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For: Gershman A, Sauria MEG, Guitart X, Vollger MR, Hook PW, Hoyt SJ, Jain M, Shumate A, Razaghi R, Koren S, Altemose N, Caldas GV, Logsdon GA, Rhie A, Eichler EE, Schatz MC, O'Neill RJ, Phillippy AM, Miga KH, Timp W. Epigenetic patterns in a complete human genome. Science 2022;376:eabj5089. [PMID: 35357915 PMCID: PMC9170183 DOI: 10.1126/science.abj5089] [Citation(s) in RCA: 164] [Impact Index Per Article: 54.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Number Cited by Other Article(s)
1
Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Monfort Anez G, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Rocha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, et alYoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Monfort Anez G, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Rocha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, Zhao SA, Zhu Y, Jarvis ED, Gerton JL, Rivas-González I, Paten B, Szpiech ZA, Huber CD, Lenz TL, Konkel MK, Yi SV, Canzar S, Watson CT, Sudmant PH, Molloy E, Garrison E, Lowe CB, Ventura M, O'Neill RJ, Koren S, Makova KD, Phillippy AM, Eichler EE. Complete sequencing of ape genomes. Nature 2025;641:401-418. [PMID: 40205052 PMCID: PMC12058530 DOI: 10.1038/s41586-025-08816-3] [Show More Authors] [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: 07/31/2024] [Accepted: 02/19/2025] [Indexed: 04/11/2025]
2
Porubsky D, Dashnow H, Sasani TA, Logsdon GA, Hallast P, Noyes MD, Kronenberg ZN, Mokveld T, Koundinya N, Nolan C, Steely CJ, Guarracino A, Dolzhenko E, Harvey WT, Rowell WJ, Grigorev K, Nicholas TJ, Goldberg ME, Oshima KK, Lin J, Ebert P, Watkins WS, Leung TY, Hanlon VCT, McGee S, Pedersen BS, Happ HC, Jeong H, Munson KM, Hoekzema K, Chan DD, Wang Y, Knuth J, Garcia GH, Fanslow C, Lambert C, Lee C, Smith JD, Levy S, Mason CE, Garrison E, Lansdorp PM, Neklason DW, Jorde LB, Quinlan AR, Eberle MA, Eichler EE. Human de novo mutation rates from a four-generation pedigree reference. Nature 2025:10.1038/s41586-025-08922-2. [PMID: 40269156 DOI: 10.1038/s41586-025-08922-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 03/20/2025] [Indexed: 04/25/2025]
3
Li Q, Keskus AG, Wagner J, Izydorczyk MB, Timp W, Sedlazeck FJ, Klein AP, Zook JM, Kolmogorov M, Schatz MC. Unraveling the hidden complexity of cancer through long-read sequencing. Genome Res 2025;35:599-620. [PMID: 40113261 PMCID: PMC12047254 DOI: 10.1101/gr.280041.124] [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] [Indexed: 03/22/2025]
4
Groza C, Ge B, Cheung WA, Pastinen T, Bourque G. Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA. Genome Res 2025;35:644-652. [PMID: 40113263 PMCID: PMC12047246 DOI: 10.1101/gr.279240.124] [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: 03/17/2024] [Accepted: 02/11/2025] [Indexed: 03/22/2025]
5
Montano C, Timp W. Evolution of genome-wide methylation profiling technologies. Genome Res 2025;35:572-582. [PMID: 40228903 PMCID: PMC12047278 DOI: 10.1101/gr.278407.123] [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] [Indexed: 04/16/2025]
6
Mahmoud M, Agustinho DP, Sedlazeck FJ. A Hitchhiker's Guide to long-read genomic analysis. Genome Res 2025;35:545-558. [PMID: 40228901 PMCID: PMC12047252 DOI: 10.1101/gr.279975.124] [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] [Indexed: 04/16/2025]
7
Rausch T, Marschall T, Korbel JO. The impact of long-read sequencing on human population-scale genomics. Genome Res 2025;35:593-598. [PMID: 40228902 PMCID: PMC12047236 DOI: 10.1101/gr.280120.124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2025]
8
Smeds L, Kamali K, Kejnovská I, Kejnovský E, Chiaromonte F, Makova KD. Non-canonical DNA in human and other ape telomere-to-telomere genomes. Nucleic Acids Res 2025;53:gkaf298. [PMID: 40226919 PMCID: PMC11995269 DOI: 10.1093/nar/gkaf298] [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: 12/13/2024] [Revised: 02/28/2025] [Accepted: 04/07/2025] [Indexed: 04/15/2025]  Open
9
Dubocanin D, Hartley GA, Sedeño Cortés AE, Mao Y, Hedouin S, Ranchalis J, Agarwal A, Logsdon GA, Munson KM, Real T, Mallory BJ, Eichler EE, Biggins S, O'Neill RJ, Stergachis AB. Conservation of dichromatin organization along regional centromeres. CELL GENOMICS 2025;5:100819. [PMID: 40147439 PMCID: PMC12008808 DOI: 10.1016/j.xgen.2025.100819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2024] [Revised: 12/20/2024] [Accepted: 02/27/2025] [Indexed: 03/29/2025]
10
Hartley GA, Okhovat M, Hoyt SJ, Fuller E, Pauloski N, Alexandre N, Alexandrov I, Drennan R, Dubocanin D, Gilbert DM, Mao Y, McCann C, Neph S, Ryabov F, Sasaki T, Storer JM, Svendsen D, Troy W, Wells J, Core L, Stergachis A, Carbone L, O'Neill RJ. Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon. CELL GENOMICS 2025;5:100808. [PMID: 40088887 PMCID: PMC12008813 DOI: 10.1016/j.xgen.2025.100808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Revised: 12/10/2024] [Accepted: 02/12/2025] [Indexed: 03/17/2025]
11
Mahlke MA, Lumerman L, Nath P, Chittenden C, Hoyt S, Koeppel J, Xu Y, Raphael R, Zaffina K, Hook PW, Timp W, Miga KH, Campbell PJ, O'Neill RJ, Altemose N, Nechemia-Arbely Y. Evolution and instability of human centromeres are accelerated by heterochromatin boundary loss and CENP-A overexpression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.03.636285. [PMID: 39975122 PMCID: PMC11838504 DOI: 10.1101/2025.02.03.636285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/21/2025]
12
Hu G, Wang Z, Tian Z, Wang K, Ji G, Wang X, Zhang X, Yang Z, Liu X, Niu R, Zhu D, Zhang Y, Duan L, Ma X, Xiong X, Kong J, Zhao X, Zhang Y, Zhao J, He S, Grover CE, Su J, Feng K, Yu G, Han J, Zang X, Wu Z, Pan W, Wendel JF, Ma X. A telomere-to-telomere genome assembly of cotton provides insights into centromere evolution and short-season adaptation. Nat Genet 2025;57:1031-1043. [PMID: 40097785 DOI: 10.1038/s41588-025-02130-4] [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: 11/23/2023] [Accepted: 02/14/2025] [Indexed: 03/19/2025]
13
Kovaka S, Hook PW, Jenike KM, Shivakumar V, Morina LB, Razaghi R, Timp W, Schatz MC. Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment. Nat Methods 2025;22:681-691. [PMID: 40155722 PMCID: PMC11978507 DOI: 10.1038/s41592-025-02631-4] [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: 03/15/2024] [Accepted: 02/16/2025] [Indexed: 04/01/2025]
14
Golub Y, Wulff A, Plösch T. From haze to horizon: epigenetic research and artificial intelligence in child and adolescent psychiatry. Eur Child Adolesc Psychiatry 2025;34:1245-1248. [PMID: 40111558 PMCID: PMC12000212 DOI: 10.1007/s00787-025-02686-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2025] [Accepted: 02/18/2025] [Indexed: 03/22/2025]
15
Fu Y, Timp W, Sedlazeck FJ. Computational analysis of DNA methylation from long-read sequencing. Nat Rev Genet 2025:10.1038/s41576-025-00822-5. [PMID: 40155770 DOI: 10.1038/s41576-025-00822-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2025] [Indexed: 04/01/2025]
16
Jayakrishnan M, Havlová M, Veverka V, Regnard C, Becker PB. Genomic context-dependent histone H3K36 methylation by three Drosophila methyltransferases and implications for dedicated chromatin readers. Nucleic Acids Res 2025;53:gkaf202. [PMID: 40164442 DOI: 10.1093/nar/gkaf202] [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: 01/20/2025] [Accepted: 03/06/2025] [Indexed: 04/02/2025]  Open
17
Koutsi M, Pouliou M, Chatzopoulos D, Champezou L, Zagkas K, Vasilogianni M, Kouroukli A, Agelopoulos M. An evolutionarily conserved constellation of functional cis-elements programs the virus-responsive fate of the human (epi)genome. Nucleic Acids Res 2025;53:gkaf207. [PMID: 40131776 PMCID: PMC11934927 DOI: 10.1093/nar/gkaf207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Revised: 02/11/2025] [Accepted: 03/04/2025] [Indexed: 03/27/2025]  Open
18
Smeds L, Kamali K, Kejnovská I, Kejnovský E, Chiaromonte F, Makova KD. Non-canonical DNA in human and other ape telomere-to-telomere genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.09.02.610891. [PMID: 39713403 PMCID: PMC11661062 DOI: 10.1101/2024.09.02.610891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/24/2024]
19
Kixmoeller K, Tarasovetc EV, Mer E, Chang YW, Black BE. Centromeric chromatin clearings demarcate the site of kinetochore formation. Cell 2025;188:1280-1296.e19. [PMID: 39855195 PMCID: PMC11890969 DOI: 10.1016/j.cell.2024.12.025] [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: 05/06/2024] [Revised: 11/24/2024] [Accepted: 12/18/2024] [Indexed: 01/27/2025]
20
Chen Y, Lin ZB, Wang SK, Wu B, Niu L, Zhong JY, Sun YM, Zheng Z, Bai X, Liu LR, Xie W, Chi W, Ye T, Luo R, Hou C, Luo F, Xiao CL. Reconstruction of diploid higher-order human 3D genome interactions from noisy Pore-C data using Dip3D. Nat Struct Mol Biol 2025:10.1038/s41594-025-01512-w. [PMID: 40038455 DOI: 10.1038/s41594-025-01512-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/05/2025] [Indexed: 03/06/2025]
21
Ramirez P, Sun W, Dehkordi SK, Zare H, Pascarella G, Carninci P, Fongang B, Bieniek KF, Frost B. Nanopore Long-Read Sequencing Unveils Genomic Disruptions in Alzheimer's Disease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.02.01.578450. [PMID: 38370753 PMCID: PMC10871260 DOI: 10.1101/2024.02.01.578450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
22
Brändl B, Steiger M, Kubelt C, Rohrandt C, Zhu Z, Evers M, Wang G, Schuldt B, Afflerbach AK, Wong D, Lum A, Halldorsson S, Djirackor L, Leske H, Magadeeva S, Smičius R, Quedenau C, Schmidt NO, Schüller U, Vik-Mo EO, Proescholdt M, Riemenschneider MJ, Zadeh G, Ammerpohl O, Yip S, Synowitz M, van Bömmel A, Kretzmer H, Müller FJ. Rapid brain tumor classification from sparse epigenomic data. Nat Med 2025;31:840-848. [PMID: 40021833 PMCID: PMC11922770 DOI: 10.1038/s41591-024-03435-3] [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: 02/07/2024] [Accepted: 11/27/2024] [Indexed: 03/03/2025]
23
Liang SA, Ren T, Zhang J, He J, Wang X, Jiang X, He Y, McCoy RC, Fu Q, Akey JM, Mao Y, Chen L. A refined analysis of Neanderthal-introgressed sequences in modern humans with a complete reference genome. Genome Biol 2025;26:32. [PMID: 39962554 PMCID: PMC11834205 DOI: 10.1186/s13059-025-03502-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2024] [Accepted: 02/11/2025] [Indexed: 02/20/2025]  Open
24
Zhang F, Li C, Yang D, Liu B, Zhou Y, Zhou Z, Zhong H, Wang Z, Chen D. Label-Free and Sequence-Independent Isothermal Amplification Strategy for the Simultaneous Detection of Genomic 5-Methylcytosine and 5-Hydroxymethylcytosine. Anal Chem 2025;97:3063-3073. [PMID: 39869504 DOI: 10.1021/acs.analchem.4c06200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2025]
25
Tsukamoto S, Mofrad MRK. Bridging scales in chromatin organization: Computational models of loop formation and their implications for genome function. J Chem Phys 2025;162:054122. [PMID: 39918128 DOI: 10.1063/5.0232328] [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: 08/06/2024] [Accepted: 11/18/2024] [Indexed: 05/08/2025]  Open
26
Castellano KR, Neitzey ML, Starovoitov A, Barrett GA, Reid NM, Vuruputoor VS, Webster CN, Storer JM, Pauloski NR, Ameral NJ, McEvoy SL, McManus MC, Puritz JB, Wegrzyn JL, O’Neill RJ. Genome Assembly of a Living Fossil, the Atlantic Horseshoe Crab Limulus polyphemus, Reveals Lineage-Specific Whole-Genome Duplications, Transposable Element-Based Centromeres, and a ZW Sex Chromosome System. Mol Biol Evol 2025;42:msaf021. [PMID: 39907027 PMCID: PMC11836539 DOI: 10.1093/molbev/msaf021] [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: 09/13/2024] [Revised: 12/16/2024] [Accepted: 01/10/2025] [Indexed: 02/06/2025]  Open
27
Wang M, Duan S, Sun Q, Liu K, Liu Y, Wang Z, Li X, Wei L, Liu Y, Nie S, Zhou K, Ma Y, Yuan H, Liu B, Hu L, Liu C, He G. YHSeqY3000 panel captures all founding lineages in the Chinese paternal genomic diversity database. BMC Biol 2025;23:18. [PMID: 39838386 PMCID: PMC11752814 DOI: 10.1186/s12915-025-02122-0] [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: 02/01/2024] [Accepted: 01/07/2025] [Indexed: 01/23/2025]  Open
28
Sobral AF, Dinis-Oliveira RJ, Barbosa DJ. CRISPR-Cas technology in forensic investigations: Principles, applications, and ethical considerations. Forensic Sci Int Genet 2025;74:103163. [PMID: 39437497 DOI: 10.1016/j.fsigen.2024.103163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2024] [Revised: 10/08/2024] [Accepted: 10/09/2024] [Indexed: 10/25/2024]
29
Ferreira MR, Carratto TMT, Frontanilla TS, Bonadio RS, Jain M, de Oliveira SF, Castelli EC, Mendes-Junior CT. Advances in forensic genetics: Exploring the potential of long read sequencing. Forensic Sci Int Genet 2025;74:103156. [PMID: 39427416 DOI: 10.1016/j.fsigen.2024.103156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 10/04/2024] [Accepted: 10/06/2024] [Indexed: 10/22/2024]
30
Luo LY, Wu H, Zhao LM, Zhang YH, Huang JH, Liu QY, Wang HT, Mo DX, EEr HH, Zhang LQ, Chen HL, Jia SG, Wang WM, Li MH. Telomere-to-telomere sheep genome assembly identifies variants associated with wool fineness. Nat Genet 2025;57:218-230. [PMID: 39779954 DOI: 10.1038/s41588-024-02037-6] [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: 03/14/2024] [Accepted: 11/19/2024] [Indexed: 01/11/2025]
31
Mastrorosa FK, Oshima KK, Rozanski AN, Harvey WT, Eichler EE, Logsdon GA. Identification and annotation of centromeric hypomethylated regions with CDR-Finder. Bioinformatics 2024;40:btae733. [PMID: 39657946 PMCID: PMC11663805 DOI: 10.1093/bioinformatics/btae733] [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: 06/07/2024] [Revised: 11/26/2024] [Accepted: 12/06/2024] [Indexed: 12/12/2024]  Open
32
Volarić M, Meštrović N, Despot-Slade E. SatXplor-a comprehensive pipeline for satellite DNA analyses in complex genome assemblies. Brief Bioinform 2024;26:bbae660. [PMID: 39708839 DOI: 10.1093/bib/bbae660] [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: 08/12/2024] [Revised: 10/31/2024] [Accepted: 12/04/2024] [Indexed: 12/23/2024]  Open
33
Iyer SV, Goodwin S, McCombie WR. Leveraging the power of long reads for targeted sequencing. Genome Res 2024;34:1701-1718. [PMID: 39567237 PMCID: PMC11610587 DOI: 10.1101/gr.279168.124] [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: 03/15/2024] [Accepted: 10/01/2024] [Indexed: 11/22/2024]
34
Koren S, Bao Z, Guarracino A, Ou S, Goodwin S, Jenike KM, Lucas J, McNulty B, Park J, Rautiainen M, Rhie A, Roelofs D, Schneiders H, Vrijenhoek I, Nijbroek K, Nordesjo O, Nurk S, Vella M, Lawrence KR, Ware D, Schatz MC, Garrison E, Huang S, McCombie WR, Miga KH, Wittenberg AHJ, Phillippy AM. Gapless assembly of complete human and plant chromosomes using only nanopore sequencing. Genome Res 2024;34:1919-1930. [PMID: 39505490 PMCID: PMC11610574 DOI: 10.1101/gr.279334.124] [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: 03/15/2024] [Accepted: 10/08/2024] [Indexed: 11/08/2024]
35
Kukla-Bartoszek M, Głombik K. Train and Reprogram Your Brain: Effects of Physical Exercise at Different Stages of Life on Brain Functions Saved in Epigenetic Modifications. Int J Mol Sci 2024;25:12043. [PMID: 39596111 PMCID: PMC11593723 DOI: 10.3390/ijms252212043] [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: 10/14/2024] [Revised: 11/05/2024] [Accepted: 11/07/2024] [Indexed: 11/28/2024]  Open
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Mohanty SK, Chiaromonte F, Makova KD. Evolutionary Dynamics of G-Quadruplexes in Human and Other Great Ape Telomere-to-Telomere Genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.05.621973. [PMID: 39574740 PMCID: PMC11580976 DOI: 10.1101/2024.11.05.621973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/02/2024]
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Kumara Mastrorosa F, Oshima KK, Rozanski AN, Harvey WT, Eichler EE, Logsdon GA. Identification and annotation of centromeric hypomethylated regions with Centromere Dip Region (CDR)-Finder. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.11.01.621587. [PMID: 39574726 PMCID: PMC11580854 DOI: 10.1101/2024.11.01.621587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2024]
38
Xia Y, Li D, Chen T, Pan S, Huang H, Zhang W, Liang Y, Fu Y, Peng Z, Zhang H, Zhang L, Peng S, Shi R, He X, Zhou S, Jiao W, Zhao X, Wu X, Zhou L, Zhou J, Ouyang Q, Tian Y, Jiang X, Zhou Y, Tang S, Shen J, Ohshima K, Tan Z. Microsatellite density landscapes illustrate short tandem repeats aggregation in the complete reference human genome. BMC Genomics 2024;25:960. [PMID: 39402450 PMCID: PMC11477012 DOI: 10.1186/s12864-024-10843-9] [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: 05/18/2024] [Accepted: 09/26/2024] [Indexed: 10/19/2024]  Open
39
Yoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Anez GM, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Roha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, et alYoo D, Rhie A, Hebbar P, Antonacci F, Logsdon GA, Solar SJ, Antipov D, Pickett BD, Safonova Y, Montinaro F, Luo Y, Malukiewicz J, Storer JM, Lin J, Sequeira AN, Mangan RJ, Hickey G, Anez GM, Balachandran P, Bankevich A, Beck CR, Biddanda A, Borchers M, Bouffard GG, Brannan E, Brooks SY, Carbone L, Carrel L, Chan AP, Crawford J, Diekhans M, Engelbrecht E, Feschotte C, Formenti G, Garcia GH, de Gennaro L, Gilbert D, Green RE, Guarracino A, Gupta I, Haddad D, Han J, Harris RS, Hartley GA, Harvey WT, Hiller M, Hoekzema K, Houck ML, Jeong H, Kamali K, Kellis M, Kille B, Lee C, Lee Y, Lees W, Lewis AP, Li Q, Loftus M, Loh YHE, Loucks H, Ma J, Mao Y, Martinez JFI, Masterson P, McCoy RC, McGrath B, McKinney S, Meyer BS, Miga KH, Mohanty SK, Munson KM, Pal K, Pennell M, Pevzner PA, Porubsky D, Potapova T, Ringeling FR, Roha JL, Ryder OA, Sacco S, Saha S, Sasaki T, Schatz MC, Schork NJ, Shanks C, Smeds L, Son DR, Steiner C, Sweeten AP, Tassia MG, Thibaud-Nissen F, Torres-González E, Trivedi M, Wei W, Wertz J, Yang M, Zhang P, Zhang S, Zhang Y, Zhang Z, Zhao SA, Zhu Y, Jarvis ED, Gerton JL, Rivas-González I, Paten B, Szpiech ZA, Huber CD, Lenz TL, Konkel MK, Yi SV, Canzar S, Watson CT, Sudmant PH, Molloy E, Garrison E, Lowe CB, Ventura M, O’Neill RJ, Koren S, Makova KD, Phillippy AM, Eichler EE. Complete sequencing of ape genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.31.605654. [PMID: 39131277 PMCID: PMC11312596 DOI: 10.1101/2024.07.31.605654] [Show More Authors] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
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Gafurov A, VinaŘ T, Medvedev P, Brejová B. Fast Context-Aware Analysis of Genome Annotation Colocalization. J Comput Biol 2024;31:946-964. [PMID: 39381845 PMCID: PMC11698669 DOI: 10.1089/cmb.2024.0667] [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] [Indexed: 10/10/2024]  Open
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Karageorgiou C, Gokcumen O, Dennis MY. Deciphering the role of structural variation in human evolution: a functional perspective. Curr Opin Genet Dev 2024;88:102240. [PMID: 39121701 PMCID: PMC11485010 DOI: 10.1016/j.gde.2024.102240] [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: 03/30/2024] [Revised: 06/27/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024]
42
Olagunju TA, Rosen BD, Neibergs HL, Becker GM, Davenport KM, Elsik CG, Hadfield TS, Koren S, Kuhn KL, Rhie A, Shira KA, Skibiel AL, Stegemiller MR, Thorne JW, Villamediana P, Cockett NE, Murdoch BM, Smith TPL. Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content. Nat Commun 2024;15:8277. [PMID: 39333471 PMCID: PMC11436988 DOI: 10.1038/s41467-024-52384-5] [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: 03/07/2024] [Accepted: 09/05/2024] [Indexed: 09/29/2024]  Open
43
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]
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/08/2024]
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Wen W, Zhong J, Zhang Z, Jia L, Chu T, Wang N, Danko CG, Wang Z. dHICA: a deep transformer-based model enables accurate histone imputation from chromatin accessibility. Brief Bioinform 2024;25:bbae459. [PMID: 39316943 PMCID: PMC11421843 DOI: 10.1093/bib/bbae459] [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: 05/16/2024] [Revised: 07/13/2024] [Accepted: 09/04/2024] [Indexed: 09/26/2024]  Open
46
Ma Z, Zuo T, Frey N, Rangrez AY. A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation. Signal Transduct Target Ther 2024;9:237. [PMID: 39307902 PMCID: PMC11418828 DOI: 10.1038/s41392-024-01946-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 07/03/2024] [Accepted: 08/01/2024] [Indexed: 09/26/2024]  Open
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Engelbrecht E, Rodriguez OL, Watson CT. Addressing Technical Pitfalls in Pursuit of Molecular Factors That Mediate Immunoglobulin Gene Regulation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024;213:651-662. [PMID: 39007649 PMCID: PMC11333172 DOI: 10.4049/jimmunol.2400131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 06/13/2024] [Indexed: 07/16/2024]
48
Pandiloski N, Horváth V, Karlsson O, Koutounidou S, Dorazehi F, Christoforidou G, Matas-Fuentes J, Gerdes P, Garza R, Jönsson ME, Adami A, Atacho DAM, Johansson JG, Englund E, Kokaia Z, Jakobsson J, Douse CH. DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor. Nat Commun 2024;15:7534. [PMID: 39214989 PMCID: PMC11364546 DOI: 10.1038/s41467-024-50765-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 07/18/2024] [Indexed: 09/04/2024]  Open
49
Hartley GA, Okhovat M, Hoyt SJ, Fuller E, Pauloski N, Alexandre N, Alexandrov I, Drennan R, Dubocanin D, Gilbert DM, Mao Y, McCann C, Neph S, Ryabov F, Sasaki T, Storer JM, Svendsen D, Troy W, Wells J, Core L, Stergachis A, Carbone L, O’Neill RJ. Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.29.610280. [PMID: 39257810 PMCID: PMC11384015 DOI: 10.1101/2024.08.29.610280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
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Hardikar S, Ren R, Ying Z, Zhou J, Horton JR, Bramble MD, Liu B, Lu Y, Liu B, Coletta LD, Shen J, Dan J, Zhang X, Cheng X, Chen T. The ICF syndrome protein CDCA7 harbors a unique DNA binding domain that recognizes a CpG dyad in the context of a non-B DNA. SCIENCE ADVANCES 2024;10:eadr0036. [PMID: 39178265 PMCID: PMC11343032 DOI: 10.1126/sciadv.adr0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 07/18/2024] [Indexed: 08/25/2024]
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