Literature DB >> 16978854

New metrics for comparative genomics.

Michael Y Galperin1, Eugene Kolker.   

Abstract

The availability of genome sequences from a variety of organisms presents an opportunity to apply this sequence information to solving the key problems of molecular biology. One of the principal roadblocks on this path is the lack of appropriate descriptors and metrics that could succinctly represent the new knowledge stemming from the genomic data. Several new metrics have recently been used in comparative genome analysis, yet challenges remain in finding an appropriate language for the emerging discipline of systems biology.

Mesh:

Year:  2006        PMID: 16978854      PMCID: PMC1764326          DOI: 10.1016/j.copbio.2006.08.007

Source DB:  PubMed          Journal:  Curr Opin Biotechnol        ISSN: 0958-1669            Impact factor:   9.740


  60 in total

Review 1.  Lateral gene transfer and the nature of bacterial innovation.

Authors:  H Ochman; J G Lawrence; E A Groisman
Journal:  Nature       Date:  2000-05-18       Impact factor: 49.962

2.  Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.

Authors:  Y I Wolf; I B Rogozin; A S Kondrashov; E V Koonin
Journal:  Genome Res       Date:  2001-03       Impact factor: 9.043

Review 3.  Missing genes in metabolic pathways: a comparative genomics approach.

Authors:  Andrei Osterman; Ross Overbeek
Journal:  Curr Opin Chem Biol       Date:  2003-04       Impact factor: 8.822

Review 4.  The value of complete microbial genome sequencing (you get what you pay for).

Authors:  Claire M Fraser; Jonathan A Eisen; Karen E Nelson; Ian T Paulsen; Steven L Salzberg
Journal:  J Bacteriol       Date:  2002-12       Impact factor: 3.490

5.  Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys.

Authors:  Michelle Sait; Philip Hugenholtz; Peter H Janssen
Journal:  Environ Microbiol       Date:  2002-11       Impact factor: 5.491

6.  Prokaryotic evolution in light of gene transfer.

Authors:  J Peter Gogarten; W Ford Doolittle; Jeffrey G Lawrence
Journal:  Mol Biol Evol       Date:  2002-12       Impact factor: 16.240

7.  Scaling laws in the functional content of genomes.

Authors:  Erik van Nimwegen
Journal:  Trends Genet       Date:  2003-09       Impact factor: 11.639

8.  Complete genome sequence of the metabolically versatile photosynthetic bacterium Rhodopseudomonas palustris.

Authors:  Frank W Larimer; Patrick Chain; Loren Hauser; Jane Lamerdin; Stephanie Malfatti; Long Do; Miriam L Land; Dale A Pelletier; J Thomas Beatty; Andrew S Lang; F Robert Tabita; Janet L Gibson; Thomas E Hanson; Cedric Bobst; Janelle L Torres y Torres; Caroline Peres; Faith H Harrison; Jane Gibson; Caroline S Harwood
Journal:  Nat Biotechnol       Date:  2003-12-14       Impact factor: 54.908

9.  Identifying protein function--a call for community action.

Authors:  Richard J Roberts
Journal:  PLoS Biol       Date:  2004-03-16       Impact factor: 8.029

10.  Genome trees constructed using five different approaches suggest new major bacterial clades.

Authors:  Y I Wolf; I B Rogozin; N V Grishin; R L Tatusov; E V Koonin
Journal:  BMC Evol Biol       Date:  2001-10-20       Impact factor: 3.260

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  15 in total

1.  From complete genome sequence to 'complete' understanding?

Authors:  Michael Y Galperin; Eugene V Koonin
Journal:  Trends Biotechnol       Date:  2010-08       Impact factor: 19.536

2.  Optimizing high performance computing workflow for protein functional annotation.

Authors:  Larissa Stanberry; Bhanu Rekepalli; Yuan Liu; Paul Giblock; Roger Higdon; Elizabeth Montague; William Broomall; Natali Kolker; Eugene Kolker
Journal:  Concurr Comput       Date:  2014-09-10       Impact factor: 1.536

Review 3.  Microbial genome analysis: the COG approach.

Authors:  Michael Y Galperin; David M Kristensen; Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Journal:  Brief Bioinform       Date:  2019-07-19       Impact factor: 11.622

4.  Interplay of heritage and habitat in the distribution of bacterial signal transduction systems.

Authors:  Michael Y Galperin; Roger Higdon; Eugene Kolker
Journal:  Mol Biosyst       Date:  2010-02-09

5.  Comparative genome biology of a serogroup B carriage and disease strain supports a polygenic nature of meningococcal virulence.

Authors:  Biju Joseph; Susanne Schneiker-Bekel; Anja Schramm-Glück; Jochen Blom; Heike Claus; Burkhard Linke; Roland F Schwarz; Anke Becker; Alexander Goesmann; Matthias Frosch; Christoph Schoen
Journal:  J Bacteriol       Date:  2010-08-13       Impact factor: 3.490

6.  Expanded microbial genome coverage and improved protein family annotation in the COG database.

Authors:  Michael Y Galperin; Kira S Makarova; Yuri I Wolf; Eugene V Koonin
Journal:  Nucleic Acids Res       Date:  2014-11-26       Impact factor: 16.971

Review 7.  Using comparative genomics to drive new discoveries in microbiology.

Authors:  Daniel H Haft
Journal:  Curr Opin Microbiol       Date:  2015-01-21       Impact factor: 7.934

8.  Rapid pair-wise synteny analysis of large bacterial genomes using web-based GeneOrder4.0.

Authors:  Padmanabhan Mahadevan; Donald Seto
Journal:  BMC Res Notes       Date:  2010-02-23

9.  UFO: a web server for ultra-fast functional profiling of whole genome protein sequences.

Authors:  Peter Meinicke
Journal:  BMC Genomics       Date:  2009-09-02       Impact factor: 3.969

10.  A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions.

Authors:  Brenton Louie; Roger Higdon; Eugene Kolker
Journal:  PLoS One       Date:  2009-10-21       Impact factor: 3.240

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