Publications

Preprints

2025

AVITI sequencing of a four-generation CEPH/Utah pedigree confirms low mutation rates at homopolymer loci despite their low sequence complexity. Hannah C Happ, Thomas A Sasani, Derek Warner, Deborah W Neklason, Aaron R Quinlan. bioRxiv

The selective dynamics of interruptions at short tandem repeats. Michael E. Goldberg, Harriet Dashnow, Kelley Harris, Aaron R Quinlan bioRxiv

2024

Sperm from infertile, oligozoospermic men have elevated mutation rates. Jason Kunisaki, Michael E Goldberg, Suchita Lulla, Thomas Sasani, Laurel Hiatt, Thomas J Nicholas, Lihua Liu, Elizabeth Torres-Arce, Yixuan Guo, Emma James, Joshua J Horns, Joemy M Ramsay, Qi Chen, James M Hotaling, Kenneth I Aston, Aaron R Quinlan. medRxiv

TRGT-denovo: accurate detection of de novo tandem repeat mutations. Mokveld T, Dolzhenko E, Dashnow H, Nicholas TJ, Sasani T, van der Sanden B, Jadhav B, Pedersen B, Kronenberg Z, Tucci A, Sharp AJ, Quinlan AR, Gilissen C, Hoischen A, Eberle MA. bioRxiv

2023

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

2025

Human de novo mutation rates from a four-generation pedigree reference. David Porubsky, Harriet Dashnow, Thomas A Sasani, Glennis A Logsdon, Pille Hallast, Michelle D Noyes, Zev N Kronenberg, Tom Mokveld, Nidhi Koundinya, Cillian Nolan, Cody J Steely, Andrea Guarracino, Egor Dolzhenko, William T Harvey, William J Rowell, Kirill Grigorev, Thomas J Nicholas, Keisuke K Oshima, Jiadong Lin, Peter Ebert, W Scott Watkins, Tiffany Y Leung, Vincent CT Hanlon, Sean McGee, Brent S Pedersen, Michael E Goldberg, Hannah C Happ, Hyeonsoo Jeong, Katherine M Munson, Kendra Hoekzema, Daniel D Chan, Yanni Wang, Jordan Knuth, Gage H Garcia, Cairbre Fanslow, Christine Lambert, Charles Lee, Joshua D Smith, Shawn Levy, Christopher E Mason, Erik Garrison, Peter M Lansdorp, Deborah W Neklason, Lynn B Jorde, Aaron R Quinlan, Michael A Eberle, Evan E Eichler. Nature

The Utah NeoSeq Project: a collaborative multidisciplinary program to facilitate genomic diagnostics in the neonatal intensive vare unit. Sabrina Malone Jenkins, Rachel N. Palmquist, Barry Moore, Steven E. Boyden, Thomas J. Nicholas, Pinar Bayrak-Toydemir, Rong Mao, J., Andrew R. Farrell, Carson H. Holt, Shawn G. Rynearson, Chelsea M. Solorzano, Alistair Ward, D. Hunter Best, Najla Al-Sweel, Dawn L. Bentley, Luca Brunelli, Clement Y. Chow, Devin W. Close, Michael J. Cormier, Malia J. Deshotel, Jacob Durtschi, Erik J. Eide, Luaiva Floyd, Eric K. Fredrickson, Makenzie L. Fulmer, Edgar J. Hernandez, Ashley L. Kapron, Mary Anne Karren, Robert G. Lewis, Christine E. Miller, L. Charles Murtaugh, Kelsey E. Nicholson, Katherine Noble, Brendan D. O’Fallon, John M. O’Shea, David C. Pattison, Brent S. Pedersen, Brandy J. Petersen, Bennet D. Peterson, Lucilla Pizzo, Hayley M. Reynolds, Paul Rindler, Carrie B. Torr, Ting Wen, H. Joseph Yost, Jian Zhao, Mark Yandell, Gabor T. Marth, Aaron R. Quinlan, John C. Carey, Brian J. Shayota, Martin Tristani-Firouzi & Joshua L. Bonkowsky. NPJ Genomic Medicine.

Identification of CNTN2 as a genetic modifier of PIGA-CDG in a family with incomplete penetrance and in Drosophila. Holly J Thorpe, Brent S Pedersen, Miranda Dietze, Nichole Link, Aaron R Quinlan, Joshua L Bonkowsky, Ashley Thomas, Clement Y Chow. The American Journal of Human Genetics.

STRchive: a dynamic resource detailing population-level and locus-specific insights at tandem repeat disease loci. Laurel Hiatt, Ben Weisburd, Egor Dolzhenko, Vincent Rubinetti, Akshay K Avvaru, Grace E VanNoy, Nehir Edibe Kurtas, Heidi L Rehm, Aaron R Quinlan, Harriet Dashnow. Genome Medicine.

A genome-wide approach for the discovery of novel repeat expansion disorders in the Undiagnosed Diseases Network cohort. Sarah Fazal, Harriet Dashnow, Maike F. Dohrn, Jacquelyn Raposo, Laurel Hiatt, Matt C. Danzi, Isaac R.L. Xu, Camilo Toro, David R. Adams, Karen Usdin, Bruce Hayward, Shipa Nadimpalli Kobren, Shamil R. Sunyaev, Rebecca C. Spillmann, Vandana Shashi, Adriana Rebelo, Guney Bademci. Genetics in Medicine.

The Platinum Pedigree: A long-read benchmark for genetic variants. Zev Kronenberg, Cillian Nolan, David Porubsky, Tom Mokveld, William J Rowell, Sangjin Lee, Egor Dolzhenko, Pi-Chuan Chang, James M Holt, Christopher T Saunders, Nathan D Olson, Sean McGee, Andrea Guarracino, Nidhi Koundinya, William T Harvey, W Scott Watkins, Katherine M Munson, Kendra Hoekzema, Khi Pin Chua, Cairbre Fanslow, Christine Lambert, Harriet Dashnow, Erik Garrison, Josh D Smith, Peter M Lansdorp, Justin M Zook, Andrew Carroll, Lynn B Jorde, Deborah W Neklason, Aaron R Quinlan, Evan E Eichler, Michael A Eberle. Nature Methods.

Vcfexpress: flexible, rapid user-expressions to filter and format VCFs. Brent S. Pedersen, Aaron R. Quinlan. Bioinformatics.

2024

Improved characterization of single-cell RNA-seq libraries with paired-end avidity sequencing. John T Chamberlin, Austin E Gillen, Aaron R. Quinlan. NAR Genomics and Bioinformatics.

De novo AHDC1 deletions identified by genome sequencing in two individuals with Xia-Gibbs syndrome.Miriam Bertrand, Gulalai Shah, Brent S Pedersen, Alexander Schulz, Anja Weise, Thomas Liehr, Peter Huppke, Stephanie DiTroia, Aaron R Quinlan, Tobias B Haack, Ralf A Husain. Molecular Syndromology

The Undiagnosed Diseases Network: characteristics of solvable applicants and diagnostic suggestions for nonaccepted ones. John J Mulvihill, Laura Findley, Weihong Ni, Janet S Sinsheimer, F Session Cole, Cecilia Esteves, Jonathan A Bernstein, John H Newman, Matthew T Wheeler, Jill R Mokry, and the Undiagnosed Diseases Network. Genetics in Medicine

Characterization and visualization of tandem repeats at genome scale. Egor Dolzhenko, Adam English, Harriet Dashnow, Guilherme De Sena Brandine, Tom Mokveld, William J Rowell, Caitlin Karniski, Zev Kronenberg, Matt C Danzi, Warren A Cheung, Chengpeng Bi, Emily Farrow, Aaron Wenger, Khi Pin Chua, Verónica Martínez-Cerdeño, Trevor D Bartley, Peng Jin, David L Nelson, Stephan Zuchner, Tomi Pastinen, Aaron R Quinlan, Fritz J Sedlazeck, Michael A Eberle. Nature Biotechnology

Placental somatic mutation in human stillbirth and live birth: a pilot case-control study of paired placental, fetal, and maternal whole genomes. Amelia D Wallace, Nathan R Blue, Terry Morgan, Tsegaselassie Workalemahu, Robert M Silver, Aaron R Quinlan. Placenta.

Dominant missense variants in SREBF2 are associated with complex dermatalogical, neurological, and skeletal abnormalities. Matthew J Moulton, Kristhen Atala, Yiming Zheng, Debdeep Dutta, Dorothy K Grange, Wen-Wen Lin, Daniel J Wegner, Jennifer A Wambach, Angela L Duker, Michael B Bober, Lisa Kratz, Carol A Wise, Ila Oxendine, Anas Khanshour, and the Undiagnosed Diseases Network. Genetics in Medicine

Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder. Jennefer N Kohler, Nicole R Legro, Dustin Baldridge, Jimann Shin, Angela Bowman, Berrak Ugur, Madelyn M Jackstadt, Leah P Shriver, Gary J Patti, Bo Zhang, Wenjia Feng, Anthony R McAdow, Pagé Goddard, Rachel A Ungar, Tanner Jensen, Kevin S Smith, Laure Fresard, Raquel Alvarez, Devon Bonner, Chloe M Reuter, Colleen McCormack, Elijah Kravets, Shruti Marwaha, James M Holt, and the Undiagnosed Diseases Network. Genetics in Medicine

Inherited genetic risk in stillbirth: a shared genomic segments analysis of high-risk pedigrees. Tsegaselassie Workalemahu, Michael J Madsen, Sarah Lopez, Jessica M Page, Nathan R Blue, Cecile Avery, Rob Sargent, Zhe Yu, Emily Guinto, D Ware Branch, Susannah Leisher, Lynn B Jorde, Aaron R Quinlan, Hilary Coon, Michael W Varner, Claire T Roberts, Deborah W Neklason, Nicola J Camp, Robert M Silver. Human Genetics and Genomics Advances

Immunological and hematological findings as major features in a patient with a new germline pathogenic CBL variant. Emilia Stellacci, Jennefer N Carter, Luca Pannone, David Stevenson, Dorsa Moslehi, Serenella Venanzi, and the Undiagnosed Diseases Network. American Journal of Medical Genetics.

Undiagnosed Disease Network collaborative approach in diagnosing rare disease in a patient with a mosaic CACNA1D variant. Kimberly M Ezell, Rory J Tinker, Yutaka Furuta, Alican Gulsevin, Lisa Bastarache, Rizwan Hamid, Joy D Cogan, Lynette Rives, Serena Neumann, Brian Corner, Mary Kozuria, John A Phillips III, and the Undiagnosed Diseases Network. American Journal of Medical Genetics

EFEMPT1 haploinsufficiency causes a Marfan-like herediatary connective tissue disorder. Irman Forghani, Steven H Lang, Matthew J Rodier, Stephanie A Bivona, and the Undiagnosed Diseases Network. American Journal of Medical Genetics

Exome and genome sequencing in a heterogeneous population of patients with rare disease: identifying predictors of a diagnosis. Jenna Pucel, Lauren C Briere, Chloe Reuter, Perman Gochyyev, and the Undiagnosed Diseases Network. Genetics in Medicine

Recurrent ATP1A1 variant Gly903Arg causes developmental delay, intellectual disability, and autism. Maike F Dohrn, Guney Bademci, Adriana P Rebelo, Médéric Jeanne, Nicholas A Borja, Danique Beijer, Matt C Danzi, Stephanie A Bivona, Paul Gueguen, Mohammad F Zafeer, and the Undiagnosed Diseases Network. Annals of Clinical and Translational Neurology

Effects of parental age and polymer composition on short tandem repeat de novo mutation rates. Michael E Goldberg, Michelle D Noyes, Evan E Eichler, Aaron R Quinlan, Kelley Harris. Genetics

De novo variants in DENND5B cause a neurodevelopmental disorder. Marcello Scala, Valeria Tomati, Matteo Ferla, Mariateresa Lena, Julie S Cohen, Ali Fatemi, Elly Brokamp, Anna Bican, John A Phillips, Mary E Koziura, Michael Nicouleau, Marlene Rio, Karine Siquier, Nathalie Boddaert, Ilaria Musante, Serena Tamburro, Simona Baldassari, Michele Iacomino, Paolo Scudieri, Maria T Acosta, David R Adams, Raquel L Alvarez, Justin Alvey, Aimee Allworth, Ashley Andrews, Euan A Ashley, Ben Afzali, Carlos A Bacino, Guney Bademci, Ashok Balasubramanyam, Dustin Baldridge, Jim Bale, Michael Bamshad, Deborah Barbouth, Pinar Bayrak-Toydemir, Anita Beck, Alan H Beggs, Edward Behrens, Gill Bejerano, Hugo J Bellen, Jimmy Bennett, Jonathan A Bernstein, Gerard T Berry, Stephanie Bivona, Elizabeth Blue, John Bohnsack, Devon Bonner, Lorenzo Botto, Lauren C Briere, Gabrielle Brown, Elizabeth A Burke, Lindsay C Burrage, Manish J Butte, Peter Byers, William E Byrd, John Carey, Olveen Carrasquillo, Thomas Cassini, Ta Chen Peter Chang, Sirisak Chanprasert, HsiaoTuan Chao, Ivan Chinn, Gary D Clark, Terra R Coakley, Laurel A Cobban, Joy D Cogan, Matthew Coggins, F Sessions Cole, Heather A Colley, Heidi Cope, Rosario Corona, William J Craigen, Andrew B Crouse, Michael Cunningham, Precilla D’Souza, Hongzheng Dai, Surendra Dasari, Joie Davis, Jyoti G Dayal, Margaret Delgado, Esteban C Dell’Angelica, Katrina Dipple, Daniel Doherty, Naghmeh Dorrani, Argenia L Doss, Emilie D Douine, Dawn Earl, David J Eckstein, Lisa T Emrick, Christine M Eng, Marni Falk, Elizabeth L Fieg, Paul G Fisher, Brent L Fogel, Irman Forghani, Jiayu Fu, William A Gahl, Ian Glass, Page C Goddard, Rena A Godfrey, Alana Grajewski, Andrea Gropman, Meghan C Halley, Rizwan Hamid, Neal Hanchard, Kelly Hassey, Nichole Hayes, Frances High, Anne Hing, Fuki M Hisama, Ingrid A Holm, Jason Hom, Martha Horike-Pyne, Alden Huang, Yan Huang, Sarah Hutchison, Wendy Introne, Rosario Isasi, Kosuke Izumi, Gail P Jarvik, Jeffrey Jarvik, Suman Jayadev, Orpa Jean-Marie, Vaidehi Jobanputra, Emerald Kaitryn, Shamika Ketkar, Dana Kiley, Gonench Kilich, Shilpa N Kobren, Isaac S Kohane, Jennefer N Kohler, Susan Korrick, Deborah Krakow, Donna M Krasnewich, Elijah Kravets, Seema R Lalani, Byron Lam, Christina Lam, Brendan C Lanpher, Ian R Lanza, Kimberly LeBlanc, Brendan H Lee, Roy Levitt, Richard A Lewis, Pengfei Liu, Xue Zhong Liu, Nicola Longo, Sandra K Loo, Joseph Loscalzo, Richard L Maas. American Journal of Human Genetics

Recurring homozygous ACTN2 variant (p.Arg506Gly) causes a recessive myopathy. Sandra Donkervoort, Payam Mohassel, Melanie O’Leary, Devon E Bonner, Taila Hartley, Nicole Acquaye, Astrid Brull, Tahseen Mozaffar, Mario A Saporta, David A Dyment, Jacinda B Sampson, Sander Pajusalu, Christina Austin‐Tse, Kyle Hurth, Julie S Cohen, Kirsty McWalter, Jodi Warman‐Chardon, Amy Crunk, A Reghan Foley, and the Undiagnosed Diseases Network. Annals of Clinical and Translational Neurology

Loss of the endoplasmic reticulum protein Tmem208 affects cell polarity, development, and viability. Debdeep Dutta, Oguz Kanca, Rishi V Shridharan, Paul C Marcogliese, Benjamin Steger, Marie Morimoto, F Graeme Frost, Ellen Macnamara, Undiagnosed Diseases Network, Michael F Wangler, Shinya Yamamoto, Andreas Jenny, David Adams, May C Malicdan, Hugo J Bellen. PNAS

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

Biallelic CRELD1 variants cause a multisystem syndrome, including neurodevelopmental phenotypes, cardiac dysrhythmias, and frequent infections. Lauren Jeffries, Emily K Mis, Kirsty McWalter, Sandra Donkervoort, Nina N Brodsky, Jean-Marie Carpier, Weizhen Ji, Cristian Ionita, Bhaskar Roy, Jon S Morrow, Armine Darbinyan, Krishna Iyer, Ritu B Aul, Siddharth Banka, Katherine R Chao, Laura Cobbold, Stacey Cohen, Helena M Custodio, Margaret Drummond-Borg, Frances Elmslie, Erika Finanger, Bryan E Hainline, Ingo Helbig, Stacy Hewson, Ying Hu, Adam Jackson, Dragana Josifova, Monica Konstantino, Meganne E Leach, Bryan Mak, David McCormick, Elisabeth McGee, Stanley Nelson, Joanne Nguyen, Kimberly Nugent, Lucy Ortega, Howard P Goodkin, Elizabeth Roeder, Sani Roy, Katie Sapp, Dimah Saade, Sanjay M Sisodiya, Karen Stals, Shelley Towner, William Wilson, and the Deciphering Developmental Disorders Consortium, the Genomics England Research Consortium, and the Undiagnosed Disease Network. Genetics in Medicine

A syndromic neurodevelopmental disorder caused by rare variants in PPFIA3. Maimuna S Paul, Sydney L Michener, Hongling Pan, Hiuling Chan, Jessica M Pfliger, Jill A Rosenfeld, Vanesa C Lerma, Alyssa Tran, Megan A Longley, Richard A Lewis, Monika Weisz-Hubshman, Mir Reza Bekheirnia, Nasim Bekheirnia, Lauren Massingham, Michael Zech, Matias Wagner, Hartmut Engels, Kirsten Cremer, Elisabeth Mangold, Sophia Peters, Jessica Trautmann, Claudia Perne, Jessica L Mester, Maria J Guillen Sacoto, Richard Person, Pamela P McDonnell, Stacey R Cohen, Laina Lusk, Ana SA Cohen, Jean-Baptiste Le Pichon, Tomi Pastinen, Dihong Zhou, Kendra Engleman, Caroline Racine, Laurence Faivre, Sébastien Moutton, Anne-Sophie Denommé-Pichon, Hyun Yong Koh, Annapurna Poduri, Jeffrey Bolton, Cordula Knopp, Dong Sun Julia Suh, Andrea Maier, Mehran Beiraghi Toosi, Ehsan Ghayoor Karimiani, Reza Maroofian, Gerald Bradley Schaefer, Vijayalakshmi Ramakumaran, Pradeep Vasudevan, Benito Banos-Pinero, Alistair T Pagnamenta, Chitra Prasad, Matthew Osmond, Sarah Schuhmann, Georgia Vasileiou, Sophie Russ-Hall, Ingrid E Scheffer, Gemma L Carvill, Heather Mefford, and the Undiagnosed Disease Network. American Journal of Human Genetics

De novo missense variants in ZBTB47 are associated with developmental delays, hypotonia, seizures, gait abnormalities, and variable movement abnormalities. Scott K Ward, Alexandrea Wadley, Chun‐hui Tsai, Paul J Benke, Lisa Emrick, Kristen Fisher, Kimberly M Houck, Hongzheng Dai, and the Undiagnosed Diseases Network. American Journal of Medical Genetics

Unraveling non-participation in genomic research: a complex interplay of barriers, facilitators, and sociocultural factors. Allyn McConkie‐Rosell, Rebecca C Spillmann, Kelly Schoch, Jennifer A Sullivan, Nicole Walley, Marie McDonald, the Undiagnosed Diseases Network, Stephen R Hooper, Vandana Shashi. Journal of Genetic Counseling

H4C5 missense variant leads to a neurodevelopmental phenotype overlapping with Angelman syndrome. Nicholas Borja, Paulo Borjas‐Mendoza, Stephanie Bivona, LéShon Peart, Joanna Gonzalez, Brittney Keira Johnson, Shengru Guo, Roman Yusupov, and the Undiagnosed Diseases Network. American Journal of Medical Genetics.

De novo variants in MRTFB have gain-of-function activity in Drosophila and are associated with a novel neurodevelopmental phenotype with dysmorphic features. Jonathan C Andrews, Jung-Wan Mok, Oguz Kanca, Sharayu Jangam, Cynthia Tifft, Ellen F Macnamara, Bianca E Russell, Lee-kai Wang, and the Undiagnosed Diseases Network. Genetics in Medicine

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 R 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 R Quinlan. GigaScience.

Settling the score: variant prioritization and Mendelian disease. Karen Eilbeck*, Aaron R 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.