifer J., Gandi, Kiran, Thompson, Natalie J., Musso, Gabe, St Onge, Peter, Ghanny, Shaun, Lam, Mandy H. Y., Butland, Gareth, Altaf-Ul, Amin M., Kanaya, Shigehiko, Shilatifard, Ali, O'Shea, Erin, Weissman, Jonathan S., Ingles, James C., Hughes, Timothy R., Parkinson, John, Gerstein, Mark, Wodak, Shoshana J., Emili, Andrew, and Greenblatt, Jack F. (2006). "Global landscape of protein complexes in the yeast Saccharomyces cerevisiae." Nature. PDF bib
topics:				DATA											P2P
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   He, X. and Zhang, J. (2006). "Transcriptional reprogramming and backup between duplicate genes: is it a genomewide phenomenon?." Genetics, 172, 1363-1367. PDF bib
topics:									FUN	GI
J   Sopko, R., Huang, D., Preston, N., Chua, G., Papp, B., Kafadar, K., Snyder, M., Oliver, S. G., Cyert, M., Hughes, T. R., Boone, C., and Andrews, B. (2006). "Mapping pathways and phenotypes by systematic gene overexpression.." Mol Cell, 21, 319-330. PDF bib
topics:				DATA				EXP
J   Guo, Xiang, Tatsuoka, Kay, and Liu, Rongxiang (2006). "Histone acetylation and transcriptional regulation in the genome of Saccharomyces cerevisiae." Bioinformatics, 22. PDF bib
topics:			CHR
J   Campillos, Mónica, von Mering, Christian, Jensen, Lars Juhl J., and Bork, Peer (2006). "Identification and analysis of evolutionarily cohesive functional modules in protein networks.." Genome Res. PDF bib
topics:							EVOL								P2P
J   Gavin, Anne-Claude, Aloy, Patrick, Grandi, Paola, Krause, Roland, Boesche, Markus, Marzioch, Martina, Rau, Christina, Jensen, Lars J., Bastuck, Sonja, Dümpelfeld, Birgit, Edelmann, Angela, Heurtier, Marie-Anne, Hoffman, Verena, Hoefert, Christian, Klein, Karin, Hudak, Manuela, Michon, Anne-Marie, Schelder, Malgorzata, Schirle, Markus, Remor, Marita, Rudi, Tatjana, Hooper, Sean, Bauer, Andreas, Bouwmeester, Tewis, Casari, Georg, Drewes, Gerard, Neubauer, Gitte, Rick, Jens M., Kuster, Bernhard, Bork, Peer, Russell, Robert B., and Superti-Furga, Giulio (2006). "Proteome survey reveals modularity of the yeast cell machinery." Nature. PDF bib
topics:				DATA											P2P
J   Keshet, Ilana, Schlesinger, Yeshayahu, Farkash, Shlomit, Rand, Eyal, Hecht, Merav, Segal, Eran, Pikarski, Eli, Young, Richard A., Niveleau, Alain, Cedar, Howard, and Simon, Itamar (2006). "Evidence for an instructive mechanism of de novo methylation in cancer cells." Nature Genetics, 38, 149-153. PDF bib
topics:				DATA								METHY
J   Li, D., Li, J., Ouyang, S., Wang, J., Wu, S., Wan, P., Zhu, Y., Xu, X., and He, F. (2006). "Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: large-scale organization and robustness.." Proteomics, 6, 456-461. PDF bib
topics:							EVOL							NS	P2P
J   Maciag, Karolina, Altschuler, Steven J., Slack, Michael D., Krogan, Nevan J., Emili, Andrew, Greenblatt, Jack F., Maniatis, Tom, and Wu, Lani F. (2006). "Systems-level analyses identify extensive coupling among gene expression machines." Mol Syst Biol, 2, msb4100045-E1-msb4100045-E14. PDF bib
topics:															P2P		REC
J   Slonim, Noam, Elemento, Olivier, and Tavazoie, Saeed (2006). "Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks." Mol Syst Biol, 2, msb4100047-E1-msb4100047-E14. PDF bib
topics:									FUN					NS
J   Pokholok, D.K., Zeitlinger, J., Hannett, N.M., Reynolds, D.B., and Young, R.A. (2006). "Activated Signal Transduction Kinases Frequently Occupy Target Genes." Science's STKE, 313, 533. PDF bib
topics:				DATA																SIG
J   Bandyopadhyay, Sourav, Sharan, Roded, and Ideker, Trey (2006). "Systematic identification of functional orthologs based on protein network comparison." Genome Res., 16(3), 428-435. PDF bib
topics:							EVOL								P2P
J   Vitkup, D., Kharchenko, P., and Wagner, A. (2006). "Influence of metabolic network structure and function on enzyme evolution." Genome Biology, 7(5), R39. PDF bib
topics:							EVOL				MET			NS
J   Warner, G. J., Adeleye, Y. A., and Ideker, T. (2006). "Interactome networks: the state of the science.." Genome Biol, 7. PDF bib
topics:															P2P				REV
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   Gat-VIks, I., Tanay, A., Raijman, D., and Shamir, Ron (2006). "A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks." Journal of Computational Biology, 13(2), 165. PDF bib
topics:																	REC	REG
J   Kharchenko, P., Chen, L., Freund, Y., Vitkup, D., and Church, G. M. (2006). "Identifying metabolic enzymes with multiple types of association evidence.." BMC Bioinformatics, 7. PDF bib
topics:											MET						REC
J   Newman, J.R.S., Ghaemmaghami, S., Ihmels, J., Breslow, D.K., Noble, M., DeRisi, J.L., and Weissman, J.S. (2006). "Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise." Nature, 441, 840-846. PDF bib
topics:								EXP
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   Segal, E., Fondufe-Mittendorf, Y., Chen, L., Thastrom, A., Field, Y., Moore, IK, Wang, JP, and Widom, J. (2006). "A genomic code for nucleosome positioning.." Nature. PDF bib
topics:			CHR	DATA													REC
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   Zhong, W. and Sternberg, P.W. (2006). "Genome-Wide Prediction of C. elegans Genetic Interactions." Science, 311(5766), 1481. PDF bib
topics:									FUN	GI							REC
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   Thomas A. Drake, Eric E. Schadt, and Aldons J. Lusis (2006). "Integrating genetic and gene expression data: application to cardiovascular and metabolic traits in mice." Mammalian Genome, 17(6), 466-479. PDF bib
topics:		ASSOC						EXP									REC	REG
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
J   Sood, P., Krek, A., Zavolan, M., Macino, G., and Rajewsky, N. (2006). "Cell-type-specific signatures of microRNAs on target mRNA expression." Proceedings of the National Academy of Sciences, 103(8), 2746-2751. PDF bib
topics:
2005
J   Almaas, Eivind, Oltvai, Zoltan, and Barabai, Albert-Laszlo L. (2005). "The Activity Reaction Core and Plasticity of Metabolic Networks.." PLoS Comput Biol, 1. PDF bib
topics:							EVOL				MET
J   Chan, C. S., Elemento, O., and Tavazoie, S. (2005). "Revealing posttranscriptional regulatory elements through network-level conservation.." PLoS Comput Biol, 1. PDF bib
topics:							EVOL									DEG	REC
J   Foat, B. C., Houshmandi, S. S., Olivas, W. M., and Bussemaker, H. J. (2005). "Profiling condition-specific, genome-wide regulation of mRNA stability in yeast.." Proc Natl Acad Sci U S A, 102, 17675-17680. PDF bib
topics:				DATA												DEG	REC
J   Jones, Richard B., Gordus, Andrew, Krall, Jordan A., and Macbeath, Gavin (2005). "A quantitative protein interaction network for the ErbB receptors using protein microarrays." Nature. PDF bib
topics:															P2P
J   Davierwala, Armaity P., Haynes, Jennifer, Li, Zhijian, Brost, Renee L., Robinson, Mark D., Yu, Lisa, Mnaimneh, Sanie, Ding, Huiming, Zhu, Hongwei, Chen, Yiqun, Cheng, Xin, Brown, Grant W., Boone, Charles, Andrews, Brenda J., and Hughes, Timothy R. (2005). "The synthetic genetic interaction spectrum of essential genes." Nat Genet, 37, 1147-1152. PDF bib
topics:									FUN	GI
J   Nariai, N., Tamada, Y., Imoto, S., and Miyano, S. (2005). "Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data.." Bioinformatics, 21 Suppl 2. PDF bib
topics:								EXP							P2P		REC	REG
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   Pokholok, D. K., Harbison, C. T., Levine, S., Cole, M., Hannett, N. M., Lee, T. I., Bell, G. W., Walker, K., Rolfe, P. A., Herbolsheimer, E., Zeitlinger, J., Lewitter, F., Gifford, D. K., and Young, R. A. (2005). "Genome-wide map of nucleosome acetylation and methylation in yeast.." Cell, 122, 517-527. PDF bib
topics:			CHR	DATA
J   Kharchenko, Peter, Church, George M., and Vitkup, Dennis (2005). "Expression dynamics of a cellular metabolic network." Molecular Systems Biology, 1, msb4100023-E1-msb4100023-E6. PDF bib
topics:								EXP			MET
J   Han, Jing-Dong J., Dupuy, Denis, Bertin, Nicolas, Cusick, Michael E., and Vidal, Marc (2005). "Effect of sampling on topology predictions of protein-protein interaction networks." Nature Biotechnology, 23, 839-844. PDF bib
topics:														NS	P2P
J   Yuan, G. C., Liu, Y. J., Dion, M. F., Slack, M. D., Wu, L. F., Altschuler, S. J., and Rando, O. J. (2005). "Genome-scale identification of nucleosome positions in S. cerevisiae.." Science, 309, 626-630. PDF bib
topics:			CHR	DATA
J   Schadt, Eric E., Lamb, John, Yang, Xia, Zhu, Jun, Edwards, Steve, Guhathakurta, Debraj, Sieberts, Solveig K., Monks, Stephanie, Reitman, Marc, Zhang, Chunsheng, Lum, Pek Y., Leonardson, Amy, Thieringer, Rolf, Metzger, Joseph M., Yang, Liming, Castle, John, Zhu, Haoyuan, Kash, Shera F., Drake, Thomas A., Sachs, Alan, and Lusis, Aldons J. (2005). "An integrative genomics approach to infer causal associations between gene expression and disease." Nature Genetics, 37, 710-717. PDF bib
topics:		ASSOC						EXP									REC	REG
J   Kelley, Ryan and Ideker, Trey (2005). "Systematic interpretation of genetic interactions using protein networks." Nature Biotechnology, 23, 561-566. PDF bib
topics:										GI					P2P		REC
J   Shlomi, T., Berkman, O., and Ruppin, E. (2005). "Regulatory on/off minimization of metabolic flux changes after genetic perturbations.." Proc Natl Acad Sci U S A, 102. PDF bib
topics:											MET							REG
J   Sachs, Karen, Perez, Omar, Pe'er, Dana, Lauffenburger, Douglas A., and Nolan, Garry P. (2005). "Causal Protein-Signaling Networks Derived from Multiparameter Single-Cell Data." Science, 308, 523-529. PDF bib
topics:																	REC			SIG
J   Siggia, E. D. (2005). "Computational methods for transcriptional regulation.." Curr Opin Genet Dev, 15, 214-221. PDF bib
topics:																	REC		REV		TRANS
J   Sonnichsen, B., Koski, L. B., Walsh, A., Marschall, P., Neumann, B., Brehm, M., Alleaume, A., Artelt, J., Bettencourt, P., Cassin, E., Hewitson, M., Holz, C., Khan, M., Lazik, S., Martin, C., Nitzsche, B., Ruer, M., Stamford, J., Winzi, M., Heinkel, R., Roder, M., Finell, J., Hantsch, H., Jones, S. J. M., Jones, M., Piano, F., Gunsalus, K. C., Oegema, K., Gonczy, P., Coulson, A., Hyman, A. A., and Echeverri, C. J. (2005). "Full-genome RNAi profiling of early embryogenesis in Caenorhabditis elegans." Nature, 434, 462-469. PDF bib
topics:				DATA					FUN
J   Sharan, R., Suthram, S., Kelley, R. M., Kuhn, T., McCuine, S., Uetz, P., Sittler, T., Karp, R. M., and Ideker, T. (2005). "Conserved patterns of protein interaction in multiple species.." Proc Natl Acad Sci U S A, 102, 1974-1979. PDF bib
topics:							EVOL								P2P
J   Lim, Lee P., Lau, Nelson C., Garrett-Engele, Philip, Grimson, Andrew, Schelter, Janell M., Castle, John, Bartel, David P., Linsley, Peter S., and Johnson, Jason M. (2005). "Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs." Nature, aop. PDF bib
topics:													MICRO			DEG
J   Fong, Stephen S., Joyce, Andrew R., and Palsson, Bernhard O. (2005). "Parallel adaptive evolution cultures of Escherichia coli lead toconvergent growth phenotypes with different gene expression states." Genome Res., 15(10), 1365-1372. PDF bib
topics:
J   Bernstein, B.E., Kamal, M., Lindblad-Toh, K., Bekiranov, S., Bailey, D.K., Huebert, D.J., McMahon, S., Karlsson, E.K., Kulbokas, E.J., Gingeras, T.R., and others (2005). "Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse." Cell, 120(2), 169-181. PDF bib
topics:			CHR	DATA
J   Chesler, E.J., Lu, L., Shou, S., Qu, Y., Gu, J., Wang, J., Hsu, H.C., Mountz, J.D., Baldwin, N.E., Langston, M.A., and others (2005). "Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function." Nature Genetics, 37, 233-242. PDF bib
topics:		ASSOC															REC	REG
J   Cusick, M.E., Klitgord, N., Vidal, M., and Hill, D.E. (2005). "Interactome: gateway into systems biology." Hum Mol Genet, 14. PDF bib
topics:														NS	P2P				REV
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   Rual, J.F., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G.F., Gibbons, F.D., Dreze, M., Ayivi-Guedehoussou, N., and others (2005). "Towards a proteome-scale map of the human protein-protein interaction network." Nature, 437(7062), 1173-1178. PDF bib
topics:				DATA											P2P
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   Butland, G., Peregrin-Alvarez, JM, Li, J., Yang, W., Yang, X., Canadien, V., Starostine, A., Richards, D., Beattie, B., Krogan, N., and others (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli.." Nature, 433(7025), 531-7. PDF bib
topics:							EVOL								P2P
J   Hahn, M.W. and Kern, A.D. (2005). "Comparative Genomics of Centrality and Essentiality in Three Eukaryotic Protein-Interaction Networks." Molecular Biology and Evolution, 22(4), 803-806. PDF bib
topics:							EVOL							NS	P2P
J   Herrgard, MJ and Palsson, BO (2005). "Untangling the web of functional and physical interactions in yeast." J Biol, 4(2), 5. PDF bib
topics:									FUN					NS	P2P
J   Li, H., Pellegrini, M., and Eisenberg, D. (2005). "Detection of parallel functional modules by comparative analysis of genome sequences." Nature Biotechnology, 23, 253-260. PDF bib
topics:							EVOL		FUN		MET
J   Qi, Y., Ye, P., and Bader, J.S. (2005). "Genetic interaction motif finding by expectation maximization -- a novel statistical model for inferring gene modules from synthetic lethality." BMC Bioinformatics, 6(1), 288. PDF bib
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J   Krek, Azra, Grun, Dominic, Poy, Matthew N., Wolf, Rachel, Rosenberg, Lauren, Epstein, Eric J., MacMenamin, Philip, da Piedade, Isabelle, Gunsalus, Kristin C., Stoffel, Markus, and Rajewsky, Nikolaus (2005). "Combinatorial microRNA target predictions." Nature Genetics, 37, 495-500. PDF bib
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J   Schuldiner, M., Collins, S.R., Thompson, N.J., Denic, V., Bhamidipati, A., Punna, T., Ihmels, J., Andrews, B., Boone, C., Greenblatt, J.F., and others (2005). "Exploration of the Function and Organization of the Yeast Early Secretory Pathway through an Epistatic Miniarray Profile." Cell, 123(3), 507-519. PDF bib
topics:				DATA					FUN	GI
J   Sharan, R., Ideker, T., Kelley, B., Shamir, R., and Karp, R.M. (2005). "Identification of Protein Complexes by Comparative Analysis of Yeast and Bacterial Protein Interaction Data." Journal of Computational Biology, 12(6), 835. PDF bib
topics:							EVOL								P2P		REC
J   Van Driessche, N., Demsar, J., Booth, E.O., Hill, P., Juvan, P., Zupan, B., Kuspa, A., and Shaulsky, G. (2005). "Epistasis analysis with global transcriptional phenotypes." Nature Genetics, 37, 471-477. PDF bib
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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
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J   Yeang, C. H., Mak, H. C., McCuine, S., Workman, C., Jaakkola, T., and Ideker, T. (2005). "Validation and refinement of gene-regulatory pathways on a network of physical interactions.." Genome Biol, 6. PDF bib
topics:															P2P		REC	REG
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
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J   Scholtens, D., Vidal, M., and Gentleman, R. (2005). "Local modeling of global interactome networks." Bioinformatics, 21(17), 3548-3557. PDF bib
topics:														NS	P2P		REC
J   de Lichtenberg, U., Jensen, L.J., Brunak, S., and Bork, P. (2005). "Dynamic Complex Formation During the Yeast Cell Cycle." Science's STKE, 307(5710), 724-727. PDF bib
topics:						DYN									P2P
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
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