Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice

by Thomas A Sasani, Aaron R Quinlan, Kelley Harris
Published 2024-02-01

Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate

by Thomas J. Nicholas, Michael J. Cormier, Aaron R. Quinlan
Published 2022-11-01

GEMINI: integrative exploration of genetic variation and genome annotations.

by Umadevi Paila, Brad A Chapman, Rory Kirchner, Aaron R Quinlan
Published 2013-01-01

Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies

by Michael J. Cormier, Brent S. Pedersen, Pinar Bayrak-Toydemir, Aaron R. Quinlan
Published 2022-11-01

Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays

by Thomas A Sasani, Kelsey R Cone, Aaron R Quinlan, Nels C Elde
Published 2018-08-01

A Systematic Review to Guide Future Efforts in the Determination of Genetic Causes of Pregnancy Loss

by Andrew Z. Carey, Nathan R. Blue, Nathan R. Blue, Michael W. Varner, Michael W. Varner, Jessica M. Page, Jessica M. Page, Nathorn Chaiyakunapruk, Nathorn Chaiyakunapruk, Aaron R. Quinlan, Aaron R. Quinlan, Aaron R. Quinlan, D. Ware Branch, D. Ware Branch, Robert M. Silver, Robert M. Silver, Tsegaselassie Workalemahu
Published 2021-12-01

Random allelic expression in the adult human body

by Stephanie N. Kravitz, Elliott Ferris, Michael I. Love, Alun Thomas, Aaron R. Quinlan, Christopher Gregg
Published 2023-01-01

Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data

by Michael J. Cormier, Jonathan R. Belyeu, Brent S. Pedersen, Joseph Brown, Johannes Köster, Aaron R. Quinlan
Published 2021-04-01

OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations

by Thomas J. Nicholas, Michael J. Cormier, Xiaomeng Huang, Yi Qiao, Gabor T. Marth, Aaron R. Quinlan
Published 2021-03-01

Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation

by Thomas A Sasani, Brent S Pedersen, Ziyue Gao, Lisa Baird, Molly Przeworski, Lynn B Jorde, Aaron R Quinlan
Published 2019-09-01

Samplot: a platform for structural variant visual validation and automated filtering

by Jonathan R. Belyeu, Murad Chowdhury, Joseph Brown, Brent S. Pedersen, Michael J. Cormier, Aaron R. Quinlan, Ryan M. Layer
Published 2021-05-01

Poxviruses capture host genes by LINE-1 retrotransposition

by Sarah M Fixsen, Kelsey R Cone, Stephen A Goldstein, Thomas A Sasani, Aaron R Quinlan, Stefan Rothenburg, Nels C Elde
Published 2022-09-01

XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data.

by Jordan A Berg, Jonathan R Belyeu, Jeffrey T Morgan, Yeyun Ouyang, Alex J Bott, Aaron R Quinlan, Jason Gertz, Jared Rutter
Published 2020-01-01

CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing.

by Amelia D Wallace, Thomas A Sasani, Jordan Swanier, Brooke L Gates, Jeff Greenland, Brent S Pedersen, Katherine E Varley, Aaron R Quinlan
Published 2021-01-01

Somalier: rapid relatedness estimation for cancer and germline studies using efficient genome sketches

by Brent S. Pedersen, Preetida J. Bhetariya, Joe Brown, Stephanie N. Kravitz, Gabor Marth, Randy L. Jensen, Mary P. Bronner, Hunter R. Underhill, Aaron R. Quinlan
Published 2020-07-01

Whole-genome sequencing analysis in families with recurrent pregnancy loss: A pilot study.

by Tsegaselassie Workalemahu, Cecile Avery, Sarah Lopez, Nathan R Blue, Amelia Wallace, Aaron R Quinlan, Hilary Coon, Derek Warner, Michael W Varner, D Ware Branch, Lynn B Jorde, Robert M Silver
Published 2023-01-01

Effective variant filtering and expected candidate variant yield in studies of rare human disease

by Brent S. Pedersen, Joe M. Brown, Harriet Dashnow, Amelia D. Wallace, Matt Velinder, Martin Tristani-Firouzi, Joshua D. Schiffman, Tatiana Tvrdik, Rong Mao, D. Hunter Best, Pinar Bayrak-Toydemir, Aaron R. Quinlan
Published 2021-07-01

STRling: a k-mer counting approach that detects short tandem repeat expansions at known and novel loci

by Harriet Dashnow, Brent S. Pedersen, Laurel Hiatt, Joe Brown, Sarah J. Beecroft, Gianina Ravenscroft, Amy J. LaCroix, Phillipa Lamont, Richard H. Roxburgh, Miriam J. Rodrigues, Mark Davis, Heather C. Mefford, Nigel G. Laing, Aaron R. Quinlan
Published 2022-12-01

Comprehensive variant calling from whole‐genome sequencing identifies a complex inversion that disrupts ZFPM2 in familial congenital diaphragmatic hernia

by Thomas J. Nicholas, Najla Al‐Sweel, Andrew Farrell, Rong Mao, Pinar Bayrak‐Toydemir, Christine E. Miller, Dawn Bentley, Rachel Palmquist, Barry Moore, Edgar J. Hernandez, Michael J. Cormier, Eric Fredrickson, Katherine Noble, Shawn Rynearson, Carson Holt, Mary Anne Karren, Joshua L. Bonkowsky, Martin Tristani‐Firouzi, Mark Yandell, Gabor Marth, Aaron R. Quinlan, Luca Brunelli, Reha M. Toydemir, Brian J. Shayota, John C. Carey, Steven E. Boyden, Sabrina Malone Jenkins
Published 2022-04-01

Publisher Correction: Combating subclonal evolution of resistant cancer phenotypes

by Samuel W. Brady, Jasmine A. McQuerry, Yi Qiao, Stephen R. Piccolo, Gajendra Shrestha, David F. Jenkins, Ryan M. Layer, Brent S. Pedersen, Ryan H. Miller, Amanda Esch, Sara R. Selitsky, Joel S. Parker, Layla A. Anderson, Brian K. Dalley, Rachel E. Factor, Chakravarthy B. Reddy, Jonathan P. Boltax, Dean Y. Li, Philip J. Moos, Joe W. Gray, Laura M. Heiser, Saundra S. Buys, Adam L. Cohen, W. Evan Johnson, Aaron R. Quinlan, Gabor Marth, Theresa L. Werner, Andrea H. Bild
Published 2018-02-01