Results 11 to 20 of about 11,509,666 (312)

Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies

Genome Biology, 2020
Recent long-read assemblies often exceed the quality and completeness of available reference genomes, making validation challenging. Here we present Merqury, a novel tool for reference-free assembly evaluation based on efficient k-mer set operations.
Arang Rhie, Brian P. Walenz, Sergey Koren, Adam M. Phillippy   +3 more
doaj   +2 more sources

The Sequence of the Human Genome [PDF]

Science, 2001
A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of ...
J. Venter, M. Adams, E. Myers, Peter W. Li, R. Mural, G. Sutton, Hamilton O. Smith, M. Yandell, C. Evans, R. Holt, J. Gocayne, P. Amanatides, R. Ballew, D. Huson, J. Wortman, Qing Zhang, C. Kodira, Xiangqun H. Zheng, Lin Chen, M. Skupski, G. Subramanian, P. Thomas, Jinghui Zhang, George L. Gabor Miklos, C. Nelson, S. Broder, A. Clark, Joe Nadeau, V. McKusick, N. Zinder, A. Levine, R. Roberts, M. Simon, C. Slayman, M. Hunkapiller, Randall A. Bolanos, A. Delcher, I. Dew, D. Fasulo, M. Flanigan, L. Florea, A. Halpern, S. Hannenhalli, S. Kravitz, S. Levy, C. Mobarry, K. Reinert, K. Remington, J. Abu-Threideh, E. Beasley, Kendra Biddick, Vivien R. Bonazzi, R. Brandon, M. Cargill, Ishwar Chandramouliswaran, R. Charlab, Kabir Chaturvedi, Z. Deng, V. D. Francesco, P. Dunn, K. Eilbeck, C. Evangelista, A. Gabrielian, W. Gan, Wangmao Ge, F. Gong, Z. Gu, P. Guan, T. J. Heiman, Maureen E. Higgins, Rui-Ru Ji, Zhaoxi Ke, K. Ketchum, Z. Lai, Yi-Ting Lei, Zhenya Li, Jiayin Li, Yong Liang, Xiaoying Lin, Fu Lu, G. Merkulov, N. Milshina, Helen M. Moore, Ashwinikumar K. Naik, Vaibhav A. Narayan, Beena A. Neelam, D. Nusskern, D. Rusch, S. Salzberg, Wei Shao, B. Shue, Jingtao Sun, Zhen Y. Wang, Aihui Wang, Xin Wang, Jian Wang, M. Wei, R. Wides, Chunlin Xiao, Chunhua Yan, Alison Yao, J. Ye, M. Zhan, Weiqing Zhang, Hongyu Zhang, Qi Zhao, Lian-rong Zheng, F. Zhong, W. Zhong, Shiaoping C. Zhu, Shaying Zhao, Dennis A. Gilbert, Suzanna Baumhueter, G. Spier, Christine Carter, A. Cravchik, T. Woodage, Feroze Ali, H. An, A. Awe, D. Baldwin, H. Baden, Mary Barnstead, I. Barrow, K. Beeson, D. Busam, Amy L. Carver, A. Center, Ming-Ming Cheng, Liz Curry, S. Danaher, L. Davenport, Raymond Desilets, S. Dietz, K. Dodson, L. Doup, S. Ferriera, Neha Garg, Andres Gluecksmann, Britney Hart, Jason Haynes, C. Haynes, C. Heiner, S. Hladun, D. Hostin, J. Houck, T. Howland, C. Ibegwam, Jeffery E. Johnson, F. Kalush, Lesley Kline, Shashi B. Koduru, A. Love, Felecia Mann, D. May, Steven McCawley, T. McIntosh, Ivy McMullen, M. Moy, Linda Moy, B. Murphy, K. Nelson, C. Pfannkoch, Eric C. Pratts, V. Puri, Hina Qureshi, Matt Reardon, Robert Rodriguez, Y. Rogers, Deanna L. Romblad, Bob Ruhfel, Richard T. Scott, Cynthia D. Sitter, Michelle Smallwood, Erin Stewart, R. Strong, Ellen Suh, R. Thomas, Ni Ni Tint, S. Tse, C. Vech, Gary Wang, J. Wetter, Sherita M. Williams, Monica S. Williams, Sandra M. Windsor, E. Winn-Deen, Keriellen Wolfe, J. Zaveri, K. Zaveri, J. F. Abril, R. Guigó, M. Campbell, K. Sjolander, Brian Karlak, A. Kejariwal, H. Mi, B. Lazareva, Thomas Hatton, A. Narechania, Karen Diemer, A. Muruganujan, Nan Guo, Shinji Sato, V. Bafna, S. Istrail, R. Lippert, R. Schwartz, B. Walenz, Shibu Yooseph, D. Allen, A. Basu, J. Baxendale, L. Blick, Marcelo Caminha, John Carnes-Stine, Parris Caulk, Y. Chiang, My D. Coyne, C. Dahlke, A. Mays, M. Dombroski, Michael Donnelly, Dale Ely, Shiva Esparham, C. Fosler, Harold C. Gire, S. Glanowski, K. Glasser, A. Glodek, M. Gorokhov, K. Graham, Barry Gropman, M. Harris, Jeremy Heil, Scott Henderson, Jeffrey Hoover, D. Jennings, Catherine Jordan, J. Jordan, John R. Kasha, Leonid Kagan, C. Kraft, A. Levitsky, Mark Lewis, Xiangjun Liu, John Lopez, Daniel S. Ma, William H. Majoros, J. McDaniel, Sean Murphy, Matthew Newman, Trung Nguyen, N. Nguyen, Marc Nodell, S. Pan, Jim Peck, Marshall W. Peterson, William Rowe, Robert Sanders, J. Scott, M. Simpson, Thomas Smith, A. Sprague, Timothy B. Stockwell, Russell J. Turner, E. Venter, Mei Wang, M. Wen, David Wu, Mitchell Wu, Ashley Xia, A. Zandieh, Xiaohong Zhu   +273 more
semanticscholar   +6 more sources

The complete sequence of a human genome

bioRxiv, 2021
In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of the human genome, which revolutionized the field of genomics.
S. Nurk, S. Koren, A. Rhie, Mikko Rautiainen, Andrey V. Bzikadze, Alla Mikheenko, Mitchell R. Vollger, Nicolas Altemose, L. Uralsky, Ariel Gershman, S. Aganezov, Savannah J. Hoyt, M. Diekhans, Glennis A. Logsdon, Michael Alonge, S. Antonarakis, M. Borchers, G. Bouffard, Shelise Y. Brooks, G. V. Caldas, Haoyu Cheng, Chen-Shan Chin, W. Chow, L. D. de Lima, Philip C. Dishuck, R. Durbin, T. Dvorkina, Ian T. Fiddes, G. Formenti, R. Fulton, A. Fungtammasan, Erik K. Garrison, Patrick G. S. Grady, Tina A. Graves-Lindsay, Ira M. Hall, Nancy F. Hansen, Gabrielle Hartley, Marina Haukness, K. Howe, M. Hunkapiller, Chirag Jain, Miten Jain, E. Jarvis, Peter Kerpedjiev, Melanie Kirsche, M. Kolmogorov, J. Korlach, Milinn Kremitzki, Heng Li, Valerie V B Maduro, T. Marschall, Ann M. McCartney, Jennifer McDaniel, Danny E. Miller, J. Mullikin, E. Myers, Nathan D. Olson, B. Paten, P. Peluso, P. Pevzner, David Porubsky, T. Potapova, E. Rogaev, J. Rosenfeld, S. Salzberg, Valerie A. Schneider, F. Sedlazeck, Kishwar Shafin, Colin J. Shew, Alaina Shumate, Y. Sims, A. Smit, Daniela C. Soto, Ivan Sovic, Jessica M. Storer, Aaron M. Streets, B. Sullivan, F. Thibaud-Nissen, J. Torrance, Justin Wagner, B. Walenz, A. Wenger, J. Wood, Chunlin Xiao, Stephanie M. Yan, Alice C. Young, S. Zarate, U. Surti, R. McCoy, M. Dennis, I. Alexandrov, J. Gerton, R. O’Neill, W. Timp, J. Zook, M. Schatz, E. Eichler, K. Miga, A. Phillippy   +98 more
semanticscholar   +1 more source

Expressing the human genome [PDF]

Nature, 2001
We have searched the human genome for genes encoding new proteins that may be involved in three nuclear gene expression processes: transcription, pre-messenger RNA splicing and polyadenylation. A plethora of potential new factors are implicated by sequence in nuclear gene expression, revealing a substantial but selective increase in complexity compared
TUPLER, Rossella, G. PERINI G., M. R. GREEN   +2 more
openaire   +3 more sources

Profiling variable-number tandem repeat variation across populations using repeat-pangenome graphs

Nature Communications, 2021
Variable number tandem repeats (VNTRs) are difficult to analyze by short-read sequencing in disease studies. Here, the authors describe a VNTR mapping strategy for short-read analyses using a repeat pangenome graph.
Tsung-Yu Lu, The Human Genome Structural Variation Consortium, Mark J. P. Chaisson   +2 more
doaj   +1 more source

Truvari: refined structural variant comparison preserves allelic diversity

Genome Biology, 2022
The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same.
Adam C. English, Vipin K. Menon, Richard A. Gibbs, Ginger A. Metcalf, Fritz J. Sedlazeck   +4 more
doaj   +1 more source

A genome-wide mutational constraint map quantified from variation in 76,156 human genomes

bioRxiv, 2022
The depletion of disruptive variation caused by purifying natural selection (constraint) has been widely used to investigate protein-coding genes underlying human disorders, but attempts to assess constraint for non-protein-coding regions have proven ...
Siwei Chen, L. Francioli, J. Goodrich, Ryan L. Collins, Qingbo S. Wang, Jessica Alföldi, N. Watts, C. Vittal, L. Gauthier, T. Poterba, Michael W. Wilson, Y. Tarasova, W. Phu, M. Yohannes, Zan Koenig, Y. Farjoun, E. Banks, S. Donnelly, S. Gabriel, N. Gupta, S. Ferriera, C. Tolonen, Sam Novod, L. Bergelson, David Roazen, Valentín Ruano-Rubio, Miguel Covarrubias, Christopher Llanwarne, Nikelle Petrillo, Gordon Wade, Thibault Jeandet, Ruchi Munshi, Kathleen M. Tibbetts, A. O’Donnell-Luria, M. Solomonson, C. Seed, Alicia R. Martin, M. Talkowski, H. Rehm, M. Daly, G. Tiao, B. Neale, D. MacArthur, K. Karczewski   +43 more
semanticscholar   +1 more source

The effects of common structural variants on 3D chromatin structure

BMC Genomics, 2020
Background Three-dimensional spatial organization of chromosomes is defined by highly self-interacting regions 0.1–1 Mb in size termed Topological Associating Domains (TADs).
Omar Shanta, Amina Noor, Human Genome Structural Variation Consortium (HGSVC), Jonathan Sebat   +3 more
doaj   +1 more source

Pan-genomics in the human genome era

Nature Reviews Genetics, 2020
Since the early days of the genome era, the scientific community has relied on a single 'reference' genome for each species, which is used as the basis for a wide range of genetic analyses, including studies of variation within and across species. As sequencing costs have dropped, thousands of new genomes have been sequenced, and scientists have come ...
Rachel M. Sherman, Steven L. Salzberg
openaire   +3 more sources

Low-level variant calling for non-matched samples using a position-based and nucleotide-specific approach

BMC Bioinformatics, 2021
Background The widespread use of next-generation sequencing has identified an important role for somatic mosaicism in many diseases. However, detecting low-level mosaic variants from next-generation sequencing data remains challenging.
Jeffrey N. Dudley, Celine S. Hong, Marwan A. Hawari, Jasmine Shwetar, Julie C. Sapp, Justin Lack, Henoke Shiferaw, NISC Comparative Sequencing Program, Jennifer J. Johnston, Leslie G. Biesecker   +9 more
doaj   +1 more source