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Mark Chaisson, Ph.D. - Publications

Affiliations: 
Genome Sciences University of Washington, Seattle, Seattle, WA 
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54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 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, ... ... Chaisson MJP, et al. Complex genetic variation in nearly complete human genomes. Biorxiv : the Preprint Server For Biology. PMID 39372794 DOI: 10.1101/2024.09.24.614721  0.738
2024 Sarwal V, Lee S, Yang J, Sankararaman S, Chaisson M, Eskin E, Mangul S. VISTA: an integrated framework for structural variant discovery. Briefings in Bioinformatics. 25. PMID 39297879 DOI: 10.1093/bib/bbae462  0.603
2024 Ma W, Chaisson MJ. Genotyping sequence-resolved copy-number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes. Biorxiv : the Preprint Server For Biology. PMID 39149335 DOI: 10.1101/2024.08.11.607269  0.38
2024 English AC, Dolzhenko E, Ziaei Jam H, McKenzie SK, Olson ND, De Coster W, Park J, Gu B, Wagner J, Eberle MA, Gymrek M, Chaisson MJP, Zook JM, Sedlazeck FJ. Analysis and benchmarking of small and large genomic variants across tandem repeats. Nature Biotechnology. PMID 38671154 DOI: 10.1038/s41587-024-02225-z  0.629
2024 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, ... ... Chaisson MJP, et al. A high-quality blue whale genome, segmental duplications, and historical demography. Molecular Biology and Evolution. PMID 38376487 DOI: 10.1093/molbev/msae036  0.578
2024 Bukhman YV, Meyer S, Chu LF, Abueg L, Antosiewicz-Bourget J, Balacco J, Brecht M, Dinatale E, Fedrigo O, Formenti G, Fungtammasan A, Giri SJ, Hiller M, Howe K, Kihara D, ... ... Chaisson MJP, et al. Chromosome level genome assembly of the Etruscan shrew Suncus etruscus. Scientific Data. 11: 176. PMID 38326333 DOI: 10.1038/s41597-024-03011-x  0.515
2024 Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Antunes A, Balacco JR, Chaisson MJP, Cheng H, Collins J, et al. Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy. Nature Biotechnology. PMID 38278971 DOI: 10.1038/s41587-023-02100-3  0.638
2023 English A, Dolzhenko E, Jam HZ, Mckenzie S, Olson ND, De Coster W, Park J, Gu B, Wagner J, Eberle MA, Gymrek M, Chaisson MJP, Zook JM, Sedlazeck FJ. Benchmarking of small and large variants across tandem repeats. Biorxiv : the Preprint Server For Biology. PMID 37961319 DOI: 10.1101/2023.10.29.564632  0.55
2023 Chaisson MJP, Sulovari A, Valdmanis PN, Miller DE, Eichler EE. Advances in the discovery and analyses of human tandem repeats. Emerging Topics in Life Sciences. PMID 37905568 DOI: 10.1042/ETLS20230074  0.614
2023 Joshi D, Diggavi S, Chaisson MJP, Kannan S. HQAlign: aligning nanopore reads for SV detection using current-level modeling. Bioinformatics (Oxford, England). 39. PMID 37738608 DOI: 10.1093/bioinformatics/btad580  0.469
2023 Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Alvarez Jerez P, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, ... ... Chaisson M, et al. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Nature Methods. PMID 37710018 DOI: 10.1038/s41592-023-01993-x  0.499
2023 Ren J, Gu B, Chaisson MJP. vamos: variable-number tandem repeats annotation using efficient motif sets. Genome Biology. 24: 175. PMID 37501141 DOI: 10.1186/s13059-023-03010-y  0.419
2023 Larivière D, Abueg L, Brajuka N, Gallardo-Alba C, Grüning B, Ko BJ, Ostrovsky A, Palmada-Flores M, Pickett BD, Rabbani K, Balacco JR, Chaisson M, Cheng H, Collins J, Denisova A, et al. Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy. Biorxiv : the Preprint Server For Biology. PMID 37425881 DOI: 10.1101/2023.06.28.546576  0.704
2023 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, ... ... Chaisson MJP, et al. A draft human pangenome reference. Nature. 617: 312-324. PMID 37165242 DOI: 10.1038/s41586-023-05896-x  0.698
2023 Lu TY, Smaruj PN, Fudenberg G, Mancuso N, Chaisson MJ. The motif composition of variable-number tandem repeats impacts gene expression. Genome Research. PMID 37037626 DOI: 10.1101/gr.276768.122  0.415
2023 Jun G, English A, Metcalf G, Yang J, Chaisson M, Pankratz N, Menon V, Salerno W, Krasheninina O, Smith A, Lane J, Blackwell T, Kang HM, Salvi S, Meng Q, et al. Structural variation across 138,134 samples in the TOPMed consortium. Research Square. PMID 36778386 DOI: 10.21203/rs.3.rs-2515453/v1  0.577
2023 Jun G, English AC, Metcalf GA, Yang J, Chaisson MJ, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, et al. Structural variation across 138,134 samples in the TOPMed consortium. Biorxiv : the Preprint Server For Biology. PMID 36747810 DOI: 10.1101/2023.01.25.525428  0.578
2023 Joshi D, Diggavi S, Chaisson MJP, Kannan S. HQAlign: Aligning nanopore reads for SV detection using current-level modeling. Arxiv. PMID 36713252  0.471
2023 Joshi D, Diggavi S, Chaisson MJP, Kannan S. HQAlign: Aligning nanopore reads for SV detection using current-level modeling. Biorxiv : the Preprint Server For Biology. PMID 36712127 DOI: 10.1101/2023.01.08.523172  0.471
2023 Kolmogorov M, Billingsley KJ, Mastoras M, Meredith M, Monlong J, Lorig-Roach R, Asri M, Jerez PA, Malik L, Dewan R, Reed X, Genner RM, Daida K, Behera S, Shafin K, ... ... Chaisson M, et al. Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation. Biorxiv : the Preprint Server For Biology. PMID 36711673 DOI: 10.1101/2023.01.12.523790  0.553
2022 Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, et al. Semi-automated assembly of high-quality diploid human reference genomes. Nature. PMID 36261518 DOI: 10.1038/s41586-022-05325-5  0.729
2022 Yang J, Chaisson MJP. TT-Mars: structural variants assessment based on haplotype-resolved assemblies. Genome Biology. 23: 110. PMID 35524317 DOI: 10.1186/s13059-022-02666-2  0.546
2022 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, et al. The Human Pangenome Project: a global resource to map genomic diversity. Nature. 604: 437-446. PMID 35444317 DOI: 10.1038/s41586-022-04601-8  0.721
2021 Lu TY, Chaisson MJP. Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs. Nature Communications. 12: 4250. PMID 34253730 DOI: 10.1038/s41467-021-24378-0  0.433
2021 Ren J, Chaisson MJP. lra: A long read aligner for sequences and contigs. Plos Computational Biology. 17: e1009078. PMID 34153026 DOI: 10.1371/journal.pcbi.1009078  0.51
2021 Rhie A, McCarthy SA, Fedrigo O, Damas J, Formenti G, Koren S, Uliano-Silva M, Chow W, Fungtammasan A, Kim J, Lee C, Ko BJ, Chaisson M, Gedman GL, Cantin LJ, et al. Towards complete and error-free genome assemblies of all vertebrate species. Nature. 592: 737-746. PMID 33911273 DOI: 10.1038/s41586-021-03451-0  0.739
2021 Zhao X, Collins RL, Lee WP, Weber AM, Jun Y, Zhu Q, Weisburd B, Huang Y, Audano PA, Wang H, Walker M, Lowther C, Fu J, Gerstein MB, ... ... Chaisson MJP, et al. Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies. American Journal of Human Genetics. PMID 33789087 DOI: 10.1016/j.ajhg.2021.03.014  0.761
2021 Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, ... ... Chaisson MJP, et al. Haplotype-resolved diverse human genomes and integrated analysis of structural variation. Science (New York, N.Y.). PMID 33632895 DOI: 10.1126/science.abf7117  0.754
2020 Porubsky D, Ebert P, Audano PA, Vollger MR, Harvey WT, Marijon P, Ebler J, Munson KM, Sorensen M, Sulovari A, Haukness M, Ghareghani M, Lansdorp PM, Paten B, ... ... Chaisson MJP, et al. Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads. Nature Biotechnology. PMID 33288906 DOI: 10.1038/s41587-020-0719-5  0.69
2020 Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, ... ... Chaisson MJP, et al. Author Correction: A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32699374 DOI: 10.1038/S41587-020-0640-Y  0.468
2020 Zook JM, Hansen NF, Olson ND, Chapman L, Mullikin JC, Xiao C, Sherry S, Koren S, Phillippy AM, Boutros PC, Sahraeian SME, Huang V, Rouette A, Alexander N, Mason CE, ... ... Chaisson MJP, et al. A robust benchmark for detection of germline large deletions and insertions. Nature Biotechnology. PMID 32541955 DOI: 10.1038/S41587-020-0538-8  0.73
2019 Sulovari A, Li R, Audano PA, Porubsky D, Vollger MR, Logsdon GA, Warren WC, Pollen AA, Chaisson MJP, Eichler EE. Human-specific tandem repeat expansion and differential gene expression during primate evolution. Proceedings of the National Academy of Sciences of the United States of America. PMID 31659027 DOI: 10.1073/Pnas.1912175116  0.673
2019 Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, et al. Multi-platform discovery of haplotype-resolved structural variation in human genomes. Nature Communications. 10: 1784. PMID 30992455 DOI: 10.1038/S41467-018-08148-Z  0.826
2019 Vollger MR, Dishuck PC, Sorensen M, Welch AE, Dang V, Dougherty ML, Graves-Lindsay TA, Wilson RK, Chaisson MJP, Eichler EE. Long-read sequence and assembly of segmental duplications. Nature Methods. 16: 88-94. PMID 30559433 DOI: 10.1038/s41592-018-0236-3  0.749
2018 Kronenberg ZN, Fiddes IT, Gordon D, Murali S, Cantsilieris S, Meyerson OS, Underwood JG, Nelson BJ, Chaisson MJP, Dougherty ML, Munson KM, Hastie AR, Diekhans M, Hormozdiari F, Lorusso N, et al. High-resolution comparative analysis of great ape genomes. Science (New York, N.Y.). 360. PMID 29880660 DOI: 10.1126/Science.Aar6343  0.808
2018 Huddleston J, Chaisson MJP, Steinberg KM, Warren W, Hoekzema K, Gordon D, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, Peluso P, Boitano M, Chin CS, Korlach J, Wilson RK, et al. Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Research. 28: 144. PMID 29295848 DOI: 10.1101/Gr.233007.117  0.792
2017 Chaisson MJ, Mukherjee S, Kannan S, Eichler EE. Resolving multicopy duplications de novo using polyploid phasing. Research in Computational Molecular Biology : ... Annual International Conference, Recomb ... : Proceedings. Recomb (Conference : 2005-). 10229: 117-133. PMID 28808695 DOI: 10.1007/978-3-319-56970-3_8  0.531
2017 Fan X, Chaisson M, Nakhleh L, Chen K. HySA: A Hybrid Structural variant Assembly approach using next generation and single-molecule sequencing technologies. Genome Research. PMID 28104618 DOI: 10.1101/Gr.214767.116  0.713
2016 Lin Y, Yuan J, Kolmogorov M, Shen MW, Chaisson M, Pevzner PA. Assembly of long error-prone reads using de Bruijn graphs. Proceedings of the National Academy of Sciences of the United States of America. PMID 27956617 DOI: 10.1073/Pnas.1604560113  0.432
2016 Huddleston J, Chaisson MJ, Meltz Steinberg K, Warren W, Hoekzema K, Gordon DS, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, Peluso P, Boitano M, Chin CS, Korlach J, Wilson RK, et al. Discovery and genotyping of structural variation from long-read haploid genome sequence data. Genome Research. PMID 27895111 DOI: 10.1101/Gr.214007.116  0.749
2016 Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, ... ... Chaisson M, et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials. Scientific Data. 3: 160025. PMID 27271295 DOI: 10.1038/Sdata.2016.25  0.694
2016 Gordon D, Huddleston J, Chaisson MJ, Hill CM, Kronenberg ZN, Munson KM, Malig M, Raja A, Fiddes I, Hillier LW, Dunn C, Baker C, Armstrong J, Diekhans M, Paten B, et al. Long-read sequence assembly of the gorilla genome. Science (New York, N.Y.). 352: aae0344. PMID 27034376 DOI: 10.1126/Science.Aae0344  0.75
2016 Grasso CS, Shinbrot E, Yu M, Liesersen M, Chaisson M, Chan A, Connolly C, Dai J, Du M, Fuchs C, Garraway L, Giannakis M, Harrison T, Hsu L, Huyghe J, et al. Abstract 136: Refining the molecular profile of colorectal tumors to expand prevention and treatment opportunities Cancer Research. 76: 136-136. DOI: 10.1158/1538-7445.Am2016-136  0.372
2015 Chaisson MJ, Wilson RK, Eichler EE. Genetic variation and the de novo assembly of human genomes. Nature Reviews. Genetics. 16: 627-40. PMID 26442640 DOI: 10.1038/nrg3933  0.749
2015 Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Hsi-Yang Fritz M, Konkel MK, Malhotra A, Stütz AM, Shi X, Paolo Casale F, ... ... Chaisson MJ, et al. An integrated map of structural variation in 2,504 human genomes. Nature. 526: 75-81. PMID 26432246 DOI: 10.1038/Nature15394  0.751
2015 Chaisson MJ, Huddleston J, Dennis MY, Sudmant PH, Malig M, Hormozdiari F, Antonacci F, Surti U, Sandstrom R, Boitano M, Landolin JM, Stamatoyannopoulos JA, Hunkapiller MW, Korlach J, Eichler EE. Resolving the complexity of the human genome using single-molecule sequencing. Nature. 517: 608-11. PMID 25383537 DOI: 10.1038/Nature13907  0.782
2014 Huddleston J, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, Sudmant PH, Graves TA, Alkan C, Dennis MY, Wilson RK, Turner SW, Korlach J, Eichler EE. Reconstructing complex regions of genomes using long-read sequencing technology. Genome Research. 24: 688-96. PMID 24418700 DOI: 10.1101/Gr.168450.113  0.778
2013 Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. STAR: ultrafast universal RNA-seq aligner. Bioinformatics (Oxford, England). 29: 15-21. PMID 23104886 DOI: 10.1093/Bioinformatics/Bts635  0.396
2012 Chaisson MJ, Tesler G. Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory. Bmc Bioinformatics. 13: 238. PMID 22988817 DOI: 10.1186/1471-2105-13-238  0.456
2011 Medvedev P, Pham S, Chaisson M, Tesler G, Pevzner P. Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 18: 1625-34. PMID 21999285 DOI: 10.1089/Cmb.2011.0151  0.452
2009 Chaisson MJ, Brinza D, Pevzner PA. De novo fragment assembly with short mate-paired reads: Does the read length matter? Genome Research. 19: 336-46. PMID 19056694 DOI: 10.1101/Gr.079053.108  0.329
2008 Chaisson MJ, Pevzner PA. Short read fragment assembly of bacterial genomes. Genome Research. 18: 324-30. PMID 18083777 DOI: 10.1101/Gr.7088808  0.485
2006 Chaisson MJ, Raphael BJ, Pevzner PA. Microinversions in mammalian evolution. Proceedings of the National Academy of Sciences of the United States of America. 103: 19824-9. PMID 17189424 DOI: 10.1073/Pnas.0603984103  0.454
2004 Chaisson M, Pevzner P, Tang H. Fragment assembly with short reads. Bioinformatics (Oxford, England). 20: 2067-74. PMID 15059830 DOI: 10.1093/Bioinformatics/Bth205  0.478
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