Publications

Reference Publication

GENCODE: reference annotation for the human and mouse genomes in 2023.

Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, Arnan C, Barnes I, Banerjee A, Bennett R, Berry A, Bignell A, Boix C, Calvet F, Cerdán-Vélez D, Cunningham F, Davidson C, Donaldson S, Dursun C, Fatima R, Giorgetti S, Giron CG, Gonzalez JM, Hardy M, Harrison PW, Hourlier T, Hollis Z, Hunt T, James B, Jiang Y, Johnson R, Kay M, Lagarde J, Martin FJ, Gómez LM, Nair S, Ni P, Pozo F, Ramalingam V, Ruffier M, Schmitt BM, Schreiber JM, Steed E, Suner MM, Sumathipala D, Sycheva I, Uszczynska-Ratajczak B, Wass E, Yang YT, Yates A, Zafrulla Z, Choudhary JS, Gerstein M, Guigo R, Hubbard TJP, Kellis M, Kundaje A, Paten B, Tress ML, Flicek P.

Nucleic Acids Res 2023 : 51 ; d1 ; D942-D949.

Previous Reference Publications

GENCODE 2021.

Frankish A, Diekhans M, Jungreis I, Lagarde J, Loveland JE, Mudge JM, Sisu C, Wright JC, Armstrong J, Barnes I, Berry A, Bignell A, Boix C, Carbonell Sala S, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Howe KL, Hunt T, Izuogu OG, Johnson R, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Riera FC, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Wolf MY, Xu J, Yang YT, Yates A, Zerbino D, Zhang Y, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Tress ML, Flicek P.

Nucleic Acids Res 2021 : 49 ; d1 ; D916-D923.

GENCODE reference annotation for the human and mouse genomes.

Frankish A, Diekhans M, Ferreira AM, Johnson R, Jungreis I, Loveland J, Mudge JM, Sisu C, Wright J, Armstrong J, Barnes I, Berry A, Bignell A, Carbonell Sala S, Chrast J, Cunningham F, Di Domenico T, Donaldson S, Fiddes IT, García Girón C, Gonzalez JM, Grego T, Hardy M, Hourlier T, Hunt T, Izuogu OG, Lagarde J, Martin FJ, Martínez L, Mohanan S, Muir P, Navarro FCP, Parker A, Pei B, Pozo F, Ruffier M, Schmitt BM, Stapleton E, Suner MM, Sycheva I, Uszczynska-Ratajczak B, Xu J, Yates A, Zerbino D, Zhang Y, Aken B, Choudhary JS, Gerstein M, Guigó R, Hubbard TJP, Kellis M, Paten B, Reymond A, Tress ML, Flicek P.

Nucleic Acids Res 2019 : 47 ; d1 ; D766-D773.

Creating reference gene annotation for the mouse C57BL6/J genome assembly.

Mudge JM, Harrow J.

Mamm Genome 2015 : 26 ; 9-10 ; 366-378.

GENCODE: the reference human genome annotation for The ENCODE Project.

Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ.

Genome Res 2012 : 22 ; 9 ; 1760-1774.

GENCODE: producing a reference annotation for ENCODE.

Harrow J, Denoeud F, Frankish A, Reymond A, Chen CK, Chrast J, Lagarde J, Gilbert JG, Storey R, Swarbreck D, Rossier C, Ucla C, Hubbard T, Antonarakis SE, Guigo R.

Genome Biol 2006 : 7 Suppl 1 ; S4.1-9.

All Publications of Participants

Evidence for widespread translation of 5' untranslated regions.

Rodriguez JM, Abascal F, Cerdán-Vélez D, Gómez LM, Vázquez J, Tress ML.

Nucleic Acids Res 2024 : 52 ; 14 ; 8112-8126.

CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing.

Carbonell-Sala S, Perteghella T, Lagarde J, Nishiyori H, Palumbo E, Arnan C, Takahashi H, Carninci P, Uszczynska-Ratajczak B, Guigó R.

Nat Commun 2024 : 15 ; 1 ; 5278.

Multiplexed single-cell characterization of alternative polyadenylation regulators.

Kowalski MH, Wessels HH, Linder J, Dalgarno C, Mascio I, Choudhary S, Hartman A, Hao Y, Kundaje A, Satija R.

Cell 2024 : 187 ; 16 ; 4408-4425.e23.

Biophysical characterization of high-confidence, small human proteins.

Whited AM, Jungreis I, Allen J, Cleveland CL, Mudge JM, Kellis M, Rinn JL, Hough LE.

Biophys Rep (N Y) 2024 : 4 ; 3 ; 100167.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification.

Pardo-Palacios FJ, Wang D, Reese F, Diekhans M, Carbonell-Sala S, Williams B, Loveland JE, De María M, Adams MS, Balderrama-Gutierrez G, Behera AK, Gonzalez Martinez JM, Hunt T, Lagarde J, Liang CE, Li H, Meade MJ, Moraga Amador DA, Prjibelski AD, Birol I, Bostan H, Brooks AM, Çelik MH, Chen Y, Du MRM, Felton C, Göke J, Hafezqorani S, Herwig R, Kawaji H, Lee J, Li JL, Lienhard M, Mikheenko A, Mulligan D, Nip KM, Pertea M, Ritchie ME, Sim AD, Tang AD, Wan YK, Wang C, Wong BY, Yang C, Barnes I, Berry AE, Capella-Gutierrez S, Cousineau A, Dhillon N, Fernandez-Gonzalez JM, Ferrández-Peral L, Garcia-Reyero N, Götz S, Hernández-Ferrer C, Kondratova L, Liu T, Martinez-Martin A, Menor C, Mestre-Tomás J, Mudge JM, Panayotova NG, Paniagua A, Repchevsky D, Ren X, Rouchka E, Saint-John B, Sapena E, Sheynkman L, Smith ML, Suner MM, Takahashi H, Youngworth IA, Carninci P, Denslow ND, Guigó R, Hunter ME, Maehr R, Shen Y, Tilgner HU, Wold BJ, Vollmers C, Frankish A, Au KF, Sheynkman GM, Mortazavi A, Conesa A, Brooks AN.

Nat Methods 2024 : 21 ; 7 ; 1349-1363.

Ribosome decision graphs for the representation of eukaryotic RNA translation complexity.

Tierney JAS, Świrski M, Tjeldnes H, Mudge JM, Kufel J, Whiffin N, Valen E, Baranov PV.

Genome Res 2024 : 34 ; 4 ; 530-538.

Single-cell long-read sequencing-based mapping reveals specialized splicing patterns in developing and adult mouse and human brain.

Joglekar A, Hu W, Zhang B, Narykov O, Diekhans M, Marrocco J, Balacco J, Ndhlovu LC, Milner TA, Fedrigo O, Jarvis ED, Sheynkman G, Korkin D, Ross ME, Tilgner HU.

Nat Neurosci 2024 : 27 ; 6 ; 1051-1063.

The T2T-CHM13 reference assembly uncovers essential WASH1 and GPRIN2 paralogues.

Cerdán-Vélez D, Tress ML.

Bioinform Adv 2024 : 4 ; 1 ; vbae029.

CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods.

Critical Assessment of Genome Interpretation Consortium.

Genome Biol 2024 : 25 ; 1 ; 53.

The UCSC Genome Browser database: 2024 update.

Raney BJ, Barber GP, Benet-Pagès A, Casper J, Clawson H, Cline MS, Diekhans M, Fischer C, Navarro Gonzalez J, Hickey G, Hinrichs AS, Kuhn RM, Lee BT, Lee CM, Le Mercier P, Miga KH, Nassar LR, Nejad P, Paten B, Perez G, Schmelter D, Speir ML, Wick BD, Zweig AS, Haussler D, Kent WJ, Haeussler M.

Nucleic Acids Res 2024 : 52 ; d1 ; D1082-D1088.

Ensembl 2024.

Harrison PW, Amode MR, Austine-Orimoloye O, Azov AG, Barba M, Barnes I, Becker A, Bennett R, Berry A, Bhai J, Bhurji SK, Boddu S, Branco Lins PR, Brooks L, Ramaraju SB, Campbell LI, Martinez MC, Charkhchi M, Chougule K, Cockburn A, Davidson C, De Silva NH, Dodiya K, Donaldson S, El Houdaigui B, Naboulsi TE, Fatima R, Giron CG, Genez T, Grigoriadis D, Ghattaoraya GS, Martinez JG, Gurbich TA, Hardy M, Hollis Z, Hourlier T, Hunt T, Kay M, Kaykala V, Le T, Lemos D, Lodha D, Marques-Coelho D, Maslen G, Merino GA, Mirabueno LP, Mushtaq A, Hossain SN, Ogeh DN, Sakthivel MP, Parker A, Perry M, Piližota I, Poppleton D, Prosovetskaia I, Raj S, Pérez-Silva JG, Salam AIA, Saraf S, Saraiva-Agostinho N, Sheppard D, Sinha S, Sipos B, Sitnik V, Stark W, Steed E, Suner MM, Surapaneni L, Sutinen K, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Ware D, Wass E, Willhoft NL, Allen J, Alvarez-Jarreta J, Chakiachvili M, Flint B, Giorgetti S, Haggerty L, Ilsley GR, Keatley J, Loveland JE, Moore B, Mudge JM, Naamati G, Tate J, Trevanion SJ, Winterbottom A, Frankish A, Hunt SE, Cunningham F, Dyer S, Finn RD, Martin FJ, Yates AD.

Nucleic Acids Res 2024 : 52 ; d1 ; D891-D899.

The status of the human gene catalogue.

Amaral P, Carbonell-Sala S, De La Vega FM, Faial T, Frankish A, Gingeras T, Guigo R, Harrow JL, Hatzigeorgiou AG, Johnson R, Murphy TD, Pertea M, Pruitt KD, Pujar S, Takahashi H, Ulitsky I, Varabyou A, Wells CA, Yandell M, Carninci P, Salzberg SL.

Nature 2023 : 622 ; 7981 ; 41-47.

GenArk: towards a million UCSC genome browsers.

Clawson H, Lee BT, Raney BJ, Barber GP, Casper J, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Nassar LR, Perez G, Wick B, Schmelter D, Speir ML, Armstrong J, Zweig AS, Kuhn RM, Kirilenko BM, Hiller M, Haussler D, Kent WJ, Haeussler M.

Genome Biol 2023 : 24 ; 1 ; 217.

The complete sequence of a human Y chromosome.

Rhie A, Nurk S, Cechova M, Hoyt SJ, Taylor DJ, Altemose N, Hook PW, Koren S, Rautiainen M, Alexandrov IA, Allen J, Asri M, Bzikadze AV, Chen NC, Chin CS, Diekhans M, Flicek P, Formenti G, Fungtammasan A, Garcia Giron C, Garrison E, Gershman A, Gerton JL, Grady PGS, Guarracino A, Haggerty L, Halabian R, Hansen NF, Harris R, Hartley GA, Harvey WT, Haukness M, Heinz J, Hourlier T, Hubley RM, Hunt SE, Hwang S, Jain M, Kesharwani RK, Lewis AP, Li H, Logsdon GA, Lucas JK, Makalowski W, Markovic C, Martin FJ, Mc Cartney AM, McCoy RC, McDaniel J, McNulty BM, Medvedev P, Mikheenko A, Munson KM, Murphy TD, Olsen HE, Olson ND, Paulin LF, Porubsky D, Potapova T, Ryabov F, Salzberg SL, Sauria MEG, Sedlazeck FJ, Shafin K, Shepelev VA, Shumate A, Storer JM, Surapaneni L, Taravella Oill AM, Thibaud-Nissen F, Timp W, Tomaszkiewicz M, Vollger MR, Walenz BP, Watwood AC, Weissensteiner MH, Wenger AM, Wilson MA, Zarate S, Zhu Y, Zook JM, Eichler EE, O'Neill RJ, Schatz MC, Miga KH, Makova KD, Phillippy AM.

Nature 2023 : 621 ; 7978 ; 344-354.

What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?

Prensner JR, Abelin JG, Kok LW, Clauser KR, Mudge JM, Ruiz-Orera J, Bassani-Sternberg M, Moritz RL, Deutsch EW, van Heesch S.

Mol Cell Proteomics 2023 : 22 ; 9 ; 100631.

SCN1A: bioinformatically informed revised boundaries for promoter and enhancer regions.

Pagni S, Custodio HM, Frankish A, Mudge JM, Mills JD, Sisodiya SM.

Hum Mol Genet 2023 : 32 ; 10 ; 1753-1763.

Evolutionary constraint and innovation across hundreds of placental mammals.

Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR, Zoonomia Consortium§, Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK.

Science 2023 : 380 ; 6643 ; eabn3943.

RNAget: an API to securely retrieve RNA quantifications.

Upchurch S, Palumbo E, Adams J, Bujold D, Bourque G, Nedzel J, Graham K, Kagda MS, Assis P, Hitz B, Righi E, Guigó R, Wold BJ, GA4GH RNA-Seq Task Team.

Bioinformatics 2023 : 39 ; 4 ; btad126.

A draft human pangenome reference.

Liao WW, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas JK, Monlong J, Abel HJ, Buonaiuto S, Chang XH, Cheng H, Chu J, Colonna V, Eizenga JM, Feng X, Fischer C, Fulton RS, Garg S, Groza C, Guarracino A, Harvey WT, Heumos S, Howe K, Jain M, Lu TY, Markello C, Martin FJ, Mitchell MW, Munson KM, Mwaniki MN, Novak AM, Olsen HE, Pesout T, Porubsky D, Prins P, Sibbesen JA, Sirén J, Tomlinson C, Villani F, Vollger MR, Antonacci-Fulton LL, Baid G, Baker CA, Belyaeva A, Billis K, Carroll A, Chang PC, Cody S, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld AL, Formenti G, Frankish A, Gao Y, Garrison NA, Giron CG, Green RE, Haggerty L, Hoekzema K, Hourlier T, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson ND, Popejoy AB, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Smith MW, Sofia HJ, Abou Tayoun AN, Thibaud-Nissen F, Tricomi FF, Wagner J, Walenz B, Wood JMD, Zimin AV, Bourque G, Chaisson MJP, Flicek P, Phillippy AM, Zook JM, Eichler EE, Haussler D, Wang T, Jarvis ED, Miga KH, Garrison E, Marschall T, Hall IM, Li H, Paten B.

Nature 2023 : 617 ; 7960 ; 312-324.

Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames.

Sandmann CL, Schulz JF, Ruiz-Orera J, Kirchner M, Ziehm M, Adami E, Marczenke M, Christ A, Liebe N, Greiner J, Schoenenberger A, Muecke MB, Liang N, Moritz RL, Sun Z, Deutsch EW, Gotthardt M, Mudge JM, Prensner JR, Willnow TE, Mertins P, van Heesch S, Hubner N.

Mol Cell 2023 : 83 ; 6 ; 994-1011.e18.

Ensembl 2023.

Martin FJ, Amode MR, Aneja A, Austine-Orimoloye O, Azov AG, Barnes I, Becker A, Bennett R, Berry A, Bhai J, Bhurji SK, Bignell A, Boddu S, Branco Lins PR, Brooks L, Ramaraju SB, Charkhchi M, Cockburn A, Da Rin Fiorretto L, Davidson C, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fatima R, Giron CG, Genez T, Ghattaoraya GS, Martinez JG, Guijarro C, Hardy M, Hollis Z, Hourlier T, Hunt T, Kay M, Kaykala V, Le T, Lemos D, Marques-Coelho D, Marugán JC, Merino GA, Mirabueno LP, Mushtaq A, Hossain SN, Ogeh DN, Sakthivel MP, Parker A, Perry M, Piližota I, Prosovetskaia I, Pérez-Silva JG, Salam AIA, Saraiva-Agostinho N, Schuilenburg H, Sheppard D, Sinha S, Sipos B, Stark W, Steed E, Sukumaran R, Sumathipala D, Suner MM, Surapaneni L, Sutinen K, Szpak M, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Walts B, Wass E, Willhoft N, Allen J, Alvarez-Jarreta J, Chakiachvili M, Flint B, Giorgetti S, Haggerty L, Ilsley GR, Loveland JE, Moore B, Mudge JM, Tate J, Thybert D, Trevanion SJ, Winterbottom A, Frankish A, Hunt SE, Ruffier M, Cunningham F, Dyer S, Finn RD, Howe KL, Harrison PW, Yates AD, Flicek P.

Nucleic Acids Res 2023 : 51 ; d1 ; D933-D941.

The UCSC Genome Browser database: 2023 update.

Nassar LR, Barber GP, Benet-Pagès A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee BT, Lee CM, Muthuraman P, Nguy B, Pereira T, Nejad P, Perez G, Raney BJ, Schmelter D, Speir ML, Wick BD, Zweig AS, Haussler D, Kuhn RM, Haeussler M, Kent WJ.

Nucleic Acids Res 2023 : 51 ; d1 ; D1188-D1195.

Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals.

Fedorova AD, Kiniry SJ, Andreev DE, Mudge JM, Baranov PV.

Nat Commun 2022 : 13 ; 1 ; 7910.

Origins and Evolution of Human Tandem Duplicated Exon Substitution Events.

Martinez-Gomez L, Cerdán-Vélez D, Abascal F, Tress ML.

Genome Biol Evol 2022 : 14 ; 12 ; evac162.

Deciphering the impact of genetic variation on human polyadenylation using APARENT2.

Linder J, Koplik SE, Kundaje A, Seelig G.

Genome Biol 2022 : 23 ; 1 ; 232.

Clinical variant interpretation and biologically relevant reference transcripts.

Pozo F, Rodriguez JM, Vázquez J, Tress ML.

NPJ Genom Med 2022 : 7 ; 1 ; 59.

APPRIS principal isoforms and MANE Select transcripts define reference splice variants.

Pozo F, Rodriguez JM, Martínez Gómez L, Vázquez J, Tress ML.

Bioinformatics 2022 : 38 ; suppl_2 ; ii89-ii94.

Standardized annotation of translated open reading frames.

Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S.

Nat Biotechnol 2022 : 40 ; 7 ; 994-999.

SCN1A overexpression, associated with a genomic region marked by a risk variant for a common epilepsy, raises seizure susceptibility.

Silvennoinen K, Gawel K, Tsortouktzidis D, Pitsch J, Alhusaini S, van Loo KMJ, Picardo R, Michalak Z, Pagni S, Martins Custodio H, Mills J, Whelan CD, de Zubicaray GI, McMahon KL, van der Ent W, Kirstein-Smardzewska KJ, Tiraboschi E, Mudge JM, Frankish A, Thom M, Wright MJ, Thompson PM, Schoch S, Becker AJ, Esguerra CV, Sisodiya SM.

Acta Neuropathol 2022 : 144 ; 1 ; 107-127.

A complete pedigree-based graph workflow for rare candidate variant analysis.

Markello C, Huang C, Rodriguez A, Carroll A, Chang PC, Eizenga J, Markello T, Haussler D, Paten B.

Genome Res 2022 : 32 ; 5 ; 893-903.

Concerted modification of nucleotides at functional centers of the ribosome revealed by single-molecule RNA modification profiling.

Bailey AD, Talkish J, Ding H, Igel H, Duran A, Mantripragada S, Paten B, Ares M.

Elife 2022 : 11 ; e76562.

A joint NCBI and EMBL-EBI transcript set for clinical genomics and research.

Morales J, Pujar S, Loveland JE, Astashyn A, Bennett R, Berry A, Cox E, Davidson C, Ermolaeva O, Farrell CM, Fatima R, Gil L, Goldfarb T, Gonzalez JM, Haddad D, Hardy M, Hunt T, Jackson J, Joardar VS, Kay M, Kodali VK, McGarvey KM, McMahon A, Mudge JM, Murphy DN, Murphy MR, Rajput B, Rangwala SH, Riddick LD, Thibaud-Nissen F, Threadgold G, Vatsan AR, Wallin C, Webb D, Flicek P, Birney E, Pruitt KD, Frankish A, Cunningham F, Murphy TD.

Nature 2022 : 604 ; 7905 ; 310-315.

Segmental duplications and their variation in a complete human genome.

Vollger MR, Guitart X, Dishuck PC, Mercuri L, Harvey WT, Gershman A, Diekhans M, Sulovari A, Munson KM, Lewis AP, Hoekzema K, Porubsky D, Li R, Nurk S, Koren S, Miga KH, Phillippy AM, Timp W, Ventura M, Eichler EE.

Science 2022 : 376 ; 6588 ; eabj6965.

The complete sequence of a human genome.

Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PGS, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O'Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM.

Science 2022 : 376 ; 6588 ; 44-53.

Complete genomic and epigenetic maps of human centromeres.

Altemose N, Logsdon GA, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Lucas JK, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH.

Science 2022 : 376 ; 6588 ; eabl4178.

Genomic and functional conservation of lncRNAs: lessons from flies.

Camilleri-Robles C, Amador R, Klein CC, Guigó R, Corominas M, Ruiz-Romero M.

Mamm Genome 2022 : 33 ; 2 ; 328-342.

Ensembl 2022.

Cunningham F, Allen JE, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Austine-Orimoloye O, Azov AG, Barnes I, Bennett R, Berry A, Bhai J, Bignell A, Billis K, Boddu S, Brooks L, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fatima R, Giron CG, Genez T, Martinez JG, Guijarro-Clarke C, Gymer A, Hardy M, Hollis Z, Hourlier T, Hunt T, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Marugán JC, Mohanan S, Mushtaq A, Naven M, Ogeh DN, Parker A, Parton A, Perry M, Piližota I, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Pérez-Silva JG, Stark W, Steed E, Sutinen K, Sukumaran R, Sumathipala D, Suner MM, Szpak M, Thormann A, Tricomi FF, Urbina-Gómez D, Veidenberg A, Walsh TA, Walts B, Willhoft N, Winterbottom A, Wass E, Chakiachvili M, Flint B, Frankish A, Giorgetti S, Haggerty L, Hunt SE, IIsley GR, Loveland JE, Martin FJ, Moore B, Mudge JM, Muffato M, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Dyer S, Harrison PW, Howe KL, Yates AD, Zerbino DR, Flicek P.

Nucleic Acids Res 2022 : 50 ; d1 ; D988-D995.

APPRIS: selecting functionally important isoforms.

Rodriguez JM, Pozo F, Cerdán-Vélez D, Di Domenico T, Vázquez J, Tress ML.

Nucleic Acids Res 2022 : 50 ; d1 ; D54-D59.

The UCSC Genome Browser database: 2022 update.

Lee BT, Barber GP, Benet-Pagès A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Muthuraman P, Nassar LR, Nguy B, Pereira T, Perez G, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Wick BD, Zweig AS, Haussler D, Kuhn RM, Haeussler M, Kent WJ.

Nucleic Acids Res 2022 : 50 ; d1 ; D1115-D1122.

Pangenomics enables genotyping of known structural variants in 5202 diverse genomes.

Sirén J, Monlong J, Chang X, Novak AM, Eizenga JM, Markello C, Sibbesen JA, Hickey G, Chang PC, Carroll A, Gupta N, Gabriel S, Blackwell TW, Ratan A, Taylor KD, Rich SS, Rotter JI, Haussler D, Garrison E, Paten B.

Science 2021 : 374 ; 6574 ; abg8871.

Non-coding regulatory elements: Potential roles in disease and the case of epilepsy.

Pagni S, Mills JD, Frankish A, Mudge JM, Sisodiya SM.

Neuropathol Appl Neurobiol 2022 : 48 ; 3 ; e12775.

Identification of high-confidence human poly(A) RNA isoform scaffolds using nanopore sequencing.

Mulroney L, Wulf MG, Schildkraut I, Tzertzinis G, Buswell J, Jain M, Olsen H, Diekhans M, Corrêa IR, Akeson M, Ettwiller L.

RNA 2022 : 28 ; 2 ; 162-176.

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer.

Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, Aguet F, Li B, Christian E, Knisbacher BA, Le PM, Hartigan CR, Keshishian H, Apffel A, Oliveira G, Zhang W, Chen S, Chow YT, Ji Z, Jungreis I, Shukla SA, Justesen S, Bachireddy P, Kellis M, Getz G, Hacohen N, Keskin DB, Carr SA, Wu CJ, Regev A.

Nat Biotechnol 2022 : 40 ; 2 ; 209-217.

Cell type-specific novel long non-coding RNA and circular RNA in the BLUEPRINT hematopoietic transcriptomes atlas.

Grassi L, Izuogu OG, Jorge NAN, Seyres D, Bustamante M, Burden F, Farrow S, Farahi N, Martin FJ, Frankish A, Mudge JM, Kostadima M, Petersen R, Lambourne JJ, Rowlston S, Martin-Rendon E, Clarke L, Downes K, Estivill X, Flicek P, Martens JHA, Yaspo ML, Stunnenberg HG, Ouwehand WH, Passetti F, Turro E, Frontini M.

Haematologica 2021 : 106 ; 10 ; 2613-2623.

The value of primary transcripts to the clinical and non-clinical genomics community: Survey results and roadmap for improvements.

Morales J, McMahon AC, Loveland J, Perry E, Frankish A, Hunt S, Armean IM, Flicek P, Cunningham F.

Mol Genet Genomic Med 2021 : 9 ; 12 ; e1786.

The clinical importance of tandem exon duplication-derived substitutions.

Martinez Gomez L, Pozo F, Walsh TA, Abascal F, Tress ML.

Nucleic Acids Res 2021 : 49 ; 14 ; 8232-8246.

Assessing the functional relevance of splice isoforms.

Pozo F, Martinez-Gomez L, Walsh TA, Rodriguez JM, Di Domenico T, Abascal F, Vazquez J, Tress ML.

NAR Genom Bioinform 2021 : 3 ; 2 ; lqab044.

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.

Jungreis I, Sealfon R, Kellis M.

Nat Commun 2021 : 12 ; 1 ; 2642.

A high-quality bonobo genome refines the analysis of hominid evolution.

Mao Y, Catacchio CR, Hillier LW, Porubsky D, Li R, Sulovari A, Fernandes JD, Montinaro F, Gordon DS, Storer JM, Haukness M, Fiddes IT, Murali SC, Dishuck PC, Hsieh P, Harvey WT, Audano PA, Mercuri L, Piccolo I, Antonacci F, Munson KM, Lewis AP, Baker C, Underwood JG, Hoekzema K, Huang TH, Sorensen M, Walker JA, Hoffman J, Thibaud-Nissen F, Salama SR, Pang AWC, Lee J, Hastie AR, Paten B, Batzer MA, Diekhans M, Ventura M, Eichler EE.

Nature 2021 : 594 ; 7861 ; 77-81.

Towards complete and error-free genome assemblies of all vertebrate species.

Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, Thibaud-Nissen F, Haggerty L, Bista I, Smith M, Haase B, Mountcastle J, Winkler S, Paez S, Howard J, Vernes SC, Lama TM, Grutzner F, Warren WC, Balakrishnan CN, Burt D, George JM, Biegler MT, Iorns D, Digby A, Eason D, Robertson B, Edwards T, Wilkinson M, Turner G, Meyer A, Kautt AF, Franchini P, Detrich HW, Svardal H, Wagner M, Naylor GJP, Pippel M, Malinsky M, Mooney M, Simbirsky M, Hannigan BT, Pesout T, Houck M, Misuraca A, Kingan SB, Hall R, Kronenberg Z, Sović I, Dunn C, Ning Z, Hastie A, Lee J, Selvaraj S, Green RE, Putnam NH, Gut I, Ghurye J, Garrison E, Sims Y, Collins J, Pelan S, Torrance J, Tracey A, Wood J, Dagnew RE, Guan D, London SE, Clayton DF, Mello CV, Friedrich SR, Lovell PV, Osipova E, Al-Ajli FO, Secomandi S, Kim H, Theofanopoulou C, Hiller M, Zhou Y, Harris RS, Makova KD, Medvedev P, Hoffman J, Masterson P, Clark K, Martin F, Howe K, Flicek P, Walenz BP, Kwak W, Clawson H, Diekhans M, Nassar L, Paten B, Kraus RHS, Crawford AJ, Gilbert MTP, Zhang G, Venkatesh B, Murphy RW, Koepfli KP, Shapiro B, Johnson WE, Di Palma F, Marques-Bonet T, Teeling EC, Warnow T, Graves JM, Ryder OA, Haussler D, O'Brien SJ, Korlach J, Lewin HA, Howe K, Myers EW, Durbin R, Phillippy AM, Jarvis ED.

Nature 2021 : 592 ; 7856 ; 737-746.

Conflicting and ambiguous names of overlapping ORFs in the SARS-CoV-2 genome: A homology-based resolution.

Jungreis I, Nelson CW, Ardern Z, Finkel Y, Krogan NJ, Sato K, Ziebuhr J, Stern-Ginossar N, Pavesi A, Firth AE, Gorbalenya AE, Kellis M.

Virology 2021 : 558 ; 145-151.

Regulatory genomic circuitry of human disease loci by integrative epigenomics.

Boix CA, James BT, Park YP, Meuleman W, Kellis M.

Nature 2021 : 590 ; 7845 ; 300-307.

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain.

Joglekar A, Prjibelski A, Mahfouz A, Collier P, Lin S, Schlusche AK, Marrocco J, Williams SR, Haase B, Hayes A, Chew JG, Weisenfeld NI, Wong MY, Stein AN, Hardwick SA, Hunt T, Wang Q, Dieterich C, Bent Z, Fedrigo O, Sloan SA, Risso D, Jarvis ED, Flicek P, Luo W, Pitt GS, Frankish A, Smit AB, Ross ME, Tilgner HU.

Nat Commun 2021 : 12 ; 1 ; 463.

The UCSC Genome Browser database: 2021 update.

Navarro Gonzalez J, Zweig AS, Speir ML, Schmelter D, Rosenbloom KR, Raney BJ, Powell CC, Nassar LR, Maulding ND, Lee CM, Lee BT, Hinrichs AS, Fyfe AC, Fernandes JD, Diekhans M, Clawson H, Casper J, Benet-Pagès A, Barber GP, Haussler D, Kuhn RM, Haeussler M, Kent WJ.

Nucleic Acids Res 2021 : 49 ; d1 ; D1046-D1057.

Ensembl 2021.

Howe KL, Achuthan P, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Charkhchi M, Cummins C, Da Rin Fioretto L, Davidson C, Dodiya K, El Houdaigui B, Fatima R, Gall A, Garcia Giron C, Grego T, Guijarro-Clarke C, Haggerty L, Hemrom A, Hourlier T, Izuogu OG, Juettemann T, Kaikala V, Kay M, Lavidas I, Le T, Lemos D, Gonzalez Martinez J, Marugán JC, Maurel T, McMahon AC, Mohanan S, Moore B, Muffato M, Oheh DN, Paraschas D, Parker A, Parton A, Prosovetskaia I, Sakthivel MP, Salam AIA, Schmitt BM, Schuilenburg H, Sheppard D, Steed E, Szpak M, Szuba M, Taylor K, Thormann A, Threadgold G, Walts B, Winterbottom A, Chakiachvili M, Chaubal A, De Silva N, Flint B, Frankish A, Hunt SE, IIsley GR, Langridge N, Loveland JE, Martin FJ, Mudge JM, Morales J, Perry E, Ruffier M, Tate J, Thybert D, Trevanion SJ, Cunningham F, Yates AD, Zerbino DR, Flicek P.

Nucleic Acids Res 2021 : 49 ; d1 ; D884-D891.

RNAcentral 2021: secondary structure integration, improved sequence search and new member databases.

RNAcentral Consortium.

Nucleic Acids Res 2021 : 49 ; d1 ; D212-D220.

Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits.

Sun C, Huang J, Wang Y, Zhao X, Su L, Thomas GWC, Zhao M, Zhang X, Jungreis I, Kellis M, Vicario S, Sharakhov IV, Bondarenko SM, Hasselmann M, Kim CN, Paten B, Penso-Dolfin L, Wang L, Chang Y, Gao Q, Ma L, Ma L, Zhang Z, Zhang H, Zhang H, Ruzzante L, Robertson HM, Zhu Y, Liu Y, Yang H, Ding L, Wang Q, Ma D, Xu W, Liang C, Itgen MW, Mee L, Cao G, Zhang Z, Sadd BM, Hahn MW, Schaack S, Barribeau SM, Williams PH, Waterhouse RM, Mueller RL.

Mol Biol Evol 2021 : 38 ; 2 ; 486-501.

Efficient dynamic variation graphs.

Eizenga JM, Novak AM, Kobayashi E, Villani F, Cisar C, Heumos S, Hickey G, Colonna V, Paten B, Garrison E.

Bioinformatics 2021 : 36 ; 21 ; 5139-5144.

Sequence diversity analyses of an improved rhesus macaque genome enhance its biomedical utility.

Warren WC, Harris RA, Haukness M, Fiddes IT, Murali SC, Fernandes J, Fernandes J, Dishuck PC, Storer JM, Raveendran M, Hillier LW, Porubsky D, Mao Y, Gordon D, Vollger MR, Lewis AP, Munson KM, DeVogelaere E, Armstrong J, Diekhans M, Walker JA, Tomlinson C, Graves-Lindsay TA, Kremitzki M, Salama SR, Audano PA, Escalona M, Maurer NW, Antonacci F, Mercuri L, Maggiolini FAM, Catacchio CR, Underwood JG, O'Connor DH, Sanders AD, Korbel JO, Ferguson B, Kubisch HM, Picker L, Kalin NH, Rosene D, Levine J, Abbott DH, Gray SB, Sanchez MM, Kovacs-Balint ZA, Kemnitz JW, Thomasy SM, Roberts JA, Kinnally EL, Capitanio JP, Skene JHP, Platt M, Cole SA, Green RE, Ventura M, Wiseman RW, Paten B, Batzer MA, Rogers J, Eichler EE.

Science 2020 : 370 ; 6523 ; eabc6617.

Abstracts from the 53rd European Society of Human Genetics (ESHG) Conference: Interactive e-Posters.

Eur J Hum Genet 2020 : 28 ; suppl 1 ; 141-797.

Progressive Cactus is a multiple-genome aligner for the thousand-genome era.

Armstrong J, Hickey G, Diekhans M, Fiddes IT, Novak AM, Deran A, Fang Q, Xie D, Feng S, Stiller J, Genereux D, Johnson J, Marinescu VD, Alföldi J, Harris RS, Lindblad-Toh K, Haussler D, Karlsson E, Jarvis ED, Zhang G, Paten B.

Nature 2020 : 587 ; 7833 ; 246-251.

A comparative genomics multitool for scientific discovery and conservation.

Zoonomia Consortium.

Nature 2020 : 587 ; 7833 ; 240-245.

Using Deep Learning to Extrapolate Protein Expression Measurements.

Barzine MP, Freivalds K, Wright JC, Opmanis M, Rituma D, Ghavidel FZ, Jarnuczak AF, Celms E, Čerāns K, Jonassen I, Lace L, Vizcaíno JA, Choudhary JS, Brazma A, Viksna J.

Proteomics 2020 : 20 ; 21-22 ; e2000009.

Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy.

Kousi M, Söylemez O, Ozanturk A, Mourtzi N, Akle S, Jungreis I, Muller J, Cassa CA, Brand H, Mokry JA, Wolf MY, Sadeghpour A, McFadden K, Lewis RA, Talkowski ME, Dollfus H, Kellis M, Davis EE, Sunyaev SR, Katsanis N.

Nat Genet 2020 : 52 ; 11 ; 1145-1150.

An analysis of tissue-specific alternative splicing at the protein level.

Rodriguez JM, Pozo F, di Domenico T, Vazquez J, Tress ML.

PLoS Comput Biol 2020 : 16 ; 10 ; e1008287.

Functional signatures of evolutionarily young CTCF binding sites.

Azazi D, Mudge JM, Odom DT, Flicek P.

BMC Biol 2020 : 18 ; 1 ; 132.

Gaussian mixture model-based unsupervised nucleotide modification number detection using nanopore-sequencing readouts.

Ding H, Bailey AD, Jain M, Olsen H, Paten B.

Bioinformatics 2020 : 36 ; 19 ; 4928-4934.

A limited set of transcriptional programs define major cell types.

Breschi A, Muñoz-Aguirre M, Wucher V, Davis CA, Garrido-Martín D, Djebali S, Gillis J, Pervouchine DD, Vlasova A, Dobin A, Zaleski C, Drenkow J, Danyko C, Scavelli A, Reverter F, Snyder MP, Gingeras TR, Guigó R.

Genome Res 2020 : 30 ; 7 ; 1047-1059.

Transcriptional activity and strain-specific history of mouse pseudogenes.

Sisu C, Muir P, Frankish A, Fiddes I, Diekhans M, Thybert D, Odom DT, Flicek P, Keane TM, Hubbard T, Harrow J, Gerstein M.

Nat Commun 2020 : 11 ; 1 ; 3695.

Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast.

Eisenberg AR, Higdon AL, Hollerer I, Fields AP, Jungreis I, Diamond PD, Kellis M, Jovanovic M, Brar GA.

Cell Syst 2020 : 11 ; 2 ; 145-160.e5.

Telomere-to-telomere assembly of a complete human X chromosome.

Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton JM, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Risques RA, Graves Lindsay TA, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM.

Nature 2020 : 585 ; 7823 ; 79-84.

Distance indexing and seed clustering in sequence graphs.

Chang X, Eizenga J, Novak AM, Sirén J, Paten B.

Bioinformatics 2020 : 36 ; suppl_1 ; i146-i153.

halSynteny: a fast, easy-to-use conserved synteny block construction method for multiple whole-genome alignments.

Krasheninnikova K, Diekhans M, Armstrong J, Dievskii A, Paten B, O'Brien S.

Gigascience 2020 : 9 ; 6 ; giaa047.

Progress, Challenges, and Surprises in Annotating the Human Genome.

Zerbino DR, Frankish A, Flicek P.

Annu Rev Genomics Hum Genet 2020 : 21 ; 55-79.

Perspectives on ENCODE.

ENCODE Project Consortium, Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM.

Nature 2020 : 583 ; 7818 ; 693-698.

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes.

Shafin K, Pesout T, Lorig-Roach R, Haukness M, Olsen HE, Bosworth C, Armstrong J, Tigyi K, Maurer N, Koren S, Sedlazeck FJ, Marschall T, Mayes S, Costa V, Zook JM, Liu KJ, Kilburn D, Sorensen M, Munson KM, Vollger MR, Monlong J, Garrison E, Eichler EE, Salama S, Haussler D, Green RE, Akeson M, Phillippy A, Miga KH, Carnevali P, Jain M, Paten B.

Nat Biotechnol 2020 : 38 ; 9 ; 1044-1053.

Transcript expression-aware annotation improves rare variant interpretation.

Cummings BB, Karczewski KJ, Kosmicki JA, Seaby EG, Watts NA, Singer-Berk M, Mudge JM, Karjalainen J, Satterstrom FK, O'Donnell-Luria AH, Poterba T, Seed C, Solomonson M, Alföldi J, Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Daly MJ, MacArthur DG.

Nature 2020 : 581 ; 7809 ; 452-458.

Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon.

Khan YA, Jungreis I, Wright JC, Mudge JM, Choudhary JS, Firth AE, Kellis M.

BMC Genet 2020 : 21 ; 1 ; 25.

Bayesian Framework for Detecting Gene Expression Outliers in Individual Samples.

Vivian J, Eizenga JM, Beale HC, Vaske OM, Paten B.

JCO Clin Cancer Inform 2020 : 4 ; 160-170.

Pangenome Graphs.

Eizenga JM, Novak AM, Sibbesen JA, Heumos S, Ghaffaari A, Hickey G, Chang X, Seaman JD, Rounthwaite R, Ebler J, Rautiainen M, Garg S, Paten B, Marschall T, Sirén J, Garrison E.

Annu Rev Genomics Hum Genet 2020 : 21 ; 139-162.

Haplotype-aware graph indexes.

Sirén J, Garrison E, Novak AM, Paten B, Durbin R.

Bioinformatics 2020 : 36 ; 2 ; 400-407.

Ensembl 2020.

Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Marugán JC, Cummins C, Davidson C, Dodiya K, Fatima R, Gall A, Giron CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Lavidas I, Le T, Lemos D, Martinez JG, Maurel T, McDowall M, McMahon A, Mohanan S, Moore B, Nuhn M, Oheh DN, Parker A, Parton A, Patricio M, Sakthivel MP, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sycheva M, Szuba M, Taylor K, Thormann A, Threadgold G, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Flint B, Frankish A, Hunt SE, IIsley G, Kostadima M, Langridge N, Loveland JE, Martin FJ, Morales J, Mudge JM, Muffato M, Perry E, Ruffier M, Trevanion SJ, Cunningham F, Howe KL, Zerbino DR, Flicek P.

Nucleic Acids Res 2020 : 48 ; d1 ; D682-D688.

UCSC Genome Browser enters 20th year.

Lee CM, Barber GP, Casper J, Clawson H, Diekhans M, Gonzalez JN, Hinrichs AS, Lee BT, Nassar LR, Powell CC, Raney BJ, Rosenbloom KR, Schmelter D, Speir ML, Zweig AS, Haussler D, Haeussler M, Kuhn RM, Kent WJ.

Nucleic Acids Res 2020 : 48 ; d1 ; D756-D761.

Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation.

Martinez-Gomez L, Abascal F, Jungreis I, Pozo F, Kellis M, Mudge JM, Tress ML.

NAR Genom Bioinform 2020 : 2 ; 1 ; lqz023.

Expert curation of the human and mouse olfactory receptor gene repertoires identifies conserved coding regions split across two exons.

Barnes IHA, Ibarra-Soria X, Fitzgerald S, Gonzalez JM, Davidson C, Hardy MP, Manthravadi D, Van Gerven L, Jorissen M, Zeng Z, Khan M, Mombaerts P, Harrow J, Logan DW, Frankish A.

BMC Genomics 2020 : 21 ; 1 ; 196.

Genotyping structural variants in pangenome graphs using the vg toolkit.

Hickey G, Heller D, Monlong J, Sibbesen JA, Sirén J, Eizenga J, Dawson ET, Garrison E, Novak AM, Paten B.

Genome Biol 2020 : 21 ; 1 ; 35.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernández JM, Gemovic B, Perovic VR, Davidović RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Törönen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijević V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Björne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Šmuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O'Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I.

Genome Biol 2019 : 20 ; 1 ; 244.

Elucidation of Codon Usage Signatures across the Domains of Life.

Novoa EM, Jungreis I, Jaillon O, Kellis M.

Mol Biol Evol 2019 : 36 ; 10 ; 2328-2339.

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.

Genome Res 2019 : 29 ; 12 ; 2073-2087.

Re-annotation of 191 developmental and epileptic encephalopathy-associated genes unmasks de novo variants in SCN1A.

Steward CA, Roovers J, Suner MM, Gonzalez JM, Uszczynska-Ratajczak B, Pervouchine D, Fitzgerald S, Viola M, Stamberger H, Hamdan FF, Ceulemans B, Leroy P, Nava C, Lepine A, Tapanari E, Keiller D, Abbs S, Sanchis-Juan A, Grozeva D, Rogers AS, Diekhans M, Guigó R, Petryszak R, Minassian BA, Cavalleri G, Vitsios D, Petrovski S, Harrow J, Flicek P, Lucy Raymond F, Lench NJ, Jonghe P, Mudge JM, Weckhuysen S, Sisodiya SM, Frankish A.

NPJ Genom Med 2019 : 4 ; 31.

Getting the Entire Message: Progress in Isoform Sequencing.

Hardwick SA, Joglekar A, Flicek P, Frankish A, Tilgner HU.

Front Genet 2019 : 10 ; 709.

A strategy for building and using a human reference pangenome.

Llamas B, Narzisi G, Schneider V, Audano PA, Biederstedt E, Blauvelt L, Bradbury P, Chang X, Chin CS, Fungtammasan A, Clarke WE, Cleary A, Ebler J, Eizenga J, Sibbesen JA, Markello CJ, Garrison E, Garg S, Hickey G, Lazo GR, Lin MF, Mahmoud M, Marschall T, Minkin I, Monlong J, Musunuri RL, Sagayaradj S, Novak AM, Rautiainen M, Regier A, Sedlazeck FJ, Siren J, Souilmi Y, Wagner J, Wrightsman T, Yokoyama TT, Zeng Q, Zook JM, Paten B, Busby B.

F1000Res 2019 : 8 ; 1751.

A plugin for the Ensembl Variant Effect Predictor that uses MaxEntScan to predict variant spliceogenicity.

Shamsani J, Kazakoff SH, Armean IM, McLaren W, Parsons MT, Thompson BA, O'Mara TA, Hunt SE, Waddell N, Spurdle AB.

Bioinformatics 2019 : 35 ; 13 ; 2315-2317.

Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay.

Pervouchine D, Popov Y, Berry A, Borsari B, Frankish A, Guigó R.

Nucleic Acids Res 2019 : 47 ; 10 ; 5293-5306.

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.

McCorkindale AL, Wahle P, Werner S, Jungreis I, Menzel P, Shukla CJ, Abreu RLP, Irizarry RA, Meyer IM, Kellis M, Zinzen RP.

Development 2019 : 146 ; 6 ; dev175265.

The UCSC Genome Browser database: 2019 update.

Haeussler M, Zweig AS, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Hinrichs AS, Gonzalez JN, Gibson D, Diekhans M, Clawson H, Casper J, Barber GP, Haussler D, Kuhn RM, Kent WJ.

Nucleic Acids Res 2019 : 47 ; d1 ; D853-D858.

RNAcentral: a hub of information for non-coding RNA sequences.

The RNAcentral Consortium.

Nucleic Acids Res 2019 : 47 ; d1 ; D221-D229.

RNAcentral: a hub of information for non-coding RNA sequences.

The RNAcentral Consortium.

Nucleic Acids Res 2019 : 47 ; d1 ; D1250-D1251.

Ensembl 2019.

Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, Bennett R, Bhai J, Billis K, Boddu S, Cummins C, Davidson C, Dodiya KJ, Gall A, Girón CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Laird MR, Lavidas I, Liu Z, Loveland JE, Marugán JC, Maurel T, McMahon AC, Moore B, Morales J, Mudge JM, Nuhn M, Ogeh D, Parker A, Parton A, Patricio M, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sparrow H, Stapleton E, Szuba M, Taylor K, Threadgold G, Thormann A, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Yates AD, Zerbino DR, Flicek P.

Nucleic Acids Res 2019 : 47 ; d1 ; D745-D751.

Corrigendum: Loose ends: almost one in five human genes still have unresolved coding status.

Abascal F, Juan D, Jungreis I, Kellis M, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML.

Nucleic Acids Res 2018 : 46 ; 22 ; 12194.

Target site specificity and in vivo complexity of the mammalian arginylome.

Wang J, Pejaver VR, Dann GP, Wolf MY, Kellis M, Huang Y, Garcia BA, Radivojac P, Kashina A.

Sci Rep 2018 : 8 ; 1 ; 16177.

Whole-Genome Alignment and Comparative Annotation.

Armstrong J, Fiddes IT, Diekhans M, Paten B.

Annu Rev Anim Biosci 2019 : 7 ; 41-64.

Chromosome assembly of large and complex genomes using multiple references.

Kolmogorov M, Armstrong J, Raney BJ, Streeter I, Dunn M, Yang F, Odom D, Flicek P, Keane TM, Thybert D, Paten B, Pham S.

Genome Res 2018 : 28 ; 11 ; 1720-1732.

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci.

Lilue J, Doran AG, Fiddes IT, Abrudan M, Armstrong J, Bennett R, Chow W, Collins J, Collins S, Czechanski A, Danecek P, Diekhans M, Dolle DD, Dunn M, Durbin R, Earl D, Ferguson-Smith A, Flicek P, Flint J, Frankish A, Fu B, Gerstein M, Gilbert J, Goodstadt L, Harrow J, Howe K, Ibarra-Soria X, Kolmogorov M, Lelliott CJ, Logan DW, Loveland J, Mathews CE, Mott R, Muir P, Nachtweide S, Navarro FCP, Odom DT, Park N, Pelan S, Pham SK, Quail M, Reinholdt L, Romoth L, Shirley L, Sisu C, Sjoberg-Herrera M, Stanke M, Steward C, Thomas M, Threadgold G, Thybert D, Torrance J, Wong K, Wood J, Yalcin B, Yang F, Adams DJ, Paten B, Keane TM.

Nat Genet 2018 : 50 ; 11 ; 1574-1583.

Towards a complete map of the human long non-coding RNA transcriptome.

Uszczynska-Ratajczak B, Lagarde J, Frankish A, Guigó R, Johnson R.

Nat Rev Genet 2018 : 19 ; 9 ; 535-548.

Variation graph toolkit improves read mapping by representing genetic variation in the reference.

Garrison E, Sirén J, Novak AM, Hickey G, Eizenga JM, Dawson ET, Jones W, Garg S, Markello C, Lin MF, Paten B, Durbin R.

Nat Biotechnol 2018 : 36 ; 9 ; 875-879.

Loose ends: almost one in five human genes still have unresolved coding status.

Abascal F, Juan D, Jungreis I, Kellis M, Martinez L, Rigau M, Rodriguez JM, Vazquez J, Tress ML.

Nucleic Acids Res 2018 : 46 ; 14 ; 7070-7084.

Genome-wide association study: Exploring the genetic basis for responsiveness to ketogenic dietary therapies for drug-resistant epilepsy.

Schoeler NE, Leu C, Balestrini S, Mudge JM, Steward CA, Frankish A, Leung MA, Mackay M, Scheffer I, Williams R, Sander JW, Cross JH, Sisodiya SM.

Epilepsia 2018 : 59 ; 8 ; 1557-1566.

A graph-based approach to diploid genome assembly.

Garg S, Rautiainen M, Novak AM, Garrison E, Durbin R, Marschall T.

Bioinformatics 2018 : 34 ; 13 ; i105-i114.

Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.

Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A.

Genome Res 2018 : 28 ; 7 ; 1096.

Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.

Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE, Haussler D, Stanke M, Paten B.

Genome Res 2018 : 28 ; 7 ; 1029-1038.

High-resolution comparative analysis of great ape genomes.

Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, Hoekzema K, Qiu R, Clark K, Raja A, Welch AE, Sorensen M, Baker C, Fulton RS, Armstrong J, Graves-Lindsay TA, Denli AM, Hoppe ER, Hsieh P, Hill CM, Pang AWC, Lee J, Lam ET, Dutcher SK, Gage FH, Warren WC, Shendure J, Haussler D, Schneider VA, Cao H, Ventura M, Wilson RK, Paten B, Pollen A, Eichler EE.

Science 2018 : 360 ; 6393 ; eaar6343.

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes.

Schlaffner CN, Pirklbauer GJ, Bender A, Steen JAJ, Choudhary JS.

J Vis Exp 2018 ; 135

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P.

Genome Res 2018 : 28 ; 4 ; 448-459.

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification.

Tardaguila M, de la Fuente L, Marti C, Pereira C, Pardo-Palacios FJ, Del Risco H, Ferrell M, Mellado M, Macchietto M, Verheggen K, Edelmann M, Ezkurdia I, Vazquez J, Tress M, Mortazavi A, Martens L, Rodriguez-Navarro S, Moreno-Manzano V, Conesa A.

Genome Res 2018 : 28 ; 3 ; 396-411.

Capturing a Long Look at Our Genetic Library.

Lagarde J, Johnson R.

Cell Syst 2018 : 6 ; 2 ; 153-155.

Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response.

Loughran G, Jungreis I, Tzani I, Power M, Dmitriev RI, Ivanov IP, Kellis M, Atkins JF.

J Biol Chem 2018 : 293 ; 12 ; 4434-4444.

Nanopore sequencing and assembly of a human genome with ultra-long reads.

Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, Tyson JR, Beggs AD, Dilthey AT, Fiddes IT, Malla S, Marriott H, Nieto T, O'Grady J, Olsen HE, Pedersen BS, Rhie A, Richardson H, Quinlan AR, Snutch TP, Tee L, Paten B, Phillippy AM, Simpson JT, Loman NJ, Loose M.

Nat Biotechnol 2018 : 36 ; 4 ; 338-345.

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

Pujar S, O'Leary NA, Farrell CM, Loveland JE, Mudge JM, Wallin C, Girón CG, Diekhans M, Barnes I, Bennett R, Berry AE, Cox E, Davidson C, Goldfarb T, Gonzalez JM, Hunt T, Jackson J, Joardar V, Kay MP, Kodali VK, Martin FJ, McAndrews M, McGarvey KM, Murphy M, Rajput B, Rangwala SH, Riddick LD, Seal RL, Suner MM, Webb D, Zhu S, Aken BL, Bruford EA, Bult CJ, Frankish A, Murphy T, Pruitt KD.

Nucleic Acids Res 2018 : 46 ; d1 ; D221-D228.

The Ensembl Genome Browser: Strategies for Accessing Eukaryotic Genome Data.

Newman V, Moore B, Sparrow H, Perry E.

Methods Mol Biol 2018 : 1757 ; 115-139.

APPRIS 2017: principal isoforms for multiple gene sets.

Rodriguez JM, Rodriguez-Rivas J, Di Domenico T, Vázquez J, Valencia A, Tress ML.

Nucleic Acids Res 2018 : 46 ; d1 ; D213-D217.

Ensembl 2018.

Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Girón CG, Gil L, Gordon L, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, To JK, Laird MR, Lavidas I, Liu Z, Loveland JE, Maurel T, McLaren W, Moore B, Mudge J, Murphy DN, Newman V, Nuhn M, Ogeh D, Ong CK, Parker A, Patricio M, Riat HS, Schuilenburg H, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Zadissa A, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Cunningham F, Yates A, Flicek P.

Nucleic Acids Res 2018 : 46 ; d1 ; D754-D761.

Computational pan-genomics: status, promises and challenges.

Computational Pan-Genomics Consortium.

Brief Bioinform 2018 : 19 ; 1 ; 118-135.

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing.

Lagarde J, Uszczynska-Ratajczak B, Carbonell S, Pérez-Lluch S, Abad A, Davis C, Gingeras TR, Frankish A, Harrow J, Guigo R, Johnson R.

Nat Genet 2017 : 49 ; 12 ; 1731-1740.

The UCSC Genome Browser database: 2018 update.

Casper J, Zweig AS, Villarreal C, Tyner C, Speir ML, Rosenbloom KR, Raney BJ, Lee CM, Lee BT, Karolchik D, Hinrichs AS, Haeussler M, Guruvadoo L, Navarro Gonzalez J, Gibson D, Fiddes IT, Eisenhart C, Diekhans M, Clawson H, Barber GP, Armstrong J, Haussler D, Kuhn RM, Kent WJ.

Nucleic Acids Res 2018 : 46 ; d1 ; D762-D769.

Genome annotation for clinical genomic diagnostics: strengths and weaknesses.

Steward CA, Parker APJ, Minassian BA, Sisodiya SM, Frankish A, Harrow J.

Genome Med 2017 : 9 ; 1 ; 49.

Most Alternative Isoforms Are Not Functionally Important.

Tress ML, Abascal F, Valencia A.

Trends Biochem Sci 2017 : 42 ; 6 ; 408-410.

Ensembl 2017.

Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Juettemann T, Keenan S, Laird MR, Lavidas I, Maurel T, McLaren W, Moore B, Murphy DN, Nag R, Newman V, Nuhn M, Ong CK, Parker A, Patricio M, Riat HS, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Wilder SP, Zadissa A, Kostadima M, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Cunningham F, Yates A, Zerbino DR, Flicek P.

Nucleic Acids Res 2017 : 45 ; d1 ; D635-D642.

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics.

Weisser H, Wright JC, Mudge JM, Gutenbrunner P, Choudhary JS.

J Proteome Res 2016 : 15 ; 12 ; 4686-4695.

The state of play in higher eukaryote gene annotation.

Mudge JM, Harrow J.

Nat Rev Genet 2016 : 17 ; 12 ; 758-772.

Alternative Splicing May Not Be the Key to Proteome Complexity.

Tress ML, Abascal F, Valencia A.

Trends Biochem Sci 2017 : 42 ; 2 ; 98-110.

Evolutionary Dynamics of Abundant Stop Codon Readthrough.

Jungreis I, Chan CS, Waterhouse RM, Fields G, Lin MF, Kellis M.

Mol Biol Evol 2016 : 33 ; 12 ; 3108-3132.

Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq).

Lagarde J, Uszczynska-Ratajczak B, Santoyo-Lopez J, Gonzalez JM, Tapanari E, Mudge JM, Steward CA, Wilming L, Tanzer A, Howald C, Chrast J, Vela-Boza A, Rueda A, Lopez-Domingo FJ, Dopazo J, Reymond A, Guigó R, Harrow J.

Nat Commun 2016 : 7 ; 12339.

Gene-specific patterns of expression variation across organs and species.

Breschi A, Djebali S, Gillis J, Pervouchine DD, Dobin A, Davis CA, Gingeras TR, Guigó R.

Genome Biol 2016 : 17 ; 1 ; 151.

Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.

Wright JC, Mudge J, Weisser H, Barzine MP, Gonzalez JM, Brazma A, Choudhary JS, Harrow J.

Nat Commun 2016 : 7 ; 11778.

DecoyPyrat: Fast Non-redundant Hybrid Decoy Sequence Generation for Large Scale Proteomics.

Wright JC, Choudhary JS.

J Proteomics Bioinform 2016 : 9 ; 6 ; 176-180.

Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction.

Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, Mudge JM, Fonseca N, Brazma A, Guigo R, Harrow J.

BMC Genomics 2015 : 16 Suppl 8 ; S2.

Comparative analysis of pseudogenes across three phyla.

Sisu C, Pei B, Leng J, Frankish A, Zhang Y, Balasubramanian S, Harte R, Wang D, Rutenberg-Schoenberg M, Clark W, Diekhans M, Rozowsky J, Hubbard T, Harrow J, Gerstein MB.

Proc Natl Acad Sci U S A 2014 : 111 ; 37 ; 13361-13366.

Comparative assembly hubs: web-accessible browsers for comparative genomics.

Nguyen N, Hickey G, Raney BJ, Armstrong J, Clawson H, Zweig A, Karolchik D, Kent WJ, Haussler D, Paten B.

Bioinformatics 2014 : 30 ; 23 ; 3293-3301.

Comparative analysis of the transcriptome across distant species.

Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R.

Nature 2014 : 512 ; 7515 ; 445-448.

Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease.

Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC.

Proc Natl Acad Sci U S A 2014 : 111 ; 33 ; E3366.

Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.

Colonna V, Ayub Q, Chen Y, Pagani L, Luisi P, Pybus M, Garrison E, Xue Y, Tyler-Smith C, 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.

Genome Biol 2014 : 15 ; 6 ; R88.

Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes.

Ezkurdia I, Juan D, Rodriguez JM, Frankish A, Diekhans M, Harrow J, Vazquez J, Valencia A, Tress ML.

Hum Mol Genet 2014 : 23 ; 22 ; 5866-5878.

Ensembl 2015.

Cunningham F, 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 SE, Janacek SH, Johnson N, Juettemann T, Kähäri AK, Keenan S, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Overduin B, Parker A, Patricio M, Perry E, Pignatelli M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Aken BL, Birney E, Harrow J, Kinsella R, Muffato M, Ruffier M, Searle SM, Spudich G, Trevanion SJ, Yates A, Zerbino DR, Flicek P.

Nucleic Acids Res 2015 : 43 ; database issue ; D662-9.

Ragout-a reference-assisted assembly tool for bacterial genomes.

Kolmogorov M, Raney B, Paten B, Pham S.

Bioinformatics 2014 : 30 ; 12 ; i302-9.

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs.

Johnson R, Guigó R.

RNA 2014 : 20 ; 7 ; 959-976.

Genome-wide association meta-analysis of human longevity identifies a novel locus conferring survival beyond 90 years of age.

Deelen J, Beekman M, Uh HW, Broer L, Ayers KL, Tan Q, Kamatani Y, Bennet AM, Tamm R, Trompet S, Guðbjartsson DF, Flachsbart F, Rose G, Viktorin A, Fischer K, Nygaard M, Cordell HJ, Crocco P, van den Akker EB, Böhringer S, Helmer Q, Nelson CP, Saunders GI, Alver M, Andersen-Ranberg K, Breen ME, van der Breggen R, Caliebe A, Capri M, Cevenini E, Collerton JC, Dato S, Davies K, Ford I, Gampe J, Garagnani P, de Geus EJ, Harrow J, van Heemst D, Heijmans BT, Heinsen FA, Hottenga JJ, Hofman A, Jeune B, Jonsson PV, Lathrop M, Lechner D, Martin-Ruiz C, Mcnerlan SE, Mihailov E, Montesanto A, Mooijaart SP, Murphy A, Nohr EA, Paternoster L, Postmus I, Rivadeneira F, Ross OA, Salvioli S, Sattar N, Schreiber S, Stefánsson H, Stott DJ, Tiemeier H, Uitterlinden AG, Westendorp RG, Willemsen G, Samani NJ, Galan P, Sørensen TI, Boomsma DI, Jukema JW, Rea IM, Passarino G, de Craen AJ, Christensen K, Nebel A, Stefánsson K, Metspalu A, Magnusson P, Blanché H, Christiansen L, Kirkwood TB, van Duijn CM, Franceschi C, Houwing-Duistermaat JJ, Slagboom PE.

Hum Mol Genet 2014 : 23 ; 16 ; 4420-4432.

Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue.

Ma J, Ward CC, Jungreis I, Slavoff SA, Schwaid AG, Neveu J, Budnik BA, Kellis M, Saghatelian A.

J Proteome Res 2014 : 13 ; 3 ; 1757-1765.

Evidence of efficient stop codon readthrough in four mammalian genes.

Loughran G, Chou MY, Ivanov IP, Ivanov IP, Jungreis I, Kellis M, Kiran AM, Baranov PV, Atkins JF.

Nucleic Acids Res 2014 : 42 ; 14 ; 8928-8938.

The Vertebrate Genome Annotation browser 10 years on.

Harrow JL, Steward CA, Frankish A, Gilbert JG, Gonzalez JM, Loveland JE, Mudge J, Sheppard D, Thomas M, Trevanion S, Wilming LG.

Nucleic Acids Res 2014 : 42 ; database issue ; D771-9.

Ensembl 2014.

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, Yates A, Zerbino DR, Searle SM.

Nucleic Acids Res 2014 : 42 ; database issue ; D749-55.

Current status and new features of the Consensus Coding Sequence database.

Farrell CM, O'Leary NA, Harte RA, Loveland JE, Wilming LG, Wallin C, Diekhans M, Barrell D, Searle SM, Aken B, Hiatt SM, Frankish A, Suner MM, Rajput B, Steward CA, Brown GR, Bennett R, Murphy M, Wu W, Kay MP, Hart J, Rajan J, Weber J, Snow C, Riddick LD, Hunt T, Webb D, Thomas M, Tamez P, Rangwala SH, McGarvey KM, Pujar S, Shkeda A, Mudge JM, Gonzalez JM, Gilbert JG, Trevanion SJ, Baertsch R, Harrow JL, Hubbard T, Ostell JM, Haussler D, Pruitt KD.

Nucleic Acids Res 2014 : 42 ; database issue ; D865-72.

Systematic evaluation of spliced alignment programs for RNA-seq data.

Engström PG, Steijger T, Sipos B, Grant GR, Kahles A, Rätsch G, Goldman N, Hubbard TJ, Harrow J, Guigó R, Bertone P, RGASP Consortium.

Nat Methods 2013 : 10 ; 12 ; 1185-1191.

Assessment of transcript reconstruction methods for RNA-seq.

Steijger T, Abril JF, Engström PG, Kokocinski F, RGASP Consortium, Hubbard TJ, Guigó R, Harrow J, Bertone P.

Nat Methods 2013 : 10 ; 12 ; 1177-1184.

Functional transcriptomics in the post-ENCODE era.

Mudge JM, Frankish A, Harrow J.

Genome Res 2013 : 23 ; 12 ; 1961-1973.

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene.

Gonzàlez-Porta M, Frankish A, Rung J, Harrow J, Brazma A.

Genome Biol 2013 : 14 ; 7 ; R70.

ENCODE data in the UCSC Genome Browser: year 5 update.

Rosenbloom KR, Sloan CA, Malladi VS, Dreszer TR, Learned K, Kirkup VM, Wong MC, Maddren M, Fang R, Heitner SG, Lee BT, Barber GP, Harte RA, Diekhans M, Long JC, Wilder SP, Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ.

Nucleic Acids Res 2013 : 41 ; database issue ; D56-63.

APPRIS: annotation of principal and alternative splice isoforms.

Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink JJ, Lopez G, Valencia A, Tress ML.

Nucleic Acids Res 2013 : 41 ; database issue ; D110-7.

The UCSC Genome Browser database: extensions and updates 2013.

Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, Raney BJ, Pohl A, Malladi VS, Li CH, Lee BT, Learned K, Kirkup V, Hsu F, Heitner S, Harte RA, Haeussler M, Guruvadoo L, Goldman M, Giardine BM, Fujita PA, Dreszer TR, Diekhans M, Cline MS, Clawson H, Barber GP, Haussler D, Kent WJ.

Nucleic Acids Res 2013 : 41 ; database issue ; D64-9.

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.

Frenkel-Morgenstern M, Gorohovski A, Lacroix V, Rogers M, Ibanez K, Boullosa C, Andres Leon E, Ben-Hur A, Valencia A.

Nucleic Acids Res 2013 : 41 ; database issue ; D142-51.

An integrated map of genetic variation from 1,092 human genomes.

1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, Kang HM, Marth GT, McVean GA.

Nature 2012 : 491 ; 7422 ; 56-65.

The GENCODE pseudogene resource.

Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB.

Genome Biol 2012 : 13 ; 9 ; R51.

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.

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 ; 9 ; 1775-1789.

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle S, Harrow J, Hubbard TJ, Guigó R, Reymond A.

Genome Res 2012 : 22 ; 9 ; 1698-1710.

Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts.

Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R, Valencia A.

Genome Res 2012 : 22 ; 7 ; 1231-1242.

Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

Ezkurdia I, del Pozo A, Frankish A, Rodriguez JM, Harrow J, Ashman K, Valencia A, Tress ML.

Mol Biol Evol 2012 : 29 ; 9 ; 2265-2283.

The importance of identifying alternative splicing in vertebrate genome annotation.

Frankish A, Mudge JM, Thomas M, Harrow J.

Database (Oxford) 2012 : 2012 ; bas014.

Tracking and coordinating an international curation effort for the CCDS Project.

Harte RA, Farrell CM, Loveland JE, Suner MM, Wilming L, Aken B, Barrell D, Frankish A, Wallin C, Searle S, Diekhans M, Harrow J, Pruitt KD.

Database (Oxford) 2012 : 2012 ; bas008.

Landscape of transcription in human cells.

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 ; 7414 ; 101-108.

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium.

Nature 2012 : 489 ; 7414 ; 57-74.

A systematic survey of loss-of-function variants in human protein-coding genes.

MacArthur DG, Balasubramanian S, Frankish A, Huang N, Morris J, Walter K, Jostins L, Habegger L, Pickrell JK, Montgomery SB, Albers CA, Zhang ZD, Conrad DF, Lunter G, Zheng H, Ayub Q, DePristo MA, Banks E, Hu M, Handsaker RE, Rosenfeld JA, Fromer M, Jin M, Mu XJ, Khurana E, Ye K, Kay M, Saunders GI, Suner MM, Hunt T, Barnes IH, Amid C, Carvalho-Silva DR, Bignell AH, Snow C, Yngvadottir B, Bumpstead S, Cooper DN, Xue Y, Romero IG, 1000 Genomes Project Consortium, Wang J, Wang J, Li Y, Gibbs RA, McCarroll SA, Dermitzakis ET, Pritchard JK, Barrett JC, Harrow J, Hurles ME, Gerstein MB, Tyler-Smith C.

Science 2012 : 335 ; 6070 ; 823-828.

Evidence for transcript networks composed of chimeric RNAs in human cells.

Djebali S, Lagarde J, Kapranov P, Lacroix V, Borel C, Mudge JM, Howald C, Foissac S, Ucla C, Chrast J, Ribeca P, Martin D, Murray RR, Yang X, Ghamsari L, Lin C, Bell I, Dumais E, Drenkow J, Tress ML, Gelpí JL, Orozco M, Valencia A, van Berkum NL, Lajoie BR, Vidal M, Stamatoyannopoulos J, Batut P, Dobin A, Harrow J, Hubbard T, Dekker J, Frankish A, Salehi-Ashtiani K, Reymond A, Antonarakis SE, Guigó R, Gingeras TR.

PLoS One 2012 : 7 ; 1 ; e28213.

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.

Lin MF, Jungreis I, Kellis M.

Bioinformatics 2011 : 27 ; 13 ; i275-82.

The origins, evolution, and functional potential of alternative splicing in vertebrates.

Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T, Howald C, Reymond A, Guigó R, Hubbard T, Harrow J.

Mol Biol Evol 2011 : 28 ; 10 ; 2949-2959.

A user's guide to the encyclopedia of DNA elements (ENCODE).

ENCODE Project Consortium.

PLoS Biol 2011 : 9 ; 4 ; e1001046.

The GENCODE exome: sequencing the complete human exome.

Coffey AJ, Kokocinski F, Calafato MS, Scott CE, Palta P, Drury E, Joyce CJ, Leproust EM, Harrow J, Hunt S, Lehesjoki AE, Turner DJ, Hubbard TJ, Palotie A.

Eur J Hum Genet 2011 : 19 ; 7 ; 827-831.

Gene inactivation and its implications for annotation in the era of personal genomics.

Balasubramanian S, Habegger L, Frankish A, MacArthur DG, Harte R, Tyler-Smith C, Harrow J, Gerstein M.

Genes Dev 2011 : 25 ; 1 ; 1-10.

Ensembl 2011.

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 ; database issue ; D800-6.

ENCODE whole-genome data in the UCSC genome browser (2011 update).

Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, Meyer LR, Sloan CA, Malladi VS, Roskin KM, Suh BB, Hinrichs AS, Clawson H, Zweig AS, Kirkup V, Fujita PA, Rhead B, Smith KE, Pohl A, Kuhn RM, Karolchik D, Haussler D, Kent WJ.

Nucleic Acids Res 2011 : 39 ; database issue ; D871-5.

The UCSC Genome Browser database: update 2011.

Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ.

Nucleic Acids Res 2011 : 39 ; database issue ; D876-82.

AnnoTrack--a tracking system for genome annotation.

Kokocinski F, Harrow J, Hubbard T.

BMC Genomics 2010 : 11 ; 538.

Long noncoding RNAs with enhancer-like function in human cells.

Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R.

Cell 2010 : 143 ; 1 ; 46-58.

Segmental duplications in the human genome reveal details of pseudogene formation.

Khurana E, Lam HY, Cheng C, Carriero N, Cayting P, Gerstein MB.

Nucleic Acids Res 2010 : 38 ; 20 ; 6997-7007.

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology.

Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP.

Nature 2010 : 465 ; 7301 ; 1033-1038.

Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates.

Zhang ZD, Frankish A, Hunt T, Harrow J, Gerstein M.

Genome Biol 2010 : 11 ; 3 ; R26.

Meeting report: a workshop on Best Practices in Genome Annotation.

Madupu R, Brinkac LM, Harrow J, Wilming LG, Böhme U, Lamesch P, Hannick LI.

Database (Oxford) 2010 : 2010 ; baq001.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

Amid C, Rehaume LM, Brown KL, Gilbert JG, Dougan G, Hancock RE, Harrow JL.

BMC Genomics 2009 : 10 ; 606.

Discovery of candidate disease genes in ENU-induced mouse mutants by large-scale sequencing, including a splice-site mutation in nucleoredoxin.

Boles MK, Wilkinson BM, Wilming LG, Liu B, Probst FJ, Harrow J, Grafham D, Hentges KE, Woodward LP, Maxwell A, Mitchell K, Risley MD, Johnson R, Hirschi K, Lupski JR, Funato Y, Miki H, Marin-Garcia P, Matthews L, Coffey AJ, Parker A, Hubbard TJ, Rogers J, Bradley A, Adams DJ, Justice MJ.

PLoS Genet 2009 : 5 ; 12 ; e1000759.

ENCODE whole-genome data in the UCSC Genome Browser.

Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, Karolchik D, Haussler D, Kent WJ.

Nucleic Acids Res 2010 : 38 ; database issue ; D620-5.

The UCSC Genome Browser database: update 2010.

Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ.

Nucleic Acids Res 2010 : 38 ; database issue ; D613-9.

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.

Nucleic Acids Res 2010 : 38 ; database issue ; D557-62.

Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity.

Liu YJ, Zheng D, Balasubramanian S, Carriero N, Khurana E, Robilotto R, Gerstein MB.

BMC Genomics 2009 : 10 ; 480.

Small RNAs originated from pseudogenes: cis- or trans-acting?

Guo X, Zhang Z, Gerstein MB, Zheng D.

PLoS Comput Biol 2009 : 5 ; 7 ; e1000449.

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, Lipman D.

Genome Res 2009 : 19 ; 7 ; 1316-1323.

Pairagon: a highly accurate, HMM-based cDNA-to-genome aligner.

Lu DV, Brown RH, Arumugam M, Brent MR.

Bioinformatics 2009 : 25 ; 13 ; 1587-1593.

Identifying protein-coding genes in genomic sequences.

Harrow J, Nagy A, Reymond A, Alioto T, Patthy L, Antonarakis SE, Guigó R.

Genome Biol 2009 : 10 ; 1 ; 201.

Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.

Balasubramanian S, Zheng D, Liu YJ, Fang G, Frankish A, Carriero N, Robilotto R, Cayting P, Gerstein M.

Genome Biol 2009 : 10 ; 1 ; R2.

Proteomics studies confirm the presence of alternative protein isoforms on a large scale.

Tress ML, Bodenmiller B, Aebersold R, Valencia A.

Genome Biol 2008 : 9 ; 11 ; R162.

The UCSC Genome Browser Database: update 2009.

Kuhn RM, Karolchik D, Zweig AS, Wang T, Smith KE, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pheasant M, Meyer L, Hsu F, Hinrichs AS, Harte RA, Giardine B, Fujita P, Diekhans M, Dreszer T, Clawson H, Barber GP, Haussler D, Kent WJ.

Nucleic Acids Res 2009 : 37 ; database issue ; D755-61.

Pseudofam: the pseudogene families database.

Lam HY, Khurana E, Fang G, Cayting P, Carriero N, Cheung KH, Gerstein MB.

Nucleic Acids Res 2009 : 37 ; database issue ; D738-43.

Retrocopy contributions to the evolution of the human genome.

Baertsch R, Diekhans M, Kent WJ, Haussler D, Brosius J.

BMC Genomics 2008 : 9 ; 466.

Dynamic instability of the major urinary protein gene family revealed by genomic and phenotypic comparisons between C57 and 129 strain mice.

Mudge JM, Armstrong SD, McLaren K, Beynon RJ, Hurst JL, Nicholson C, Robertson DH, Wilming LG, Harrow JL.

Genome Biol 2008 : 9 ; 5 ; R91.

An endogenous small interfering RNA pathway in Drosophila.

Czech B, Malone CD, Zhou R, Stark A, Schlingeheyde C, Dus M, Perrimon N, Kellis M, Wohlschlegel JA, Sachidanandam R, Hannon GJ, Brennecke J.

Nature 2008 : 453 ; 7196 ; 798-802.

Using native and syntenically mapped cDNA alignments to improve de novo gene finding.

Stanke M, Diekhans M, Baertsch R, Haussler D.

Bioinformatics 2008 : 24 ; 5 ; 637-644.

Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, Almeida J, Forbes S, Gilbert JG, Halls K, Harrow JL, Hart E, Howe K, Jackson DK, Palmer S, Roberts AN, Sims S, Stewart CA, Traherne JA, Trevanion S, Wilming L, Rogers J, de Jong PJ, Elliott JF, Sawcer S, Todd JA, Trowsdale J, Beck S.

Immunogenetics 2008 : 60 ; 1 ; 1-18.

The UCSC Genome Browser Database: 2008 update.

Karolchik D, Kuhn RM, Baertsch R, Barber GP, Clawson H, Diekhans M, Giardine B, Harte RA, Hinrichs AS, Hsu F, Kober KM, Miller W, Pedersen JS, Pohl A, Raney BJ, Rhead B, Rosenbloom KR, Smith KE, Stanke M, Thakkapallayil A, Trumbower H, Wang T, Zweig AS, Haussler D, Kent WJ.

Nucleic Acids Res 2008 : 36 ; database issue ; D773-9.

Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories.

Zhang ZD, Cayting P, Weinstock G, Gerstein M.

Mol Biol Evol 2008 : 25 ; 1 ; 131-143.

Determination and validation of principal gene products.

Tress ML, Wesselink JJ, Frankish A, López G, Goldman N, Löytynoja A, Massingham T, Pardi F, Whelan S, Harrow J, Valencia A.

Bioinformatics 2008 : 24 ; 1 ; 11-17.

The vertebrate genome annotation (Vega) database.

Wilming LG, Gilbert JG, Howe K, Trevanion S, Hubbard T, Harrow JL.

Nucleic Acids Res 2008 : 36 ; database issue ; D753-60.

Targeted discovery of novel human exons by comparative genomics.

Siepel A, Diekhans M, Brejová B, Langton L, Stevens M, Comstock CL, Davis C, Ewing B, Oommen S, Lau C, Yu HC, Li J, Roe BA, Green P, Gerhard DS, Temple G, Haussler D, Brent MR.

Genome Res 2007 : 17 ; 12 ; 1763-1773.

28-way vertebrate alignment and conservation track in the UCSC Genome Browser.

Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ.

Genome Res 2007 : 17 ; 12 ; 1797-1808.

Efficient targeted transcript discovery via array-based normalization of RACE libraries.

Djebali S, Kapranov P, Foissac S, Lagarde J, Reymond A, Ucla C, Wyss C, Drenkow J, Dumais E, Murray RR, Lin C, Szeto D, Denoeud F, Calvo M, Frankish A, Harrow J, Makrythanasis P, Vidal M, Salehi-Ashtiani K, Antonarakis SE, Gingeras TR, Guigó R.

Nat Methods 2008 : 5 ; 7 ; 629-635.

Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions.

Denoeud F, Kapranov P, Ucla C, Frankish A, Castelo R, Drenkow J, Lagarde J, Alioto T, Manzano C, Chrast J, Dike S, Wyss C, Henrichsen CN, Holroyd N, Dickson MC, Taylor R, Hance Z, Foissac S, Myers RM, Rogers J, Hubbard T, Harrow J, Guigó R, Gingeras TR, Antonarakis SE, Reymond A.

Genome Res 2007 : 17 ; 6 ; 746-759.

The ENCODE Project at UC Santa Cruz.

Thomas DJ, Rosenbloom KR, Clawson H, Hinrichs AS, Trumbower H, Raney BJ, Karolchik D, Barber GP, Harte RA, Hillman-Jackson J, Kuhn RM, Rhead BL, Smith KE, Thakkapallayil A, Zweig AS, ENCODE Project Consortium, Haussler D, Kent WJ.

Nucleic Acids Res 2007 : 35 ; database issue ; D663-7.

The UCSC genome browser database: update 2007.

Kuhn RM, Karolchik D, Zweig AS, Trumbower H, Thomas DJ, Thakkapallayil A, Sugnet CW, Stanke M, Smith KE, Siepel A, Rosenbloom KR, Rhead B, Raney BJ, Pohl A, Pedersen JS, Hsu F, Hinrichs AS, Harte RA, Diekhans M, Clawson H, Bejerano G, Barber GP, Baertsch R, Haussler D, Kent WJ.

Nucleic Acids Res 2007 : 35 ; database issue ; D668-73.

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

ENCODE Project Consortium, Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, Kuehn MS, Taylor CM, Neph S, Koch CM, Asthana S, Malhotra A, Adzhubei I, Greenbaum JA, Andrews RM, Flicek P, Boyle PJ, Cao H, Carter NP, Clelland GK, Davis S, Day N, Dhami P, Dillon SC, Dorschner MO, Fiegler H, Giresi PG, Goldy J, Hawrylycz M, Haydock A, Humbert R, James KD, Johnson BE, Johnson EM, Frum TT, Rosenzweig ER, Karnani N, Lee K, Lefebvre GC, Navas PA, Neri F, Parker SC, Sabo PJ, Sandstrom R, Shafer A, Vetrie D, Weaver M, Wilcox S, Yu M, Collins FS, Dekker J, Lieb JD, Tullius TD, Crawford GE, Sunyaev S, Noble WS, Dunham I, Denoeud F, Reymond A, Kapranov P, Rozowsky J, Zheng D, Castelo R, Frankish A, Harrow J, Ghosh S, Sandelin A, Hofacker IL, Baertsch R, Keefe D, Dike S, Cheng J, Hirsch HA, Sekinger EA, Lagarde J, Abril JF, Shahab A, Flamm C, Fried C, Hackermüller J, Hertel J, Lindemeyer M, Missal K, Tanzer A, Washietl S, Korbel J, Emanuelsson O, Pedersen JS, Holroyd N, Taylor R, Swarbreck D, Matthews N, Dickson MC, Thomas DJ, Weirauch MT, Gilbert J, Drenkow J, Bell I, Zhao X, Srinivasan KG, Sung WK, Ooi HS, Chiu KP, Foissac S, Alioto T, Brent M, Pachter L, Tress ML, Valencia A, Choo SW, Choo CY, Ucla C, Manzano C, Wyss C, Cheung E, Clark TG, Brown JB, Ganesh M, Patel S, Tammana H, Chrast J, Henrichsen CN, Kai C, Kawai J, Nagalakshmi U, Wu J, Lian Z, Lian J, Newburger P, Zhang X, Bickel P, Mattick JS, Carninci P, Hayashizaki Y, Weissman S, Hubbard T, Myers RM, Rogers J, Stadler PF, Lowe TM, Wei CL, Ruan Y, Struhl K, Gerstein M, Antonarakis SE, Fu Y, Green ED, Karaöz U, Siepel A, Taylor J, Liefer LA, Wetterstrand KA, Good PJ, Feingold EA, Guyer MS, Cooper GM, Asimenos G, Dewey CN, Hou M, Nikolaev S, Montoya-Burgos JI, Löytynoja A, Whelan S, Pardi F, Massingham T, Huang H, Zhang NR, Holmes I, Mullikin JC, Ureta-Vidal A, Paten B, Seringhaus M, Church D, Rosenbloom K, Kent WJ, Stone EA, NISC Comparative Sequencing Program, Baylor College of Medicine Human Genome Sequencing Center, Washington University Genome Sequencing Center, Broad Institute, Children's Hospital Oakland Research Institute, Batzoglou S, Goldman N, Hardison RC, Haussler D, Miller W, Sidow A, Trinklein ND, Zhang ZD, Barrera L, Stuart R, King DC, Ameur A, Enroth S, Bieda MC, Kim J, Bhinge AA, Jiang N, Liu J, Yao F, Vega VB, Lee CW, Ng P, Shahab A, Yang A, Moqtaderi Z, Zhu Z, Xu X, Squazzo S, Oberley MJ, Inman D, Singer MA, Richmond TA, Munn KJ, Rada-Iglesias A, Wallerman O, Komorowski J, Fowler JC, Couttet P, Bruce AW, Dovey OM, Ellis PD, Langford CF, Nix DA, Euskirchen G, Hartman S, Urban AE, Kraus P, Van Calcar S, Heintzman N, Kim TH, Wang K, Qu C, Hon G, Luna R, Glass CK, Rosenfeld MG, Aldred SF, Cooper SJ, Halees A, Lin JM, Shulha HP, Zhang X, Xu M, Haidar JN, Yu Y, Ruan Y, Iyer VR, Green RD, Wadelius C, Farnham PJ, Ren B, Harte RA, Hinrichs AS, Trumbower H, Clawson H, Hillman-Jackson J, Zweig AS, Smith K, Thakkapallayil A, Barber G, Kuhn RM, Karolchik D, Armengol L, Bird CP, de Bakker PI, Kern AD, Lopez-Bigas N, Martin JD, Stranger BE, Woodroffe A, Davydov E, Dimas A, Eyras E, Hallgrímsdóttir IB, Huppert J, Zody MC, Abecasis GR, Estivill X, Bouffard GG, Guan X, Hansen NF, Idol JR, Maduro VV, Maskeri B, McDowell JC, Park M, Thomas PJ, Young AC, Blakesley RW, Muzny DM, Sodergren E, Wheeler DA, Worley KC, Jiang H, Weinstock GM, Gibbs RA, Graves T, Fulton R, Mardis ER, Wilson RK, Clamp M, Cuff J, Gnerre S, Jaffe DB, Chang JL, Lindblad-Toh K, Lander ES, Koriabine M, Nefedov M, Osoegawa K, Yoshinaga Y, Zhu B, de Jong PJ.

Nature 2007 : 447 ; 7146 ; 799-816.

The implications of alternative splicing in the ENCODE protein complement.

Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A.

Proc Natl Acad Sci U S A 2007 : 104 ; 13 ; 5495-5500.

EGASP: the human ENCODE Genome Annotation Assessment Project.

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.

Genome Biol 2006 : 7 Suppl 1 ; S2.1-31.