Comparative Genomics – Bioinformatics Centre - University of Copenhagen

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Bioinformatics Centre > Research > Comparative Genomics

Comparative Genomics

The completion of more than 40 vertebrate genomes allows us to study the evolutionary process at unprecedented resolution, not only shedding light on the process itself, but also on the structure and function of the genomes.  Our work involves the development of new methods for comparative analysis, their genome-wide application, interpretation of results in the light of high-throughput functional genomics data, and, in some cases, experimental collaborations to validate specific biological hypothesis. A main focus of the group is the study of non-protein-coding RNA, which have proven to be vital for virtually all cellular processes. Specific projects include comparative discovery of RNA genes, RNA secondary structure prediction, combined RNA sequence and structure alignment, and experimental collaborations on candidates for A-to-I RNA edting and on candidates of cis-regulatory structures within protein-coding genes.  

Publications

 2009

  • Han, J., J. S. Pedersen, S. C. Kwon, C. D. Belair, Y. K. Kim, K. H. Yeom, W. Y. Yang, D. Haussler, R. Blelloch, N. V. Kim (2009). Posttranscriptional Crossregulation between Drosha and DGCR8. Cell. 136: 75-84.

 2008

  • Karolchik, D., R. M. Kuhn, R. Baertsch, G. P. Barber, H. Clawson, M. Diekhans, B. Giardine, R. A. Harte, A. S. Hinrichs, F. Hsu, K. M. Kober, W. Miller, J. S. Pedersen, A. Pohl, B. J. Raney, B. Rhead, K. R. Rosenbloom, K. E. Smith, M. Stanke, A. Thakkapallayil, H. Trumbower, T. Wang, A. S. Zweig, D. Haussler and W. J. Kent (2008). The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res. 36: D773-9.

2007

  • Drosophila 12 Genomes Consortium (2007). Evolution of genes and genomes on the Drosophila phylogeny. Nature. 450: 203-18.
  • Stark, A.*, M. F. Lin*, P. Kheradpour*, J. S. Pedersen*, L. Parts, J. W. Carlson, M. A. Crosby, M. D. Rasmussen, S. Roy, A. N. Deoras, J. G. Ruby, J. Brennecke, H. F. curators, B. D. G. Project, E. Hodges, A. S. Hinrichs, A. Caspi, B. Paten, S. W. Park, M. V. Han, M. L. Maeder, B. J. Polansky, B. E. Robson, S. Aerts, J. van Helden, B. Hassan, D. G. Gilbert, D. A. Eastman, M. Rice, M. Weir, M. W. Hahn, Y. Park, C. N. Dewey, L. Pachter, W. J. Kent, D. Haussler, E. C. Lai, D. P. Bartel, G. J. Hannon, T. C. Kaufman, M. B. Eisen, A. G. Clark, D. Smith, S. E. Celniker, W. M. Gelbart and M. Kellis (2007). Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450: 219-32.
  • ENCODE Project Consortium (2007). Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 447: 799-816.
  • Kuhn, R. M., D. Karolchik, A. S. Zweig, H. Trumbower, D. J. Thomas, A. Thakkapallayil, C. W. Sugnet, M. Stanke, K. E. Smith, A. Siepel, K. R. Rosenbloom, B. Rhead, B. J. Raney, A. Pohl, J. S. Pedersen, F. Hsu, A. S. Hinrichs, R. A. Harte, M. Diekhans, H. Clawson, G. Bejerano, G. P. Barber, R. Baertsch, D. Haussler and W. J. Kent (2007). The UCSC genome browser database: update 2007. Nucleic Acids Res. 35: D668-73.
  • Ohlson, J., J. S. Pedersen, D. Haussler and M. Ohman (2007). Editing modifies the GABA(A) receptor subunit alpha3. RNA. 13: 698-703.
  • Washietl, S., J. S. Pedersen, J. O. Korbel, C. Stocsits, A. R. Gruber, J. Hackermüller, J. Hertel, M. Lindemeyer, K. Reiche, A. Tanzer, C. Ucla, C. Wyss, S. E. Antonarakis, F. Denoeud, J. Lagarde, J. Drenkow, P. Kapranov, T. R. Gingeras, R. Guigo, M. Snyder, M. B. Gerstein, A. Reymond, I. L. Hofacker and P. F. Stadler (2007). Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 17: 852-64.


2006

  • Hinrichs, A. S., D. Karolchik, R. Baertsch, G. P. Barber, G. Bejerano, H. Clawson, M. Diekhans, T. S. Furey, R. A. Harte, F. Hsu, J. Hillman-Jackson, R. M. Kuhn, J. S. Pedersen, A. Pohl, B. J. Raney, K. R. Rosenbloom, A. Siepel, K. E. Smith, C. W. Sugnet, A. Sultan-Qurraie, D. J. Thomas, H. Trumbower, R. J. Weber, M. Weirauch, A. S. Zweig, D. Haussler and W. J. Kent (2006). The UCSC Genome Browser Database: update 2006. Nucleic Acids Res. 34: D590-8.
  • Pedersen, J. S., G. Bejerano, A. Siepel, K. Rosenbloom, K. Lindblad-Toh, E. S. Lander, J. Kent, W. Miller and D. Haussler (2006). Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2: e33.
  • Pollard, K. S., S. R. Salama, B. King, A. D. Kern, T. Dreszer, S. Katzman, A. Siepel, J. S. Pedersen, G. Bejerano, R. Baertsch, K. R. Rosenbloom, J. Kent and D. Haussler (2006). Forces shaping the fastest evolving regions in the human genome. PLoS Genet. 2: e168.
  • Pollard, K. S., S. R. Salama, N. Lambert, M. A. Lambot, S. Coppens, J. S. Pedersen, S. Katzman, B. King, C. Onodera, A. Siepel, A. D. Kern, C. Dehay, H. Igel, M. Ares, P. Vanderhaeghen and D. Haussler (2006). An RNA gene expressed during cortical development evolved rapidly in humans. Nature. 443: 167-72.


2005

  • Siepel, A., G. Bejerano, J. S. Pedersen, A. S. Hinrichs, M. Hou, K. Rosenbloom, H. Clawson, J. Spieth, L. W. Hillier, S. Richards, G. M. Weinstock, R. K. Wilson, R. A. Gibbs, W. J. Kent, W. Miller and D. Haussler (2005). Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15: 1034-50.


2004

  • Pedersen, J. S.*, R. Forsberg*, I. M. Meyer and J. Hein (2004). An evolutionary model for protein-coding regions with conserved RNA structure. Mol Biol Evol. 21: 1913-22.
  • Pedersen, J. S.*, I. M. Meyer*, R. Forsberg, P. Simmonds and J. Hein (2004). A comparative method for finding and folding RNA secondary structures within protein-coding regions. Nucleic Acids Res. 32: 4925-36.


2003

  • Pedersen, J. S. and J. Hein (2003). Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics. 19: 219-27.