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2012

• Chen, R., Mias, G.I., Li-Pook-Than, J., Jiang, L., Lam, H.Y., Miriami, E., Karczewski, K.J., Hariharan, M., Dewey, F.E., Cheng, Y., et al. (2012). Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148, 1293-1307.
• Ciofani, M., Madar, A., Galan, C., Sellars, M., Mace, K., Pauli, F., Agarwal, A., Huang, W., Parkurst, C.N., Muratet, M., et al. (2012). A validated regulatory network for th17 cell specification. Cell 151, 289-303.
• Ellis, M.J., Ding, L., Shen, D., Luo, J., Suman, V.J., Wallis, J.W., Van Tine, B.A., Hoog, J., Goiffon, R.J., Goldstein, T.C., et al. (2012). Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature 486, 353-360.
• Garnett, M.J., Edelman, E.J., Heidorn, S.J., Greenman, C.D., Dastur, A., Lau, K.W., Greninger, P., Thompson, I.R., Luo, X., Soares, J., et al. (2012). Systematic identification of genomic markers of drug sensitivity in cancer cells. Nature 483, 570-575.
• Jostins, L., Ripke, S., Weersma, R., Duerr, R., McGovern, D., Hui, K., Lee, J., Schumm, L., Sharma, Y., Anderson, C., et al. (2012). Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 491, 119–124.
• Koren, O., Goodrich, J.K., Cullender, T.C., Spor, A., Laitinen, K., Backhed, H.K., Gonzalez, A., Werner, J.J., Angenent, L.T., Knight, R., et al. (2012). Host remodeling of the gut microbiome and metabolic changes during pregnancy. Cell 150, 470-480.
• Lau, E., Kluger, H., Varsano, T., Lee, K., Scheffler, I., Rimm, D.L., Ideker, T., and Ronai, Z.A. (2012). PKCepsilon promotes oncogenic functions of ATF2 in the nucleus while blocking its apoptotic function at mitochondria. Cell 148, 543-555.
• Lin, Y.Y., Kiihl, S., Suhail, Y., Liu, S.Y., Chou, Y.H., Kuang, Z., Lu, J.Y., Khor, C.N., Lin, C.L., Bader, J.S., et al. (2012). Functional dissection of lysine deacetylases reveals that HDAC1 and p300 regulate AMPK. Nature 482, 251-255.
• Molenaar, J.J., Koster, J., Zwijnenburg, D.A., van Sluis, P., Valentijn, L.J., van der Ploeg, I., Hamdi, M., van Nes, J., Westerman, B.A., van Arkel, J., et al. (2012). Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature 483, 589-593.
• Neph, S., Stergachis, A.B., Reynolds, A., Sandstrom, R., Borenstein, E., and Stamatoyannopoulos, J.A. (2012). Circuitry and dynamics of human transcription factor regulatory networks. Cell 150, 1274-1286.
• Northcott, P.A., Shih, D.J., Peacock, J., Garzia, L., Morrissy, A.S., Zichner, T., Stutz, A.M., Korshunov, A., Reimand, J., Schumacher, S.E., et al. (2012). Subgroup-specific structural variation across 1,000 medulloblastoma genomes. Nature 488, 49-56.
• O'Roak, B.J., Vives, L., Girirajan, S., Karakoc, E., Krumm, N., Coe, B.P., Levy, R., Ko, A., Lee, C., Smith, J.D., et al. (2012). Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485, 246-250.
• Powell, A.E., Wang, Y., Li, Y., Poulin, E.J., Means, A.L., Washington, M.K., Higginbotham, J.N., Juchheim, A., Prasad, N., Levy, S.E., et al. (2012). The pan-ErbB negative regulator Lrig1 is an intestinal stem cell marker that functions as a tumor suppressor. Cell 149, 146-158.
• Shah, S.P., Roth, A., Goya, R., Oloumi, A., Ha, G., Zhao, Y., Turashvili, G., Ding, J., Tse, K., Haffari, G., et al. (2012). The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 486, 395-399.

2011

• Dawson, M.A., Prinjha, R.K., Dittmann, A., Giotopoulos, G., Bantscheff, M., Chan, W.I., Robson, S.C., Chung, C.W., Hopf, C., Savitski, M.M., et al. (2011). Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. Nature 478, 529-533.
• Edwards, A.M., Isserlin, R., Bader, G.D., Frye, S.V., Willson, T.M., and Yu, F.H. (2011). Too many roads not taken. Nature 470, 163-165.
• Emanuele, M.J., Elia, A.E., Xu, Q., Thoma, C.R., Izhar, L., Leng, Y., Guo, A., Chen, Y.N., Rush, J., Hsu, P.W., et al. (2011). Global identification of modular cullin-RING ligase substrates. Cell 147, 459-474.
• Gieger, C., Radhakrishnan, A., Cvejic, A., Tang, W., Porcu, E., Pistis, G., Serbanovic-Canic, J., Elling, U., Goodall, A.H., Labrune, Y., et al. (2011). New gene functions in megakaryopoiesis and platelet formation. Nature 480, 201-208.
• Green, R.A., Kao, H.L., Audhya, A., Arur, S., Mayers, J.R., Fridolfsson, H.N., Schulman, M., Schloissnig, S., Niessen, S., Laband, K., et al. (2011). A high-resolution C. elegans essential gene network based on phenotypic profiling of a complex tissue. Cell 145, 470-482.
• Guruharsha, K.G., Rual, J.F., Zhai, B., Mintseris, J., Vaidya, P., Vaidya, N., Beekman, C., Wong, C., Rhee, D.Y., Cenaj, O., et al. (2011). A protein complex network of Drosophila melanogaster. Cell 147, 690-703.
• Ideker, T., Dutkowski, J., and Hood, L. (2011). Boosting signal-to-noise in complex biology: prior knowledge is power. Cell 144, 860-863.
• Muegge, B.D., Kuczynski, J., Knights, D., Clemente, J.C., Gonzalez, A., Fontana, L., Henrissat, B., Knight, R., and Gordon, J.I. (2011). Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. Science 332, 970-974.
• Nichols, R.J., Sen, S., Choo, Y.J., Beltrao, P., Zietek, M., Chaba, R., Lee, S., Kazmierczak, K.M., Lee, K.J., Wong, A., et al. (2011). Phenotypic landscape of a bacterial cell. Cell 144, 143-156.
• Paul, P., van den Hoorn, T., Jongsma, M.L., Bakker, M.J., Hengeveld, R., Janssen, L., Cresswell, P., Egan, D.A., van Ham, M., Ten Brinke, A., et al. (2011). A Genome-wide multidimensional RNAi screen reveals pathways controlling MHC class II antigen presentation. Cell 145, 268-283.
• Sang, L., Miller, J.J., Corbit, K.C., Giles, R.H., Brauer, M.J., Otto, E.A., Baye, L.M., Wen, X., Scales, S.J., Kwong, M., et al. (2011). Mapping the NPHP-JBTS-MKS protein network reveals ciliopathy disease genes and pathways. Cell 145, 513-528.
• Seebacher, J., and Gavin, A.C. (2011). SnapShot: Protein-protein interaction networks. Cell 144, 1000, 1000 e1001.
• Su, Z., Huang, W., and Gu, X. (2011). Comment on "Positive selection of tyrosine loss in metazoan evolution". Science 332, 917; author reply 917.

2010

• Bandyopadhyay, S., Mehta, M., Kuo, D., Sung, M.K., Chuang, R., Jaehnig, E.J., Bodenmiller, B., Licon, K., Copeland, W., Shales, M., et al. (2010). Rewiring of genetic networks in response to DNA damage. Science 330, 1385-1389.
• Behrends, C., Sowa, M.E., Gygi, S.P., and Harper, J.W. (2010). Network organization of the human autophagy system. Nature 466, 68-76.
• Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E.D., Sevier, C.S., Ding, H., Koh, J.L., Toufighi, K., Mostafavi, S., et al. (2010). The genetic landscape of a cell. Science 327, 425-431.
• Hudson, T.J., Anderson, W., Artez, A., Barker, A.D., Bell, C., Bernabe, R.R., Bhan, M.K., Calvo, F., Eerola, I., Gerhard, D.S., et al. (2010). International network of cancer genome projects. Nature 464, 993-998.
• Huttlin, E.L., Jedrychowski, M.P., Elias, J.E., Goswami, T., Rad, R., Beausoleil, S.A., Villen, J., Haas, W., Sowa, M.E., and Gygi, S.P. (2010). A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 143, 1174-1189.
• Kim, J., Lee, J.E., Heynen-Genel, S., Suyama, E., Ono, K., Lee, K., Ideker, T., Aza-Blanc, P., and Gleeson, J.G. (2010). Functional genomic screen for modulators of ciliogenesis and cilium length. Nature 464, 1048-1051.
• Konig, R., Stertz, S., Zhou, Y., Inoue, A., Hoffmann, H.H., Bhattacharyya, S., Alamares, J.G., Tscherne, D.M., Ortigoza, M.B., Liang, Y., et al. (2010). Human host factors required for influenza virus replication. Nature 463, 813-817.
• Kumar, D., Nath, L., Kamal, M.A., Varshney, A., Jain, A., Singh, S., and Rao, K.V. (2010). Genome-wide analysis of the host intracellular network that regulates survival of Mycobacterium tuberculosis. Cell 140, 731-743.
• Li, X., Gianoulis, T.A., Yip, K.Y., Gerstein, M., and Snyder, M. (2010). Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses. Cell 143, 639-650.
• Moore, M.J., Wang, Q., Kennedy, C.J., and Silver, P.A. (2010). An alternative splicing network links cell-cycle control to apoptosis. Cell 142, 625-636.
• Pinto, D., Pagnamenta, A.T., Klei, L., Anney, R., Merico, D., Regan, R., Conroy, J., Magalhaes, T.R., Correia, C., Abrahams, B.S., et al. (2010). Functional impact of global rare copy number variation in autism spectrum disorders. Nature 466, 368-372.
• Pospisilik, J.A., Schramek, D., Schnidar, H., Cronin, S.J., Nehme, N.T., Zhang, X., Knauf, C., Cani, P.D., Aumayr, K., Todoric, J., et al. (2010). Drosophila genome-wide obesity screen reveals hedgehog as a determinant of brown versus white adipose cell fate. Cell 140, 148-160.
• Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K.S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., Yamada, T., et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464, 59-65.
• Ravasi, T., Suzuki, H., Cannistraci, C.V., Katayama, S., Bajic, V.B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N., et al. (2010). An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140, 744-752.
• van Wageningen, S., Kemmeren, P., Lijnzaad, P., Margaritis, T., Benschop, J.J., de Castro, I.J., van Leenen, D., Groot Koerkamp, M.J., Ko, C.W., Miles, A.J., et al. (2010). Functional overlap and regulatory links shape genetic interactions between signaling pathways. Cell 143, 991-1004.
• Zielinska, D.F., Gnad, F., Wisniewski, J.R., and Mann, M. (2010). Precision mapping of an in vivo N-glycoproteome reveals rigid topological and sequence constraints. Cell 141, 897-907.

2009

• Jackson, P.K. (2009). Navigating the deubiquitinating proteome with a CompPASS. Cell 138, 222-224.
• Jorgensen, C., Sherman, A., Chen, G.I., Pasculescu, A., Poliakov, A., Hsiung, M., Larsen, B., Wilkinson, D.G., Linding, R., and Pawson, T. (2009). Cell-specific information processing in segregating populations of Eph receptor ephrin-expressing cells. Science 326, 1502-1509.
• Keiser, M.J., Setola, V., Irwin, J.J., Laggner, C., Abbas, A.I., Hufeisen, S.J., Jensen, N.H., Kuijer, M.B., Matos, R.C., Tran, T.B., et al. (2009). Predicting new molecular targets for known drugs. Nature 462, 175-181.
• Leidel, S., Pedrioli, P.G., Bucher, T., Brost, R., Costanzo, M., Schmidt, A., Aebersold, R., Boone, C., Hofmann, K., and Peter, M. (2009). Ubiquitin-related modifier Urm1 acts as a sulphur carrier in thiolation of eukaryotic transfer RNA. Nature 458, 228-232.
• Mummery-Widmer, J.L., Yamazaki, M., Stoeger, T., Novatchkova, M., Bhalerao, S., Chen, D., Dietzl, G., Dickson, B.J., and Knoblich, J.A. (2009). Genome-wide analysis of Notch signalling in Drosophila by transgenic RNAi. Nature 458, 987-992.
• Quigley, D.A., To, M.D., Perez-Losada, J., Pelorosso, F.G., Mao, J.H., Nagase, H., Ginzinger, D.G., and Balmain, A. (2009). Genetic architecture of mouse skin inflammation and tumour susceptibility. Nature 458, 505-508.
• Sowa, M.E., Bennett, E.J., Gygi, S.P., and Harper, J.W. (2009). Defining the human deubiquitinating enzyme interaction landscape. Cell 138, 389-403.
• Tan, C.S., Pasculescu, A., Lim, W.A., Pawson, T., Bader, G.D., and Linding, R. (2009). Positive selection of tyrosine loss in metazoan evolution. Science 325, 1686-1688.
• Zhang, E.E., Liu, A.C., Hirota, T., Miraglia, L.J., Welch, G., Pongsawakul, P.Y., Liu, X., Atwood, A., Huss, J.W., 3rd, Janes, J., et al. (2009). A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell 139, 199-210.

2008

• Ideker, T. (2008). Forging new ties between E. coli genes. Cell 133, 1135-1137.
• Ley, R.E., Hamady, M., Lozupone, C., Turnbaugh, P.J., Ramey, R.R., Bircher, J.S., Schlegel, M.L., Tucker, T.A., Schrenzel, M.D., Knight, R., et al. (2008). Evolution of mammals and their gut microbes. Science 320, 1647-1651.
• Mahrus, S., Trinidad, J.C., Barkan, D.T., Sali, A., Burlingame, A.L., and Wells, J.A. (2008). Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini. Cell 134, 866-876.
• Muller, F.J., Laurent, L.C., Kostka, D., Ulitsky, I., Williams, R., Lu, C., Park, I.H., Rao, M.S., Shamir, R., Schwartz, P.H., et al. (2008). Regulatory networks define phenotypic classes of human stem cell lines. Nature 455, 401-405.
• Roguev, A., Bandyopadhyay, S., Zofall, M., Zhang, K., Fischer, T., Collins, S.R., Qu, H., Shales, M., Park, H.O., Hayles, J., et al. (2008). Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast. Science 322, 405-410.
• Yu, H., Braun, P., Yildirim, M.A., Lemmens, I., Venkatesan, K., Sahalie, J., Hirozane-Kishikawa, T., Gebreab, F., Li, N., Simonis, N., et al. (2008). High-quality binary protein interaction map of the yeast interactome network. Science 322, 104-110.

2006

• Alper, H., Moxley, J., Nevoigt, E., Fink, G.R., and Stephanopoulos, G. (2006). Engineering yeast transcription machinery for improved ethanol tolerance and production. Science 314, 1565-1568.
• Deplancke, B., Mukhopadhyay, A., Ao, W., Elewa, A.M., Grove, C.A., Martinez, N.J., Sequerra, R., Doucette-Stamm, L., Reece-Hoyes, J.S., Hope, I.A., et al. (2006). A gene-centered C. elegans protein-DNA interaction network. Cell 125, 1193-1205.
• Gilchrist, M., Thorsson, V., Li, B., Rust, A.G., Korb, M., Roach, J.C., Kennedy, K., Hai, T., Bolouri, H., and Aderem, A. (2006). Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4. Nature 441, 173-178.
• Krogan, N.J., Cagney, G., Yu, H., Zhong, G., Guo, X., Ignatchenko, A., Li, J., Pu, S., Datta, N., Tikuisis, A.P., et al. (2006). Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature 440, 637-643.
• Pan, X., Ye, P., Yuan, D.S., Wang, X., Bader, J.S., and Boeke, J.D. (2006). A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 124, 1069-1081.
• Workman, C.T., Mak, H.C., McCuine, S., Tagne, J.B., Agarwal, M., Ozier, O., Begley, T.J., Samson, L.D., and Ideker, T. (2006). A systems approach to mapping DNA damage response pathways. Science 312, 1054-1059.

2004

• Hood, L., Heath, J.R., Phelps, M.E., and Lin, B. (2004). Systems biology and new technologies enable predictive and preventative medicine. Science 306, 640-643.
• Tong, A.H., Lesage, G., Bader, G.D., Ding, H., Xu, H., Xin, X., Young, J., Berriz, G.F., Brost, R.L., Chang, M., et al. (2004). Global mapping of the yeast genetic interaction network. Science 303, 808-813.

2002

• Ho, Y., Gruhler, A., Heilbut, A., Bader, G.D., Moore, L., Adams, S.L., Millar, A., Taylor, P., Bennett, K., Boutilier, K., et al. (2002). Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183.
• Tong, A.H., Drees, B., Nardelli, G., Bader, G.D., Brannetti, B., Castagnoli, L., Evangelista, M., Ferracuti, S., Nelson, B., Paoluzi, S., et al. (2002). A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science 295, 321-324.

2001

• Ideker, T., Thorsson, V., Ranish, J.A., Christmas, R., Buhler, J., Eng, J.K., Bumgarner, R., Goodlett, D.R., Aebersold, R., and Hood, L. (2001). Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929-934.
• Tong, A.H., Evangelista, M., Parsons, A.B., Xu, H., Bader, G.D., Page, N., Robinson, M., Raghibizadeh, S., Hogue, C.W., Bussey, H., et al. (2001). Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294, 2364-2368.