Gerstein Lab Publications
Genomics: Analysis of Pseudogenes and Intergenic Regions
We were the first group to assign pseudogenes comprehensively to the human genome and, for comparison, to the genomes of other organisms. Collectively, these studies enable us to determine the common "pseudofamilies" in various genomes and to address important evolutionary questions about the type of proteins that were present in the past history of an organism. In particular, they enabled us to show that there are dramatic differences in the repertoire of pseudogenes in the human genome versus those of other organisms with the human having many more processed pseudogenes (associated with highly transcribed genes such as those of the ribosome), whereas the genomes of other organisms have many more pseudogenes associated with environmental response proteins and horizontal transfer events. Our large scale assignment of pseudogenes also enabled us to precisely calibrate neutral rates of mutation in the genome. Finally, we were able to couple our pseudogene assignments with results of tiling array experiments probing the activity of intergenic regions. These studies enabled us to suggest that pseudogenes might not actually be dead at all, but that many of them are quite alive and actively transcribed. Our work with pseudogenes, and tiling arrays, and intergenic analysis has required the development of many novel technologies such as automatic assignment pipelines and statistical scoring schemes.
S Balasubramanian, L Habegger, A Frankish, DG MacArthur, R Harte, C Tyler-Smith, J Harrow, M Gerstein (2011). Genes Dev 25:1-10.
E Khurana, HY Lam, C Cheng, N Carriero, P Cayting, MB Gerstein (2010). Nucleic Acids Res 38:6997-7007.
ME Holford, E Khurana, KH Cheung, M Gerstein (2010). Bioinformatics 26:i71-8.
ZD Zhang, A Frankish, T Hunt, J Harrow, M Gerstein (2010). Genome Biol 11:R26.
YJ Liu, D Zheng, S Balasubramanian, N Carriero, E Khurana, R Robilotto, MB Gerstein (2009). BMC Genomics 10:480.
X Guo, Z Zhang, MB Gerstein, D Zheng (2009). PLoS Comput Biol 5:e1000449.
S Balasubramanian, D Zheng, YJ Liu, G Fang, A Frankish, N Carriero, R Robilotto, P Cayting, M Gerstein (2009). Genome Biol 10:R2.
HY Lam, E Khurana, G Fang, P Cayting, N Carriero, KH Cheung, MB Gerstein (2008). Nucleic Acids Res 37:D738-43.
ZD Zhang, P Cayting, G Weinstock, M Gerstein (2008). Mol Biol Evol 25:131-43.
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 Guigó, J Harrow, MB Gerstein (2007). Genome Res 17:839-51.
JE Karro, Y Yan, D Zheng, Z Zhang, N Carriero, P Cayting, P Harrrison, M Gerstein (2007). Nucleic Acids Res 35:D55-60.
D Zheng, MB Gerstein (2006). Genome Biol 7 Suppl 1:S13.1-10.
M Gerstein, D Zheng (2006). Sci Am 295:48-55.
Z Zhang, N Carriero, D Zheng, J Karro, PM Harrison, M Gerstein (2006). Bioinformatics 22:1437-9.
D Zheng, Z Zhang, PM Harrison, J Karro, N Carriero, M Gerstein (2005). J Mol Biol 349:27-45.
PM Harrison, D Zheng, Z Zhang, N Carriero, M Gerstein (2005). Nucleic Acids Res 33:2374-83.
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.
Y Liu, PM Harrison, V Kunin, M Gerstein (2004). Genome Biol 5:R64.
Z Zhang, M Gerstein (2004). Curr Opin Genet Dev 14:328-35.
Z Zhang, N Carriero, M Gerstein (2004). Trends Genet 20:62-7.
Z Zhang, PM Harrison, Y Liu, M Gerstein (2003). Genome Res 13:2541-58.
PM Harrison, N Carriero, Y Liu, M Gerstein (2003). J Mol Biol 333:885-92.
Z Zhang, M Gerstein (2003). Nucleic Acids Res 31:5338-48.
Z Zhang, M Gerstein (2003). Gene 312:61-72.
Z Zhang, M Gerstein (2003). Genomics 81:468-80.
PM Harrison, D Milburn, Z Zhang, P Bertone, M Gerstein (2003). Nucleic Acids Res 31:1033-7.
P Harrison, A Kumar, N Lan, N Echols, M Snyder, M Gerstein (2002). J Mol Biol 316:409-19.
PM Harrison, M Gerstein (2002). J Mol Biol 318:1155-74.
PM Harrison, H Hegyi, S Balasubramanian, NM Luscombe, P Bertone, N Echols, T Johnson, M Gerstein (2002). Genome Res 12:272-80.
ZL Zhang, PM Harrison, M Gerstein (2002). J Mol Biol 323:811-22.
Z Zhang, P Harrison, M Gerstein (2002). Genome Res 12:1466-82.
S Balasubramanian, P Harrison, H Hegyi, P Bertone, N Luscombe, N Echols, P McGarvey, Z Zhang, M Gerstein (2002). Pharmacogenomics 3:393-402.
N Echols, P Harrison, S Balasubramanian, NM Luscombe, P Bertone, Z Zhang, M Gerstein (2002). Nucleic Acids Res 30:2515-23.
PM Harrison, N Echols, MB Gerstein (2001). Nucleic Acids Res 29:818-30.
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