Author

Carl A. Baker

University of Washington

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Genomics· 4 Bioinformatics· 1 Evolutionary Biology· 1 Genetics· 1

Signature Assays, Organisms & Methods

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Organism:human· 7 Assay:whole-genome sequencing· 6 Approach:statistical model· 5 Approach:experimental assay· 4 Research Focus:genome assembly· 4 Research Focus:variant calling· 4 Research Focus:benchmarking· 2 Research Focus:database / resource· 2

Frequent Co-Authors

Katherine M. MunsoniD· 7 shared David PorubskỳiD· 6 shared Evan E. EichleriD· 6 shared Kendra HoekzemaiD· 6 shared Arang RhieiD· 4 shared Ashley D. SandersiD· 4 shared Sergey KoreniD· 4 shared Sergey NurkiD· 4 shared

Activity by Year

2019-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 45 mutual co-author links

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7 shared papersGenomics

Katherine M. MunsonORCID

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7 papers

Recent·Most cited

A global map for introgressed structural variation and selection in humans

PingHsun Hsieh, Natthapon Soisangwan, David Gordon, Athef Javidh, William T. Harvey, David Porubskỳ, Kendra Hoekzema, Carl A. Baker, Katherine M. Munson, Christopher Kinipi, Matthew Leavesley, Nicolas Brucato, Murray P. Cox, François‐Xavier Ricaut, Irene Gallego Romero, Evan E. Eichler

Long-read phased assemblies from two Papuans plus 47 HPRC genomes map archaic introgressed structural variants, revealing 11 candidate archaic centromeres and 16 candidate adaptive SVs.

Science · Jun 11, 2026Peer-reviewedEvolutionary Biology✦ In-depth digest

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

Glenn Hickey, Jean Monlong, Jana Ebler, Adam M. Novak, Jordan M. Eizenga, Yan Ping Gao, Haley Abel, Lucinda Fulton, Mobin Asri, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, Guillaume Bourque, Silvia Buonaiuto, , Valérie Schneider

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

Nature Biotechnology · May 10, 2023Peer-reviewedBioinformatics

A Draft Human Pangenome Reference

Wen‐Wei Liao, Mobin Asri, Jana Ebler, Daniel Doerr, Marina Haukness, Glenn Hickey, Shuangjia Lu, Julian Lucas, Jean Monlong, Haley Abel, Silvia Buonaiuto, Xian H. Chang, Haoyu Cheng, Justin Chu, Vincenza Colonna, , Francesca Floriana Tricomi

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

Nature · May 10, 2023Peer-reviewedGenomics

Recombination between heterologous human acrocentric chromosomes

Andrea Guarracino, Silvia Buonaiuto, Leonardo Gomes de Lima, Tamara Potapova, Arang Rhie, Sergey Koren, BORIS Y. RUBINSTEIN, Christian Fischer, Haley Abel, Lucinda L. Antonacci-Fulton, Mobin Asri, Gunjan Baid, Carl A. Baker, Anastasiya Belyaeva, Konstantinos Billis, , Ashley D. Sanders

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

Nature · May 10, 2023Peer-reviewedGenomics

Alpha satellite insertion close to an ancestral centromeric region

Giuliana Giannuzzi, Glennis A. Logsdon, Nicolas Chatron, Danny E. Miller, Julie Reversat, Katherine M. Munson, Kendra Hoekzema, Marie‐Noëlle Bonnet‐Dupeyron, Pierre‐Antoine Rollat‐Farnier, Carl A. Baker, Damien Sanlaville, Evan E. Eichler, Caroline Schluth‐Bolard, Alexandre Reymond

The paper reports a de novo alpha satellite DNA insertion near an ancestral centromere, showing it lacks centromeric functionality and does not disrupt genes or methylation.

Molecular Biology and Evolution · Aug 13, 2021Peer-reviewedGenetics

The structure, function, and evolution of a complete human chromosome 8

Glennis A. Logsdon, Mitchell Robert Vollger, PingHsun Hsieh, Yafei Mao, Mikhail A. Liskovykh, Sergey Koren, Sergey Nurk, Ludovica Mercuri, Philip C. Dishuck, Arang Rhie, Leonardo Gomes de Lima, Tatiana Dvorkina, David Porubskỳ, William T. Harvey, Alla Mikheenko, , Evan E. Eichler

This paper completes the linear assembly of human chromosome 8, resolves long-standing gaps, and analyzes the evolutionary history of its centromeric regions across great apes.

Nature · Apr 7, 2021Peer-reviewedGenomics

Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads

Mitchell Robert Vollger, Glennis A. Logsdon, Peter A. Audano, Arvis Sulovari, David Porubskỳ, Paul S. Peluso, Aaron M. Wenger, Gregory T. Concepcion, Zev N. Kronenberg, Katherine M. Munson, Carl A. Baker, Ashley D. Sanders, Diana C.J. Spierings, Peter M. Lansdorp, Urvashi Surti, , Evan E. Eichler

This study compares HiFi and CLR long-read sequencing for human genome assembly, finding HiFi provides better continuity and accuracy in complex regions but not centromeres or segmental duplications.

Annals of Human Genetics · Nov 11, 2019Peer-reviewedGenomics