Publications by authors named "Mark Chaisson"

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Long-read sequencing identifies FGF14 repeat expansions in Parkinson's disease.
Fulya Akçimen, Kensuke Daida, Lara M Lange, Abraham Moller, Abigail Miano-Burkhardt, Mark Chaisson

Brain· December 2025

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Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes.
Walfred Ma, Mark J P Chaisson

Nat Genet· November 2025

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Author Correction: Complex genetic variation in nearly complete human genomes.
Glennis A Logsdon, Peter Ebert, Peter A Audano, Mark Loftus, David Porubsky, Mark J P Chaisson

Nature· September 2025

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Complex genetic variation in nearly complete human genomes.
Glennis A Logsdon, Peter Ebert, Peter A Audano, Mark Loftus, David Porubsky, Mark J P Chaisson

Nature· August 2025

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Long-read sequencing identifies repeat expansions in Parkinson's disease.
Fulya Akçimen, Kensuke Daida, Lara M Lange, Abraham Moller, Abigail Miano-Burkhardt, Mark Chaisson

medRxiv· August 2025

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Identification of GGC Repeat Expansions in ZFHX3 among Chilean Movement Disorder Patients.
Paula Saffie-Awad, Abraham Moller, Kensuke Daida, Pilar Alvarez Jerez, Zhongbo Chen, Mark J P Chaisson

Mov Disord· July 2025

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Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes.
Walfred Ma, Mark Jp Chaisson

bioRxiv· April 2025

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Analysis and benchmarking of small and large genomic variants across tandem repeats.
Adam C English, Egor Dolzhenko, Helyaneh Ziaei Jam, Sean K McKenzie, Nathan D Olson, Mark J P Chaisson

Nat Biotechnol· March 2025

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Identification of GGC Repeat Expansions in Among Chilean Movement Disorder Patients.
Paula Saffie-Awad, Abraham Moller, Kensuke Daida, Pilar Alvarez Jerez, Zhongbo Chen, Mark Jp Chaisson

medRxiv· March 2025

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An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes.
Chong Li, Marc Jan Bonder, Sabriya Syed, Matthew Jensen, , Mark J P Chaisson

Genome Res· December 2024

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Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation.
Kimberley J Billingsley, Melissa Meredith, Kensuke Daida, Pilar Alvarez Jerez, Shloka Negi, Mark Chaisson

bioRxiv· December 2024

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Complex genetic variation in nearly complete human genomes.
Glennis A Logsdon, Peter Ebert, Peter A Audano, Mark Loftus, David Porubsky, Mark J P Chaisson

bioRxiv· September 2024

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VISTA: an integrated framework for structural variant discovery.
Varuni Sarwal, Seungmo Lee, Jianzhi Yang, Sriram Sankararaman, Mark Chaisson

Brief Bioinform· July 2024

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Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy.
Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjorn Grüning, Mark J P Chaisson

Nat Biotechnol· March 2024

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A High-Quality Blue Whale Genome, Segmental Duplications, and Historical Demography.
Yury V Bukhman, Phillip A Morin, Susanne Meyer, Li-Fang Chu, Jeff K Jacobsen, Mark J P Chaisson

Mol Biol Evol· March 2024

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Chromosome level genome assembly of the Etruscan shrew Suncus etruscus.
Yury V Bukhman, Susanne Meyer, Li-Fang Chu, Linelle Abueg, Jessica Antosiewicz-Bourget, Mark J P Chaisson

Sci Data· February 2024

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Advances in the discovery and analyses of human tandem repeats.
Mark J P Chaisson, Arvis Sulovari, Paul N Valdmanis, Danny E Miller, Evan E Eichler

Emerg Top Life Sci· December 2023

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Benchmarking of small and large variants across tandem repeats.
Adam English, Egor Dolzhenko, Helyaneh Ziaei Jam, Sean Mckenzie, Nathan D Olson, Mark J P Chaisson

bioRxiv· November 2023

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Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation.
Mikhail Kolmogorov, Kimberley J Billingsley, Mira Mastoras, Melissa Meredith, Jean Monlong, Mark Chaisson

Nat Methods· October 2023

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HQAlign: aligning nanopore reads for SV detection using current-level modeling.
Dhaivat Joshi, Suhas Diggavi, Mark J P Chaisson, Sreeram Kannan

Bioinformatics· October 2023

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vamos: variable-number tandem repeats annotation using efficient motif sets.
Jingwen Ren, Bida Gu, Mark J P Chaisson

Genome Biol· July 2023

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Scalable, accessible, and reproducible reference genome assembly and evaluation in Galaxy.
Delphine Larivière, Linelle Abueg, Nadolina Brajuka, Cristóbal Gallardo-Alba, Bjorn Grüning, Mark Chaisson

bioRxiv· June 2023

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A draft human pangenome reference.
Wen-Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Mark J P Chaisson

Nature· May 2023

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The motif composition of variable number tandem repeats impacts gene expression.
Tsung-Yu Lu, Paulina N Smaruj, Geoffrey Fudenberg, Nicholas Mancuso, Mark J P Chaisson

Genome Res· April 2023

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Structural variation across 138,134 samples in the TOPMed consortium.
Goo Jun, Adam C English, Ginger A Metcalf, Jianzhi Yang, Mark Jp Chaisson

Res Sq· February 2023

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