Publications

Preprints

2023

Epistasis between mutator alleles contributes to germline mutation rate variability in laboratory mice. Thomas A Sasani, Aaron R Quinlan, Kelley Harris. bioRxiv

Resolving the unsolved: Comprehensive assessment of tandem repeats at scale Egor Dolzhenko, Adam English, Harriet Dashnow, Guilherme De Sena Brandine, Tom Mokveld, William J. Rowell, Caitlin Karniski, Zev Kronenberg, Matt C. Danzi, Warren Cheung, Chengpeng Bi, Emily Farrow, Aaron Wenger, Verónica Martínez-Cerdeño, Trevor D Bartley, Peng Jin, David Nelson, Stephan Zuchner, Tomi Pastinen,
Aaron R Quinlan, Fritz J. Sedlazeck, Michael A Eberle. bioRxiv

2022

Variable RNA sampling biases mediate concordance of single-cell and nucleus sequencing across cell types. John T Chamberlin, Younghee Lee, Gabor T Marth, Aaron R Quinlan. bioRxiv

Estimation of offspring genetic risk scores using parental genotypes. Adebayo Adesomo, Tsegaselassie Workalemahu, Matthew Givens, Mark Yandell, Aaron R Quinlan, Martin Tristani-Firouzi, Sarah Heerboth, Robert Silver, Nathan R Blue. medRxiv.

Peer-reviewed manuscripts

2023

Familial aggregation of stillbirth: A pedigree analysis of a matched case–control study. Tsegaselassie Workalemahu, Jessica M Page, Huong Meeks, Zhe Yu, Emily Guinto, Alison Fraser, Michael W Varner, Lauren H Theilen, Aaron R Quinlan, Hilary Coon, Daniel A Enquobahrie, Cande V Ananth, Fasil Tekola‐Ayele, Lynn B Jorde, Robert M Silver. BJOG: An International Journal of Obstetrics & Gynaecology

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

Random allelic expression in the adult human body. Stephanie N Kravitz, Elliott Ferris, Michael I Love, Alun Thomas, Aaron R Quinlan, Christopher Gregg. Cell Reports

2022

Extensive recombination-driven coronavirus diversification expands the pool of potential pandemic pathogens. Stephen A. Goldstein, Joe Brown, Brent S Pedersen, Aaron R. Quinlan, Nels C. Elde. Genome Biology and Evolution

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

Annotation of structural variants with reported allele frequencies and related metrics from multiple datasets using SVAFotate. Thomas J Nicholas, Michael J Cormier, Aaron R Quinlan. BMC Bioinformatics

Combining genetic constraint with predictions of alternative splicing to prioritize deleterious splicing in rare disease studies. Michael J Cormier, Brent S Pedersen, Pinar Bayrak-Toydemir, Aaron R Quinlan. BMC Bioinformatics

Poxviruses capture host genes by LINE-1 retrotransposition. Sarah M. Fixsen, Kelsey R. Cone, Stephen A. Goldstein, Thomas A. Sasani, Aaron R. Quinlan, Stefan Rothenburg, Nels C. Elde. eLife.

Integrating precision medicine into the standard of care for male infertility: what will it take? Jason Kunisaki, Aaron Quinlan, Kenneth I Aston, James Hotaling. European Urology

Searching thousands of genomes to classify somatic and novel structural variants using STIX. Murad Chowdhury, Brent S Pedersen, Fritz J Sedlazeck, Aaron R Quinlan, Ryan M Layer. Nature Methods

trfermikit: a tool to discover VNTR-associated deletions. Peter McHale & Aaron R Quinlan. Bioinformatics.

2021

Genes affecting ionizing radiation survival identified through combined exome sequencing and functional screening. Meenal Gupta, Xiangfei Liu, Sharon N. Teraoka, Jocyndra A. Wright, Richard A. Gatti, Aaron R. Quinlan, Patrick Concannon. Human Mutation

Effective variant filtering and expected candidate variant yield in studies of rare human disease. Brent S. Pedersen, Joseph Brown, Harriet Dashnow, Amelia D. Wallace, Matt Velinder, Tatiana Tvrdik, Rong Mao, D. Hunter Best, Pinar Bayrak-Toydemir, Aaron R. Quinlan. NPJ Genomic Medicine.

Go Get Data (GGD) is a framework that facilitates reproducible access to genomic data. Michael J. Cormier, Jonathan R. Belyeu, Brent S. Pedersen, Joseph Brown, Johannes Koster, Aaron R. Quinlan. Nature Communications.

Samplot: a platform for structural variant visual validation and automated filtering. Jonathan R. Belyeu, Murad Chowdhury, Joseph Brown, Brent S. Pedersen, Michael J. Cormier, Aaron R. Quinlan, Ryan M. Layer. Genome Biology.

De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families. Jonathan R. Belyeu, Harrison Brand, Harold Wang, Xuefang Zhao, Brent S. Pedersen, Julie Feusier, Meenal Gupta, Thomas J. Nicholas, Lisa Baird, Bernie Devlin, Stephan J. Sanders, Lynn B. Jorde, Michael E. Talkowski, Aaron R. Quinlan. AJHG.

OncoGEMINI: software for investigating tumor variants from multiple biopsies with integrated cancer annotations. Thomas J. Nicholas, Michael J. Cormier, Xiaomeng Huang, Yi Qiao, Gabor T. Marth, Aaron R. Quinlan. Genome Medicine.

Unfazed: parent-of-origin detection for large and small de novo variants. Jonathan R Belyeu, Thomas A Sasani, Brent S Pedersen, Aaron R. Quinlan. Bioinformatics.

Balancing efficient analysis and storage of quantitative genomics data with the D4 format and d4tools. Hao Hou, Brent Pedersen, Aaron R. Quinlan. Nature Computational Science.

CaBagE: a Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing. Amelia Wallace, Thomas A. Sasani, Jordan Swanier, Brooke L. Gates, Jeff Greenland, Brent S. Pedersen, K-T Varley, Aaron R. Quinlan. PLoS One.

2020

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

Germline mutation rates in young adults predict longevity and reproductive lifespan.] Richard M. Cawthon, Huong D. Meeks, Thomas A. Sasani, Ken R. Smith, Richard A. Kerber, Elizabeth O’Brien, Lisa Baird, Melissa M. Dixon, Andreas P. Peiffer, Mark F. Leppert, Aaron R. Quinlan, Lynn B. Jorde. Scientific Reports.

XPRESSyourself: Enhancing, standardizing, and automating ribosome profiling computational analyses yields improved insight into data.] Jordan A. Berg, Jonathan R. Belyeu, Jeffrey T. Morgan, Yeyun Ouyang, Alex J. Bott, Aaron R. Quinlan, Jason Gertz, Jared Rutter. PLoS Computational Biology.

2019

Large, three-generation CEPH families reveal post-zygotic mosaicism and variability in germline mutation accumulation. Thomas. A Sasani, Brent S. Pedersen, Ziyue Gao, Lisa Baird, Molly Przeworski, Lynn B. Jorde, Aaron R. Quinlan. eLife.

Duphold: scalable, depth-based annotation and curation of high-confidence structural variant calls. Brent S. Pedersen, Aaron R. Quinlan. GigaScience.

Overlooked roles of DNA damage and maternal age in generating human germline mutations. Ziyue Gao, Priya Moorjani, Thomas A. Sasani, Brent S. Pedersen, Aaron R. Quinlan, Lynn B. Jorde, Guy Amster, Molly Przeworski. PNAS.

Coexpression patterns define epigenetic regulators associated with neurological dysfunction. Leandros Boukas, James M. Havrilla, Peter F. Hickey, Aaron R. Quinlan, Hans T. Bjornsson, Kasper D. Hansen. Genome Research.

2018

A map of constrained coding regions in the human genome. James M. Havrilla, Brent S. Pedersen, Ryan M. Layer, Aaron R. Quinlan*. Nature Genetics.

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder. An JY, Lin K, Zhu L, Werling DM, Dong S, Brand H, Wang HZ, Zhao X, Schwartz GB, Collins RL, Currall BB, Dastmalchi C, Dea J, Duhn C, Gilson MC, Klei L, Liang L, Markenscoff-Papadimitriou E, Pochareddy S, Ahituv N, Buxbaum JD, Coon H, Daly MJ, Kim YS, Marth GT, Neale BM, Aaron R. Quinlan, Rubenstein JL, Sestan N, State MW, Willsey AJ, Talkowski ME, Devlin B, Roeder K, Sanders SJ. Science.

Long read sequencing reveals poxvirus evolution through rapid homogenization of gene arrays. Sasani TA, Cone KR, Aaron R. Quinlan, Elde NC. eLife.

Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy. Ostrander BEP, Butterfield RJ, Pedersen BS, Farrell AJ, Layer RM, Ward A, Miller C, DiSera T, Filloux FM, Candee MS, Newcomb T, Bonkowsky JL, Marth GT, Aaron R. Quinlan. NPJ Genomic Medicine.

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features. Simovski B, Kanduri C, Gundersen S, Titov D, Domanska D, Bock C, Bossini-Castillo L, Chikina M, Favorov A, Layer RM, Mironov AA, Aaron R. Quinlan, Sheffield NC, Trynka G, Sandve GK. Nucleic Acids Research.

SV-plaudit: A cloud-based framework for manually curating thousands of structural variants. Belyeu JR, Nicholas TJ, Pedersen BS, Sasani TA, Havrilla JM, Kravitz SN, Conway ME, Lohman BK, Aaron R. Quinlan, Layer RM.Gigascience.

hts-nim: scripting high-performance genomic analyses. Pedersen BS, Aaron R. Quinlan. Bioinformatics.

An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Donna M Werling, Harrison Brand, Joon-Yong An, Matthew R Stone, Joseph T Glessner, Lingxue Zhu, Ryan L Collins, Shan Dong, Ryan M Layer, Eiriene-Chloe Markenscoff-Papadimitriou, Andrew Farrell, Grace B Schwartz, Benjamin B Currall, Jeanselle Dea, Clif Duhn, Carolyn Erdman, Michael Gilson, Robert E Handsaker, Seva Kashin, Lambertus Klei, Jeffrey D Mandell, Tomasz J Nowakowski, Yuwen Liu, Sirisha Pochareddy, Louw Smith, Michael F Walker, Harold Z Wang, Mathew J Waterman, Xin He, Arnold R Kriegstein, John L Rubenstein, Nenad Sestan, Steven A McCarroll, Ben M Neale, Hilary Coon, A. Jeremy Willsey, Joseph D Buxbaum, Mark J Daly, Matthew W State, Aaron R. Quinlan, Gabor T Marth, Kathryn Roeder, Bernie Devlin, Michael E Talkowski, Stephan J Sanders. Nature Genetics.

Nanopore sequencing and assembly of a human genome with ultra-long reads. Miten Jain, Sergey Koren, Josh Quick, Arthur C Rand, Thomas A Sasani, John R Tyson, Andrew D Beggs, Alexander T Dilthey, Ian T Fiddes, Sunir Malla, Hannah Marriott, Karen H Miga, Tom Nieto, Justin O’Grady, Hugh E Olsen, Brent S Pedersen, Arang Rhie, Hollian Richardson, Aaron R. Quinlan, Terrance P Snutch, Louise Tee, Benedict Paten, Adam M. Phillippy, Jared T Simpson, Nicholas James Loman, Matthew Loose. Nature Biotechnology.

GIGGLE: a search engine for large-scale integrated genome analysis. Ryan M. Layer, Brent S. Pedersen, Tonya DiSera, Gabor T. Marth, Jason Gertz, Aaron R. Quinlan. Nature Methods.

mosdepth: quick coverage calculation for genomes and exomes. Brent S. Pedersen and Aaron R. Quinlan. Bioinformatics.

2017

Indexcov: fast coverage quality control for whole-genome sequencing. Brent S. Pedersen, Ryan L Collins, Michael E Talkowski, Aaron Quinlan. GigaScience.

Settling the score: variant prioritization and Mendelian disease. Karen Eilbeck*, Aaron Quinlan*, Mark Yandell. Nature Reviews Genetics.

Combating subclonal evolution of resistant cancer phenotypes. Andrea Bild, Samuel Brady, Jasmine McQuerry, Yi Qiao, Stephen Piccolo, Gajendra Shrestha, Ryan Layer, Brent Pedersen, David Jenkins, Ryan Miller, Amanda Esch, Sara Selitsky, Joel Parker, Layla Anderson, Chakravarthy Reddy, Jonathan Boltax, Dean Li, Philip Moos, Joe Gray, Laura Heiser, W. Evan Johnson, Saundra Buys, Adam Cohen, Aaron R. Quinlan, Gabor Marth, Theresa Werner, Brian Dalley, and Rachel Factor. Nature Communications.

Identification of ATIC as a novel target for chemoradiosensitization. Xiangfei Liu, Uma Devi Paila, Sharon N. Teraoka, Jocyndra A. Wright, Xin Huang, Aaron R. Quinlan, Richard A. Gatti and Patrick Concannon. International Journal of Radiation Oncology.

Who’s Who? Detecting and Resolving Sample Anomalies in Human DNA Sequencing Studies with Peddy. Brent S. Pedersen and Aaron R. Quinlan. American Journal of Human Genetics.

cyvcf2: fast, flexible variant analysis with Python. Brent S. Pedersen and Aaron R. Quinlan. Bioinformatics.