This site is no longer maintained and is provided for reference only. Some functionality or links may not work. Please contact support for all enquiries.
Publications | Quantomics

Publications

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
Europe PubMed Central: 20838655 NCBI PubMed: 20838655
Severin J, Beal K, Vilella AJ, Fitzgerald S, Schuster M, Gordon L, Ureta-Vidal A, Flicek P, Herrero J
BMC Bioinformatics (2010) 11:240
Europe PubMed Central: 20459813 NCBI PubMed: 20459813
Gruber AR, Findeiß S, Washietl S, Hofacker IL, Stadler PF
Pac Symp Biocomput (2010) 15:69-79
Europe PubMed Central: 19908359 NCBI PubMed: 19908359
Kehr S, Bartschat S, Stadler PF, Tafer H
Bioinformatics (2011) 27:279-80
Europe PubMed Central: 21076148 NCBI PubMed: 21076148
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
Europe PubMed Central: 20855026 NCBI PubMed: 20855026
McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F
Bioinformatics (2010) 26:2069-70
Europe PubMed Central: 20562413 NCBI PubMed: 20562413
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
Europe PubMed Central: 20459805 NCBI PubMed: 20459805
Rios D, McLaren WM, Chen Y, Birney E, Stabenau A, Flicek P, Cunningham F
BMC Bioinformatics (2010) 11:238
Europe PubMed Central: 20459810 NCBI PubMed: 20459810
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
Europe PubMed Central: 20360741 NCBI PubMed: 20360741
Tafer H, Amman F, Eggenhoffer F, Stadler PF, Hofacker IL
Bioinformatics (2011) 27:1934-1940
Europe PubMed Central: 21593134 NCBI PubMed: 21593134
Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J.
Nature (2010) 464:250-255
Europe PubMed Central: 20164839 NCBI PubMed: 20164839
Tafer H, Kehr S, Hertel J, Hofacker IL, Stadler PF
Bioinformatics (2010) 26:610-615
Europe PubMed Central: 20015949 NCBI PubMed: 20015949
Bussotti G , Raineri E , Erb I , Zytnicki M , Wilm A , Beaudoing E , Bucher P , Notredame C
Nucleic Acids Research (2011) 39:6886-6895
Europe PubMed Central: 21624887 NCBI PubMed: 21624887
Langenberger D, Pundhir S, Ekstrøm CT, Stadler PF, Hoffmann S, Gorodkin J
Bioinformatics (2011) 28:17-24
Europe PubMed Central: 22053076 NCBI PubMed: 22053076
Fasold M, Langenberger D, Binder H, Stadler PF, Hoffmann S
Nucleic Acids Res. (2011) 39:W112-7
Europe PubMed Central: 21622957 NCBI PubMed: 21622957
Esteve-Codina A, Kofler R, Palmieri N, Bussotti G, Notredame C, Perez-Enciso M
BMC Genomics (2011) 12:552
Europe PubMed Central: 22067327 NCBI PubMed: 22067327
Kemena C, Taly JF, Kleinjung J, Notredame C
Bioinformatics (2011) 27:3385-91
Europe PubMed Central: 22039207 NCBI PubMed: 22039207
Taly JF, Magis C, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Kemena C, Notredame C
Nat Protoc (2011) 6:1669-82
Europe PubMed Central: 21979275 NCBI PubMed: 21979275
Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C
Nucleic Acids Res. (2011) 39:W13-7
Europe PubMed Central: 21558174 NCBI PubMed: 21558174
Kinsella RJ, Kahari A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, Kersey P, Flicek P
Database (Oxford) (2011) 2011:bar030
Europe PubMed Central: 21785142 NCBI PubMed: 21785142
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fairley S, Fitzgerald S, Gil L, Gordon L, Hendrix M, Hourlier T, Johnson N, Kahari AK, Keefe D, Keenan S, Kinsella R, Komorowska M, Koscielny G, Kulesha E, Larsson P, Longden I, McLaren W, Muffato M, Overduin B, Pignatelli M, Pritchard B, Riat HS, Ritchie GR, Ruffier M, Schuster M, Sobral D, Tang YA, Taylor K, Trevanion S, Vandrovcova J, White S, Wilson M, Wilder SP, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernandez-Suarez XM, Harrow J, Herrero J, Hubbard TJ, Parker A, Proctor G, Spudich G, Vogel J, Yates A, Zadissa A, Searle SM
Nucleic Acids Res. (2012) 40:D84-90
Europe PubMed Central: 22086963 NCBI PubMed: 22086963
Fadista J, Bendixen C
PLoS ONE (2012) 7:e31025
Europe PubMed Central: 22363540 NCBI PubMed: 22363540
Jiang L, Sorensen P, Thomsen B, Edwards SM, Skarman A, Rontved CM, Lund MS, Workman CT
Physiol. Genomics (2012) 44:305-17
Europe PubMed Central: 22234994 NCBI PubMed: 22234994
Skarman A, Shariati M, Janss L, Jiang L, Sorensen P
BMC Bioinformatics (2012) 13:73
Europe PubMed Central: 22554182 NCBI PubMed: 22554182
Rius J, Cores F, Solsona F, van Hemert JI, Koetsier J, Notredame C
BMC Bioinformatics (2011) 12:150
Europe PubMed Central: 21569428 NCBI PubMed: 21569428
Arnold P, Erb I, Pachkov M, Molina N, van Nimwegen E
Bioinformatics (2012) 28:487-94
Europe PubMed Central: 22334039 NCBI PubMed: 22334039
Chang JM, Di Tommaso P, Taly JF, Notredame C
BMC Bioinformatics (2012) 13 Suppl 4:S1
Europe PubMed Central: 22536955 NCBI PubMed: 22536955
Meuwissen TH, Luan T, Woolliams JA
J. Anim. Breed. Genet. (2011) 128:429-39
Europe PubMed Central: 22059576 NCBI PubMed: 22059576
Erb I, Gonzalez-Vallinas JR, Bussotti G, Blanco E, Eyras E, Notredame C
Nucleic Acids Res. (2012) 40:e52
Europe PubMed Central: 22230796 NCBI PubMed: 22230796
Kadri NK, Koks PD, Meuwissen TH
Genet. Sel. Evol. (2012) 44:7
Europe PubMed Central: 22443295 NCBI PubMed: 22443295
Luan T, Woolliams JA, Odegard J, Dolezal M, Roman-Ponce SI, Bagnato A, Meuwissen TH
Genet. Sel. Evol. (2012) 44:28
Europe PubMed Central: 22937985 NCBI PubMed: 22937985
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J
Nucleic Acids Res. (2013) 41 (W1):W475-W479
Europe PubMed Central: 23630321 NCBI PubMed: 23630321
Huang Y, Li Y, Burt DW, Chen H, Zhang Y, Qian W, Kim H, Gan S, Zhao Y, Li J, Yi K, Feng H, Zhu P, Li B, Liu Q, Fairley S, Magor KE, Du Z, Hu X, Goodman L, Tafer H, Vignal A, Lee T, Kim KW, Sheng Z, An Y, Searle S, Herrero J, Groenen MA, Crooijmans RP, Faraut T, Cai Q, Webster RG, Aldridge JR, Warren WC, Bartschat S, Kehr S, Marz M, Stadler PF, Smith J, Kraus RH, Zhao Y, Ren L, Fei J, Morisson M, Kaiser P, Griffin DK, Rao M, Pitel F, Wang J, Li N
Nat. Genet. (2013) 45:776-783
Europe PubMed Central: 23749191 NCBI PubMed: 23749191
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
Nucleic Acids Res. (2013) 41 (D1):D48-55
Europe PubMed Central: 23203987 NCBI PubMed: 23203987
Sonesson AK, Woolliams JA, Meuwissen TH
Genet. Sel. Evol. (2012) 44:27
Europe PubMed Central: 22898324 NCBI PubMed: 22898324
Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R
Genome Res. (2012) 22:1775-1789
Europe PubMed Central: 22955988 NCBI PubMed: 22955988
Sabarinathan R, Tafer H, Seemann SE, Hofacker IL, Stadler PF, Gorodkin J
Hum. Mutat. (2013) 34:546-556
Europe PubMed Central: 23315997 NCBI PubMed: 23315997
Hertel J, Bartschat S, Wintsche A, Otto C, , Stadler PF
RNA Biol (2012) 9:231-241
Europe PubMed Central: 22617875 NCBI PubMed: 22617875
Groenen MA, Archibald AL, Uenishi H, Tuggle CK, Takeuchi Y, Rothschild MF, Rogel-Gaillard C, Park C, Milan D, Megens HJ, Li S, Larkin DM, Kim H, Frantz LA, Caccamo M, Ahn H, Aken BL, Anselmo A, Anthon C, Auvil L, Badaoui B, Beattie CW, Bendixen C, Berman D, Blecha F, Blomberg J, Bolund L, Bosse M, Botti S, Bujie Z, Bystrom M, Capitanu B, Carvalho-Silva D, Chardon P, Chen C, Cheng R, Choi SH, Chow W, Clark RC, Clee C, Crooijmans RP, Dawson HD, Dehais P, De Sapio F, Dibbits B, Drou N, Du ZQ, Eversole K, Fadista J, Fairley S, Faraut T, Faulkner GJ, Fowler KE, Fredholm M, Fritz E, Gilbert JG, Giuffra E, Gorodkin J, Griffin DK, Harrow JL, Hayward A, Howe K, Hu ZL, Humphray SJ, Hunt T, Hornshøj H, Jeon JT, Jern P, Jones M, Jurka J, Kanamori H, Kapetanovic R, Kim J, Kim JH, Kim KW, Kim TH, Larson G, Lee K, Lee KT, Leggett R, Lewin HA, Li Y, Liu W, Loveland JE, Lu Y, Lunney JK, Ma J, Madsen O, Mann K, Matthews L, McLaren S, Morozumi T, Murtaugh MP, Narayan J, Nguyen DT, Ni P, Oh SJ, Onteru S, Panitz F, Park EW, Park HS, Pascal G, Paudel Y, Perez-Enciso M, Ramirez-Gonzalez R, Reecy JM, Rodriguez-Zas S, Rohrer GA, Rund L, Sang Y, Schachtschneider K, Schraiber JG, Schwartz J, Scobie L, Scott C, Searle S, Servin B, Southey BR, Sperber G, Stadler P, Sweedler JV, Tafer H, Thomsen B, Wali R, Wang J, Wang J, White S, Xu X, Yerle M, Zhang G, Zhang J, Zhang J, Zhao S, Rogers J, Churcher C, Schook LB
Nature (2012) 491:393-398
Europe PubMed Central: 23151582 NCBI PubMed: 23151582
Ehsani A, Sørensen P, Pomp D, Allan M, Janss L
BMC Genomics (2012) 13:456
Europe PubMed Central: 22950759 NCBI PubMed: 22950759
Bartschat S, Kehr S, Tafer H, Stadler PF, Hertel J
Bioinformatics (2014) 30:115-116
Europe PubMed Central: 24174566 NCBI PubMed: 24174566
Kehr S, Bartschat S, Tafer H, Stadler PF, Hertel J
Mol. Biol. Evol. (2014) 31:455-467
Europe PubMed Central: 24162733 NCBI PubMed: 24162733
Nitsche A, Doose G, Tafer H, Robinson M, Saha NR, Gerdol M, Canapa A, Hoffmann S, Amemiya CT, Stadler PF
Europe PubMed Central: 24174405 NCBI PubMed: 24174405
Chang JM, Taly JF, Erb I, Sung TY, Hsu WL, Tang CY, Notredame C, Su EC
PLoS ONE (2013) 8:e75542
Europe PubMed Central: 24146760 NCBI PubMed: 24146760
Kemena C, Bussotti G, Capriotti E, Marti-Renom MA, Notredame C
Bioinformatics (2013) 29:1112-1119
Europe PubMed Central: 23449094 NCBI PubMed: 23449094
Knowles DG, Röder M, Merkel A, Guigó R
Bioinformatics (2013) 29:614-621
Europe PubMed Central: 23329413 NCBI PubMed: 23329413
Magis C, Taly JF, Bussotti G, Chang JM, Di Tommaso P, Erb I, Espinosa-Carrasco J, Notredame C
Methods Mol. Biol. (2014) 1079:117-129
Europe PubMed Central: 24170398 NCBI PubMed: 24170398
Magis C, Di Tommaso P, Notredame C
Nucleic Acids Res. (2013) 41:W358-62
Europe PubMed Central: 23716642 NCBI PubMed: 23716642
Rius J, Cores F, Solsona F, van Hemert JI, Koetsier J, Notredame C
BMC Bioinformatics (2011) 12:150
Europe PubMed Central: 21569428 NCBI PubMed: 21569428
Steijger T, Abril JF, Engström PG, Kokocinski F, , Abril JF, Akerman M, Alioto T, Ambrosini G, Antonarakis SE, Behr J, Bertone P, Bohnert R, Bucher P, Cloonan N, Derrien T, Djebali S, Du J, Dudoit S, Engström PG, Gerstein M, Gingeras TR, Gonzalez D, Grimmond SM, Guigó R, Habegger L, Harrow J, Hubbard TJ, Iseli C, Jean G, Kahles A, Kokocinski F, Lagarde J, Leng J, Lefebvre G, Lewis S, Mortazavi A, Niermann P, Rätsch G, Reymond A, Ribeca P, Richard H, Rougemont J, Rozowsky J, Sammeth M, Sboner A, Schulz MH, Searle SM, Solorzano ND, Solovyev V, Stanke M, Steijger T, Stevenson BJ, Stockinger H, Valsesia A, Weese D, White S, Wold BJ, Wu J, Wu TD, Zeller G, Zerbino D, Zhang MQ, Hubbard TJ, Guigó R, Harrow J, Bertone P
Nat. Methods (2013) 10:1177-1184
Europe PubMed Central: 24185837 NCBI PubMed: 24185837
Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigó R
Genome Res. (2012) 22:1616-1625
Europe PubMed Central: 22955974 NCBI PubMed: 22955974
International Sheep Genomics Consortium, Archibald AL, Cockett NE, Dalrymple BP, Faraut T, Kijas JW, Maddox JF, McEwan JC, Hutton Oddy V, Raadsma HW, Wade C, Wang J, Wang W, Xun X
Anim. Genet. (2010) 41:449-453
Europe PubMed Central: 20809919 NCBI PubMed: 20809919
Flicek P, Amode MR, Barrell D, Beal K, Billis K, Brent S, Carvalho-Silva D, Clapham P, Coates G, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt S, Johnson N, Juettemann T, Kähäri AK, Keenan S, Kulesha E, Martin FJ, Maurel T, McLaren WM, Murphy DN, Nag R, Overduin B, Pignatelli M, Pritchard B, Pritchard E, Riat HS, Ruffier M, Sheppard D, Taylor K, Thormann A, Trevanion SJ, Vullo A, Wilder SP, Wilson M, Zadissa A, Aken BL, Birney E, Cunningham F, Harrow J, Herrero J, Hubbard TJ, Kinsella R, Muffato M, Parker A, Spudich G, Yates A, Zerbino DR, Searle SM
Nucleic Acids Res. (2014) 42:D749-55
Europe PubMed Central: 24316576 NCBI PubMed: 24316576
Schreiber F, Patricio M, Muffato M, Pignatelli M, Bateman A
Nucleic Acids Res. (2014) 42:D922-5
Europe PubMed Central: 24194607 NCBI PubMed: 24194607
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
Nucleic Acids Res. (2010) 38:D557-62
Europe PubMed Central: 19906699 NCBI PubMed: 19906699
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S, Gordon L, Hendrix M, Hourlier T, Johnson N, Kähäri A, Keefe D, Keenan S, Kinsella R, Kokocinski F, Kulesha E, Larsson P, Longden I, McLaren W, Overduin B, Pritchard B, Riat HS, Rios D, Ritchie GR, Ruffier M, Schuster M, Sobral D, Spudich G, Tang YA, Trevanion S, Vandrovcova J, Vilella AJ, White S, Wilder SP, Zadissa A, Zamora J, Aken BL, Birney E, Cunningham F, Dunham I, Durbin R, Fernández-Suarez XM, Herrero J, Hubbard TJ, Parker A, Proctor G, Vogel J, Searle SM
Nucleic Acids Res. (2011) 39:D800-6
Europe PubMed Central: d.o.i.: 10.1093/nar/gkq1064 NCBI PubMed: d.o.i.: 10.1093/nar/gkq1064
Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR
Nature (2012) 489:101-108
Europe PubMed Central: doi:10.1038/nature11233 NCBI PubMed: doi:10.1038/nature11233
Orobitg, Miquel, Fernando Cores, Fernando Guirado, Concepció Roig, and Cedric Notredame
The Journal of Supercomputing (2013) 65/3:1076-1088
Europe PubMed Central: D.o.i.: 10.1007/s11227-012-0856-9 NCBI PubMed: D.o.i.: 10.1007/s11227-012-0856-9
Liu AY, Woolliams JA
Genet Res (Camb) (2010) 92:157-166
Europe PubMed Central: 10.1017/S0016672310000145 NCBI PubMed: 10.1017/S0016672310000145