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Author Details

Mark J P Chaisson
University of Southern California
2004
43
26
PMIDPaper TitleJournal TitlePublished Year
36712127HQAlign: Aligning nanopore reads for SV detection using current-level modeling.bioRxiv2023
37961319Benchmarking of small and large variants across tandem repeats.bioRxiv2023
37905568Advances in the discovery and analyses of human tandem repeats.Emerg Top Life Sci2023
37710018Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.Nat Methods2023
37738608HQAlign: aligning nanopore reads for SV detection using current-level modeling.Bioinformatics2023
37501141vamos: variable-number tandem repeats annotation using efficient motif sets.Genome Biol2023
37425881Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.bioRxiv2023
37037626The motif composition of variable number tandem repeats impacts gene expression.Genome Res2023
36747810Structural variation across 138,134 samples in the TOPMed consortium.bioRxiv2023
36778386Structural variation across 138,134 samples in the TOPMed consortium.Res Sq2023
36713252HQAlign: Aligning nanopore reads for SV detection using current-level modeling.ArXiv2023
36344967A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.BMC Biol2022
35444317The Human Pangenome Project: a global resource to map genomic diversity.Nature2022
35524317TT-Mars: structural variants assessment based on haplotype-resolved assemblies.Genome Biol2022
33288906Fully phased human genome assembly without parental data using single-cell strand sequencing and long reads.Nat Biotechnol2021
33911273Towards complete and error-free genome assemblies of all vertebrate species.Nature2021
33789087Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies.Am J Hum Genet2021
33632895Haplotype-resolved diverse human genomes and integrated analysis of structural variation.Science2021
34153026lra: A long read aligner for sequences and contigs.PLoS Comput Biol2021
32541955A robust benchmark for detection of germline large deletions and insertions.Nat Biotechnol2020
32699374Author Correction: A robust benchmark for detection of germline large deletions and insertions.Nat Biotechnol2020
30559433Long-read sequence and assembly of segmental duplications.Nat Methods2019
31659027Human-specific tandem repeat expansion and differential gene expression during primate evolution.Proc Natl Acad Sci U S A2019
29295848Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data.Genome Res2018
29880660High-resolution comparative analysis of great ape genomes.Science2018
30452458Deleterious mitochondrial DNA point mutations are overrepresented in Drosophila expressing a proofreading-defective DNA polymerase γ.PLoS Genet2018
27895111Discovery and genotyping of structural variation from long-read haploid genome sequence data.Genome Res2017
28104618HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies.Genome Res2017
28808695Resolving multicopy duplications <i>de novo</i> using polyploid phasing.Res Comput Mol Biol2017
27034376Long-read sequence assembly of the gorilla genome.Science2016
27956617Assembly of long error-prone reads using de Bruijn graphs.Proc Natl Acad Sci U S A2016
27271295Extensive sequencing of seven human genomes to characterize benchmark reference materials.Sci Data2016
25383537Resolving the complexity of the human genome using single-molecule sequencing.Nature2015
26432246An integrated map of structural variation in 2,504 human genomes.Nature2015
26442640Genetic variation and the de novo assembly of human genomes.Nat Rev Genet2015
24418700Reconstructing complex regions of genomes using long-read sequencing technology.Genome Res2014
23104886STAR: ultrafast universal RNA-seq aligner.Bioinformatics2013
22988817Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory.BMC Bioinformatics2012
21999285Paired de bruijn graphs: a novel approach for incorporating mate pair information into genome assemblers.J Comput Biol2011
19056694De novo fragment assembly with short mate-paired reads: Does the read length matter?Genome Res2009
18083777Short read fragment assembly of bacterial genomes.Genome Res2008
17189424Microinversions in mammalian evolution.Proc Natl Acad Sci U S A2006
15059830Fragment assembly with short reads.Bioinformatics2004
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Collaborators

Evan E Eichler
University of Washington
Co-authored papers 18
Adam M Phillippy
National Human Genome Research Institute, National Institutes of Health
Co-authored papers 7
Richard K Wilson
The Ohio State University
Co-authored papers 7
Pavel A Pevzner
University of California
Co-authored papers 6
Tina Graves
McDonnell Genome Institute, Washington University
Co-authored papers 6
Tobias Marschall
Center for Digital Medicine, Heinrich Heine University Dusseldorf
Co-authored papers 6
Fritz J Sedlazeck
Baylor College of Medicine
Co-authored papers 6
Benedict Paten
UC Santa Cruz Genomics Institute, University of California
Co-authored papers 6
Ryan E Mills
University of Michigan Medical School ann arbor
Co-authored papers 5
Joyce Lee
Co-authored papers 5
Ken Chen
University of Texas MD Anderson Cancer Center
Co-authored papers 4
Christopher E Mason
Feil Family Brain and Mind Research Institute.
Co-authored papers 4
Paul Flicek
European Bioinformatics Institute
Co-authored papers 4
Alex R Hastie
Co-authored papers 4
Can Alkan
Bilkent University
Co-authored papers 4
Jan O Korbel
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 4
Ali Bashir
Google Accelerated Science Team, Google Inc
Co-authored papers 4
David Haussler
Genomics Institute, University of California Santa Cruz
Co-authored papers 4
Justin M Zook
National Institute of Standards and Technology
Co-authored papers 4
Xian Fan
Rice University
Co-authored papers 4
Adam C English
Baylor College of Medicine Human Genome Sequencing Center
Co-authored papers 4
Ian T Fiddes
Liver Center and Diabetes Center, University of California san francisco
Co-authored papers 4
Mark Gerstein
Yale University
Co-authored papers 3
Michael C Schatz
Johns Hopkins University
Co-authored papers 3
Noah Spies
Stanford University
Co-authored papers 3
Stephen T Sherry
National Center for Biotechnology Information, National Institutes of Health
Co-authored papers 3
Nathan D Olson
National Institute of Standards and Technology
Co-authored papers 3
Chunlin Xiao
Chongqing Aier Eye Hospital
Co-authored papers 3
Weichen Zhou
Chengdu First People's Hospital
Co-authored papers 3
Fereydoun Hormozdiari
University of California davis
Co-authored papers 3
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