Literature DB >> 12194990

Databases and tools for browsing genomes.

Ewan Birney1, Michele Clamp, Tim Hubbard.   

Abstract

To maximize the value of genome sequences they need to be integrated with other types of biological data and with each other. The entire collection of data then needs to be made available in a way that is easy to view and mine for complex relationships. The recently determined vertebrate genome sequences of human and mouse are so large that building the infrastructure to manage these datasets is a major challenge. This article reviews the database systems and tools for analysis that have so far been developed to address this.

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Year:  2002        PMID： 12194990     DOI： 10.1146/annurev.genom.3.030502.101529

Source DB:  PubMed          Journal:  Annu Rev Genomics Hum Genet        ISSN： 1527-8204            Impact factor:   8.929


  9 in total

1.  Ensembl 2004.

Authors:  E Birney; D Andrews; P Bevan; M Caccamo; G Cameron; Y Chen; L Clarke; G Coates; T Cox; J Cuff; V Curwen; T Cutts; T Down; R Durbin; E Eyras; X M Fernandez-Suarez; P Gane; B Gibbins; J Gilbert; M Hammond; H Hotz; V Iyer; A Kahari; K Jekosch; A Kasprzyk; D Keefe; S Keenan; H Lehvaslaiho; G McVicker; C Melsopp; P Meidl; E Mongin; R Pettett; S Potter; G Proctor; M Rae; S Searle; G Slater; D Smedley; J Smith; W Spooner; A Stabenau; J Stalker; R Storey; A Ureta-Vidal; C Woodwark; M Clamp; T Hubbard
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

2.  Computational gene prediction using multiple sources of evidence.

Authors:  Jonathan E Allen; Mihaela Pertea; Steven L Salzberg
Journal:  Genome Res       Date:  2004-01       Impact factor: 9.043

3.  Ensembl 2002: accommodating comparative genomics.

Authors:  M Clamp; D Andrews; D Barker; P Bevan; G Cameron; Y Chen; L Clark; T Cox; J Cuff; V Curwen; T Down; R Durbin; E Eyras; J Gilbert; M Hammond; T Hubbard; A Kasprzyk; D Keefe; H Lehvaslaiho; V Iyer; C Melsopp; E Mongin; R Pettett; S Potter; A Rust; E Schmidt; S Searle; G Slater; J Smith; W Spooner; A Stabenau; J Stalker; E Stupka; A Ureta-Vidal; I Vastrik; E Birney
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

4.  Development of human protein reference database as an initial platform for approaching systems biology in humans.

Authors:  Suraj Peri; J Daniel Navarro; Ramars Amanchy; Troels Z Kristiansen; Chandra Kiran Jonnalagadda; Vineeth Surendranath; Vidya Niranjan; Babylakshmi Muthusamy; T K B Gandhi; Mads Gronborg; Nieves Ibarrola; Nandan Deshpande; K Shanker; H N Shivashankar; B P Rashmi; M A Ramya; Zhixing Zhao; K N Chandrika; N Padma; H C Harsha; A J Yatish; M P Kavitha; Minal Menezes; Dipanwita Roy Choudhury; Shubha Suresh; Neelanjana Ghosh; R Saravana; Sreenath Chandran; Subhalakshmi Krishna; Mary Joy; Sanjeev K Anand; V Madavan; Ansamma Joseph; Guang W Wong; William P Schiemann; Stefan N Constantinescu; Lily Huang; Roya Khosravi-Far; Hanno Steen; Muneesh Tewari; Saghi Ghaffari; Gerard C Blobe; Chi V Dang; Joe G N Garcia; Jonathan Pevsner; Ole N Jensen; Peter Roepstorff; Krishna S Deshpande; Arul M Chinnaiyan; Ada Hamosh; Aravinda Chakravarti; Akhilesh Pandey
Journal:  Genome Res       Date:  2003-10       Impact factor: 9.043

5.  Genome annotation of Anopheles gambiae using mass spectrometry-derived data.

Authors:  Dário E Kalume; Suraj Peri; Raghunath Reddy; Jun Zhong; Mobolaji Okulate; Nirbhay Kumar; Akhilesh Pandey
Journal:  BMC Genomics       Date:  2005-09-19       Impact factor: 3.969

6.  Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry.

Authors:  Frank Desiere; Eric W Deutsch; Alexey I Nesvizhskii; Parag Mallick; Nichole L King; Jimmy K Eng; Alan Aderem; Rose Boyle; Erich Brunner; Samuel Donohoe; Nelson Fausto; Ernst Hafen; Lee Hood; Michael G Katze; Kathleen A Kennedy; Floyd Kregenow; Hookeun Lee; Biaoyang Lin; Dan Martin; Jeffrey A Ranish; David J Rawlings; Lawrence E Samelson; Yuzuru Shiio; Julian D Watts; Bernd Wollscheid; Michael E Wright; Wei Yan; Lihong Yang; Eugene C Yi; Hui Zhang; Ruedi Aebersold
Journal:  Genome Biol       Date:  2004-12-10       Impact factor: 13.583

7.  Current awareness on comparative and functional genomics.

Authors: 
Journal:  Comp Funct Genomics       Date:  2003

8.  Rapid and Sensitive Detection of Breast Cancer Cells in Patient Blood with Nuclease-Activated Probe Technology.

Authors:  Sven Kruspe; David D Dickey; Kevin T Urak; Giselle N Blanco; Matthew J Miller; Karen C Clark; Elliot Burghardt; Wade R Gutierrez; Sneha D Phadke; Sukriti Kamboj; Timothy Ginader; Brian J Smith; Sarah K Grimm; James Schappet; Howard Ozer; Alexandra Thomas; James O McNamara; Carlos H Chan; Paloma H Giangrande
Journal:  Mol Ther Nucleic Acids       Date:  2017-08-12       Impact factor: 8.886

Review 9.  Death of a dogma: eukaryotic mRNAs can code for more than one protein.

Authors:  Hélène Mouilleron; Vivian Delcourt; Xavier Roucou
Journal:  Nucleic Acids Res       Date:  2015-11-17       Impact factor: 16.971
  9 in total

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