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Page 1
Alignathon: a competitive assessment of whole-genome alignment methods.
Earl D, Nguyen N, Hickey G, Harris RS, Fitzgerald S, Beal K, Seledtsov I, Molodtsov V, Raney BJ, Clawson H, Kim J, Kemena C, Chang JM, Erb I, Poliakov A, Hou M, Herrero J, Kent WJ, Solovyev V, Darling AE, Ma J, Notredame C, Brudno M, Dubchak I, Haussler D, Paten B. Earl D, et al. Among authors: fitzgerald s. Genome Res. 2014 Dec;24(12):2077-89. doi: 10.1101/gr.174920.114. Epub 2014 Oct 1. Genome Res. 2014. PMID: 25273068 Free PMC article.
Genome-wide nucleotide-level mammalian ancestor reconstruction.
Paten B, Herrero J, Fitzgerald S, Beal K, Flicek P, Holmes I, Birney E. Paten B, et al. Among authors: fitzgerald s. Genome Res. 2008 Nov;18(11):1829-43. doi: 10.1101/gr.076521.108. Epub 2008 Oct 10. Genome Res. 2008. PMID: 18849525 Free PMC article.
eHive: an artificial intelligence workflow system for genomic analysis.
Severin J, Beal K, Vilella AJ, Fitzgerald S, Schuster M, Gordon L, Ureta-Vidal A, Flicek P, Herrero J. Severin J, et al. Among authors: fitzgerald s. BMC Bioinformatics. 2010 May 11;11:240. doi: 10.1186/1471-2105-11-240. BMC Bioinformatics. 2010. PMID: 20459813 Free PMC article.
Ensembl comparative genomics resources.
Herrero J, Muffato M, Beal K, Fitzgerald S, Gordon L, Pignatelli M, Vilella AJ, Searle SM, Amode R, Brent S, Spooner W, Kulesha E, Yates A, Flicek P. Herrero J, et al. Among authors: fitzgerald s. Database (Oxford). 2016 Feb 20;2016:bav096. doi: 10.1093/database/bav096. Print 2016. Database (Oxford). 2016. PMID: 26896847 Free PMC article.
A high-resolution map of human evolutionary constraint using 29 mammals.
Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, Washietl S, Kheradpour P, Ernst J, Jordan G, Mauceli E, Ward LD, Lowe CB, Holloway AK, Clamp M, Gnerre S, Alföldi J, Beal K, Chang J, Clawson H, Cuff J, Di Palma F, Fitzgerald S, Flicek P, Guttman M, Hubisz MJ, Jaffe DB, Jungreis I, Kent WJ, Kostka D, Lara M, Martins AL, Massingham T, Moltke I, Raney BJ, Rasmussen MD, Robinson J, Stark A, Vilella AJ, Wen J, Xie X, Zody MC; Broad Institute Sequencing Platform and Whole Genome Assembly Team; Baldwin J, Bloom T, Chin CW, Heiman D, Nicol R, Nusbaum C, Young S, Wilkinson J, Worley KC, Kovar CL, Muzny DM, Gibbs RA; Baylor College of Medicine Human Genome Sequencing Center Sequencing Team; Cree A, Dihn HH, Fowler G, Jhangiani S, Joshi V, Lee S, Lewis LR, Nazareth LV, Okwuonu G, Santibanez J, Warren WC, Mardis ER, Weinstock GM, Wilson RK; Genome Institute at Washington University; Delehaunty K, Dooling D, Fronik C, Fulton L, Fulton B, Graves T, Minx P, Sodergren E, Birney E, Margulies EH, Herrero J, Green ED, Haussler D, Siepel A, Goldman N, Pollard KS, Pedersen JS, Lander ES, Kellis M. Lindblad-Toh K, et al. Among authors: fitzgerald s. Nature. 2011 Oct 12;478(7370):476-82. doi: 10.1038/nature10530. Nature. 2011. PMID: 21993624 Free PMC article.
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.
Mudge JM, Jungreis I, Hunt T, Gonzalez JM, Wright JC, Kay M, Davidson C, Fitzgerald S, Seal R, Tweedie S, He L, Waterhouse RM, Li Y, Bruford E, Choudhary JS, Frankish A, Kellis M. Mudge JM, et al. Among authors: fitzgerald s. Genome Res. 2019 Dec;29(12):2073-2087. doi: 10.1101/gr.246462.118. Epub 2019 Sep 19. Genome Res. 2019. PMID: 31537640 Free PMC article.
Ensembl 2013.
Flicek P, Ahmed I, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, García-Girón C, Gordon L, Hourlier T, Hunt S, Juettemann T, Kähäri AK, Keenan S, Komorowska M, Kulesha E, Longden I, Maurel T, McLaren WM, Muffato M, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sheppard D, Sobral D, Taylor K, Thormann A, Trevanion S, White S, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Harrow J, Herrero J, Hubbard TJ, Johnson N, Kinsella R, Parker A, Spudich G, Yates A, Zadissa A, Searle SM. Flicek P, et al. Among authors: fitzgerald s. Nucleic Acids Res. 2013 Jan;41(Database issue):D48-55. doi: 10.1093/nar/gks1236. Epub 2012 Nov 30. Nucleic Acids Res. 2013. PMID: 23203987 Free PMC article.
Insights into hominid evolution from the gorilla genome sequence.
Scally A, Dutheil JY, Hillier LW, Jordan GE, Goodhead I, Herrero J, Hobolth A, Lappalainen T, Mailund T, Marques-Bonet T, McCarthy S, Montgomery SH, Schwalie PC, Tang YA, Ward MC, Xue Y, Yngvadottir B, Alkan C, Andersen LN, Ayub Q, Ball EV, Beal K, Bradley BJ, Chen Y, Clee CM, Fitzgerald S, Graves TA, Gu Y, Heath P, Heger A, Karakoc E, Kolb-Kokocinski A, Laird GK, Lunter G, Meader S, Mort M, Mullikin JC, Munch K, O'Connor TD, Phillips AD, Prado-Martinez J, Rogers AS, Sajjadian S, Schmidt D, Shaw K, Simpson JT, Stenson PD, Turner DJ, Vigilant L, Vilella AJ, Whitener W, Zhu B, Cooper DN, de Jong P, Dermitzakis ET, Eichler EE, Flicek P, Goldman N, Mundy NI, Ning Z, Odom DT, Ponting CP, Quail MA, Ryder OA, Searle SM, Warren WC, Wilson RK, Schierup MH, Rogers J, Tyler-Smith C, Durbin R. Scally A, et al. Among authors: fitzgerald s. Nature. 2012 Mar 7;483(7388):169-75. doi: 10.1038/nature10842. Nature. 2012. PMID: 22398555 Free PMC article.
Ensembl's 10th year.
Flicek P, Aken BL, 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 YA, Trevanion S, Vilella A, Vogel J, White S, Wilder SP, Zadissa A, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Smith J, Searle SM. Flicek P, et al. Among authors: fitzgerald s. Nucleic Acids Res. 2010 Jan;38(Database issue):D557-62. doi: 10.1093/nar/gkp972. Epub 2009 Nov 11. Nucleic Acids Res. 2010. PMID: 19906699 Free PMC article.
1,118 results