Literature DB >> 12671656

Comparative genomics: genome-wide analysis in metazoan eukaryotes.

Abel Ureta-Vidal1, Laurence Ettwiller, Ewan Birney.   

Abstract

The increasing number of complete and nearly complete metazoan genome sequences provides a significant amount of material for large-scale comparative genomic analysis. Finding new effective methods to analyse such enormous datasets has been the object of intense research. Three main areas in comparative genomics have recently shown important developments: whole-genome alignment, gene prediction and regulatory-region prediction. Each of these areas improves the methods of deciphering long genomic sequences and uncovering what lies hidden in them.

Mesh:

Year:  2003        PMID: 12671656     DOI: 10.1038/nrg1043

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  73 in total

1.  CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting.

Authors:  Eugene Berezikov; Victor Guryev; Ronald H A Plasterk; Edwin Cuppen
Journal:  Genome Res       Date:  2003-12-12       Impact factor: 9.043

Review 2.  Comparative genomic analysis as a tool for biological discovery.

Authors:  Marcelo A Nobrega; Len A Pennacchio
Journal:  J Physiol       Date:  2004-01-01       Impact factor: 5.182

3.  Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites.

Authors:  Gregory E Crawford; Ingeborg E Holt; James C Mullikin; Denise Tai; Robert Blakesley; Gerard Bouffard; Alice Young; Catherine Masiello; Eric D Green; Tyra G Wolfsberg; Francis S Collins
Journal:  Proc Natl Acad Sci U S A       Date:  2004-01-19       Impact factor: 11.205

4.  Sockeye: a 3D environment for comparative genomics.

Authors:  Stephen B Montgomery; Tamara Astakhova; Mikhail Bilenky; Ewan Birney; Tony Fu; Maik Hassel; Craig Melsopp; Marcin Rak; A Gordon Robertson; Monica Sleumer; Asim S Siddiqui; Steven J M Jones
Journal:  Genome Res       Date:  2004-05       Impact factor: 9.043

5.  Mauve: multiple alignment of conserved genomic sequence with rearrangements.

Authors:  Aaron C E Darling; Bob Mau; Frederick R Blattner; Nicole T Perna
Journal:  Genome Res       Date:  2004-07       Impact factor: 9.043

6.  Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions.

Authors:  Yutaka Suzuki; Riu Yamashita; Matsuyuki Shirota; Yuta Sakakibara; Joe Chiba; Junko Mizushima-Sugano; Kenta Nakai; Sumio Sugano
Journal:  Genome Res       Date:  2004-09       Impact factor: 9.043

Review 7.  Charting gene regulatory networks: strategies, challenges and perspectives.

Authors:  Gong-Hong Wei; De-Pei Liu; Chih-Chuan Liang
Journal:  Biochem J       Date:  2004-07-01       Impact factor: 3.857

8.  Separating significant matches from spurious matches in DNA sequences.

Authors:  Hugo Devillers; Sophie Schbath
Journal:  J Comput Biol       Date:  2011-12-09       Impact factor: 1.479

9.  An ORFeome-based analysis of human transcription factor genes and the construction of a microarray to interrogate their expression.

Authors:  David N Messina; Jarret Glasscock; Warren Gish; Michael Lovett
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043

10.  Long-range comparison of human and mouse Sprr loci to identify conserved noncoding sequences involved in coordinate regulation.

Authors:  Natalia Martin; Satyakam Patel; Julia A Segre
Journal:  Genome Res       Date:  2004-12       Impact factor: 9.043

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