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Mark Chaisson
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STAR: ultrafast universal RNA-seq aligner
A Dobin, CA Davis, F Schlesinger, J Drenkow, C Zaleski, S Jha, P Batut, ...
Bioinformatics 29 (1), 15-21, 2013
384302013
An integrated map of structural variation in 2,504 human genomes
PH Sudmant, T Rausch, EJ Gardner, RE Handsaker, A Abyzov, ...
Nature 526 (7571), 75-81, 2015
23662015
Towards complete and error-free genome assemblies of all vertebrate species
A Rhie, SA McCarthy, O Fedrigo, J Damas, G Formenti, S Koren, ...
Nature 592 (7856), 737-746, 2021
14222021
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory
MJ Chaisson, G Tesler
BMC bioinformatics 13, 1-18, 2012
12202012
Resolving the complexity of the human genome using single-molecule sequencing
MJP Chaisson, J Huddleston, MY Dennis, PH Sudmant, M Malig, ...
Nature 517 (7536), 608-611, 2015
8512015
Multi-platform discovery of haplotype-resolved structural variation in human genomes
MJP Chaisson, AD Sanders, X Zhao, A Malhotra, D Porubsky, T Rausch, ...
Nature communications 10 (1), 1784, 2019
7602019
Extensive sequencing of seven human genomes to characterize benchmark reference materials
JM Zook, D Catoe, J McDaniel, L Vang, N Spies, A Sidow, Z Weng, Y Liu, ...
Scientific data 3 (1), 1-26, 2016
6712016
Short read fragment assembly of bacterial genomes
MJ Chaisson, PA Pevzner
Genome research 18 (2), 324-330, 2008
5952008
Haplotype-resolved diverse human genomes and integrated analysis of structural variation
P Ebert, PA Audano, Q Zhu, B Rodriguez-Martin, D Porubsky, MJ Bonder, ...
Science 372 (6537), eabf7117, 2021
4422021
Genetic variation and the de novo assembly of human genomes
MJP Chaisson, RK Wilson, EE Eichler
Nature Reviews Genetics 16 (11), 627-640, 2015
4092015
Discovery and genotyping of structural variation from long-read haploid genome sequence data
J Huddleston, MJP Chaisson, KM Steinberg, W Warren, K Hoekzema, ...
Genome research 27 (5), 677-685, 2017
3922017
De novo fragment assembly with short mate-paired reads: Does the read length matter?
MJ Chaisson, D Brinza, PA Pevzner
Genome research 19 (2), 336-346, 2009
3822009
High-resolution comparative analysis of great ape genomes
ZN Kronenberg, IT Fiddes, D Gordon, S Murali, S Cantsilieris, ...
Science 360 (6393), eaar6343, 2018
3682018
Long-read sequence assembly of the gorilla genome
D Gordon, J Huddleston, MJP Chaisson, CM Hill, ZN Kronenberg, ...
Science 352 (6281), aae0344, 2016
3472016
A draft human pangenome reference
WW Liao, M Asri, J Ebler, D Doerr, M Haukness, G Hickey, S Lu, JK Lucas, ...
Nature 617 (7960), 312-324, 2023
3302023
Fragment assembly with short reads
M Chaisson, P Pevzner, H Tang
Bioinformatics 20 (13), 2067-2074, 2004
3012004
Assembly of long error-prone reads using de Bruijn graphs
Y Lin, J Yuan, M Kolmogorov, MW Shen, M Chaisson, PA Pevzner
Proceedings of the National Academy of Sciences 113 (52), E8396-E8405, 2016
2912016
Reconstructing complex regions of genomes using long-read sequencing technology
J Huddleston, S Ranade, M Malig, F Antonacci, M Chaisson, L Hon, ...
Genome research 24 (4), 688-696, 2014
2872014
A robust benchmark for detection of germline large deletions and insertions
JM Zook, NF Hansen, ND Olson, L Chapman, JC Mullikin, C Xiao, ...
Nature biotechnology 38 (11), 1347-1355, 2020
2752020
The Human Pangenome Project: a global resource to map genomic diversity
T Wang, L Antonacci-Fulton, K Howe, HA Lawson, JK Lucas, AM Phillippy, ...
Nature 604 (7906), 437-446, 2022
2492022
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