Author: pwang
Date: 2012-11-07 16:47:03 -0800 (Wed, 07 Nov 2012)
New Revision: 30758
Modified:
new_cytoscape_website/trunk/who_is_using.html
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Add CNS publication list
Modified: new_cytoscape_website/trunk/who_is_using.html
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<div class="blockfull">
<h2>Share Your Work!</h2>
<p>If you have Cytoscape-related publications, news/blog articles, or
artworks, share them with others by <a href="community.html">social media
services</a>.</p>
+
+ 2012<br /><ul>
+<li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li></ul>
+2011<br /><ul>
+<li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>Ideker, T., Dutkowski, J., and Hood, L. (2011). Boosting
signal-to-noise in complex biology: prior knowledge is power. Cell 144, 860-863.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>Seebacher, J., and Gavin, A.C. (2011). SnapShot: Protein-protein
interaction networks. Cell 144, 1000, 1000 e1001.
+</li><li>Su, Z., Huang, W., and Gu, X. (2011). Comment on "Positive selection
of tyrosine loss in metazoan evolution". Science 332, 917; author reply 917.
+</li></ul>
+2010<br /><ul>
+<li>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.
+</li><li>Behrends, C., Sowa, M.E., Gygi, S.P., and Harper, J.W. (2010).
Network organization of the human autophagy system. Nature 466, 68-76.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li></ul>
+2009<br /><ul>
+<li>Jackson, P.K. (2009). Navigating the deubiquitinating proteome with a
CompPASS. Cell 138, 222-224.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li></ul>
+2008<br /><ul>
+<li>Ideker, T. (2008). Forging new ties between E. coli genes. Cell 133,
1135-1137.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li></ul>
+2006<br /><ul>
+<li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li><li>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.
+</li></ul>
+2004<br /><ul>
+<li>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.
+</li><li>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.
+</li></ul>
+2002<br /><ul>
+<li>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.
+</li><li>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.
+</li></ul>
+2001<br /><ul>
+<li>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.
+</li><li>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.
+</li></ul>
+
</div>
</div>
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