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Vertebrate Genomics Team - Publications


The following is a list of publications for the Vertebrate Genomics Team.

Ensembl:


2011

Flicek, P. Amode, M.R., et al. (2011)
Nucleic Acids Res. 39 (Database issue), D800-6.

Guberman, J.M., Ai, J., et al. (2011)
Database (Oxford) 2011 bar041.

Kinsella, R.J., Kahari, A., et al. (2011)
Database, doi: 10.1093/database/bar030.

Oakley, D.J., Iyer, V., et al. (2011)
Database (Oxford) 2011 bar028.

Ringwald, M., Iyer, V., et al. (2011)
Nucleic Acids Res. 39 (Database issue), D849-55.

Spudich, G.M. and Fernandez-Suarez, X.M. (2011)
Curr. Protoc. Hum. Genet. Chapter 6 Unit6.11.

2010

Chen, Y., et al. (2010)
BMC Genomics 11, 293.

Fernández-Suárez, X.M. and Schuster, M.K. (2010)
Curr. Protoc. Bioinformatics 2007 Chapter 1, Unit 1.15.

McLaren, W., et al. (2010)
Bioinformatics 26, 2069-2070.

Rios, D., et al. (2010)
BMC Bioinformatics 11, 238.

Spudich, G. and Fernández-Suárez, X.M. (2010)
BMC Genomics 11, 295.

Flicek P., Aken B.L., Ballester B., Beal K., Bragin E., Brent S., Chen Y., Clapham P., Coates G., Fairley S., Fitzgerald S., Fernandez-Banet J., Gordon L., Gräf S., Haider S., Hammond M., Howe K., Jenkinson A., Johnson N., Kähäri A., Keefe D., Keenan S., Kinsella R., Kokocinski F., Koscielny G., Kulesha E., Lawson D., Longden I., Massingham T., McLaren W., Megy K., Overduin B., Pritchard B., Rios D., Ruffier M., Schuster M., Slater G., Smedley D., Spudich G., Tang Y.A., Trevanion S., Vilella A., Vogel J., White S., Wilder S.P., Zadissa A., Birney E., Cunningham F., Dunham I., Durbin R., Fernández-Suarez X.M., Herrero J., Hubbard T.J., Parker A., Proctor G., Smith J., Searle S.M. (2010)
Ensembl's 10th year.
Nucleic Acids Research 38: D557-D562.
abstract full-text PDF

2009 and earlier

Flicek P, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Eyre T, Fitzgerald S, Fernandez-Banet J, Gräf S, Haider S, Hammond M, Holland R, Howe KL, Howe K, Johnson N, Jenkinson A, Kähäri A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Megy K, Meidl P, Overduin B, Parker A, Pritchard B, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Slater G, Smedley D, Spudich G, Trevanion S, Vilella AJ, Vogel J, White S, Wood M, Birney E, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Herrero J, Hubbard TJ, Kasprzyk A, Proctor G, Smith J, Ureta-Vidal A, Searle S. 2008.
Ensembl 2008.
Nucleic Acids Res. Epub 2007 Nov 13.
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Hubbard TJ, Aken BL, Beal K, Ballester B, Caccamo M, Chen Y, Clarke L, Coates G, Cunningham F, Cutts T, Down T, Dyer SC, Fitzgerald S, Fernandez-Banet J, Graf S, Haider S, Hammond M, Herrero J, Holland R, Howe K, Howe K, Johnson N, Kahari A, Keefe D, Kokocinski F, Kulesha E, Lawson D, Longden I, Melsopp C, Megy K, Meidl P, Ouverdin B, Parker A, Prlic A, Rice S, Rios D, Schuster M, Sealy I, Severin J, Slater G, Smedley D, Spudich G, Trevanion S, Vilella A, Vogel J, White S, Wood M, Cox T, Curwen V, Durbin R, Fernandez-Suarez XM, Flicek P, Kasprzyk A, Proctor G, Searle S, Smith J, Ureta-Vidal A, Birney E. 2007.
Ensembl 2007.
Nucleic Acids Res. 35(Database issue):D610-7.
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Cunningham F, Rios D, Griffiths M, Smith J, Ning Z, Cox T, Flicek P, Marin-Garcin P, Herrero J, Rogers J, van der Weyden L, Bradley A, Birney E, Adams DJ. 2006.
TranscriptSNPView: a genome-wide catalog of mouse coding variation.
Nat Genet. 38(8):853.
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Birney E, Andrews D, Caccamo M, Chen Y, Clarke L, Coates G, Cox T, Cunningham F, Curwen V, Cutts T, Down T, Durbin R, Fernandez-Suarez XM, Flicek P, Graf S, Hammond M, Herrero J, Howe K, Iyer V, Jekosch K, Kahari A, Kasprzyk A, Keefe D, Kokocinski F, Kulesha E, London D, Longden I, Melsopp C, Meidl P, Overduin B, Parker A, Proctor G, Prlic A, Rae M, Rios D, Redmond S, Schuster M, Sealy I, Searle S, Severin J, Slater G, Smedley D, Smith J, Stabenau A, Stalker J, Trevanion S, Ureta-Vidal A, Vogel J, White S, Woodwark C, Hubbard TJ. 2006.
Ensembl 2006.
Nucleic Acids Res. 34(Database issue):D556-61.
abstract full-text HTML

For more Ensembl Related publications see http://www.ensembl.org/info/about/publications.html

Research:


2011

Bateman, A., Agrawal, S., et al. (2011)
RNA 17 (11), 1941-6.

Boyle, A.P., Song, L., et al. (2011)
Genome Res. 21 (3), 456-64.

Church, D.M., Schneider, V.A., et al. (2011)
PLoS Biol. 9 (7), e1001091.

Conrad, D.F., Keebler, J.E., et al. (2011)
Nat. Genet. 43 (7), 712-4.

Danecek, P., Auton, A., et al. (2011)
Bioinformatics 27 (15), 2156-8.

ENCODE Project Consortium. (2011)
PLoS Biol. 9 (4), e1001046.

Faure, A.J., Seoighe, C. and Mulder, N.J. (2011)
BMC Bioinformatics 12 Art. No.: 29.

Gaudet, P., Bairoch, A., et al. (2011)
Database (Oxford) 2011 baq027.

Gaudet, P., Bairoch, A., et al. (2011)
Nucleic Acids Res. 39 (Database issue), D7-D10.

Gravel, S., Henn, B.M., et al. (2011)
Proc. Natl. Acad. Sci. U. S. A. 108 (29), 11983-8.

Kohonen-Corish, M.R., Macrae, F., et al. (2011)
Deciphering the colon cancer genes-report of the InSiGHTHuman Variome Project Workshop, UNESCO, Paris 2010.
Hum. Mutat. 32 (4), 491-4.

Lindblad-Toh, K., Garber, M., et al. (2011)
Nature 478 (7370), 476-82.

Lipman, D., Flicek, P., et al. (2011)
Genome Biol. 12 (3), 402.

Locke, D.P., Hillier, L.W., et al. (2011)
Nature 469 (7331), 529-33.

Malone, C.M.P., Domaschenz, R., et al. (2011)
Exp. Cell Res. 317 (11), 1590-602.

Marth, G.T., Yu, F., et al. (2011)
Genome Biol. 12 (9), R84.

Mills, R.E., Walter, K., et al. (2011)
Nature 470 (7332), 59-65.

Pignatelli, M., and Moya, A. (2011)
PLoS One 6 (5), Art. No.: e19984.

Reimundo, P., Pignatelli, M., et al. (2011)
J. Bacteriol. 193 (14), 3684-5.

Renfree, M.B., Papenfuss, A.T., et al. (2011)
Genome Biol. 12 (8), R81.

Smedley, D., Salimova, E. and Rosenthal, N. (2011)
Methods 53, 411-6.

Song, L., Zhang, Z., et al. (2011)
Genome Res. 21 (10), 1757-67.

Vilella, A.J., Birney, E., et al. (2011)
Genome Biol. 12 (2), Art. No.: 401.

2010

Atanur, S.S., et al. (2010)
Genome Res. 20, 791-803.

Ballester, B., et al. (2010)
BMC Genomics 11, 294.

Daelemans, C., et al. (2010)
BMC Genetics 11, 25.

Dalgleish, R., et al. (2010)
Genome Med. 2, 24.

Gheldof, N., et al. (2010)
Nucleic Acids Res. 38, 4325-36.

Gruenberger, M., et al. (2010)
BMC Res. Notes 3, 16.

McDaniell, R., et al. (2010)
Science 328, 235-239.

Peric-Hupkes, D., et al. (2010)
Mol. Cell 38, 603-613.

Schmidt, D., et al. (2010)
Genome Res. 20, 578-588.

Schmidt, D., et al. (2010)
Science 328, 1036-1040.

Severin, J., et al. (2010)
BMC Bioinformatics 11, 240.

Database (Oxford) 2010, baq014.

Sudbery, I., et al. (2010)
BMC Genomics 11, 175.

Swertz, M.A., et al. (2010)
Genome Biol. 11, R27.

Warren, W.C., et al. (2010)
Nature 464, 757-762.

Ye, K., et al. (2010)
J. Proteomics Bioinform. 3, 99-100.

2009 and earlier

Flicek P. 2009.
The need for speed.
Genome Biol. 2009 Mar 27;10(3):212. [Epub ahead of print]
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Carlile M, Swan D, Jackson K, Preston-Fayers K, Ballester B, Flicek P, Werner A 2009.
Strand selective generation of endo-siRNAs from the Na/phosphate transporter gene Slc34a1 in murine tissues.
Nucleic Acids Res. 2009 Feb 23. [Epub ahead of print]
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Morley RH, Lachani K, Keefe D, Gilchrist MJ, Flicek P, Smith JC, Wardle FC 2009.
A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation.
Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3829-34. Epub 2009 Feb 18.
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Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, Koch CM, Dunham I, Bieda M, Xu X, Farnham PJ, Kapranov P, Nix DA, Gingeras TR, Zhang X, Holster H, Jiang N, Green RD, Song JS, McCuine SA, Anton E, Nguyen L, Trinklein ND, Ye Z, Ching K, Hawkins D, Ren B, Scacheri PC, Rozowsky J, Karpikov A, Euskirchen G, Weissman S, Gerstein M, Snyder M, Yang A, Moqtaderi Z, Hirsch H, Shulha HP, Fu Y, Weng Z, Struhl K, Myers RM, Lieb JD, Liu XS. 2008.
Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets.
Genome Res. 2008 Mar;18(3):393-403.
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Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Howe KL, Jackson DK, Miretti MM, Fiegler H, Marioni JC, Birney E, Hubbard TJ, Carter NP, Tavaré S, Beck S. 2008.
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs).
Genome Res. 2008 Sep;18(9):1518-29.
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Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, Gräf S, Johnson N, Herrero J, Tomazou EM, Thorne NP, Bäckdahl L, Herberth M, Howe KL, Jackson DK, Miretti MM, Marioni JC, Birney E, Hubbard TJ, Durbin R, Tavaré S, Beck S. 2008.
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis.
Nat Biotechnol. Jul;26(7):779-85.
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Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D, Montgomery S, Tavaré S, Deloukas P, Dermitzakis ET. 2007.
Population genomics of human gene expression.
Nature Genetics. Nat Genet. 39(10):1217-24. Epub 2007 Sep 16
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Graf S, Nielsen FG, Kurtz S, Huynen MA, Birney E, Stunnenberg H, Flicek P. 2007.
Optimized design and assessment of whole genome tiling arrays.
Bioinformatics. 23(13):i195-i204.
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Oeder S, Mages J, Flicek P, Lang R. 2007.
Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.
BMC Genomics. 8:200.
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Koch CM, Andrews RM, Flicek P, Dillon SC, Karaoz U, Clelland GK, Wilcox S, Beare DM, Fowler JC, Couttet P, James KD, Lefebvre GC, Bruce AW, Dovey OM, Ellis PD, Dhami P, Langford CF, Weng Z, Birney E, Carter NP, Vetrie D, Dunham I. 2007.
The landscape of histone modifications across 1% of the human genome in five human cell lines.
Genome Res. 17(6):691-707.
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Flicek P, Brent MR. 2006.
Using several pair-wise informant sequences for de novo prediction of alternatively spliced transcripts.
Genome Biol. 7 Suppl 1:S8.1-9.
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Guigó R, Flicek P, Abril JF, Reymond A, Lagarde J, Denoeud F, Antonarakis S, Ashburner M, Bajic VB, Birney E, Castelo R, Eyras E, Ucla C, Gingeras TR, Harrow J, Hubbard T, Lewis SE, Reese MG. 2006.
EGASP: the human ENCODE Genome Annotation Assessment Project.
Genome Biol. 7 Suppl 1:S2.1-31.
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Eyras E, Reymond A, Castelo R, Bye JM, Camara F, Flicek P, Huckle EJ, Parra G, Shteynberg DD, Wyss C, Rogers J, Antonarakis SE, Birney E, Guigo R, Brent MR. 2005.
Gene finding in the chicken genome.
BMC Bioinformatics. 6:131.
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Flicek P, Keibler E, Hu P, Korf I, Brent MR. 2003.
Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map.
Genome Res. 13(1):46-54.
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Korf I, Flicek P, Duan D, Brent MR. 2001.
Integrating genomic homology into gene structure prediction. Bioinformatics. 17 Suppl 1:S140-8.
abstract full-text PDF


Major Collaborative Projects and International Consortia:


International Cancer Genome Consortium. (2010)
Nature 464, 993-998.

Wilkinson, P., et al. (2010)
Nucleic Acids Res. 38 (Database issue), D570-576.

Zouberakis, M., et al. (2010)
Database (Oxford) 2010, baq010.

STAR Consortium, Saar K, Beck A, Bihoreau MT, Birney E, Brocklebank D, Chen Y, Cuppen E, Demonchy S, Dopazo J, Flicek P, Foglio M, Fujiyama A, Gut IG, Gauguier D, Guigo R, Guryev V, Heinig M, Hummel O, Jahn N, Klages S, Kren V, Kube M, Kuhl H, Kuramoto T, Kuroki Y, Lechner D, Lee YA, Lopez-Bigas N, Lathrop GM, Mashimo T, Medina I, Mott R, Patone G, Perrier-Cornet JA, Platzer M, Pravenec M, Reinhardt R, Sakaki Y, Schilhabel M, Schulz H, Serikawa T, Shikhagaie M, Tatsumoto S, Taudien S, Toyoda A, Voigt B, Zelenika D, Zimdahl H, Hubner N. 2008.
SNP and haplotype mapping for genetic analysis in the rat.
Nat Genet. May;40(5):560-6.
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Warren WC, Hillier LW, Marshall Graves JA, Birney E, Ponting CP, Grützner F, Belov K, Miller W, Clarke L, Chinwalla AT, Yang SP, Heger A, Locke DP, Miethke P, Waters PD, Veyrunes F, Fulton L, Fulton B, Graves T, Wallis J, Puente XS, López-Otín C, Ordóñez GR, Eichler EE, Chen L, Cheng Z, Deakin JE, Alsop A, Thompson K, Kirby P, Papenfuss AT, Wakefield MJ, Olender T, Lancet D, Huttley GA, Smit AF, Pask A, Temple-Smith P, Batzer MA, Walker JA, Konkel MK, Harris RS, Whittington CM, Wong ES, Gemmell NJ, Buschiazzo E, Vargas Jentzsch IM, Merkel A, Schmitz J, Zemann A, Churakov G, Kriegs JO, Brosius J, Murchison EP, Sachidanandam R, Smith C, Hannon GJ, Tsend-Ayush E, McMillan D, Attenborough R, Rens W, Ferguson-Smith M, Lefèvre CM, Sharp JA, Nicholas KR, Ray DA, Kube M, Reinhardt R, Pringle TH, Taylor J, Jones RC, Nixon B, Dacheux JL, Niwa H, Sekita Y, Huang X, Stark A, Kheradpour P, Kellis M, Flicek P, Chen Y, Webber C, Hardison R, Nelson J, Hallsworth-Pepin K, Delehaunty K, Markovic C, Minx P, Feng Y, Kremitzki C, Mitreva M, Glasscock J, Wylie T, Wohldmann P, Thiru P, Nhan MN, Pohl CS, Smith SM, Hou S, Renfree MB, Mardis ER, Wilson RK. 2008.
Genome analysis of the platypus reveals unique signatures of evolution.
Nature. May 8;453(7192):175-83.
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The ENCODE Project Consortium. 2007.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.
Nature. 447(7146):799-816.
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International Chicken Genome Sequencing Consortium. 2004.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Nature. 432(7018):695-716.
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Hillier LW, Fulton RS, Fulton LA, Graves TA, Pepin KH, Wagner-McPherson C, Layman D, Maas J, Jaeger S, Walker R, Wylie K, Sekhon M, Becker MC, O'Laughlin MD, Schaller ME, Fewell GA, Delehaunty KD, Miner TL, Nash WE, Cordes M, Du H, Sun H, Edwards J, Bradshaw-Cordum H, Ali J, Andrews S, Isak A, Vanbrunt A, Nguyen C, Du F, Lamar B, Courtney L, Kalicki J, Ozersky P, Bielicki L, Scott K, Holmes A, Harkins R, Harris A, Strong CM, Hou S, Tomlinson C, Dauphin-Kohlberg S, Kozlowicz-Reilly A, Leonard S, Rohlfing T, Rock SM, Tin-Wollam AM, Abbott A, Minx P, Maupin R, Strowmatt C, Latreille P, Miller N, Johnson D, Murray J, Woessner JP, Wendl MC, Yang SP, Schultz BR, Wallis JW, Spieth J, Bieri TA, Nelson JO, Berkowicz N, Wohldmann PE, Cook LL, Hickenbotham MT, Eldred J, Williams D, Bedell JA, Mardis ER, Clifton SW, Chissoe SL, Marra MA, Raymond C, Haugen E, Gillett W, Zhou Y, James R, Phelps K, Iadanoto S, Bubb K, Simms E, Levy R, Clendenning J, Kaul R, Kent WJ, Furey TS, Baertsch RA, Brent MR, Keibler E, Flicek P, Bork P, Suyama M, Bailey JA, Portnoy ME, Torrents D, Chinwalla AT, Gish WR, Eddy SR, McPherson JD, Olson MV, Eichler EE, Green ED, Waterston RH, Wilson RK. 2003.
The DNA sequence of human chromosome 7.
Nature. 424(6945):157-64.
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Mouse Genome Sequencing Consortium. 2002.
Initial sequencing and comparative analysis of the mouse genome.
Nature. 420(6915):520-62.
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Reviews and Commentary:

Flicek P.
Gene Prediction: compare and CONTRAST. 2007.
Genome Biol. 8:233.
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Cotton RG, Appelbe W, Auerbach AD, Becker K, Bodmer W, Boone DJ, Boulyjenkov V, Brahmachari S, Brody L, Brookes A, Brown AF, Byers P, Cantu JM, Cassiman JJ, Claustres M, Concannon P, den Dunnen JT, Flicek P, Gibbs R, Hall J, Hasler J, Katz M, Kwok PY, Laradi S, Lindblom A, Maglott D, Marsh S, Masimirembwa CM, Minoshima S, de Ramirez AM, Pagon R, Ramesar R, Ravine D, Richards S, Rimoin D, Ring HZ, Scriver CR, Sherry S, Shimizu N, Stein L, Tadmouri GO, Taylor G and Watson M. 2007.
Recommendations of the 2006 Human Variome Project meeting.
Nat Genet. 39(4):433-6.
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A long time ago, in a galaxy far, far away:


Miner TJ, Shriver CD, Flicek P, Miner FC, Jaques DP, Maniscalco-Theberge ME, Krag DN. 1999.
Guidelines for the Safe Use of Radioactive Materials During the Localization and Resection of the Sentinel Lymph Node.
Annals of Surgical Oncology, 6:75-82
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Albright BJ, Bartschat K, Flicek P. 1993.
Core Potentials for Quasi-one-electron Systems.
Journal of Physics B: Atomic, Molecular and Optical Physics, 26:337-344
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