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For: Numanagić I, Gökkaya AS, Zhang L, Berger B, Alkan C, Hach F. Fast characterization of segmental duplications in genome assemblies. Bioinformatics 2018;34:i706-i714. [PMID: 30423092 PMCID: PMC6129265 DOI: 10.1093/bioinformatics/bty586] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
Number Cited by Other Article(s)
1
Zhang S, Xu N, Fu L, Yang X, Ma K, Li Y, Yang Z, Li Z, Feng Y, Jiang X, Han J, Hu R, Zhang L, Lian D, de Gennaro L, Paparella A, Ryabov F, Meng D, He Y, Wu D, Yang C, Mao Y, Bian X, Lu Y, Antonacci F, Ventura M, Shepelev VA, Miga KH, Alexandrov IA, Logsdon GA, Phillippy AM, Su B, Zhang G, Eichler EE, Lu Q, Shi Y, Sun Q, Mao Y. Integrated analysis of the complete sequence of a macaque genome. Nature 2025;640:714-721. [PMID: 40011769 PMCID: PMC12003069 DOI: 10.1038/s41586-025-08596-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 01/03/2025] [Indexed: 02/28/2025]
2
Real TD, Hebbar P, Yoo D, Antonacci F, Pačar I, Diekhans M, Mikol GJ, Popoola OG, Mallory BJ, Vollger MR, Dishuck PC, Guitart X, Rozanski AN, Munson KM, Hoekzema K, Ranchalis JE, Neph SJ, Sedeño-Cortes AE, Paten B, Salama SR, Stergachis AB, Eichler EE. Genetic diversity and regulatory features of human-specific NOTCH2NL duplications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.14.643395. [PMID: 40166283 PMCID: PMC11956922 DOI: 10.1101/2025.03.14.643395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
3
Zhang Z, Gupta I, Pevzner PA. GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions. Bioinformatics 2025;41:btaf058. [PMID: 39908455 PMCID: PMC11842051 DOI: 10.1093/bioinformatics/btaf058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Revised: 12/02/2024] [Accepted: 02/03/2025] [Indexed: 02/07/2025]  Open
4
Jeong H, Dishuck PC, Yoo D, Harvey WT, Munson KM, Lewis AP, Kordosky J, Garcia GH, Human Genome Structural Variation Consortium (HGSVC), Yilmaz F, Hallast P, Lee C, Pastinen T, Eichler EE. Structural polymorphism and diversity of human segmental duplications. Nat Genet 2025;57:390-401. [PMID: 39779957 PMCID: PMC11821543 DOI: 10.1038/s41588-024-02051-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Accepted: 12/04/2024] [Indexed: 01/11/2025]
5
Park JS, Choi Y, Kim JH, Lee C, Jeong MG, Jeong YI, Kang YJ, Chung YS, Choi HK. Development of a web-based high-throughput marker design program: CAPS (cleaved amplified polymorphic sequence) Maker. PLANT METHODS 2024;20:192. [PMID: 39719584 DOI: 10.1186/s13007-024-01319-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2024] [Accepted: 12/17/2024] [Indexed: 12/26/2024]
6
Moulistanos A, Papasakellariou K, Kavakiotis I, Gkagkavouzis K, Karaiskou N, Antonopoulou E, Triantafyllidis A, Papakostas S. Genomic Signatures of Domestication in European Seabass (Dicentrarchus labrax L.) Reveal a Potential Role for Epigenetic Regulation in Adaptation to Captivity. Ecol Evol 2024;14:e70512. [PMID: 39629177 PMCID: PMC11612516 DOI: 10.1002/ece3.70512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2024] [Revised: 10/17/2024] [Accepted: 10/18/2024] [Indexed: 12/07/2024]  Open
7
Fornezza S, Delvecchio VS, Harvey WT, Dishuck PC, Eichler EE, Giannuzzi G. AGAP duplicons associate with structural diversity at Chromosome 10q11.22. Genome Res 2024;34:1487-1499. [PMID: 39322278 PMCID: PMC11534156 DOI: 10.1101/gr.279454.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 09/10/2024] [Indexed: 09/27/2024]
8
González-Pech RA, Shepherd J, Fuller ZL, LaJeunesse TC, Parkinson JE. The genome of a giant clam zooxanthella (Cladocopium infistulum) offers few clues to adaptation as an extracellular symbiont with high thermotolerance. BMC Genomics 2024;25:914. [PMID: 39354409 PMCID: PMC11443893 DOI: 10.1186/s12864-024-10822-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 09/20/2024] [Indexed: 10/03/2024]  Open
9
de Lima LG, Guarracino A, Koren S, Potapova T, McKinney S, Rhie A, Solar SJ, Seidel C, Fagen B, Walenz BP, Bouffard GG, Brooks SY, Peterson M, Hall K, Crawford J, Young AC, Pickett BD, Garrison E, Phillippy AM, Gerton JL. The formation and propagation of human Robertsonian chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.24.614821. [PMID: 39386535 PMCID: PMC11463614 DOI: 10.1101/2024.09.24.614821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
10
Soto DC, Uribe-Salazar JM, Kaya G, Valdarrago R, Sekar A, Haghani NK, Hino K, La GN, Mariano NAF, Ingamells C, Baraban AE, Turner TN, Green ED, Simó S, Quon G, Andrés AM, Dennis MY. Gene expansions contributing to human brain evolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.26.615256. [PMID: 39386494 PMCID: PMC11463660 DOI: 10.1101/2024.09.26.615256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
11
Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D, Paisie CA, Harvey WT, Zhao X, Martino GV, Henglin M, Munson KM, Rabbani K, Chin CS, Gu B, Ashraf H, Austine-Orimoloye O, Balachandran P, Bonder MJ, Cheng H, Chong Z, Crabtree J, Gerstein M, Guethlein LA, Hasenfeld P, Hickey G, Hoekzema K, Hunt SE, Jensen M, Jiang Y, Koren S, Kwon Y, Li C, Li H, Li J, Norman PJ, Oshima KK, Paten B, Phillippy AM, Pollock NR, Rausch T, Rautiainen M, Scholz S, Song Y, Söylev A, Sulovari A, Surapaneni L, Tsapalou V, Zhou W, Zhou Y, Zhu Q, Zody MC, Mills RE, Devine SE, Shi X, Talkowski ME, Chaisson MJP, Dilthey AT, Konkel MK, Korbel JO, Lee C, Beck CR, Eichler EE, Marschall T. Complex genetic variation in nearly complete human genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.24.614721. [PMID: 39372794 PMCID: PMC11451754 DOI: 10.1101/2024.09.24.614721] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
12
Liang X, Duan Q, Li B, Wang Y, Bu Y, Zhang Y, Kuang Z, Mao L, An X, Wang H, Yang X, Wan N, Feng Z, Shen W, Miao W, Chen J, Liu S, Storz JF, Liu J, Nevo E, Li K. Genomic structural variation contributes to evolved changes in gene expression in high-altitude Tibetan sheep. Proc Natl Acad Sci U S A 2024;121:e2322291121. [PMID: 38913905 PMCID: PMC11228492 DOI: 10.1073/pnas.2322291121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/06/2024] [Indexed: 06/26/2024]  Open
13
Jeong H, Dishuck PC, Yoo D, Harvey WT, Munson KM, Lewis AP, Kordosky J, Garcia GH, Human Genome Structural Variation Consortium (HGSVC), Yilmaz F, Hallast P, Lee C, Pastinen T, Eichler EE. Structural polymorphism and diversity of human segmental duplications. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.04.597452. [PMID: 38895457 PMCID: PMC11185583 DOI: 10.1101/2024.06.04.597452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
14
Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bornberg-Bauer E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJC, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PGS, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Pond SLK, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McGarvey KM, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O'Neill RJ, Eichler EE, Phillippy AM. The complete sequence and comparative analysis of ape sex chromosomes. Nature 2024;630:401-411. [PMID: 38811727 PMCID: PMC11168930 DOI: 10.1038/s41586-024-07473-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 04/26/2024] [Indexed: 05/31/2024]
15
Laudanski K, Elmadhoun O, Mathew A, Kahn-Pascual Y, Kerfeld MJ, Chen J, Sisniega DC, Gomez F. Anesthetic Considerations for Patients with Hereditary Neuropathy with Liability to Pressure Palsies: A Narrative Review. Healthcare (Basel) 2024;12:858. [PMID: 38667620 PMCID: PMC11050561 DOI: 10.3390/healthcare12080858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 03/28/2024] [Accepted: 03/29/2024] [Indexed: 04/28/2024]  Open
16
Zhang S, Xu N, Fu L, Yang X, Li Y, Yang Z, Feng Y, Ma K, Jiang X, Han J, Hu R, Zhang L, de Gennaro L, Ryabov F, Meng D, He Y, Wu D, Yang C, Paparella A, Mao Y, Bian X, Lu Y, Antonacci F, Ventura M, Shepelev VA, Miga KH, Alexandrov IA, Logsdon GA, Phillippy AM, Su B, Zhang G, Eichler EE, Lu Q, Shi Y, Sun Q, Mao Y. Comparative genomics of macaques and integrated insights into genetic variation and population history. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.07.588379. [PMID: 38645259 PMCID: PMC11030432 DOI: 10.1101/2024.04.07.588379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
17
Hickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Human Pangenome Reference Consortium, Marschall T, Li H, Paten B, Human Pangenome Reference Consortium, Abel HJ, Antonacci-Fulton LL, Asri M, Baid G, Baker CA, Belyaeva A, Billis K, Bourque G, Buonaiuto S, Carroll A, Chaisson MJP, Chang PC, Chang XH, Cheng H, Chu J, Cody S, Colonna V, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Doerr D, Ebert P, Ebler J, Eichler EE, Eizenga JM, Fairley S, Fedrigo O, Felsenfeld AL, Feng X, Fischer C, Flicek P, Formenti G, Frankish A, Fulton RS, Gao Y, Garg S, Garrison E, Garrison NA, Giron CG, Green RE, Groza C, Guarracino A, Haggerty L, Hall IM, Harvey WT, Haukness M, Haussler D, Heumos S, Hickey G, Hoekzema K, Hourlier T, Howe K, Jain M, Jarvis ED, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Li H, Liao WW, Lu S, Lu TY, Lucas JK, Magalhães H, Marco-Sola S, Marijon P, Markello C, Marschall T, Martin FJ, McCartney A, McDaniel J, Miga KH, Mitchell MW, Monlong J, Mountcastle J, Munson KM, Mwaniki MN, Nattestad M, Novak AM, Nurk S, Olsen HE, Olson ND, Paten B, et alHickey G, Monlong J, Ebler J, Novak AM, Eizenga JM, Gao Y, Human Pangenome Reference Consortium, Marschall T, Li H, Paten B, Human Pangenome Reference Consortium, Abel HJ, Antonacci-Fulton LL, Asri M, Baid G, Baker CA, Belyaeva A, Billis K, Bourque G, Buonaiuto S, Carroll A, Chaisson MJP, Chang PC, Chang XH, Cheng H, Chu J, Cody S, Colonna V, Cook DE, Cook-Deegan RM, Cornejo OE, Diekhans M, Doerr D, Ebert P, Ebler J, Eichler EE, Eizenga JM, Fairley S, Fedrigo O, Felsenfeld AL, Feng X, Fischer C, Flicek P, Formenti G, Frankish A, Fulton RS, Gao Y, Garg S, Garrison E, Garrison NA, Giron CG, Green RE, Groza C, Guarracino A, Haggerty L, Hall IM, Harvey WT, Haukness M, Haussler D, Heumos S, Hickey G, Hoekzema K, Hourlier T, Howe K, Jain M, Jarvis ED, Ji HP, Kenny EE, Koenig BA, Kolesnikov A, Korbel JO, Kordosky J, Koren S, Lee H, Lewis AP, Li H, Liao WW, Lu S, Lu TY, Lucas JK, Magalhães H, Marco-Sola S, Marijon P, Markello C, Marschall T, Martin FJ, McCartney A, McDaniel J, Miga KH, Mitchell MW, Monlong J, Mountcastle J, Munson KM, Mwaniki MN, Nattestad M, Novak AM, Nurk S, Olsen HE, Olson ND, Paten B, Pesout T, Phillippy AM, Popejoy AB, Porubsky D, Prins P, Puiu D, Rautiainen M, Regier AA, Rhie A, Sacco S, Sanders AD, Schneider VA, Schultz BI, Shafin K, Sibbesen JA, Sirén J, Smith MW, Sofia HJ, Tayoun ANA, Thibaud-Nissen F, Tomlinson C, Tricomi FF, Villani F, Vollger MR, Wagner J, Walenz B, Wang T, Wood JMD, Zimin AV, Zook JM. Pangenome graph construction from genome alignments with Minigraph-Cactus. Nat Biotechnol 2024;42:663-673. [PMID: 37165083 PMCID: PMC10638906 DOI: 10.1038/s41587-023-01793-w] [Show More Authors] [Citation(s) in RCA: 91] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 04/18/2023] [Indexed: 05/12/2023]
18
Bukhman YV, Morin PA, Meyer S, Chu LF, Jacobsen JK, Antosiewicz-Bourget J, Mamott D, Gonzales M, Argus C, Bolin J, Berres ME, Fedrigo O, Steill J, Swanson SA, Jiang P, Rhie A, Formenti G, Phillippy AM, Harris RS, Wood JMD, Howe K, Kirilenko BM, Munegowda C, Hiller M, Jain A, Kihara D, Johnston JS, Ionkov A, Raja K, Toh H, Lang A, Wolf M, Jarvis ED, Thomson JA, Chaisson MJP, Stewart R. A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography. Mol Biol Evol 2024;41:msae036. [PMID: 38376487 PMCID: PMC10919930 DOI: 10.1093/molbev/msae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/21/2024]  Open
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Chaisson MJP, Sulovari A, Valdmanis PN, Miller DE, Eichler EE. Advances in the discovery and analyses of human tandem repeats. Emerg Top Life Sci 2023;7:361-381. [PMID: 37905568 PMCID: PMC10806765 DOI: 10.1042/etls20230074] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/18/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023]
20
Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJ, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PG, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O’Neill RJ, Eichler E, Phillippy AM. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569198. [PMID: 38077089 PMCID: PMC10705393 DOI: 10.1101/2023.11.30.569198] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]
21
Yang Y, Wu Z, Wu Z, Li T, Shen Z, Zhou X, Wu X, Li G, Zhang Y. A near-complete assembly of asparagus bean provides insights into anthocyanin accumulation in pods. PLANT BIOTECHNOLOGY JOURNAL 2023;21:2473-2489. [PMID: 37558431 PMCID: PMC10651155 DOI: 10.1111/pbi.14142] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 07/11/2023] [Accepted: 07/23/2023] [Indexed: 08/11/2023]
22
Bredemeyer KR, Hillier L, Harris AJ, Hughes GM, Foley NM, Lawless C, Carroll RA, Storer JM, Batzer MA, Rice ES, Davis BW, Raudsepp T, O'Brien SJ, Lyons LA, Warren WC, Murphy WJ. Single-haplotype comparative genomics provides insights into lineage-specific structural variation during cat evolution. Nat Genet 2023;55:1953-1963. [PMID: 37919451 PMCID: PMC10845050 DOI: 10.1038/s41588-023-01548-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/20/2023] [Indexed: 11/04/2023]
23
Sun M, Yao C, Shu Q, He Y, Chen G, Yang G, Xu S, Liu Y, Xue Z, Wu J. Telomere-to-telomere pear (Pyrus pyrifolia) reference genome reveals segmental and whole genome duplication driving genome evolution. HORTICULTURE RESEARCH 2023;10:uhad201. [PMID: 38023478 PMCID: PMC10681005 DOI: 10.1093/hr/uhad201] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/01/2023] [Indexed: 12/01/2023]
24
Yang C, Zhou Y, Song Y, Wu D, Zeng Y, Nie L, Liu P, Zhang S, Chen G, Xu J, Zhou H, Zhou L, Qian X, Liu C, Tan S, Zhou C, Dai W, Xu M, Qi Y, Wang X, Guo L, Fan G, Wang A, Deng Y, Zhang Y, Jin J, He Y, Guo C, Guo G, Zhou Q, Xu X, Yang H, Wang J, Xu S, Mao Y, Jin X, Ruan J, Zhang G. The complete and fully-phased diploid genome of a male Han Chinese. Cell Res 2023;33:745-761. [PMID: 37452091 PMCID: PMC10542383 DOI: 10.1038/s41422-023-00849-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/29/2023] [Indexed: 07/18/2023]  Open
25
Liu Q, Xie B, Gao Y, Xu S, Lu Y. A protocol for applying low-coverage whole-genome sequencing data in structural variation studies. STAR Protoc 2023;4:102433. [PMID: 37432854 PMCID: PMC10362160 DOI: 10.1016/j.xpro.2023.102433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/23/2023] [Accepted: 06/12/2023] [Indexed: 07/13/2023]  Open
26
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. The complete sequence of a human Y chromosome. Nature 2023;621:344-354. [PMID: 37612512 PMCID: PMC10752217 DOI: 10.1038/s41586-023-06457-y] [Citation(s) in RCA: 183] [Impact Index Per Article: 91.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
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Meadows JRS, Kidd JM, Wang GD, Parker HG, Schall PZ, Bianchi M, Christmas MJ, Bougiouri K, Buckley RM, Hitte C, Nguyen AK, Wang C, Jagannathan V, Niskanen JE, Frantz LAF, Arumilli M, Hundi S, Lindblad-Toh K, Ginja C, Agustina KK, André C, Boyko AR, Davis BW, Drögemüller M, Feng XY, Gkagkavouzis K, Iliopoulos G, Harris AC, Hytönen MK, Kalthoff DC, Liu YH, Lymberakis P, Poulakakis N, Pires AE, Racimo F, Ramos-Almodovar F, Savolainen P, Venetsani S, Tammen I, Triantafyllidis A, vonHoldt B, Wayne RK, Larson G, Nicholas FW, Lohi H, Leeb T, Zhang YP, Ostrander EA. Genome sequencing of 2000 canids by the Dog10K consortium advances the understanding of demography, genome function and architecture. Genome Biol 2023;24:187. [PMID: 37582787 PMCID: PMC10426128 DOI: 10.1186/s13059-023-03023-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 07/25/2023] [Indexed: 08/17/2023]  Open
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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, et alLiao 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. A draft human pangenome reference. Nature 2023;617:312-324. [PMID: 37165242 PMCID: PMC10172123 DOI: 10.1038/s41586-023-05896-x] [Show More Authors] [Citation(s) in RCA: 467] [Impact Index Per Article: 233.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 02/28/2023] [Indexed: 05/12/2023]
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Berger B, Yu YW. Navigating bottlenecks and trade-offs in genomic data analysis. Nat Rev Genet 2023;24:235-250. [PMID: 36476810 PMCID: PMC10204111 DOI: 10.1038/s41576-022-00551-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2022] [Indexed: 12/12/2022]
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Payne ZL, Penny GM, Turner TN, Dutcher SK. A gap-free genome assembly of Chlamydomonas reinhardtii and detection of translocations induced by CRISPR-mediated mutagenesis. PLANT COMMUNICATIONS 2023;4:100493. [PMID: 36397679 PMCID: PMC10030371 DOI: 10.1016/j.xplc.2022.100493] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/26/2022] [Accepted: 11/15/2022] [Indexed: 05/04/2023]
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Harringmeyer OS, Hoekstra HE. Chromosomal inversion polymorphisms shape the genomic landscape of deer mice. Nat Ecol Evol 2022;6:1965-1979. [PMID: 36253543 PMCID: PMC9715431 DOI: 10.1038/s41559-022-01890-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 08/17/2022] [Indexed: 12/15/2022]
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Toh H, Yang C, Formenti G, Raja K, Yan L, Tracey A, Chow W, Howe K, Bergeron LA, Zhang G, Haase B, Mountcastle J, Fedrigo O, Fogg J, Kirilenko B, Munegowda C, Hiller M, Jain A, Kihara D, Rhie A, Phillippy AM, Swanson SA, Jiang P, Clegg DO, Jarvis ED, Thomson JA, Stewart R, Chaisson MJP, Bukhman YV. A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes. BMC Biol 2022;20:245. [DOI: 10.1186/s12915-022-01427-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/29/2022] [Indexed: 11/09/2022]  Open
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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. Segmental duplications and their variation in a complete human genome. Science 2022;376:eabj6965. [PMID: 35357917 PMCID: PMC8979283 DOI: 10.1126/science.abj6965] [Citation(s) in RCA: 190] [Impact Index Per Article: 63.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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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. A complete reference genome improves analysis of human genetic variation. Science 2022;376:eabl3533. [PMID: 35357935 PMCID: PMC9336181 DOI: 10.1126/science.abl3533] [Citation(s) in RCA: 196] [Impact Index Per Article: 65.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Išerić H, Alkan C, Hach F, Numanagić I. Fast characterization of segmental duplication structure in multiple genome assemblies. Algorithms Mol Biol 2022;17:4. [PMID: 35303886 PMCID: PMC8932185 DOI: 10.1186/s13015-022-00210-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 02/08/2022] [Indexed: 11/29/2022]  Open
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Lou H, Gao Y, Xie B, Wang Y, Zhang H, Shi M, Ma S, Zhang X, Liu C, Xu S. Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references. Cell Syst 2022;13:321-333.e6. [PMID: 35180379 DOI: 10.1016/j.cels.2022.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 11/09/2021] [Accepted: 01/27/2022] [Indexed: 12/17/2022]
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Neubert K, Zuchantke E, Leidenfrost RM, Wünschiers R, Grützke J, Malorny B, Brendebach H, Al Dahouk S, Homeier T, Hotzel H, Reinert K, Tomaso H, Busch A. Testing assembly strategies of Francisella tularensis genomes to infer an evolutionary conservation analysis of genomic structures. BMC Genomics 2021;22:822. [PMID: 34773979 PMCID: PMC8590783 DOI: 10.1186/s12864-021-08115-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 10/12/2021] [Indexed: 02/08/2023]  Open
38
Raj Kolora SR, Owens GL, Vazquez JM, Stubbs A, Chatla K, Jainese C, Seeto K, McCrea M, Sandel MW, Vianna JA, Maslenikov K, Bachtrog D, Orr JW, Love M, Sudmant PH. Origins and evolution of extreme life span in Pacific Ocean rockfishes. Science 2021;374:842-847. [PMID: 34762458 PMCID: PMC8923369 DOI: 10.1126/science.abg5332] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Li K, Jiang W, Hui Y, Kong M, Feng LY, Gao LZ, Li P, Lu S. Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution. MOLECULAR PLANT 2021;14:1745-1756. [PMID: 34171481 DOI: 10.1016/j.molp.2021.06.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 05/04/2023]
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Vervoort L, Dierckxsens N, Pereboom Z, Capozzi O, Rocchi M, Shaikh TH, Vermeesch JR. 22q11.2 Low Copy Repeats Expanded in the Human Lineage. Front Genet 2021;12:706641. [PMID: 34335701 PMCID: PMC8320366 DOI: 10.3389/fgene.2021.706641] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/23/2021] [Indexed: 11/13/2022]  Open
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Abdullaev ET, Umarova IR, Arndt PF. Modelling segmental duplications in the human genome. BMC Genomics 2021;22:496. [PMID: 34215180 PMCID: PMC8254307 DOI: 10.1186/s12864-021-07789-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 06/10/2021] [Indexed: 11/22/2022]  Open
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Khorsand P, Denti L, Human Genome Structural Variant Consortium, Bonizzoni P, Chikhi R, Hormozdiari F. Comparative genome analysis using sample-specific string detection in accurate long reads. BIOINFORMATICS ADVANCES 2021;1:vbab005. [PMID: 36700094 PMCID: PMC9710709 DOI: 10.1093/bioadv/vbab005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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Dog10K_Boxer_Tasha_1.0: A Long-Read Assembly of the Dog Reference Genome. Genes (Basel) 2021;12:genes12060847. [PMID: 34070911 PMCID: PMC8228171 DOI: 10.3390/genes12060847] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 12/27/2022]  Open
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Zhong J, Tang C, Peng W, Xie M, Sun Y, Tang Q, Xiao Q, Yang J. A novel essential protein identification method based on PPI networks and gene expression data. BMC Bioinformatics 2021;22:248. [PMID: 33985429 PMCID: PMC8120700 DOI: 10.1186/s12859-021-04175-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Accepted: 05/06/2021] [Indexed: 02/08/2023]  Open
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Halo JV, Pendleton AL, Shen F, Doucet AJ, Derrien T, Hitte C, Kirby LE, Myers B, Sliwerska E, Emery S, Moran JV, Boyko AR, Kidd JM. Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes. Proc Natl Acad Sci U S A 2021;118:e2016274118. [PMID: 33836575 PMCID: PMC7980453 DOI: 10.1073/pnas.2016274118] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
46
Guan J, Xu Y, Yu Y, Fu J, Ren F, Guo J, Zhao J, Jiang Q, Wei J, Xie H. Genome structure variation analyses of peach reveal population dynamics and a 1.67 Mb causal inversion for fruit shape. Genome Biol 2021;22:13. [PMID: 33402202 PMCID: PMC7784018 DOI: 10.1186/s13059-020-02239-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/14/2020] [Indexed: 12/11/2022]  Open
47
The structure, function and evolution of a complete human chromosome 8. Nature 2021;593:101-107. [PMID: 33828295 PMCID: PMC8099727 DOI: 10.1038/s41586-021-03420-7] [Citation(s) in RCA: 208] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 03/04/2021] [Indexed: 02/07/2023]
48
Uchiyama Y, Yamaguchi D, Iwama K, Miyatake S, Hamanaka K, Tsuchida N, Aoi H, Azuma Y, Itai T, Saida K, Fukuda H, Sekiguchi F, Sakaguchi T, Lei M, Ohori S, Sakamoto M, Kato M, Koike T, Takahashi Y, Tanda K, Hyodo Y, Honjo RS, Bertola DR, Kim CA, Goto M, Okazaki T, Yamada H, Maegaki Y, Osaka H, Ngu LH, Siew CG, Teik KW, Akasaka M, Doi H, Tanaka F, Goto T, Guo L, Ikegawa S, Haginoya K, Haniffa M, Hiraishi N, Hiraki Y, Ikemoto S, Daida A, Hamano SI, Miura M, Ishiyama A, Kawano O, Kondo A, Matsumoto H, Okamoto N, Okanishi T, Oyoshi Y, Takeshita E, Suzuki T, Ogawa Y, Handa H, Miyazono Y, Koshimizu E, Fujita A, Takata A, Miyake N, Mizuguchi T, Matsumoto N. Efficient detection of copy-number variations using exome data: Batch- and sex-based analyses. Hum Mutat 2020;42:50-65. [PMID: 33131168 DOI: 10.1002/humu.24129] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 09/29/2020] [Accepted: 10/15/2020] [Indexed: 12/16/2022]
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Criscuolo A. On the transformation of MinHash-based uncorrected distances into proper evolutionary distances for phylogenetic inference. F1000Res 2020;9:1309. [PMID: 33335719 PMCID: PMC7713896 DOI: 10.12688/f1000research.26930.1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/12/2020] [Indexed: 12/29/2022]  Open
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Feng C, Dai M, Liu Y, Chen M. Sequence repetitiveness quantification and de novo repeat detection by weighted k-mer coverage. Brief Bioinform 2020;22:5855256. [PMID: 32591772 DOI: 10.1093/bib/bbaa086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 04/10/2020] [Accepted: 04/22/2020] [Indexed: 11/12/2022]  Open
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