During the year 2005, the lab continued its research progress along the same lines that we had previously.
1) Genome annotation
2) Understanding protein function in terms of networks
3) Structural genomics
4) Biophysical analysis of macromolecular motions.
Additionally, we also wrote a number of papers that explored various social aspects of large-scale scientific collaboration and we engaged in a number of multi-disciplinary collaborations.
In relation to the genomics, we accomplished two things. First of all, we had two papers, Harrison et al and Zheng et al, which looked at transcribed pseudogenes in the human genome and tried to show that even though pseudogenes are thought of as dead copies of genes, they might actually have some activity in them in relationship to transcription. In Royce et al, 2005, we developed some approaches for scoring microarrays, which is very important for the analysis of these intergenic regions. In Balasubramanian et al, we also continued on our genomic analysis, focusing on variations merging nets with a particularly well-known protein family and trying to predict which SNPs were deleterious.
Continuing the structural work, Alexandrov et al and Voss et al, reported work using normal modes to predict RNA packing and to look at motions.
In protein networks, Lu et al assessed the degree to which we could predict networks, and in Douglas et al, we developed a new tool for visualizing networks derived from connected genes, but also networks related to scientific co-publication.
In the broader context of connecting computing to molecular biology, we wrote a number of papers on the ideas behind database interoperation. In Cheung et al, we developed a prototype system for assessing the interoperation of databases related to yeast. In Smith et al, we looked at the degree to which computer security consideration significantly impede database interoperation.
Finally, we also had a number of novel experimental collaborations this year. At the end of the year, in Ptacek et al, we were participants in a large multi-disciplinary team that published a paper unraveling the phosphorylome, the network of all protein-protein interactions involved in phosphorylation, an important signalling process.
P Bertone, V Trifonov, JS Rozowsky, F Schubert, O Emanuelsson, J Karro, MY Kao, M Snyder, M Gerstein (2006). Genome Res 16: 271-81.
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)
DM Gelperin, MA White, ML Wilkinson, Y Kon, LA Kung, KJ Wise, N Lopez-Hoyo, L Jiang, S Piccirillo, H Yu, M Gerstein, ME Dumont, EM Phizicky, M Snyder, EJ Grayhack (2005). Genes Dev 19: 2816-26.
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.
SE Hartman, P Bertone, AK Nath, TE Royce, M Gerstein, S Weissman, M Snyder (2005). Genes Dev 19: 2953-68.
A Smith, D Greenbaum, SM Douglas, M Long, M Gerstein (2005). Genome Biol 6: 119.
SM Douglas, GT Montelione, M Gerstein (2005). Genome Biol 6: R80.
T Coric, D Zheng, M Gerstein, CM Canessa (2005). J Physiol 568: 725-35.
LJ Lu, Y Xia, A Paccanaro, H Yu, M Gerstein (2005). Genome Res 15: 945-53.
TE Royce, JS Rozowsky, P Bertone, M Samanta, V Stolc, S Weissman, M Snyder, M Gerstein (2005). Trends Genet 21: 466-75.
KH Cheung, KY Yip, A Smith, R Deknikker, A Masiar, M Gerstein (2005). Bioinformatics 21 Suppl 1: i85-96.
D Zheng, Z Zhang, PM Harrison, J Karro, N Carriero, M Gerstein (2005). J Mol Biol 349: 27-45.
P Bertone, M Gerstein, M Snyder (2005). Chromosome Res 13: 259-74.
Y Gilad, SA Rifkin, P Bertone, M Gerstein, KP White (2005). Genome Res 15: 674-80.
PM Harrison, D Zheng, Z Zhang, N Carriero, M Gerstein (2005). Nucleic Acids Res 33: 2374-83.
D Huber, D Boyd, Y Xia, MH Olma, M Gerstein, J Beckwith (2005). J Bacteriol 187: 2983-91.
TB Acton, KC Gunsalus, R Xiao, LC Ma, J Aramini, MC Baran, YW Chiang, T Climent, B Cooper, NG Denissova, SM Douglas, JK Everett, CK Ho, D Macapagal, PK Rajan, R Shastry, LY Shih, GV Swapna, M Wilson, M Wu, M Gerstein, M Inouye, JF Hunt, GT Montelione (2005). Methods Enzymol 394: 210-43.
S Balasubramanian, Y Xia, E Freinkman, M Gerstein (2005). Nucleic Acids Res 33: 1710-21.
H Grosshans, T Johnson, KL Reinert, M Gerstein, FJ Slack (2005). Dev Cell 8: 321-30.
V Alexandrov, U Lehnert, N Echols, D Milburn, D Engelman, M Gerstein (2005). Protein Sci 14: 633-43.
NR Voss, M Gerstein (2005). J Mol Biol 346: 477-92.
N Carriero, MV Osier, KH Cheung, PL Miller, M Gerstein, H Zhao, B Wu, S Rifkin, J Chang, H Zhang, K White, K Williams, M Schultz (2005). J Am Med Inform Assoc 12: 90-8.
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