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Literature DB >> 12519964

The SNP Consortium website: past, present and future.

Gudmundur A Thorisson¹, Lincoln D Stein.

Abstract

The SNP Consortium website (http://snp.cshl.org) has undergone many changes since its initial conception three years ago. The database back end has been changed from the venerable ACeDB to the more scalable MySQL engine. Users can access the data via gene or single nucleotide polymorphism (SNP) keyword searches and browse or dump SNP data to textfiles. A graphical genome browsing interface shows SNPs mapped onto the genome assembly in the context of externally available gene predictions and other features. SNP allele frequency and genotype data are available via FTP-download and on individual SNP report web pages. SNP linkage maps are available for download and for browsing in a comparative map viewer. All software components of the data coordinating center (DCC) website (http://snp.cshl.org) are open source.

Mesh：

Year: 2003 PMID： 12519964 PMCID： PMC165499 DOI： 10.1093/nar/gkg052

Source DB: PubMed Journal: Nucleic Acids Res ISSN： 0305-1048 Impact factor: 16.971

14 in total

1. dbSNP: the NCBI database of genetic variation.

Authors: S T Sherry; M H Ward; M Kholodov; J Baker; L Phan; E M Smigielski; K Sirotkin
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

2. RefSeq and LocusLink: NCBI gene-centered resources.

Authors: K D Pruitt; D R Maglott
Journal: Nucleic Acids Res Date: 2001-01-01 Impact factor: 16.971

3. The structure of haplotype blocks in the human genome.

Authors: Stacey B Gabriel; Stephen F Schaffner; Huy Nguyen; Jamie M Moore; Jessica Roy; Brendan Blumenstiel; John Higgins; Matthew DeFelice; Amy Lochner; Maura Faggart; Shau Neen Liu-Cordero; Charles Rotimi; Adebowale Adeyemo; Richard Cooper; Ryk Ward; Eric S Lander; Mark J Daly; David Altshuler
Journal: Science Date: 2002-05-23 Impact factor: 47.728

4. The human genome browser at UCSC.

Authors: W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal: Genome Res Date: 2002-06 Impact factor: 9.043

5. The generic genome browser: a building block for a model organism system database.

Authors: Lincoln D Stein; Christopher Mungall; ShengQiang Shu; Michael Caudy; Marco Mangone; Allen Day; Elizabeth Nickerson; Jason E Stajich; Todd W Harris; Adrian Arva; Suzanna Lewis
Journal: Genome Res Date: 2002-10 Impact factor: 9.043

6. The Bioperl toolkit: Perl modules for the life sciences.

Authors: Jason E Stajich; David Block; Kris Boulez; Steven E Brenner; Stephen A Chervitz; Chris Dagdigian; Georg Fuellen; James G R Gilbert; Ian Korf; Hilmar Lapp; Heikki Lehväslaiho; Chad Matsalla; Chris J Mungall; Brian I Osborne; Matthew R Pocock; Peter Schattner; Martin Senger; Lincoln D Stein; Elia Stupka; Mark D Wilkinson; Ewan Birney
Journal: Genome Res Date: 2002-10 Impact factor: 9.043

7. Gramene: a resource for comparative grass genomics.

Authors: Doreen Ware; Pankaj Jaiswal; Junjian Ni; Xiaokang Pan; Kuan Chang; Kenneth Clark; Leonid Teytelman; Steve Schmidt; Wei Zhao; Samuel Cartinhour; Susan McCouch; Lincoln Stein
Journal: Nucleic Acids Res Date: 2002-01-01 Impact factor: 16.971

8. Scriptable access to the Caenorhabditis elegans genome sequence and other ACEDB databases.

Authors: L D Stein; J Thierry-Mieg
Journal: Genome Res Date: 1998-12 Impact factor: 9.043

9. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms.

Authors: R Sachidanandam; D Weissman; S C Schmidt; J M Kakol; L D Stein; G Marth; S Sherry; J C Mullikin; B J Mortimore; D L Willey; S E Hunt; C G Cole; P C Coggill; C M Rice; Z Ning; J Rogers; D R Bentley; P Y Kwok; E R Mardis; R T Yeh; B Schultz; L Cook; R Davenport; M Dante; L Fulton; L Hillier; R H Waterston; J D McPherson; B Gilman; S Schaffner; W J Van Etten; D Reich; J Higgins; M J Daly; B Blumenstiel; J Baldwin; N Stange-Thomann; M C Zody; L Linton; E S Lander; D Altshuler
Journal: Nature Date: 2001-02-15 Impact factor: 49.962

10. The distributed annotation system.

Authors: R D Dowell; R M Jokerst; A Day; S R Eddy; L Stein
Journal: BMC Bioinformatics Date: 2001-10-10 Impact factor: 3.169

37 in total

Review 1. "Are we there yet?": Deciding when one has demonstrated specific genetic causation in complex diseases and quantitative traits.

Authors: Grier P Page; Varghese George; Rodney C Go; Patricia Z Page; David B Allison
Journal: Am J Hum Genet Date: 2003-09-17 Impact factor: 11.025

2. Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data.

Authors: Rasmus Nielsen; Melissa J Hubisz; Andrew G Clark
Journal: Genetics Date: 2004-09-15 Impact factor: 4.562

3. Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array.

Authors: Hajime Matsuzaki; Halina Loi; Shoulian Dong; Ya-Yu Tsai; Joy Fang; Jane Law; Xiaojun Di; Wei-Min Liu; Geoffrey Yang; Guoying Liu; Jing Huang; Giulia C Kennedy; Thomas B Ryder; Gregory A Marcus; P Sean Walsh; Mark D Shriver; Jennifer M Puck; Keith W Jones; Rui Mei
Journal: Genome Res Date: 2004-03 Impact factor: 9.043

4. The Bermuda Triangle: The Pragmatics, Policies, and Principles for Data Sharing in the History of the Human Genome Project.

Authors: Kathryn Maxson Jones; Rachel A Ankeny; Robert Cook-Deegan
Journal: J Hist Biol Date: 2018-12 Impact factor: 1.326

5. An interactive bovine in silico SNP database (IBISS).

Authors: Rachel J Hawken; Wesley C Barris; Sean M McWilliam; Brian P Dalrymple
Journal: Mamm Genome Date: 2004-10 Impact factor: 2.957

6. Quantitative detection of individual cleaved DNA molecules on surfaces using gold nanoparticles and scanning electron microscope imaging.

Authors: Bei Nie; Michael R Shortreed; Lloyd M Smith
Journal: Anal Chem Date: 2006-03-01 Impact factor: 6.986

Review 7. Genomics and policymaking: from static models to complex systems?

Authors: Bartha Maria Knoppers
Journal: Hum Genet Date: 2009-02-28 Impact factor: 4.132

8. A two-stage pruning algorithm for likelihood computation for a population tree.

Authors: Arindam RoyChoudhury; Joseph Felsenstein; Elizabeth A Thompson
Journal: Genetics Date: 2008-09-09 Impact factor: 4.562

Review 9. Nutrigenetics and nutrigenomics: viewpoints on the current status and applications in nutrition research and practice.

Authors: Michael Fenech; Ahmed El-Sohemy; Leah Cahill; Lynnette R Ferguson; Tapaeru-Ariki C French; E Shyong Tai; John Milner; Woon-Puay Koh; Lin Xie; Michelle Zucker; Michael Buckley; Leah Cosgrove; Trevor Lockett; Kim Y C Fung; Richard Head
Journal: J Nutrigenet Nutrigenomics Date: 2011-05-28

10. Single nucleotide polymorphisms in microRNA binding sites of oncogenes: implications in cancer and pharmacogenomics.

Authors: Mayakannan Manikandan; Arasambattu Kannan Munirajan
Journal: OMICS Date: 2013-11-28