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2019 2
2020 18
2021 18
2022 23
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2026 6

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Page 1
Lossless Pangenome Indexing Using Tag Arrays.
Eskandar P, Paten B, Sirén J. Eskandar P, et al. Res Sq [Preprint]. 2026 Jan 18:rs.3.rs-8233501. doi: 10.21203/rs.3.rs-8233501/v1. Res Sq. 2026. PMID: 41646363 Free PMC article. Preprint.
Origin and evolution of acrocentric chromosomes in human and great apes.
Solar SJ, Hebbar P, de Lima LG, Sweeten A, Rhie A, Potapova T, de Gennaro L, Guarracino A, Kim J, Pickett BD, Paten B, Wilson MA, Koren S, Garrison E, Eichler EE, Ventura M, Gerton JL, Phillippy AM. Solar SJ, et al. bioRxiv [Preprint]. 2025 Dec 23:2025.12.22.696095. doi: 10.64898/2025.12.22.696095. bioRxiv. 2025. PMID: 41497641 Free PMC article. Preprint.
Making genomic data FAIR through effective Data Portals.
Speir ML, Teh WK, Perry MD, Schwartz R, Nejad P, Harris T, Fischer C, Diekhans M, Lee BT, Paten B, Kent WJ, Haeussler M. Speir ML, et al. Sci Data. 2025 Nov 28;12(1):1872. doi: 10.1038/s41597-025-06142-x. Sci Data. 2025. PMID: 41315456 Free PMC article.
Ensembl 2026.
Yates AD, Austine-Orimoloye O, Azov AG, Barba M, Barnes I, Barrera-Enriquez VP, Becker A, Bennett R, Berry A, Bhai J, Bhurji SK, Branco Lins PR, Brooks L, Budhanuru Ramaraju S, Campbell LI, Carbajo Martinez M, Carpenter J, Charkhchi M, Cortes LA, Davidson C, Dickson S, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Fairbrother-Browne A, Falola O, Fatima R, Gonzalez Martinez J, Gurbich T, Hall H, Hardy M, Hollis Z, Hunt T, Kay M, Kaikala V, Lazar A, Lemos D, Lodha D, Mathlouthi N, Merino GA, Merritt R, Mirabueno LP, Mushtaq A, Nakib Hossain S, Pérez-Silva JG, Piližota I, Poppleton D, Prosovetskaia I, Raj S, Salam AIA, Saraf S, Sinha S, Sipos B, Sitnik V, Suner MM, Surapaneni L, Tierney JAS, Urbina-Gómez D, Veidenberg A, Walsh TA, Allen JM, Alvarez-Jarreta J, Cheema J, Batista da Rocha J, De Silva NH, Tricomi FF, Giorgetti S, Ilsley GR, Keatley J, Loveland JE, Mudge JM, Naamati G, Tate J, Willhoft NL, Winterbottom A, Flint BR, Frankish A, Haggerty L, Hunt SE, Clark EL, Dyer SC, Freeberg MA, Martin FJ, Finn RD. Yates AD, et al. Nucleic Acids Res. 2026 Jan 6;54(D1):D1053-D1060. doi: 10.1093/nar/gkaf1239. Nucleic Acids Res. 2026. PMID: 41296548 Free PMC article.
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.
Chang X, Novak AM, Eizenga JM, Sirén J, Monlong J, Negi S, Andreace F, Nag S, Kyriakidis K, Hickey G, Hwang S, Délot EC, Carroll A, Shafin K, Chang PC, Okamoto F, Paten B. Chang X, et al. Res Sq [Preprint]. 2025 Oct 23:rs.3.rs-7747403. doi: 10.21203/rs.3.rs-7747403/v1. Res Sq. 2025. PMID: 41282249 Free PMC article. Preprint.
Cross-tissue molecular responses in the liver and blood after toxicant exposures.
Zhang B, Miao B, Fu S, Shao W, Coarfa C, Kumar R, Kuntala P, Park B, Grimm S, Jangid R, Svoboda L, Xing X, Li D, Liu S, Hamanaka R, Lalancette C, Sartor M, Krapp C, Crawford G, Patisaul H, Wiltshire T, Biswal S, Mutlu G, Rajagopalan S, Tang WY, Bartolomei M, Walker C, Dolinoy D, Colacino J, Aylor D, Wang T. Zhang B, et al. Res Sq [Preprint]. 2025 Oct 10:rs.3.rs-7610132. doi: 10.21203/rs.3.rs-7610132/v1. Res Sq. 2025. PMID: 41282178 Free PMC article. Preprint.
Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe.
Chang X, Novak AM, Eizenga JM, Sirén J, Monlong J, Negi S, Andreace F, Nag S, Kyriakidis K, Hickey G, Hwang S, Délot EC, Carroll A, Shafin K, Chang PC, Okamoto F, Paten B; Human Pangenome Reference Consortium. Chang X, et al. bioRxiv [Preprint]. 2025 Oct 1:2025.09.29.678807. doi: 10.1101/2025.09.29.678807. bioRxiv. 2025. PMID: 41256518 Free PMC article. Preprint.
Toxicogenomic Insights into Environmental Toxicant Exposures: The TaRGET II Resource.
Zhang BA, Miao B, Fu S, Coarfa C, Kumar R, Kuntala PK, Park B, Grimm SL, Jangid R, Colacino JA, Svoboda LK, Shao W, Xing X, Li D, Liu S, Hamanaka RB, Lalancette C, Sartor MA, Krapp C, Crawford GE, Patisaul HB, Wiltshire T; TaRGET II Consortium; Aylor D, Biswal S, Mutlu GM, Rajagopalan S, Tang WY, Wang T, Dolinoy DC, Bartolomei MS, Walker CL. Zhang BA, et al. Res Sq [Preprint]. 2025 Aug 20:rs.3.rs-7285514. doi: 10.21203/rs.3.rs-7285514/v1. Res Sq. 2025. PMID: 40894060 Free PMC article. Preprint.
Defining and cataloging variants in pangenome graphs.
Nowbandegani PS, Zhang S, Hu H, Li H, O'Connor LJ. Nowbandegani PS, et al. bioRxiv [Preprint]. 2025 Aug 4:2025.08.04.668502. doi: 10.1101/2025.08.04.668502. bioRxiv. 2025. PMID: 40799530 Free PMC article. Preprint.
Comprehensive Transcriptomic and Epigenomic Insights into Environmental Toxicant Exposures: The TaRGET II Resource.
Zhang BA, Miao B, Fu S, Coarfa C, Kumar R, Kuntala PK, Park B, Grimm SL, Jangid R, Colacino JA, Svoboda LK, Shao W, Xing X, Li D, Liu S, Hamanaka RB, Lalancette C, Sartor MA, Krapp C, Crawford GE, Patisaul HB, Wiltshire T; TaRGET II Consortium; Aylor D, Biswal S, Mutlu GM, Rajagopalan S, Tang WY, Wang T, Dolinoy DC, Bartolomei MS, Walker C. Zhang BA, et al. bioRxiv [Preprint]. 2025 Jul 31:2025.07.28.667191. doi: 10.1101/2025.07.28.667191. bioRxiv. 2025. PMID: 40766696 Free PMC article. Preprint.
Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.
Porubsky D, Yoo D, Dishuck PC, Koundinya N, Souche E, Harvey WT, Munson KM, Hoekzema K, Chan DD, Leung TY, Santos MS, Meynants S, Swillen A, Breckpot J, Tsapalou V, Hasenfeld P, Korbel JO, Lansdorp PM, Vermeesch JR, Eichler EE. Porubsky D, et al. bioRxiv [Preprint]. 2025 Jul 7:2025.07.04.662981. doi: 10.1101/2025.07.04.662981. bioRxiv. 2025. PMID: 40631282 Free PMC article. Preprint.
Lossless Pangenome Indexing Using Tag Arrays.
Eskandar P, Paten B, Sirén J. Eskandar P, et al. bioRxiv [Preprint]. 2025 May 15:2025.05.12.653561. doi: 10.1101/2025.05.12.653561. bioRxiv. 2025. PMID: 40463112 Free PMC article. Preprint.
Highly accurate assembly polishing with DeepPolisher.
Mastoras M, Asri M, Brambrink L, Hebbar P, Kolesnikov A, Cook DE, Nattestad M, Lucas J, Won TS, Chang PC, Carroll A, Paten B, Shafin K; and the Human Pangenome Reference Consortium. Mastoras M, et al. Genome Res. 2025 Jul 1;35(7):1595-1608. doi: 10.1101/gr.280149.124. Genome Res. 2025. PMID: 40389286 Free PMC article.
WashU Epigenome Browser update 2025.
Seng C, Liu S, Zhang W, Zhuo X, Li D, Wang T. Seng C, et al. Nucleic Acids Res. 2025 Jul 7;53(W1):W554-W561. doi: 10.1093/nar/gkaf387. Nucleic Acids Res. 2025. PMID: 40322916 Free PMC article.
Severus detects somatic structural variation and complex rearrangements in cancer genomes using long-read sequencing.
Keskus AG, Bryant A, Ahmad T, Yoo B, Aganezov S, Goretsky A, Donmez A, Lansdon LA, Rodriguez I, Park J, Liu Y, Cui X, Gardner J, McNulty B, Sacco S, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Cook DE, Chang PC, Kolesnikov A, Carroll A, Molloy EK, Bi C, Walter A, Gibson M, Pushel I, Guest E, Pastinen T, Shafin K, Miga KH, Malikic S, Day CP, Robine N, Sahinalp C, Dean M, Farooqi MS, Paten B, Kolmogorov M. Keskus AG, et al. Nat Biotechnol. 2026 Feb;44(2):247-257. doi: 10.1038/s41587-025-02618-8. Epub 2025 Apr 4. Nat Biotechnol. 2026. PMID: 40185952 Free PMC article.
Advancing long-read nanopore genome assembly and accurate variant calling for rare disease detection.
Negi S, Stenton SL, Berger SI, Canigiula P, McNulty B, Violich I, Gardner J, Hillaker T, O'Rourke SM, O'Leary MC, Carbonell E, Austin-Tse C, Lemire G, Serrano J, Mangilog B, VanNoy G, Kolmogorov M, Vilain E, O'Donnell-Luria A, Délot E, Miga KH, Monlong J, Paten B. Negi S, et al. Am J Hum Genet. 2025 Feb 6;112(2):428-449. doi: 10.1016/j.ajhg.2025.01.002. Epub 2025 Jan 24. Am J Hum Genet. 2025. PMID: 39862869 Free PMC article.
Ensembl 2025.
Dyer SC, Austine-Orimoloye O, Azov AG, Barba M, Barnes I, Barrera-Enriquez VP, Becker A, Bennett R, Beracochea M, Berry A, Bhai J, Bhurji SK, Boddu S, Branco Lins PR, Brooks L, Ramaraju SB, Campbell LI, Martinez MC, Charkhchi M, Cortes LA, Davidson C, Denni S, Dodiya K, Donaldson S, El Houdaigui B, El Naboulsi T, Falola O, Fatima R, Genez T, Martinez JG, Gurbich T, Hardy M, Hollis Z, Hunt T, Kay M, Kaykala V, Lemos D, Lodha D, Mathlouthi N, Merino GA, Merritt R, Mirabueno LP, Mushtaq A, Hossain SN, Pérez-Silva JG, Perry M, Piližota I, Poppleton D, Prosovetskaia I, Raj S, Salam AIA, Saraf S, Saraiva-Agostinho N, Sinha S, Sipos B, Sitnik V, Steed E, Suner MM, Surapaneni L, Sutinen K, Tricomi FF, Tsang I, Urbina-Gómez D, Veidenberg A, Walsh TA, Willhoft NL, Allen J, Alvarez-Jarreta J, Chakiachvili M, Cheema J, da Rocha JB, De Silva NH, Giorgetti S, Haggerty L, Ilsley GR, Keatley J, Loveland JE, Moore B, Mudge JM, Naamati G, Tate J, Trevanion SJ, Winterbottom A, Flint B, Frankish A, Hunt SE, Finn RD, Freeberg MA, Harrison PW, Martin FJ, Yates AD. Dyer SC, et al. Nucleic Acids Res. 2025 Jan 6;53(D1):D948-D957. doi: 10.1093/nar/gkae1071. Nucleic Acids Res. 2025. PMID: 39656687 Free PMC article.
The UCSC Genome Browser database: 2025 update.
Perez G, Barber GP, Benet-Pages A, Casper J, Clawson H, Diekhans M, Fischer C, Gonzalez JN, Hinrichs AS, Lee CM, Nassar LR, Raney BJ, Speir ML, van Baren MJ, Vaske CJ, Haussler D, Kent WJ, Haeussler M. Perez G, et al. Nucleic Acids Res. 2025 Jan 6;53(D1):D1243-D1249. doi: 10.1093/nar/gkae974. Nucleic Acids Res. 2025. PMID: 39460617 Free PMC article.
DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies.
Park J, Cook DE, Chang PC, Kolesnikov A, Brambrink L, Mier JC, Gardner J, McNulty B, Sacco S, Keskus A, Bryant A, Ahmad T, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Yoo B, Pushel I, Lansdon LA, Bi C, Walter A, Gibson M, Pastinen T, Farooqi MS, Robine N, Miga KH, Carroll A, Kolmogorov M, Paten B, Shafin K. Park J, et al. bioRxiv [Preprint]. 2024 Aug 19:2024.08.16.608331. doi: 10.1101/2024.08.16.608331. bioRxiv. 2024. Update in: Nat Biotechnol. 2025 Oct 16. doi: 10.1038/s41587-025-02839-x. PMID: 39229187 Free PMC article. Updated. Preprint.
Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional regulation.
Foltz JA, Tran J, Wong P, Fan C, Schmidt E, Fisk B, Becker-Hapak M, Russler-Germain DA, Johnson J, Marin ND, Cubitt CC, Pence P, Rueve J, Pureti S, Hwang K, Gao F, Zhou AY, Foster M, Schappe T, Marsala L, Berrien-Elliott MM, Cashen AF, Bednarski JJ, Fertig E, Griffith OL, Griffith M, Wang T, Petti AA, Fehniger TA. Foltz JA, et al. Sci Immunol. 2024 Jun 28;9(96):eadk4893. doi: 10.1126/sciimmunol.adk4893. Epub 2024 Jun 28. Sci Immunol. 2024. PMID: 38941480 Free PMC article.
Cis-regulatory evolution of the recently expanded Ly49 gene family.
Fan C, Xing X, Murphy SJH, Poursine-Laurent J, Schmidt H, Parikh BA, Yoon J, Choudhary MNK, Saligrama N, Piersma SJ, Yokoyama WM, Wang T. Fan C, et al. Nat Commun. 2024 Jun 6;15(1):4839. doi: 10.1038/s41467-024-48990-y. Nat Commun. 2024. PMID: 38844462 Free PMC article.
Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads.
Keskus A, Bryant A, Ahmad T, Yoo B, Aganezov S, Goretsky A, Donmez A, Lansdon LA, Rodriguez I, Park J, Liu Y, Cui X, Gardner J, McNulty B, Sacco S, Shetty J, Zhao Y, Tran B, Narzisi G, Helland A, Cook DE, Chang PC, Kolesnikov A, Carroll A, Molloy EK, Pushel I, Guest E, Pastinen T, Shafin K, Miga KH, Malikic S, Day CP, Robine N, Sahinalp C, Dean M, Farooqi MS, Paten B, Kolmogorov M. Keskus A, et al. medRxiv [Preprint]. 2024 Mar 26:2024.03.22.24304756. doi: 10.1101/2024.03.22.24304756. medRxiv. 2024. PMID: 38585974 Free PMC article. Preprint.
Structurally divergent and recurrently mutated regions of primate genomes.
Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Yoo D, Gordon DS, Fair T, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Mao Y, Shi Y, Sun Q, Lu Q, Paten B, Bakken TE, Pollen AA, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Mao Y, et al. Cell. 2024 Mar 14;187(6):1547-1562.e13. doi: 10.1016/j.cell.2024.01.052. Epub 2024 Feb 29. Cell. 2024. PMID: 38428424 Free PMC article.
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. Harrison PW, et al. Nucleic Acids Res. 2024 Jan 5;52(D1):D891-D899. doi: 10.1093/nar/gkad1049. Nucleic Acids Res. 2024. PMID: 37953337 Free PMC article.
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. Raney BJ, et al. Nucleic Acids Res. 2024 Jan 5;52(D1):D1082-D1088. doi: 10.1093/nar/gkad987. Nucleic Acids Res. 2024. PMID: 37953330 Free PMC article.
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. Rhie A, et al. Nature. 2023 Sep;621(7978):344-354. doi: 10.1038/s41586-023-06457-y. Epub 2023 Aug 23. Nature. 2023. PMID: 37612512 Free PMC article.
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, … See abstract for full author list ➔ Liao WW, et al. Nature. 2023 May;617(7960):312-324. doi: 10.1038/s41586-023-05896-x. Epub 2023 May 10. Nature. 2023. PMID: 37165242 Free PMC article.
Structurally divergent and recurrently mutated regions of primate genomes.
Mao Y, Harvey WT, Porubsky D, Munson KM, Hoekzema K, Lewis AP, Audano PA, Rozanski A, Yang X, Zhang S, Gordon DS, Wei X, Logsdon GA, Haukness M, Dishuck PC, Jeong H, Del Rosario R, Bauer VL, Fattor WT, Wilkerson GK, Lu Q, Paten B, Feng G, Sawyer SL, Warren WC, Carbone L, Eichler EE. Mao Y, et al. bioRxiv [Preprint]. 2023 Mar 7:2023.03.07.531415. doi: 10.1101/2023.03.07.531415. bioRxiv. 2023. Update in: Cell. 2024 Mar 14;187(6):1547-1562.e13. doi: 10.1016/j.cell.2024.01.052. PMID: 36945442 Free PMC article. Updated. Preprint.
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. Nassar LR, et al. Nucleic Acids Res. 2023 Jan 6;51(D1):D1188-D1195. doi: 10.1093/nar/gkac1072. Nucleic Acids Res. 2023. PMID: 36420891 Free PMC article.
LungMAP Portal Ecosystem: Systems-level Exploration of the Lung.
Gaddis N, Fortriede J, Guo M, Bardes EE, Kouril M, Tabar S, Burns K, Ardini-Poleske ME, Loos S, Schnell D, Jin K, Iyer B, Du Y, Huo BX, Bhattacharjee A, Korte J, Munshi R, Smith V, Herbst A, Kitzmiller JA, Clair GC, Carson JP, Adkins J, Morrisey EE, Pryhuber GS, Misra R, Whitsett JA, Sun X, Heathorn T, Paten B, Prasath VBS, Xu Y, Tickle T, Aronow BJ, Salomonis N. Gaddis N, et al. Am J Respir Cell Mol Biol. 2024 Feb;70(2):129-139. doi: 10.1165/rcmb.2022-0165OC. Am J Respir Cell Mol Biol. 2024. PMID: 36413377 Free PMC article.
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. Martin FJ, et al. Nucleic Acids Res. 2023 Jan 6;51(D1):D933-D941. doi: 10.1093/nar/gkac958. Nucleic Acids Res. 2023. PMID: 36318249 Free PMC article.
GBZ file format for pangenome graphs.
Sirén J, Paten B. Sirén J, et al. Bioinformatics. 2022 Nov 15;38(22):5012-5018. doi: 10.1093/bioinformatics/btac656. Bioinformatics. 2022. PMID: 36179091 Free PMC article.
Recurrent inversion polymorphisms in humans associate with genetic instability and genomic disorders.
Porubsky D, Höps W, Ashraf H, Hsieh P, Rodriguez-Martin B, Yilmaz F, Ebler J, Hallast P, Maria Maggiolini FA, Harvey WT, Henning B, Audano PA, Gordon DS, Ebert P, Hasenfeld P, Benito E, Zhu Q; Human Genome Structural Variation Consortium (HGSVC); Lee C, Antonacci F, Steinrücken M, Beck CR, Sanders AD, Marschall T, Eichler EE, Korbel JO. Porubsky D, et al. Cell. 2022 May 26;185(11):1986-2005.e26. doi: 10.1016/j.cell.2022.04.017. Epub 2022 May 6. Cell. 2022. PMID: 35525246 Free PMC article.
The Human Pangenome Project: a global resource to map genomic diversity.
Wang T, Antonacci-Fulton L, Howe K, Lawson HA, Lucas JK, Phillippy AM, Popejoy AB, Asri M, Carson C, Chaisson MJP, Chang X, Cook-Deegan R, Felsenfeld AL, Fulton RS, Garrison EP, Garrison NA, Graves-Lindsay TA, Ji H, Kenny EE, Koenig BA, Li D, Marschall T, McMichael JF, Novak AM, Purushotham D, Schneider VA, Schultz BI, Smith MW, Sofia HJ, Weissman T, Flicek P, Li H, Miga KH, Paten B, Jarvis ED, Hall IM, Eichler EE, Haussler D; Human Pangenome Reference Consortium. Wang T, et al. Nature. 2022 Apr;604(7906):437-446. doi: 10.1038/s41586-022-04601-8. Epub 2022 Apr 20. Nature. 2022. PMID: 35444317 Free PMC article. Review.
WashU Epigenome Browser update 2022.
Li D, Purushotham D, Harrison JK, Hsu S, Zhuo X, Fan C, Liu S, Xu V, Chen S, Xu J, Ouyang S, Wu AS, Wang T. Li D, et al. Nucleic Acids Res. 2022 Jul 5;50(W1):W774-W781. doi: 10.1093/nar/gkac238. Nucleic Acids Res. 2022. PMID: 35412637 Free PMC article.
Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies.
Mc Cartney AM, Shafin K, Alonge M, Bzikadze AV, Formenti G, Fungtammasan A, Howe K, Jain C, Koren S, Logsdon GA, Miga KH, Mikheenko A, Paten B, Shumate A, Soto DC, Sović I, Wood JMD, Zook JM, Phillippy AM, Rhie A. Mc Cartney AM, et al. Nat Methods. 2022 Jun;19(6):687-695. doi: 10.1038/s41592-022-01440-3. Epub 2022 Mar 31. Nat Methods. 2022. PMID: 35361931 Free PMC article.
A complete reference genome improves analysis of human genetic variation.
Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, Rhie A, Meredith M, Martin S, Lee J, Koren S, Rosenfeld JA, Paten B, Layer R, Chin CS, Sedlazeck FJ, Hansen NF, Miller DE, Phillippy AM, Miga KH, McCoy RC, Dennis MY, Zook JM, Schatz MC. Aganezov S, et al. Science. 2022 Apr;376(6588):eabl3533. doi: 10.1126/science.abl3533. Epub 2022 Apr 1. Science. 2022. PMID: 35357935 Free PMC article.
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. Nurk S, et al. Science. 2022 Apr;376(6588):44-53. doi: 10.1126/science.abj6987. Epub 2022 Mar 31. Science. 2022. PMID: 35357919 Free PMC article.
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. Altemose N, et al. Science. 2022 Apr;376(6588):eabl4178. doi: 10.1126/science.abl4178. Epub 2022 Apr 1. Science. 2022. PMID: 35357911 Free PMC article.
CoLoRd: compressing long reads.
Kokot M, Gudyś A, Li H, Deorowicz S. Kokot M, et al. Nat Methods. 2022 Apr;19(4):441-444. doi: 10.1038/s41592-022-01432-3. Epub 2022 Mar 28. Nat Methods. 2022. PMID: 35347321 Free PMC article.
Variant interpretation: UCSC Genome Browser Recommended Track Sets.
Benet-Pagès A, Rosenbloom KR, Nassar LR, Lee CM, Raney BJ, Clawson H, Schmelter D, Casper J, Gonzalez JN, Perez G, Lee BT, Zweig AS, Kent WJ, Haeussler M, Kuhn RM. Benet-Pagès A, et al. Hum Mutat. 2022 Aug;43(8):998-1011. doi: 10.1002/humu.24335. Epub 2022 Feb 7. Hum Mutat. 2022. PMID: 35088925 Free PMC article.
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. Sirén J, et al. Science. 2021 Dec 17;374(6574):abg8871. doi: 10.1126/science.abg8871. Epub 2021 Dec 17. Science. 2021. PMID: 34914532 Free PMC article.
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. Cunningham F, et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D988-D995. doi: 10.1093/nar/gkab1049. Nucleic Acids Res. 2022. PMID: 34791404 Free PMC article.
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. Lee BT, et al. Nucleic Acids Res. 2022 Jan 7;50(D1):D1115-D1122. doi: 10.1093/nar/gkab959. Nucleic Acids Res. 2022. PMID: 34718705 Free PMC article.
UCSC Cell Browser: visualize your single-cell data.
Speir ML, Bhaduri A, Markov NS, Moreno P, Nowakowski TJ, Papatheodorou I, Pollen AA, Raney BJ, Seninge L, Kent WJ, Haeussler M. Speir ML, et al. Bioinformatics. 2021 Dec 7;37(23):4578-4580. doi: 10.1093/bioinformatics/btab503. Bioinformatics. 2021. PMID: 34244710 Free PMC article.
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. Mao Y, et al. Nature. 2021 Jun;594(7861):77-81. doi: 10.1038/s41586-021-03519-x. Epub 2021 May 5. Nature. 2021. PMID: 33953399 Free PMC article.
The Need for a Human Pangenome Reference Sequence.
Miga KH, Wang T. Miga KH, et al. Annu Rev Genomics Hum Genet. 2021 Aug 31;22:81-102. doi: 10.1146/annurev-genom-120120-081921. Epub 2021 Apr 30. Annu Rev Genomics Hum Genet. 2021. PMID: 33929893 Free PMC article. Review.
Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease.
Zhang B, Kim MY, Elliot G, Zhou Y, Zhao G, Li D, Lowdon RF, Gormley M, Kapidzic M, Robinson JF, McMaster MT, Hong C, Mazor T, Hamilton E, Sears RL, Pehrsson EC, Marra MA, Jones SJM, Bilenky M, Hirst M, Wang T, Costello JF, Fisher SJ. Zhang B, et al. Dev Cell. 2021 May 3;56(9):1238-1252.e5. doi: 10.1016/j.devcel.2021.04.001. Epub 2021 Apr 22. Dev Cell. 2021. PMID: 33891899 Free PMC article.
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, 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. Warren WC, et al. Science. 2020 Dec 18;370(6523):eabc6617. doi: 10.1126/science.abc6617. Science. 2020. PMID: 33335035 Free PMC article.
Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads.
Porubsky D, Ebert P, Audano PA, Vollger MR, Harvey WT, Marijon P, Ebler J, Munson KM, Sorensen M, Sulovari A, Haukness M, Ghareghani M; Human Genome Structural Variation Consortium; Lansdorp PM, Paten B, Devine SE, Sanders AD, Lee C, Chaisson MJP, Korbel JO, Eichler EE, Marschall T. Porubsky D, et al. Nat Biotechnol. 2021 Mar;39(3):302-308. doi: 10.1038/s41587-020-0719-5. Epub 2020 Dec 7. Nat Biotechnol. 2021. PMID: 33288906 Free PMC article.
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. Navarro Gonzalez J, et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D1046-D1057. doi: 10.1093/nar/gkaa1070. Nucleic Acids Res. 2021. PMID: 33221922 Free PMC article.
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. Armstrong J, et al. Nature. 2020 Nov;587(7833):246-251. doi: 10.1038/s41586-020-2871-y. Epub 2020 Nov 11. Nature. 2020. PMID: 33177663 Free PMC article.
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. Howe KL, et al. Nucleic Acids Res. 2021 Jan 8;49(D1):D884-D891. doi: 10.1093/nar/gkaa942. Nucleic Acids Res. 2021. PMID: 33137190 Free PMC article.
Cell-type-specific 3D epigenomes in the developing human cortex.
Song M, Pebworth MP, Yang X, Abnousi A, Fan C, Wen J, Rosen JD, Choudhary MNK, Cui X, Jones IR, Bergenholtz S, Eze UC, Juric I, Li B, Maliskova L, Lee J, Liu W, Pollen AA, Li Y, Wang T, Hu M, Kriegstein AR, Shen Y. Song M, et al. Nature. 2020 Nov;587(7835):644-649. doi: 10.1038/s41586-020-2825-4. Epub 2020 Oct 14. Nature. 2020. PMID: 33057195 Free PMC article.
Cellular diversity of the regenerating caudal fin.
Hou Y, Lee HJ, Chen Y, Ge J, Osman FOI, McAdow AR, Mokalled MH, Johnson SL, Zhao G, Wang T. Hou Y, et al. Sci Adv. 2020 Aug 12;6(33):eaba2084. doi: 10.1126/sciadv.aba2084. eCollection 2020 Aug. Sci Adv. 2020. PMID: 32851162 Free PMC article.
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. Shafin K, et al. Nat Biotechnol. 2020 Sep;38(9):1044-1053. doi: 10.1038/s41587-020-0503-6. Epub 2020 May 4. Nat Biotechnol. 2020. PMID: 32686750 Free PMC article.
An Evolutionary Insertion in the Mxra8 Receptor-Binding Site Confers Resistance to Alphavirus Infection and Pathogenesis.
Kim AS, Zimmerman O, Fox JM, Nelson CA, Basore K, Zhang R, Durnell L, Desai C, Bullock C, Deem SL, Oppenheimer J, Shapiro B, Wang T, Cherry S, Coyne CB, Handley SA, Landis MJ, Fremont DH, Diamond MS. Kim AS, et al. Cell Host Microbe. 2020 Mar 11;27(3):428-440.e9. doi: 10.1016/j.chom.2020.01.008. Epub 2020 Feb 18. Cell Host Microbe. 2020. PMID: 32075743 Free PMC article.
WashU Epigenome Browser update 2019.
Li D, Hsu S, Purushotham D, Sears RL, Wang T. Li D, et al. Nucleic Acids Res. 2019 Jul 2;47(W1):W158-W165. doi: 10.1093/nar/gkz348. Nucleic Acids Res. 2019. PMID: 31165883 Free PMC article.