Gerstein Lab Publications
Proteomics: Prediction and Analysis of Protein Networks
We are amongst the first groups to describe how many weak functional genomic features could be systematically integrated with data mining techniques to predict protein networks (comprising protein interactions and other functional linkages). Some of the features integrated were obviously related to protein interactions (e.g. expression correlations) but many others such as (e.g. essentiality) were less so. We have had a number of localization and interaction predictions experimentally verified. In more recent work, we were able to calibrate the degree to which the data quality and the specific mining approach is associated with the strength of the predictions. In addition, we have studied the structure of protein networks, both on a large-scale in terms of global statistics (e.g. the diameter) and on a small-scale in terms of local network motifs (e.g. hubs). In particular, we have correlated network hubs with gene essentiality. Most importantly, we were the first to study the dynamics of regulatory networks. This allowed us to discover changing transient hubs and systematic patterns of connectivity rewiring in the yeast regulatory network. We were able to show for the first time that network dramatically changes in different conditions. 2007 snippet describing some of the lab's work in networks [html] [doc]
early 2009 description of some of the lab's work in networks for a general audience [html] [doc]
early 2009 description of some of the lab's work in networks, referenced, for a more technical audience [html] [doc]
C Cheng, KK Yan, W Hwang, J Qian, N Bhardwaj, J Rozowsky, ZJ Lu, W Niu, P Alves, M Kato, M Snyder, M Gerstein (2011). PLoS Comput Biol 7:e1002190.
N Bhardwaj, A Abyzov, D Clarke, C Shou, MB Gerstein (2011). Protein Sci 20:1745-54.
C Shou, N Bhardwaj, HY Lam, KK Yan, PM Kim, M Snyder, MB Gerstein (2011). PLoS Comput Biol 7:e1001050.
N Bhardwaj, PM Kim, MB Gerstein (2010). Sci Signal 3:ra79.
N Bhardwaj, MB Carson, A Abyzov, KK Yan, H Lu, MB Gerstein (2010). PLoS Comput Biol 6:e1000755.
HY Lam, PM Kim, J Mok, R Tonikian, SS Sidhu, BE Turk, M Snyder, MB Gerstein (2010). BMC Bioinformatics 11:243.
KK Yan, G Fang, N Bhardwaj, RP Alexander, M Gerstein (2010). Proc Natl Acad Sci U S A 107:9186-91.
PV Patel, TA Gianoulis, RD Bjornson, KY Yip, DM Engelman, MB Gerstein (2010). Genome Res 20:960-71.
N Bhardwaj, KK Yan, MB Gerstein (2010). Proc Natl Acad Sci U S A 107:6841-6.
C Cheng, X Fu, P Alves, M Gerstein (2009). Genome Biol 10:R90.
KY Yip, PM Kim, D McDermott, M Gerstein (2009). BMC Bioinformatics 10:241.
RP Alexander, PM Kim, T Emonet, MB Gerstein (2009). Sci Signal 2:pe44.
Y Xia, EA Franzosa, MB Gerstein (2009). PLoS Comput Biol 5:e1000413.
KY Yip, M Gerstein (2009). Bioinformatics 25:243-50.
PM Kim, A Sboner, Y Xia, M Gerstein (2008). Mol Syst Biol 4:179.
KY Yip, P Patel, PM Kim, DM Engelman, D McDermott, M Gerstein (2008). Bioinformatics 24:290-2.
PM Kim, JO Korbel, MB Gerstein (2007). Proc Natl Acad Sci U S A 104:20274-9.
LJ Lu, A Sboner, YJ Huang, HX Lu, TA Gianoulis, KY Yip, PM Kim, GT Montelione, MB Gerstein (2007). Trends Biochem Sci 32:320-31.
H Yu, R Jansen, G Stolovitzky, M Gerstein (2007). Bioinformatics 23:2163-73.
X Zhu, M Gerstein, M Snyder (2007). Genes Dev 21:1010-24.
H Yu, PM Kim, E Sprecher, V Trifonov, M Gerstein (2007). PLoS Comput Biol 3:e59.
PM Kim, LJ Lu, Y Xia, MB Gerstein (2006). Science 314:1938-41.
KY Yip, H Yu, PM Kim, M Schultz, M Gerstein (2006). Bioinformatics 22:2968-70.
H Yu, M Gerstein (2006). Proc Natl Acad Sci U S A 103:14724-31.
H Yu, Y Xia, V Trifonov, M Gerstein (2007). Genome Biol 7:R55.
NJ Krogan, G Cagney, H Yu, G Zhong, X Guo, A Ignatchenko, J Li, S Pu, N Datta, AP Tikuisis, T Punna, JM Peregrín-Alvarez, M Shales, X Zhang, M Davey, MD Robinson, A Paccanaro, JE Bray, A Sheung, B Beattie, DP Richards, V Canadien, A Lalev, F Mena, P Wong, A Starostine, MM Canete, J Vlasblom, S Wu, C Orsi, SR Collins, S Chandran, R Haw, JJ Rilstone, K Gandi, NJ Thompson, G Musso, P St Onge, S Ghanny, MH Lam, G Butland, AM Altaf-Ul, S Kanaya, A Shilatifard, E O'Shea, JS Weissman, CJ Ingles, TR Hughes, J Parkinson, M Gerstein, SJ Wodak, A Emili, JF Greenblatt (2006). Nature 440:637-43.
H Yu, A Paccanaro, V Trifonov, M Gerstein (2006). Bioinformatics 22:823-9.
Y Xia, LJ Lu, M Gerstein (2006). J Mol Biol 357:339-49.
A Paccanaro, V Trifonov, H Yu, M Gerstein (2005). International Joint Conference on Neural Networks (IJCNN, Jul. 31-Aug. 4, Montreal, Canada), pages 161 - 166, vol. 1
LJ Lu, Y Xia, H Yu, A Rives, H Lu, F Schubert, M Gerstein (2005). Data Analysis and Visualization in Genomics and Proteomics (Wiley, NY)
J Ptacek, G Devgan, G Michaud, H Zhu, X Zhu, J Fasolo, H Guo, G Jona, A Breitkreutz, R Sopko, RR McCartney, MC Schmidt, N Rachidi, SJ Lee, AS Mah, L Meng, MJ Stark, DF Stern, C De Virgilio, M Tyers, B Andrews, M Gerstein, B Schweitzer, PF Predki, M Snyder (2005). Nature 438:679-84.
SM Douglas, GT Montelione, M Gerstein (2005). Genome Biol 6:R80.
LJ Lu, Y Xia, A Paccanaro, H Yu, M Gerstein (2005). Genome Res 15:945-53.
N Lin, B Wu, R Jansen, M Gerstein, H Zhao (2004). BMC Bioinformatics 5:154.
NM Luscombe, MM Babu, H Yu, M Snyder, SA Teichmann, M Gerstein (2004). Nature 431:308-12.
MM Babu, NM Luscombe, L Aravind, M Gerstein, SA Teichmann (2004). Curr Opin Struct Biol 14:283-91.
Y Xia, H Yu, R Jansen, M Seringhaus, S Baxter, D Greenbaum, H Zhao, M Gerstein (2004). Annu Rev Biochem 73:1051-87.
H Yu, NM Luscombe, HX Lu, X Zhu, Y Xia, JD Han, N Bertin, S Chung, M Vidal, M Gerstein (2004). Genome Res 14:1107-18.
H Yu, D Greenbaum, H Xin Lu, X Zhu, M Gerstein (2004). Trends Genet 20:227-31.
H Yu, X Zhu, D Greenbaum, J Karro, M Gerstein (2004). Nucleic Acids Res 32:328-37.
S Li, CM Armstrong, N Bertin, H Ge, S Milstein, M Boxem, PO Vidalain, JD Han, A Chesneau, T Hao, DS Goldberg, N Li, M Martinez, JF Rual, P Lamesch, L Xu, M Tewari, SL Wong, LV Zhang, GF Berriz, L Jacotot, P Vaglio, J Reboul, T Hirozane-Kishikawa, Q Li, HW Gabel, A Elewa, B Baumgartner, DJ Rose, H Yu, S Bosak, R Sequerra, A Fraser, SE Mango, WM Saxton, S Strome, S Van Den Heuvel, F Piano, J Vandenhaute, C Sardet, M Gerstein, L Doucette-Stamm, KC Gunsalus, JW Harper, ME Cusick, FP Roth, DE Hill, M Vidal (2004). Science 303:540-3.
Z Zhang, M Gerstein (2003). Nat Biotechnol 21:1295-7.
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.
J Qian, J Lin, NM Luscombe, H Yu, M Gerstein (2003). Bioinformatics 19:1917-26.
H Yu, NM Luscombe, J Qian, M Gerstein (2003). Trends Genet 19:422-7.
R Jansen, D Greenbaum, M Gerstein (2002). Genome Res 12:37-46.
M Gerstein, N Lan, R Jansen (2002). Science 295:284-7.
R Jansen, N Lan, J Qian, M Gerstein (2003). J Struct Funct Genomics 2:71-81.
AM Edwards, B Kus, R Jansen, D Greenbaum, J Greenblatt, M Gerstein (2002). Trends Genet 18:529-36.
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