Search Results - "English, Adam C"

Truvari: refined structural variant comparison preserves allelic diversity by English, Adam C, Menon, Vipin K, Gibbs, Richard A, Metcalf, Ginger A, Sedlazeck, Fritz J

“…The fundamental challenge of multi-sample structural variant (SV) analysis such as merging and benchmarking is identifying when two SVs are the same. Common…”
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Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology by English, Adam C, Richards, Stephen, Han, Yi, Wang, Min, Vee, Vanesa, Qu, Jiaxin, Qin, Xiang, Muzny, Donna M, Reid, Jeffrey G, Worley, Kim C, Gibbs, Richard A

“…Many genomes have been sequenced to high-quality draft status using Sanger capillary electrophoresis and/or newer short-read sequence data and whole genome…”
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Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects by Regier, Allison A., Farjoun, Yossi, Larson, David E., Krasheninina, Olga, Kang, Hyun Min, Howrigan, Daniel P., Chen, Bo-Juen, Kher, Manisha, Banks, Eric, Ames, Darren C., English, Adam C., Li, Heng, Xing, Jinchuan, Zhang, Yeting, Matise, Tara, Abecasis, Goncalo R., Salerno, Will, Zody, Michael C., Neale, Benjamin M., Hall, Ira M.

“…Hundreds of thousands of human whole genome sequencing (WGS) datasets will be generated over the next few years. These data are more valuable in aggregate:…”
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PBHoney: identifying genomic variants via long-read discordance and interrupted mapping by English, Adam C, Salerno, William J, Reid, Jeffrey G

“…As resequencing projects become more prevalent across a larger number of species, accurate variant identification will further elucidate the nature of genetic…”
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Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2 by Beck, Christine R., Carvalho, Claudia M.B., Akdemir, Zeynep C., Sedlazeck, Fritz J., Song, Xiaofei, Meng, Qingchang, Hu, Jianhong, Doddapaneni, Harsha, Chong, Zechen, Chen, Edward S., Thornton, Philip C., Liu, Pengfei, Yuan, Bo, Withers, Marjorie, Jhangiani, Shalini N., Kalra, Divya, Walker, Kimberly, English, Adam C., Han, Yi, Chen, Ken, Muzny, Donna M., Ira, Grzegorz, Shaw, Chad A., Gibbs, Richard A., Hastings, P.J., Lupski, James R.

“…DNA rearrangements resulting in human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used long- and short-read sequencing…”
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Assessing structural variation in a personal genome-towards a human reference diploid genome by English, Adam C, Salerno, William J, Hampton, Oliver A, Gonzaga-Jauregui, Claudia, Ambreth, Shruthi, Ritter, Deborah I, Beck, Christine R, Davis, Caleb F, Dahdouli, Mahmoud, Ma, Singer, Carroll, Andrew, Veeraraghavan, Narayanan, Bruestle, Jeremy, Drees, Becky, Hastie, Alex, Lam, Ernest T, White, Simon, Mishra, Pamela, Wang, Min, Han, Yi, Zhang, Feng, Stankiewicz, Pawel, Wheeler, David A, Reid, Jeffrey G, Muzny, Donna M, Rogers, Jeffrey, Sabo, Aniko, Worley, Kim C, Lupski, James R, Boerwinkle, Eric, Gibbs, Richard A

“…Characterizing large genomic variants is essential to expanding the research and clinical applications of genome sequencing. While multiple data types and…”
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PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations by Wang, Min, Beck, Christine R, English, Adam C, Meng, Qingchang, Buhay, Christian, Han, Yi, Doddapaneni, Harsha V, Yu, Fuli, Boerwinkle, Eric, Lupski, James R, Muzny, Donna M, Gibbs, Richard A

“…Generation of long (>5 Kb) DNA sequencing reads provides an approach for interrogation of complex regions in the human genome. Currently, large-insert whole…”
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SVachra: a tool to identify genomic structural variation in mate pair sequencing data containing inward and outward facing reads by Hampton, Oliver A, English, Adam C, Wang, Mark, Salerno, William J, Liu, Yue, Muzny, Donna M, Han, Yi, Wheeler, David A, Worley, Kim C, Lupski, James R, Gibbs, Richard A

“…Characterization of genomic structural variation (SV) is essential to expanding the research and clinical applications of genome sequencing. Reliance upon…”
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Prevalence of alternative splicing choices in Arabidopsis thaliana by English, Adam C, Patel, Ketan S, Loraine, Ann E

“…Around 14% of protein-coding genes of Arabidopsis thaliana genes from the TAIR9 genome release are annotated as producing multiple transcript variants through…”
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A robust benchmark for detection of germline large deletions and insertions by Zook, Justin M., Hansen, Nancy F., Olson, Nathan D., Chapman, Lesley, Mullikin, James C., Xiao, Chunlin, Sherry, Stephen, Koren, Sergey, Phillippy, Adam M., Boutros, Paul C., Sahraeian, Sayed Mohammad E., Huang, Vincent, Rouette, Alexandre, Alexander, Noah, Mason, Christopher E., Hajirasouliha, Iman, Ricketts, Camir, Lee, Joyce, Tearle, Rick, Fiddes, Ian T., Barrio, Alvaro Martinez, Wala, Jeremiah, Carroll, Andrew, Ghaffari, Noushin, Rodriguez, Oscar L., Bashir, Ali, Jackman, Shaun, Farrell, John J., Wenger, Aaron M., Alkan, Can, Soylev, Arda, Schatz, Michael C., Garg, Shilpa, Church, George, Marschall, Tobias, Chen, Ken, Fan, Xian, English, Adam C., Rosenfeld, Jeffrey A., Zhou, Weichen, Mills, Ryan E., Sage, Jay M., Davis, Jennifer R., Kaiser, Michael D., Oliver, John S., Catalano, Anthony P., Chaisson, Mark J. P., Spies, Noah, Sedlazeck, Fritz J., Salit, Marc

“…New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution and…”
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Making Theological Progress with David Deutsch's Theory of Explanations by English, Adam C.

“…Theological progress occurs when explanations are contested, revised, and upgraded. But what are explanations? According to the physicist David Deutsch, an…”
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Theology Remixed: Christianity as Story, Game, Language, Culture by English, Adam C

“…Jesus didn't fall back on parables because he lacked the right words. Parables were the exact way Jesus intended to communicate. What pictures or analogies…”
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Analysis and benchmarking of small and large genomic variants across tandem repeats by English, Adam C, Dolzhenko, Egor, Ziaei Jam, Helyaneh, McKenzie, Sean K, Olson, Nathan D, De Coster, Wouter, Park, Jonghun, Gu, Bida, Wagner, Justin, Eberle, Michael A, Gymrek, Melissa, Chaisson, Mark J P, Zook, Justin M, Sedlazeck, Fritz J

“…Tandem repeats (TRs) are highly polymorphic in the human genome, have thousands of associated molecular traits and are linked to over 60 disease phenotypes…”
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xAtlas: scalable small variant calling across heterogeneous next-generation sequencing experiments by Farek, Jesse, Hughes, Daniel, Salerno, William, Zhu, Yiming, Pisupati, Aishwarya, Mansfield, Adam, Krasheninina, Olga, English, Adam C, Metcalf, Ginger, Boerwinkle, Eric, Muzny, Donna M, Gibbs, Richard, Khan, Ziad, Sedlazeck, Fritz J

“…Abstract Background The growing volume and heterogeneity of next-generation sequencing (NGS) data complicate the further optimization of identifying DNA…”
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Author Correction: A robust benchmark for detection of germline large deletions and insertions by Zook, Justin M., Hansen, Nancy F., Olson, Nathan D., Chapman, Lesley, Mullikin, James C., Xiao, Chunlin, Sherry, Stephen, Koren, Sergey, Phillippy, Adam M., Boutros, Paul C., Sahraeian, Sayed Mohammad E., Huang, Vincent, Rouette, Alexandre, Alexander, Noah, Mason, Christopher E., Hajirasouliha, Iman, Ricketts, Camir, Lee, Joyce, Tearle, Rick, Fiddes, Ian T., Barrio, Alvaro Martinez, Wala, Jeremiah, Carroll, Andrew, Ghaffari, Noushin, Rodriguez, Oscar L., Bashir, Ali, Jackman, Shaun, Farrell, John J., Wenger, Aaron M., Alkan, Can, Soylev, Arda, Schatz, Michael C., Garg, Shilpa, Church, George, Marschall, Tobias, Chen, Ken, Fan, Xian, English, Adam C., Rosenfeld, Jeffrey A., Zhou, Weichen, Mills, Ryan E., Sage, Jay M., Davis, Jennifer R., Kaiser, Michael D., Oliver, John S., Catalano, Anthony P., Chaisson, Mark J. P., Spies, Noah, Sedlazeck, Fritz J., Salit, Marc

“…An amendment to this paper has been published and can be accessed via a link at the top of the paper…”
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Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine [version 1; peer review: 1 approved, 1 approved with reservations] by Mahmoud, Medhat, Gener, Alejandro Rafael, Khayat, Michael M, English, Adam C, Balaji, Advait, Zhou, Anbo, Hehn, Andreas, Fungtammasan, Arkarachai, Chrisman, Brianna Sierra, Chin, Chen-Shan, Lin, Chiao-Feng, Lo, Chun-Hsuan, Liao, Chunxiao, Carvalho, Claudia M. B, Diesh, Colin, Symer, David E, Kalra, Divya, Albin, Dreycey, Aliyev, Elbay, Dawson, Eric T, Venner, Eric, Foertter, Fernanda, Bae, Gigon, Du, Haowei, Daw, Joyjit, Wang, Junzhou, Akagi, Keiko, Phan, Lon, Jochum, Michael, Edrisi, Mohammadamin, Shah, Nirav N, Wang, Qi, Fullem, Robert, Zheng, Rong, Kalla, Sara E, Mitra, Shakuntala, Treangen, Todd J, Mahaganapathy, Vaidhyanathan, Malladi, Venkat Sai, Menon, Vipin K, Fu, Yilei, Yin, Yongze, Feng, Yuanqing, Hefferon, Tim, Sedlazeck, Fritz J, Busby, Ben

“…In October 2019, 46 scientists from around the world participated in the first National Center for Biotechnology Information (NCBI) Structural Variation (SV)…”
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"Science Cannot Stop with Science": Maurice Blondel and the Sciences by English, Adam C.

“…Maurice Blondel, best known for his 1893 work on Action, offers a window on the world of philosophers who negotiated the scientific disciplines at the turn of…”
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Association Analysis of Common Structural Variants in the Alzheimer’s Disease Sequencing Project by Lee, Songmi, English, Adam C, Xia, Rui, Peloso, Gina M., Bis, Joshua C, Lin, Honghuang, Choi, Seung Hoan, Heard‐Costa, Nancy, DeStefano, Anita L., Sedlazeck, Fritz J, Fornage, Myriam

“…Background Structural variants (SV), genomic rearrangements of >50 base pairs, are an important source of genetic variation and have a great impact on gene…”
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Church without prisoners: On the twentieth anniversary of A Peculiar People by English, Adam C.

“…This article reassesses the seminal ideas of Rodney Clapp’s 1996 A Peculiar People on the occasion of its twentieth anniversary. Clapp observes that…”
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The Cyrilian Solution: Cyril of Jerusalem and Saul Kripke on Naming God by English, Adam C.

“…Cyril of Jerusalem's proposed theology of the Trinity has been labeled generic. That is, the term "God" identifies not so much a species of being or an…”
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