Whole genome sequence of Treponema pallidum ssp. pallidum, strain Mexico A, suggests recombination between yaws and syphilis strains. by Helena Pětrošová, Marie Zobaníková, Darina Čejková, Lenka Mikalová, Petra Pospíšilová, Michal Strouhal, Lei Chen, Xiang Qin, Donna M Muzny, George M Weinstock, David Šmajs

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Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. by Adam C English, Stephen Richards, Yi Han, Min Wang, Vanesa Vee, Jiaxin Qu, Xiang Qin, Donna M Muzny, Jeffrey G Reid, Kim C Worley, Richard A Gibbs

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SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads by Oliver A. Hampton, Adam C. English, Mark Wang, William J. Salerno, Yue Liu, Donna M. Muzny, Yi Han, David A. Wheeler, Kim C. Worley, James R. Lupski, Richard A. Gibbs

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Somatic mutations of esophageal adenocarcinoma: a comparison between Black and White patients by Hyeyeun Lim, Marie-Claude Gingras, Jing Zhao, Jinyoung Byun, Patricia D. Castro, Spiridon Tsavachidis, Jianhong Hu, Harshavardhan Doddapaneni, Yi Han, Donna M. Muzny, Richard A. Gibbs, Christopher I. Amos, Aaron P. Thrift

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Whole genome sequences of three Treponema pallidum ssp. pertenue strains: yaws and syphilis treponemes differ in less than 0.2% of the genome sequence. by Darina Cejková, Marie Zobaníková, Lei Chen, Petra Pospíšilová, Michal Strouhal, Xiang Qin, Lenka Mikalová, Steven J Norris, Donna M Muzny, Richard A Gibbs, Lucinda L Fulton, Erica Sodergren, George M Weinstock, David Smajs

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Transmission event of SARS-CoV-2 delta variant reveals multiple vaccine breakthrough infections by Timothy Farinholt, Harsha Doddapaneni, Xiang Qin, Vipin Menon, Qingchang Meng, Ginger Metcalf, Hsu Chao, Marie-Claude Gingras, Vasanthi Avadhanula, Paige Farinholt, Charu Agrawal, Donna M. Muzny, Pedro A. Piedra, Richard A. Gibbs, Joseph Petrosino

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Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression. by Dan Vanderpool, Bui Quang Minh, Robert Lanfear, Daniel Hughes, Shwetha Murali, R Alan Harris, Muthuswamy Raveendran, Donna M Muzny, Mark S Hibbins, Robert J Williamson, Richard A Gibbs, Kim C Worley, Jeffrey Rogers, Matthew W Hahn

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Complete genome sequence of Treponema paraluiscuniculi, strain Cuniculi A: the loss of infectivity to humans is associated with genome decay. by David Šmajs, Marie Zobaníková, Michal Strouhal, Darina Čejková, Shannon Dugan-Rocha, Petra Pospíšilová, Steven J Norris, Tom Albert, Xiang Qin, Kym Hallsworth-Pepin, Christian Buhay, Donna M Muzny, Lei Chen, Richard A Gibbs, George M Weinstock

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The gut mycobiome of the Human Microbiome Project healthy cohort by Andrea K. Nash, Thomas A. Auchtung, Matthew C. Wong, Daniel P. Smith, Jonathan R. Gesell, Matthew C. Ross, Christopher J. Stewart, Ginger A. Metcalf, Donna M. Muzny, Richard A. Gibbs, Nadim J. Ajami, Joseph F. Petrosino

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Whole exome sequencing identifies novel genes for fetal hemoglobin response to hydroxyurea in children with sickle cell anemia. by Vivien A Sheehan, Jacy R Crosby, Aniko Sabo, Nicole A Mortier, Thad A Howard, Donna M Muzny, Shannon Dugan-Perez, Banu Aygun, Kerri A Nottage, Eric Boerwinkle, Richard A Gibbs, Russell E Ware, Jonathan M Flanagan

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Genetic Burden Contributing to Extremely Low or High Bone Mineral Density in a Senior Male Population From the Osteoporotic Fractures in Men Study (MrOS) by Shan Chen, Mahim Jain, Shalini Jhangiani, Zeynep C Akdemir, Philippe M Campeau, Robert F Klein, Carrie Nielson, Hongzheng Dai, Donna M Muzny, Eric Boerwinkle, Richard A Gibbs, Eric S Orwoll, James R Lupski, Jennifer E Posey, Brendan Lee

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Modeling nonsegmented negative-strand RNA virus (NNSV) transcription with ejective polymerase collisions and biased diffusion by Felipe-Andrés Piedra, David Henke, Anubama Rajan, Donna M. Muzny, Harsha Doddapaneni, Vipin K. Menon, Kristi L. Hoffman, Matthew C. Ross, Sara J. Javornik Cregeen, Ginger Metcalf, Richard A. Gibbs, Joseph F. Petrosino, Vasanthi Avadhanula, Pedro A. Piedra, Pedro A. Piedra

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NODAL variants are associated with a continuum of laterality defects from simple D-transposition of the great arteries to heterotaxy by Zain Dardas, Jawid M. Fatih, Angad Jolly, Moez Dawood, Haowei Du, Christopher M. Grochowski, Edward G. Jones, Shalini N. Jhangiani, Xander H. T. Wehrens, Pengfei Liu, Weimin Bi, Eric Boerwinkle, Jennifer E. Posey, Donna M. Muzny, Richard A. Gibbs, James R. Lupski, Zeynep Coban-Akdemir, Shaine A. Morris

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Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential. by Carl J Yeoman, Suleyman Yildirim, Susan M Thomas, A Scott Durkin, Manolito Torralba, Granger Sutton, Christian J Buhay, Yan Ding, Shannon P Dugan-Rocha, Donna M Muzny, Xiang Qin, Richard A Gibbs, Steven R Leigh, Rebecca Stumpf, Bryan A White, Sarah K Highlander, Karen E Nelson, Brenda A Wilson

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PCM1 is necessary for focal ciliary integrity and is a candidate for severe schizophrenia by Tanner O. Monroe, Melanie E. Garrett, Maria Kousi, Ramona M. Rodriguiz, Sungjin Moon, Yushi Bai, Steven C. Brodar, Karen L. Soldano, Jeremiah Savage, Thomas F. Hansen, Donna M. Muzny, Richard A. Gibbs, Lawrence Barak, Patrick F. Sullivan, Allison E. Ashley-Koch, Akira Sawa, William C. Wetsel, Thomas Werge, Nicholas Katsanis

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Oligonucleotide capture sequencing of the SARS-CoV-2 genome and subgenomic fragments from COVID-19 individuals. by Harsha Doddapaneni, Sara Javornik Cregeen, Richard Sucgang, Qingchang Meng, Xiang Qin, Vasanthi Avadhanula, Hsu Chao, Vipin Menon, Erin Nicholson, David Henke, Felipe-Andres Piedra, Anubama Rajan, Zeineen Momin, Kavya Kottapalli, Kristi L Hoffman, Fritz J Sedlazeck, Ginger Metcalf, Pedro A Piedra, Donna M Muzny, Joseph F Petrosino, Richard A Gibbs

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Hybrid de novo genome assembly and centromere characterization of the gray mouse lemur (Microcebus murinus) by Peter A. Larsen, R. Alan Harris, Yue Liu, Shwetha C. Murali, C. Ryan Campbell, Adam D. Brown, Beth A. Sullivan, Jennifer Shelton, Susan J. Brown, Muthuswamy Raveendran, Olga Dudchenko, Ido Machol, Neva C. Durand, Muhammad S. Shamim, Erez Lieberman Aiden, Donna M. Muzny, Richard A. Gibbs, Anne D. Yoder, Jeffrey Rogers, Kim C. Worley

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Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds by Marina Naval-Sanchez, Quan Nguyen, Sean McWilliam, Laercio R. Porto-Neto, Ross Tellam, Tony Vuocolo, Antonio Reverter, Miguel Perez-Enciso, Rudiger Brauning, Shannon Clarke, Alan McCulloch, Wahid Zamani, Saeid Naderi, Hamid Reza Rezaei, Francois Pompanon, Pierre Taberlet, Kim C. Worley, Richard A. Gibbs, Donna M. Muzny, Shalini N. Jhangiani, Noelle Cockett, Hans Daetwyler, James Kijas

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The impact of the Turkish population variome on the genomic architecture of rare disease traits by Zeynep Coban-Akdemir, Xiaofei Song, Francisco C. Ceballos, Davut Pehlivan, Ender Karaca, Yavuz Bayram, Tadahiro Mitani, Tomasz Gambin, Tugce Bozkurt-Yozgatli, Shalini N. Jhangiani, Donna M. Muzny, Richard A. Lewis, Pengfei Liu, Eric Boerwinkle, Ada Hamosh, Richard A. Gibbs, V. Reid Sutton, Nara Sobreira, Claudia M.B. Carvalho, Chad A. Shaw, Jennifer E. Posey, David Valle, James R. Lupski

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Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder by Elizabeth A. Normand, Alicia Braxton, Salma Nassef, Patricia A. Ward, Francesco Vetrini, Weimin He, Vipulkumar Patel, Chunjing Qu, Lauren E. Westerfield, Samantha Stover, Avinash V. Dharmadhikari, Donna M. Muzny, Richard A. Gibbs, Hongzheng Dai, Linyan Meng, Xia Wang, Rui Xiao, Pengfei Liu, Weimin Bi, Fan Xia, Magdalena Walkiewicz, Ignatia B. Van den Veyver, Christine M. Eng, Yaping Yang

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