Search Results - "Hart, Reece"

HGVS Recommendations for the Description of Sequence Variants: 2016 Update by den Dunnen, Johan T., Dalgleish, Raymond, Maglott, Donna R., Hart, Reece K., Greenblatt, Marc S., McGowan-Jordan, Jean, Roux, Anne-Francoise, Smith, Timothy, Antonarakis, Stylianos E., Taschner, Peter E.M.

“…ABSTRACT The consistent and unambiguous description of sequence variants is essential to report and exchange information on the analysis of a genome. In…”
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SeqRepo: A system for managing local collections of biological sequences by Hart, Reece K, Prlić, Andreas

“…Access to biological sequence data, such as genome, transcript, or protein sequence, is at the core of many bioinformatics analysis workflows. The National…”
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VariantValidator: Accurate validation, mapping, and formatting of sequence variation descriptions by Freeman, Peter J., Hart, Reece K., Gretton, Liam J., Brookes, Anthony J., Dalgleish, Raymond

“…The Human Genome Variation Society (HGVS) variant nomenclature is widely used to describe sequence variants in scientific publications, clinical reports, and…”
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A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature by Hart, Reece K, Rico, Rudolph, Hare, Emily, Garcia, John, Westbrook, Jody, Fusaro, Vincent A

“…Biological sequence variants are commonly represented in scientific literature, clinical reports and databases of variation using the mutation nomenclature…”
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hgvs: A Python package for manipulating sequence variants using HGVS nomenclature: 2018 Update by Wang, Meng, Callenberg, Keith M., Dalgleish, Raymond, Fedtsov, Alexandre, Fox, Naomi K., Freeman, Peter J., Jacobs, Kevin B., Kaleta, Piotr, McMurry, Andrew J., Prlić, Andreas, Rajaraman, Veena, Hart, Reece K.

“…The Human Genome Variation Society (HGVS) nomenclature guidelines encourage the accurate and standard description of DNA, RNA, and protein sequence variants in…”
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Somatic cancer variant curation and harmonization through consensus minimum variant level data by Ritter, Deborah I, Roychowdhury, Sameek, Roy, Angshumoy, Rao, Shruti, Landrum, Melissa J, Sonkin, Dmitriy, Shekar, Mamatha, Davis, Caleb F, Hart, Reece K, Micheel, Christine, Weaver, Meredith, Van Allen, Eliezer M, Parsons, Donald W, McLeod, Howard L, Watson, Michael S, Plon, Sharon E, Kulkarni, Shashikant, Madhavan, Subha

“…To truly achieve personalized medicine in oncology, it is critical to catalog and curate cancer sequence variants for their clinical relevance. The Somatic…”
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The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification by Wagner, Alex H., Babb, Lawrence, Alterovitz, Gil, Baudis, Michael, Brush, Matthew, Cameron, Daniel L., Cline, Melissa, Griffith, Malachi, Griffith, Obi L., Hunt, Sarah E., Kreda, David, Lee, Jennifer M., Li, Stephanie, Lopez, Javier, Moyer, Eric, Nelson, Tristan, Patel, Ronak Y., Riehle, Kevin, Robinson, Peter N., Rynearson, Shawn, Schuilenburg, Helen, Tsukanov, Kirill, Walsh, Brian, Konopko, Melissa, Rehm, Heidi L., Yates, Andrew D., Freimuth, Robert R., Hart, Reece K.

“…Maximizing the personal, public, research, and clinical value of genomic information will require the reliable exchange of genetic variation data. We report…”
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Development and application of a computable genotype model in the GA4GH Variation Representation Specification by Goar, Wesley, Babb, Lawrence, Chamala, Srikar, Cline, Melissa, Freimuth, Robert R, Hart, Reece K, Kuzma, Kori, Lee, Jennifer, Nelson, Tristan, Prlić, Andreas, Riehle, Kevin, Smith, Anastasia, Stahl, Kathryn, Yates, Andrew D, Rehm, Heidi L, Wagner, Alex H

“…As the diversity of genomic variation data increases with our growing understanding of the role of variation in health and disease, it is critical to develop…”
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Pathogenicity Interpretation in the Age of Precision Medicine: The 2015 Annual Scientific Meeting of the Human Genome Variation Society by Oetting, William S., Brenner, Steven E., Brookes, Anthony J., Greenblatt, Marc S., Hart, Reece K., Karchin, Rachel, Sunyaev, Shamil R., Taschner, Peter E.

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Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization by Pappu, Rohit V, Hart, Reece K, Ponder, Jay W

“…Global energy optimization of a molecular system is difficult due to the well-known “multiple minimum” problem. The rugged potential energy surface (PES)…”
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Unison: an integrated platform for computational biology discovery by Hart, Reece K, Mukhyala, Kiran

“…This paper describes the design and applications of Unison, a comprehensive and integrated warehouse of protein sequences, diverse precomputed predictions, and…”
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31. A cross-consortia initiative for aligning the definitions and descriptions of gene fusions by Wagner, Alex, Hart, Reece, den Dunnen, Johan, Bruford, Elspeth, Hastings, Ros, DiStefano, Marina, Kim, Myungshin, Moore, Sarah, Raca, Gordana

“…Despite the well-established role of gene fusions in oncogenic processes, current practices for characterizing and annotating gene fusion events in the…”
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Abstract 1096: Harmonization standards from the Variant Interpretation for Cancer Consortium by Wagner, Alex H., Hart, Reece K., Babb, Larry, Freimuth, Robert R., Coffman, Adam, Liang, Yonghao, Pitel, Beth, Roy, Angshumoy, Brush, Matthew, Lee, Jennifer, Lu, Anna, Coard, Thomas, Rao, Shruti, Ritter, Deborah, Walsh, Brian, Mockus, Susan, Horak, Peter, King, Ian, Sonkin, Dmitriy, Madhavan, Subha, Raca, Gordana, Chakravarty, Debyani, Griffith, Malachi, Griffith, Obi L.

“…The use of clinical gene sequencing is now commonplace, and genome analysts and molecular pathologists are often tasked with the labor-intensive process of…”
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Exploring the similarities between potential smoothing and simulated annealing by Hart, Reece K., Pappu, Rohit V., Ponder, Jay W.

“…Simulated annealing and potential function smoothing are two widely used approaches for global energy optimization of molecular systems. Potential smoothing as…”
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Abstract P4-12-07: Technical evaluation of multigene testing for hereditary breast and ovarian cancer by Lincoln, Stephen, Kurian, Allison, Desmond, Andrea, Nilsen, Geoffrey, Jacobs, Kevin, Yang, Shan, Hart, Reece, Monzon, Federico, Ellisen, Leif, Ford, James

“…Introduction: Next Generation Sequencing, or NGS technology is gaining acceptance in diagnostic laboratories for multigene panel testing. However questions…”
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Pathogenicity Interpretation in the Age of Precision Medicine: The 2015 Annual Scientific Meeting of the Human Genome Variation Society: HUMAN MUTATION by Oetting, William S., Brenner, Steven E., Brookes, Anthony J., Greenblatt, Marc S., Hart, Reece K., Karchin, Rachel, Sunyaev, Shamil R., Taschner, Peter E.

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59. Integrating cytogenomic and sequence variants in the GA4GH variation representation specification by Wagner, Alex, Babb, Lawrence, Freimuth, Robert, Pitel, Beth, Krysiak, Kilannin, Roy, Angshumoy, Coard, Thomas, Lu, Anna, King, Ian, Sonkin, Dmitriy, Lee, Jennifer, Raca, Gordana, Griffith, Malachi, Griffith, Obi, Hart, Reece

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Potential function smoothing with applications to molecular docking by Hart, Reece Kimball

“…Structure prediction is often modelled as an optimization problem in which a computer must minimize the potential energy of a molecular system in terms of its…”
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Systematic and fully automated identification of protein sequence patterns by Hart, R K, Royyuru, A K, Stolovitzky, G, Califano, A

“…We present an efficient algorithm to systematically and automatically identify patterns in protein sequence families. The procedure is based on the Splash…”
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Potential function smoothing with applications to molecular docking by Hart, Reece Kimball

“…Structure prediction is often modelled as an optimization problem in which a computer must minimize the potential energy of a molecular system in terms of its…”
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