5 Favorites as of March 2012, mostly focussed on networks and systems

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.
MB Gerstein, ZJ Lu, EL Van Nostrand, C Cheng, BI Arshinoff, T Liu, KY Yip, R Robilotto, A Rechtsteiner, K Ikegami, P Alves, A Chateigner, M Perry, M Morris, RK Auerbach, X Feng, J Leng, A Vielle, W Niu, K Rhrissorrakrai, A Agarwal, RP Alexander, G Barber, CM Brdlik, J Brennan, JJ Brouillet, A Carr, MS Cheung, H Clawson, S Contrino, LO Dannenberg, AF Dernburg, A Desai, L Dick, AC Dose, J Du, T Egelhofer, S Ercan, G Euskirchen, B Ewing, EA Feingold, R Gassmann, PJ Good, P Green, F Gullier, M Gutwein, MS Guyer, L Habegger, T Han, JG Henikoff, SR Henz, A Hinrichs, H Holster, T Hyman, AL Iniguez, J Janette, M Jensen, M Kato, WJ Kent, E Kephart, V Khivansara, E Khurana, JK Kim, P Kolasinska-Zwierz, EC Lai, I Latorre, A Leahey, S Lewis, P Lloyd, L Lochovsky, RF Lowdon, Y Lubling, R Lyne, M MacCoss, SD Mackowiak, M Mangone, S McKay, D Mecenas, G Merrihew, DM Miller, A Muroyama, JI Murray, SL Ooi, H Pham, T Phippen, EA Preston, N Rajewsky, G Ratsch, H Rosenbaum, J Rozowsky, K Rutherford, P Ruzanov, M Sarov, R Sasidharan, A Sboner, P Scheid, E Segal, H Shin, C Shou, FJ Slack, C Slightam, R Smith, WC Spencer, EO Stinson, S Taing, T Takasaki, D Vafeados, K Voronina, G Wang, NL Washington, CM Whittle, B Wu, KK Yan, G Zeller, Z Zha, M Zhong, X Zhou, modENCODE Consortium, J Ahringer, S Strome, KC Gunsalus, G Micklem, XS Liu, V Reinke, SK Kim, LW Hillier, S Henikoff, F Piano, M Snyder, L Stein, JD Lieb, RH Waterston (2010). Science 330: 1775-87.

Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl Acad Sci U S A 107: 9186-91.

Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
D Zheng, A Frankish, R Baertsch, P Kapranov, A Reymond, SW Choo, Y Lu, F Denoeud, SE Antonarakis, M Snyder, Y Ruan, CL Wei, TR Gingeras, R Guigo, J Harrow, MB Gerstein (2007). Genome Res 17: 839-51.

Relating three-dimensional structures to protein networks provides evolutionary insights.
PM Kim, LJ Lu, Y Xia, MB Gerstein (2006). Science 314: 1938-41.

A Bayesian networks approach for predicting protein-protein interactions from genomic data.
R Jansen, H Yu, D Greenbaum, Y Kluger, NJ Krogan, S Chung, A Emili, M Snyder, JF Greenblatt, M Gerstein (2003). Science 302: 449-53.

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