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Publications

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.
Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Ann Blomberg L, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM
PLoS Biol. (2010) 8:e1000475
UK PubMed Central: 20838655 NCBI PubMed: 20838655
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
BMC Bioinformatics (2010) 11:240
UK PubMed Central: 20459813 NCBI PubMed: 20459813
RNAZ 2.0: IMPROVED NONCODING RNA DETECTION.
Gruber AR, Findeiß S, Washietl S, Hofacker IL, Stadler PF
Pac Symp Biocomput (2010) 15:69-79
UK PubMed Central: 19908359 NCBI PubMed: 19908359
PLEXY: efficient target prediction for box C/D snoRNAs.
Kehr S, Bartschat S, Stadler PF, Tafer H
Bioinformatics (2011) 27:279-80
UK PubMed Central: 21076148 NCBI PubMed: 21076148
A genome scan for quantitative trait loci affecting milk somatic cell score in Israeli and Italian Holstein cows by means of selective DNA pooling with single- and multiple-marker mapping.
Tal-Stein R, Fontanesi L, Dolezal M, Scotti E, Bagnato A, Russo V, Canavesi F, Friedmann A, Soller M, Lipkin E
J. Dairy Sci. (2010) 93:4913-27
UK PubMed Central: 20855026 NCBI PubMed: 20855026
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.
McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F
Bioinformatics (2010) 26:2069-70
UK PubMed Central: 20562413 NCBI PubMed: 20562413
Ensembl variation resources.
Chen Y, Cunningham F, Rios D, McLaren WM, Smith J, Pritchard B, Spudich GM, Brent S, Kulesha E, Marin-Garcia P, Smedley D, Birney E, Flicek P
BMC Genomics (2010) 11:293
UK PubMed Central: 20459805 NCBI PubMed: 20459805
A database and API for variation, dense genotyping and resequencing data.
Rios D, McLaren WM, Chen Y, Birney E, Stabenau A, Flicek P, Cunningham F
BMC Bioinformatics (2010) 11:238
UK PubMed Central: 20459810 NCBI PubMed: 20459810
The genome of a songbird.
Warren WC, Clayton DF, Ellegren H, Arnold AP, Hillier LW, Kunstner A, Searle S, White S, Vilella AJ, Fairley S, Heger A, Kong L, Ponting CP, Jarvis ED, Mello CV, Minx P, Lovell P, Velho TA, Ferris M, Balakrishnan CN, Sinha S, Blatti C, London SE, Li Y, Lin YC, George J, Sweedler J, Southey B, Gunaratne P, Watson M, Nam K, Backstrom N, Smeds L, Nabholz B, Itoh Y, Whitney O, Pfenning AR, Howard J, Volker M, Skinner BM, Griffin DK, Ye L, McLaren WM, Flicek P, Quesada V, Velasco G, Lopez-Otin C, Puente XS, Olender T, Lancet D, Smit AF, Hubley R, Konkel MK, Walker JA, Batzer MA, Gu W, Pollock DD, Chen L, Cheng Z, Eichler EE, Stapley J, Slate J, Ekblom R, Birkhead T, Burke T, Burt D, Scharff C, Adam I, Richard H, Sultan M, Soldatov A, Lehrach H, Edwards SV, Yang SP, Li X, Graves T, Fulton L, Nelson J, Chinwalla A, Hou S, Mardis ER, Wilson RK
Nature (2010) 464:757-62
UK PubMed Central: 20360741 NCBI PubMed: 20360741
Fast Accessibility-Based Prediction of RNA-RNA Interactions
Tafer H, Amman F, Eggenhoffer F, Stadler PF, Hofacker IL
Bioinformatics (Accepted) :
UK PubMed Central: