Genome informatics

Apart from human genome resequencing, projects that Richard is connected to include:

• the SGRP yeast sequence variation and population genomics project;
• the TreeFam database of animal gene families;
• the Ensembl resource for vertebrate genome annotation;
• the WormBase model organism database for C. elegans;
• the MitoCheck study of mitosis regulation in human cells;
• the Pfam database of protein domain families; and
• the ACEDB genome database.

• 1000 Genomes Project, a deep catalogue of human genetic variation.
• SGRP, Saccharomyces Genome Resequencing Project.
• WormBase is the repository of mapping, sequencing and phenotypic information for C. elegans and several related nematodes. It also contains large amounts of data from manually curated papers and genome wide studies.
• TreeFam, tree families database.
• Margarita, inferring genealogies from population genotype data and using these to map disease loci.
• MAQ, software for mapping short sequencing reads

• MitoCheck
• Saccharomyces Genome Resequencing Project
• TreeFam

• MitoCheck, regulation of mitosis by phosphorylation.
• AceDB
• PFam
• EnsEMBL

• The Sequence Alignment/Map format and SAMtools.

  Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R and 1000 Genome Project Data Processing Subgroup

  Bioinformatics (Oxford, England) 2009;25;16;2078-9

  PUBMED: 19505943; PMC: 2723002; DOI: 10.1093/bioinformatics/btp352

• The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

  Pruitt KD, Harrow J, Harte RA, Wallin C, Diekhans M, Maglott DR, Searle S, Farrell CM, Loveland JE, Ruef BJ, Hart E, Suner MM, Landrum MJ, Aken B, Ayling S, Baertsch R, Fernandez-Banet J, Cherry JL, Curwen V, Dicuccio M, Kellis M, Lee J, Lin MF, Schuster M, Shkeda A, Amid C, Brown G, Dukhanina O, Frankish A, Hart J, Maidak BL, Mudge J, Murphy MR, Murphy T, Rajan J, Rajput B, Riddick LD, Snow C, Steward C, Webb D, Weber JA, Wilming L, Wu W, Birney E, Haussler D, Hubbard T, Ostell J, Durbin R and Lipman D

  Genome research 2009;19;7;1316-23

  PUBMED: 19498102; PMC: 2704439; DOI: 10.1101/gr.080531.108

• Population genomics of domestic and wild yeasts.

  Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V, Tsai IJ, Bergman CM, Bensasson D, O'Kelly MJ, van Oudenaarden A, Barton DB, Bailes E, Nguyen AN, Jones M, Quail MA, Goodhead I, Sims S, Smith F, Blomberg A, Durbin R and Louis EJ

  Nature 2009;458;7236;337-41

  PUBMED: 19212322; PMC: 2659681; DOI: 10.1038/nature07743

• Inferring selection on amino acid preference in protein domains.

  Moses AM and Durbin R

  Molecular biology and evolution 2008;26;3;527-36

  PUBMED: 19095755; PMC: 2716081; DOI: 10.1093/molbev/msn286

• Accurate whole human genome sequencing using reversible terminator chemistry.

  Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Keira Cheetham R, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IM, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DM, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Huw Jones TA, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Ernest Sohna Sohna J, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R and Smith AJ

  Nature 2008;456;7218;53-9

  PUBMED: 18987734; PMC: 2581791; DOI: 10.1038/nature07517

• Mapping short DNA sequencing reads and calling variants using mapping quality scores.

  Li H, Ruan J and Durbin R

  Genome research 2008;18;11;1851-8

  PUBMED: 18714091; PMC: 2577856; DOI: 10.1101/gr.078212.108

• Mapping trait loci by use of inferred ancestral recombination graphs.

  Minichiello MJ and Durbin R

  American journal of human genetics 2006;79;5;910-22

  PUBMED: 17033967; PMC: 1698562; DOI: 10.1086/508901

• TreeFam: a curated database of phylogenetic trees of animal gene families.

  Li H, Coghlan A, Ruan J, Coin LJ, Hériché JK, Osmotherly L, Li R, Liu T, Zhang Z, Bolund L, Wong GK, Zheng W, Dehal P, Wang J and Durbin R

  Nucleic acids research 2006;34;Database issue;D572-80

  PUBMED: 16381935; PMC: 1347480; DOI: 10.1093/nar/gkj118

Team

No team members listed