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J

James Holt

computational biology, pacbio

19H-index
99Paper Count
1.6KCitation Count
Published Papers 18
Publication Date
Complex structural variant visualization with SVTopo
err2025-10-11
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errOAAI
errJonathan R. Belyeu; William J. Rowell; Juniper A. Lake; James Matthew Holt; Zev Kronenberg; Christopher T. Saunders; Michael A. Eberle
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The Platinum Pedigree: a long-read benchmark for genetic variants
err2025-08-04
err0
errOAAI
errZev 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; Cody J. Steely; Sean McGee; Andrea Guarracino; Nidhi Koundinya; William T. Harvey; W. Scott Watkins; Katherine M. Munson; Kendra Hoekzema; Khi Pin Chua; Xiao Chen; Cairbre Fanslow; Christine Lambert; Harriet Dashnow; Erik Garrison; Joshua 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
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Jointly benchmarking small and structural variant calls with vcfdist
err2024-10-02
err0
errOAAI
errDunn, Tim; Zook, Justin M.; Holt, James M.; Narayanasamy, Satish
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Loss of function of FAM177A1, a Golgi complex localized protein, causes a novel neurodevelopmental disorder
err2024-09-01
err2
PREAI
errKohler, Jennefer N.; Legro, Nicole R.; Baldridge, Dustin; Shin, Jimann; Bowman, Angela; Ugur, Berrak; Jackstadt, Madelyn M.; Shriver, Leah P.; Patti, Gary J.; Zhang, Bo; Feng, Wenjia; McAdow, Anthony R.; Goddard, Page; Ungar, Rachel A.; Jensen, Tanner; Smith, Kevin S.; Fresard, Laure; Alvarez, Raquel; Bonner, Devon; Reuter, Chloe M.; McCormack, Colleen; Kravets, Elijah; Marwaha, Shruti; Holt, James M.; Worthey, Elizabeth A.; Ashley, Euan A.; Montgomery, Stephen B.; Fisher, Paul G.; Postlethwait, John; De Camilli, Pietro; Solnica-Krezel, Lila; Bernstein, Jonathan A.; Wheeler, Matthew T.
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The landscape of reported VUS in multi-gene panel and genomic testing: Time for a change
err2023-12-01
err36
errOAAI
errRehm, Heidi L.; Alaimo, Joseph T.; Aradhya, Swaroop; Bayrak-Toydemir, Pinar; Best, Hunter; Brandon, Rhonda; Buchan, Jillian G.; Chao, Elizabeth C.; Chen, Elaine; Clifford, Jacob; Cohen, Ana S. A.; Conlin, Laura K.; Das, Soma; Davis, Kyle W.; del Gaudio, Daniela; Del Viso, Florencia; Divincenzo, Christina; Eisenberg, Marcia; Guidugli, Lucia; Hammer, Monia B.; Harrison, Steven M.; Hatchell, Kathryn E.; Dyer, Lindsay Havens; Hoang, Lily U.; Holt, James M.; Jobanputra, Vaidehi; Karbassi, Izabela D.; Kearney, Hutton M.; Kelly, Melissa A.; Kelly, Jacob M.; Kluge, Michelle L.; Komala, Timothy; Kruszka, Paul; Lau, Lynette; Lebo, Matthew S.; Marshall, Christian R.; Mcknight, Dianalee; Mcwalter, Kirsty; Meng, Yan; Nagan, Narasimhan; Neckelmann, Christian S.; Neerman, Nir; Niu, Zhiyv; Paolillo, Vitoria K.; Paolucci, Sarah A.; Perry, Denise; Pesaran, Tina; Radtke, Kelly; Rasmussen, Kristen J.; Retterer, Kyle; Saunders, Carol J.; Spiteri, Elizabeth; Stanley, Christine; Szuto, Anna; Taft, Ryan J.; Thiffault, Isabelle; Thomas, Brittany C.; Thomas-Wilson, Amanda; Thorpe, Erin; Tidwell, Timothy J.; Towne, Meghan C.; Zouk, Hana
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Polishing De Novo Nanopore Assemblies of Bacteria and Eukaryotes With FMLRC2
err2023-03-03
err15
errOAAI
errMak, Q. X. Charles; Wick, Ryan R.; Holt, James Matthew; Wang, Jeremy R.
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Finding merit in impurity: Designing a cost-effective workflow for saliva genome sequencing
err2022-03-01
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errOAAI
errSosonkina, Nadiya; Kelly, Melissa; Holt, James; Bick, David; Nakouzi, Ghunwa
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Expansion of long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders and multiple congenital anomalies
err2022-03-01
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errOAAI
errHiatt, Susan; Lawlor, James; Handley, Lori; Bonnstetter, Zachary; Jenkins, Jerry; Lovell, John; Holt, James; Finnila, Candice; Thompson, Michelle; Latner, Donald; Partridge, Christopher; Plott, Christopher; Boston, Lori Beth; Williams, Melissa; Bowling, Kevin; Grimwood, Jane; Schmutz, Jeremy; Cooper, Gregory
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Long-read genome sequencing secondary processing pipelines provide variant call accuracy that exceeds current clinical standards for short-read genome sequencing
err2022-03-01
err0
errOAAI
errHolt, James; Handley, Lori; Lawlor, James; Hiatt, Susan; Cooper, Gregory; Grimwood, Jane; Nakouzi, Ghunwa
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Reducing Sanger confirmation testing through false positive prediction algorithms
err2021-07-01
err8
errOAAI
errHolt, James M.; Kelly, Melissa; Sundlof, Brett; Nakouzi, Ghunwa; Bick, David; Lyon, Elaine
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Long-read genome sequencing for the molecular diagnosis of neurodevelopmental disorders
err2021-04-01
err33
errOAAI
errHiatt, Susan M.; Lawlor, James M. J.; Handley, Lori H.; Ramaker, Ryne C.; Rogers, Brianne B.; Partridge, E. Christopher; Boston, Lori Beth; Williams, Melissa; Plott, Christopher B.; Jenkins, Jerry; Gray, David E.; Holt, James M.; Bowling, Kevin M.; Bebin, E. Martina; Grimwood, Jane; Schmutz, Jeremy; Cooper, Gregory M.
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Clinical Diagnosis through Whole-Genome Sequencing
err2019-12-30
err1
errOAAI
errHurst, Anna C. E.; Wilk, Melissa A.; Holt, James M.; Lyon, Elaine; Bick, David
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Kilquist syndrome: A novel syndromic hearing loss disorder caused by homozygous deletion of SLC12A2
err2019-03-12
err35
errOAAI
errMacnamara, Ellen F.; Koehler, Alanna E.; D'Souza, Precilla; Estwick, Tyra; Lee, Paul; Vezina, Gilbert; Fauni, Harper; Braddock, Stephen R.; Torti, Erin; Holt, James Matthew; Sharma, Prashant; Malicdan, May Christine, V; Tifft, Cynthia J.; Acosta, Maria T.; Adams, David R.; Aday, Aaron; Alejandro, Mercedes E.; Allard, Patrick; Ashley, Euan A.; Azamian, Mahshid S.; Bacino, Carlos A.; Bademci, Guney; Baker, Eva; Balasubramanyam, Ashok; Baldridge, Dustin; Barbouth, Deborah; Batzli, Gabriel F.; Beggs, Alan H.; Bellen, Hugo J.; Bernstein, Jonathan A.; Berry, Gerard T.; Bican, Anna; Bick, David P.; Birch, Camille L.; Bivona, Stephanie; Bonnenmann, Carsten; Bonner, Devon; Boone, Braden E.; Bostwick, Bret L.; Briere, Lauren C.; Brokamp, Elly; Brown, Donna M.; Brush, Matthew; Burke, Elizabeth A.; Burrage, Lindsay C.; Butte, Manish J.; Carrasquillo, Olveen; Chang, Ta Chen Peter; Chao, Hsiao-Tuan; Clark, Gary D.; Coakley, Terra R.; Cobban, Laurel A.; Cogan, Joy D.; Cole, F. Sessions; Colley, Heather A.; Cooper, Cynthia M.; Cope, Heidi; Craigen, William J.; Dasari, Surendra; Davids, Mariska; Davidson, Jean M.; Dayal, Jyoti G.; Dell'Angelica, Esteban C.; Dhar, Shweta U.; Dorrani, Naghmeh; Dorset, Daniel C.; Douine, Emilie D.; Draper, David D.; Duncan, Annika M. DriesLaura; Eckstein, David J.; Emrick, Lisa T.; Eng, Christine M.; Enns, Gregory M.; Esteves, Cecilia; Fernandez, Liliana; Ferreira, Carlos; Fieg, Elizabeth L.; Fisher, Paul G.; Fogel, Brent L.; Forghani, Irman; Friedman, Noah D.; Gahl, William A.; Godfrey, Rena A.; Goldman, Alica M.; Goldstein, David B.; Gourdine, Jean-Philippe F.; Grajewski, Alana; Groden, Catherine A.; Gropman, Andrea L.; Haendel, Melissa; Hamid, Rizwan; Hanchard, Neil A.; High, Frances; Holm, Ingrid A.; Hom, Jason; Huang, Alden; Huang, Yong; Isasi, Rosario; Jamal, Fariha; Jiang, Yong-hui; Johnston, Jean M.; Jones, Angela L.; Karaviti, Lefkothea; Kelley, Emily G.; Koeller, David M.; Kohane, Isaac S.; Kohler, Jennefer N.; Krakow, Deborah; Krasnewich, Donna M.; Korrick, Susan; Koziura, Mary; Krier, Joel B.; Kyle, Jennifer E.; Lalani, Seema R.; Lam, Byron; Lanpher, Brendan C.; Lanza, Ian R.; Lau, C. Christopher; Lazar, Jozef; LeBlanc, Kimberly; Lee, Brendan H.; Lee, Hane; Levitt, Roy; Levy, Shawn E.; Lewis, Richard A.; Lincoln, Sharyn A.; Liu, Pengfei; Xue; Liu, Zhong; Loo, Sandra K.; Loscalzo, Joseph; Maas, Richard L.; MacRae, Calum A.; Maduro, Valerie V.; Majcherska, Marta M.; Mamounas, Laura A.; Manolio, Teri A.; Markello, Thomas C.; Marom, Ronit; Martin, Martin G.; Martinez-Agosto, Julian A.; Marwaha, Shruti; May, Thomas; McCauley, Jacob; McConkie-Rosell, Allyn; McCormack, Colleen E.; McCray, Alexa T.; Merker, Jason D.; Metz, Thomas O.; Might, Matthew; Morava-Kozicz, Eva; Moretti, Paolo M.; Morimoto, Marie; Mulvihill, John J.; Murdock, David R.; Nath, Avi; Nelson, Stan F.; Newberry, J. Scott; Newman, John H.; Nicholas, Sarah K.; Novacic, Donna; Oglesbee, Devin; Orengo, James P.; Pak, Stephen; Pallais, J. Carl; Palmer, Christina G. S.; Papp, Jeanette C.; Parker, Neil H.; Pena, Loren Dm; Phillips, John A., III; Posey, Jennifer E.; Postlethwait, John H.; Potocki, Lorraine; Pusey, Barbara N.; Renteria, Genecee; Reuter, Chloe M.; Rives, Lynette; Robertson, Amy K.; Rodan, Lance H.; Rosenfeld, Jill A.; Rowley, Robb K.; Sacco, Ralph; Sampson, Jacinda B.; Samson, Susan L.; Saporta, Mario; Schaechter, Judy; Schedl, Timothy; Schoch, Kelly; Scott, Daryl A.; Shakachite, Lisa; Shashi, Vandana; Shields, Kathleen; Shin, Jimann; Signer, Rebecca; Sillari, Catherine H.; Silverman, Edwin K.; Sinsheimer, Janet S.; Smith, Kevin S.; Solnica-Krezel, Lilianna; Spillmann, Rebecca C.; Stoler, Joan M.; Stong, Nicholas; Sullivan, Jennifer A.; Sweetser, David A.; Tamburro, Cecelia P.; Tan, Queenie K-G; Tekin, Mustafa; Telischi, Fred; Thorson, Willa; Toro, Camilo; Tran, Alyssa A.; Urv, Tiina K.; Vogel, Tiphanie P.; Waggott, Daryl M.; Wahl, Colleen E.; Walley, Nicole M.; Walsh, Chris A.; Walker, Melissa; Wambach, Jennifer; Wan, Jijun; Wang, Lee-kai; Wangler, Michael F.; Ward, Patricia A.; Waters, Katrina M.; Webb-Robertson, Bobbie-Jo M.; Wegner, Daniel; Westerfield, Monte; Wheeler, Matthew T.; Wise, Anastasia L.; Wolfe, Lynne A.; Woods, Jeremy D.; Worthey, Elizabeth A.; Yamamoto, Shinya; Yang, John; Yoon, Amanda J.; Yu, Guoyun; Zastrow, Diane B.; Zhao, Chunli; Zuchner, Stephan
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The Evolutionary Fates of a Large Segmental Duplication in Mouse
err2016-09-01
err17
errOAAI
errMorgan, Andrew P.; Holt, J. Matthew; McMullan, Rachel C.; Bell, Timothy A.; Clayshulte, Amelia M. -F.; Didion, John P.; Yadgary, Liran; Thybert, David; Odom, Duncan T.; Flicek, Paul; McMillan, Leonard; de Villena, Fernando Pardo-Manuel
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R2d2 Drives Selfish Sweeps in the House Mouse
err2016-02-15
err53
errOAAI
errDidion, John P.; Morgan, Andrew P.; Yadgary, Liran; Bell, Timothy A.; McMullan, Rachel C.; de Solorzano, Lydia Ortiz; Britton-Davidian, Janice; Bult, Carol J.; Campbell, Karl J.; Castiglia, Riccardo; Ching, Yung-Hao; Chunco, Amanda J.; Crowley, James J.; Chesler, Elissa J.; Foerster, Daniel W.; French, John E.; Gabriel, Sofia I.; Gatti, Daniel M.; Garland, Theodore; Giagia-Athanasopoulou, Eva B.; Gimenez, Mabel D.; Grize, Sofia A.; Gunduz, Islam; Holmes, Andrew; Hauffe, Heidi C.; Herman, Jeremy S.; Holt, James M.; Hua, Kunjie; Jolley, Wesley J.; Lindholm, Anna K.; Lopez-Fuster, Maria J.; Mitsainas, George; Mathias, Maria da Luz; McMillan, Leonard; Morgado Ramalhinho, Maria da Graca; Rehermann, Barbara; Rosshart, Stephan P.; Searle, Jeremy B.; Shiao, Meng-Shin; Solano, Emanuela; Svenson, Karen L.; Thomas-Laemont, Patricia; Threadgill, David W.; Ventura, Jacint; Weinstock, George M.; Pomp, Daniel; Churchill, Gary A.; de Villena, Fernando Pardo-Manuel
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Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance (vol 47, pg 353, 2015)
err2015-05-27
err3
errOAAI
errCrowley, James J.; Zhabotynsky, Vasyl; Sun, Wei; Huang, Shunping; Pakatci, Isa Kemal; Kim, Yunjung; Wang, Jeremy R.; Morgan, Andrew P.; Calaway, John D.; Aylor, David L.; Yun, Zaining; Bell, Timothy A.; Buus, Ryan J.; Calaway, Mark E.; Didion, John P.; Gooch, Terry J.; Robinson, Stephanie D. Hansen Nashiya N.; Shaw, Ginger D.; Spence, Jason S.; Quackenbush, Corey R.; Barrick, Cordelia J.; Nonneman, Randal J.; Kim, Kyunisu; Xenakis, James; Xie, Yuying; Valdar, William; Lenarcic, Alan B.; Wang, Wei; Welsh, Catherine E.; Fu, Chen-Ping; Zhang, Zhaojun; Holt, James; Guo, Zhishan; Threadgill, David W.; Tarantino, Lisa M.; Miller, Darla R.; Zou, Fei; McMillan, Leonard; Sullivan, Patrick F.; de Villena, Fernando Pardo-Manuel
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Analyses of allele-specific gene expression in highly divergent mouse crosses identifies pervasive allelic imbalance
err2015-03-02
err165
errOAAI
errCrowley, James J.; Zhabotynsky, Vasyl; Sun, Wei; Huang, Shunping; Pakatci, Isa Kemal; Kim, Yunjung; Wang, Jeremy R.; Morgan, Andrew P.; Calaway, John D.; Aylor, David L.; Yun, Zaining; Bell, Timothy A.; Buus, Ryan J.; Calaway, Mark E.; Didion, John P.; Gooch, Terry J.; Hansen, Stephanie D.; Robinson, Nashiya N.; Shaw, Ginger D.; Spence, Jason S.; Quackenbush, Corey R.; Barrick, Cordelia J.; Nonneman, Randal J.; Kim, Kyungsu; Xenakis, James; Xie, Yuying; Valdar, William; Lenarcic, Alan B.; Wang, Wei; Welsh, Catherine E.; Fu, Chen-Ping; Zhang, Zhaojun; Holt, James; Guo, Zhishan; Threadgill, David W.; Tarantino, Lisa M.; Miller, Darla R.; Zou, Fei; McMillan, Leonard; Sullivan, Patrick F.; de Villena, Fernando Pardo-Manuel
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A novel multi-alignment pipeline for high-throughput sequencing data
err2014-06-18
err37
errOAAI
errHuang, Shunping; Holt, James; Kao, Chia-Yu; McMillan, Leonard; Wang, Wei
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