Search Results - "Shefchek, Kent"

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species by Mungall, Christopher J, McMurry, Julie A, Köhler, Sebastian, Balhoff, James P, Borromeo, Charles, Brush, Matthew, Carbon, Seth, Conlin, Tom, Dunn, Nathan, Engelstad, Mark, Foster, Erin, Gourdine, J P, Jacobsen, Julius O B, Keith, Dan, Laraway, Bryan, Lewis, Suzanna E, NguyenXuan, Jeremy, Shefchek, Kent, Vasilevsky, Nicole, Yuan, Zhou, Washington, Nicole, Hochheiser, Harry, Groza, Tudor, Smedley, Damian, Robinson, Peter N, Haendel, Melissa A

“…The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges…”
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KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response by Reese, Justin T., Unni, Deepak, Callahan, Tiffany J., Cappelletti, Luca, Ravanmehr, Vida, Carbon, Seth, Shefchek, Kent A., Good, Benjamin M., Balhoff, James P., Fontana, Tommaso, Blau, Hannah, Matentzoglu, Nicolas, Harris, Nomi L., Munoz-Torres, Monica C., Haendel, Melissa A., Robinson, Peter N., Joachimiak, Marcin P., Mungall, Christopher J.

“…Integrated, up-to-date data about SARS-CoV-2 and COVID-19 is crucial for the ongoing response to the COVID-19 pandemic by the biomedical research community…”
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KG-Hub—building and exchanging biological knowledge graphs by Caufield, J Harry, Putman, Tim, Schaper, Kevin, Unni, Deepak R, Hegde, Harshad, Callahan, Tiffany J, Cappelletti, Luca, Moxon, Sierra A T, Ravanmehr, Vida, Carbon, Seth, Chan, Lauren E, Cortes, Katherina, Shefchek, Kent A, Elsarboukh, Glass, Balhoff, Jim, Fontana, Tommaso, Matentzoglu, Nicolas, Bruskiewich, Richard M, Thessen, Anne E, Harris, Nomi L, Munoz-Torres, Monica C, Haendel, Melissa A, Robinson, Peter N, Joachimiak, Marcin P, Mungall, Christopher J, Reese, Justin T

“…Abstract Motivation Knowledge graphs (KGs) are a powerful approach for integrating heterogeneous data and making inferences in biology and many other domains,…”
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Navigating the Phenotype Frontier: The Monarch Initiative by McMurry, Julie A, Köhler, Sebastian, Washington, Nicole L, Balhoff, James P, Borromeo, Charles, Brush, Matthew, Carbon, Seth, Conlin, Tom, Dunn, Nathan, Engelstad, Mark, Foster, Erin, Gourdine, Jean-Philippe, Jacobsen, Julius O B, Keith, Daniel, Laraway, Bryan, Xuan, Jeremy Nguyen, Shefchek, Kent, Vasilevsky, Nicole A, Yuan, Zhou, Lewis, Suzanna E, Hochheiser, Harry, Groza, Tudor, Smedley, Damian, Robinson, Peter N, Mungall, Christopher J, Haendel, Melissa A

“…The principles of genetics apply across the entire tree of life. At the cellular level we share biological mechanisms with species from which we diverged…”
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Underrepresentation of Phenotypic Variability of 16p13.11 Microduplication Syndrome Assessed With an Online Self-Phenotyping Tool (Phenotypr): Cohort Study by Li, Jianqiao, Hojlo, Margaret A, Chennuri, Sampath, Gujral, Nitin, Paterson, Heather L, Shefchek, Kent A, Genetti, Casie A, Cohn, Emily L, Sewalk, Kara C, Garvey, Emily A, Buttermore, Elizabeth D, Anderson, Nickesha C, Beggs, Alan H, Agrawal, Pankaj B, Brownstein, John S, Haendel, Melissa A, Holm, Ingrid A, Gonzalez-Heydrich, Joseph, Brownstein, Catherine A

“…16p13.11 microduplication syndrome has a variable presentation and is characterized primarily by neurodevelopmental and physical phenotypes resulting from copy…”
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Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery by Mungall, Christopher J., Washington, Nicole L., Nguyen-Xuan, Jeremy, Condit, Christopher, Smedley, Damian, Köhler, Sebastian, Groza, Tudor, Shefchek, Kent, Hochheiser, Harry, Robinson, Peter N., Lewis, Suzanna E., Haendel, Melissa A.

“…ABSTRACT The Matchmaker Exchange application programming interface (API) allows searching a patient's genotypic or phenotypic profiles across clinical sites,…”
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Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery by Gourdine, Jean-Philippe F, Brush, Matthew H, Vasilevsky, Nicole A, Shefchek, Kent, Köhler, Sebastian, Matentzoglu, Nicolas, Munoz-Torres, Monica C, McMurry, Julie A, Zhang, Xingmin Aaron, Robinson, Peter N, Haendel, Melissa A

“…While abnormalities related to carbohydrates (glycans) are frequent for patients with rare and undiagnosed diseases as well as in many common diseases, these…”
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Genomic Insights into the Emerging Human Pathogen Mycobacterium massiliense by Tettelin, Hervé, Sampaio, Elizabeth P, Daugherty, Sean C, Hine, Erin, Riley, David R, Sadzewicz, Lisa, Sengamalay, Naomi, Shefchek, Kent, Su, Qi, Tallon, Luke J, Conville, Patricia, Olivier, Kenneth N, Holland, Steven M, Fraser, Claire M, Zelazny, Adrian M

“…Mycobacterium massiliense (Mycobacterium abscessus group) is an emerging pathogen causing pulmonary disease and skin and soft tissue infections. We report the…”
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Genome Sequence of Enterobacter radicincitans DSM16656T, a Plant Growth-Promoting Endophyte by Witzel, Katja, Gwinn-Giglio, Michelle, Nadendla, Suvarna, Shefchek, Kent, Ruppel, Silke

“…Enterobacter radicincitans sp. nov. DSM16656T represents a new species of the genus Enterobacter which is a biological nitrogen-fixing endophytic bacterium…”
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Genome sequence of Enterobacter radicincitans DSM16656(T), a plant growth-promoting endophyte by Witzel, Katja, Gwinn-Giglio, Michelle, Nadendla, Suvarna, Shefchek, Kent, Ruppel, Silke

“…Enterobacter radicincitans sp. nov. DSM16656(T) represents a new species of the genus Enterobacter which is a biological nitrogen-fixing endophytic bacterium…”
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A Simple Standard for Sharing Ontological Mappings (SSSOM) by Matentzoglu, Nicolas, Balhoff, James P, Bello, Susan M, Bizon, Chris, Brush, Matthew, Callahan, Tiffany J, Chute, Christopher G, Duncan, William D, Evelo, Chris T, Gabriel, Davera, Graybeal, John, Gray, Alasdair, Gyori, Benjamin M, Haendel, Melissa, Harmse, Henriette, Harris, Nomi L, Harrow, Ian, Hegde, Harshad B, Hoyt, Amelia L, Hoyt, Charles T, Jiao, Dazhi, Jiménez-Ruiz, Ernesto, Jupp, Simon, Kim, Hyeongsik, Koehler, Sebastian, Liener, Thomas, Long, Qinqin, Malone, James, McLaughlin, James A, McMurry, Julie A, Moxon, Sierra, Munoz-Torres, Monica C, Osumi-Sutherland, David, Overton, James A, Peters, Bjoern, Putman, Tim, Queralt-Rosinach, Núria, Shefchek, Kent, Solbrig, Harold, Thessen, Anne, Tudorache, Tania, Vasilevsky, Nicole, Wagner, Alex H, Mungall, Christopher J

“…Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between…”
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The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species by Putman, Tim E, Schaper, Kevin, Matentzoglu, Nicolas, Rubinetti, Vincent P, Alquaddoomi, Faisal S, Cox, Corey, Caufield, J Harry, Elsarboukh, Glass, Gehrke, Sarah, Hegde, Harshad, Reese, Justin T, Braun, Ian, Bruskiewich, Richard M, Cappelletti, Luca, Carbon, Seth, Caron, Anita R, Chan, Lauren E, Chute, Christopher G, Cortes, Katherina G, De Souza, Vinícius, Fontana, Tommaso, Harris, Nomi L, Hartley, Emily L, Hurwitz, Eric, Jacobsen, Julius O B, Krishnamurthy, Madan, Laraway, Bryan J, McLaughlin, James A, McMurry, Julie A, Moxon, Sierra A T, Mullen, Kathleen R, O’Neil, Shawn T, Shefchek, Kent A, Stefancsik, Ray, Toro, Sabrina, Vasilevsky, Nicole A, Walls, Ramona L, Whetzel, Patricia L, Osumi-Sutherland, David, Smedley, Damian, Robinson, Peter N, Mungall, Christopher J, Haendel, Melissa A, Munoz-Torres, Monica C

“…Abstract Bridging the gap between genetic variations, environmental determinants, and phenotypic outcomes is critical for supporting clinical diagnosis and…”
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The Clinical Variant Analysis Tool: Analyzing the evidence supporting reported genomic variation in clinical practice by Chin, Hui-Lin, Gazzaz, Nour, Huynh, Stephanie, Handra, Iulia, Warnock, Lynn, Moller-Hansen, Ashley, Boerkoel, Pierre, Jacobsen, Julius O.B., du Souich, Christèle, Zhang, Nan, Shefchek, Kent, Prentice, Leah M., Washington, Nicole, Haendel, Melissa, Armstrong, Linlea, Clarke, Lorne, Li, Wenhui Laura, Smedley, Damian, Robinson, Peter N., Boerkoel, Cornelius F.

“…Genomic test results, regardless of laboratory variant classification, require clinical practitioners to judge the applicability of a variant for medical…”
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Plain-language medical vocabulary for precision diagnosis by Vasilevsky, Nicole A., Foster, Erin D., Engelstad, Mark E., Carmody, Leigh, Might, Matt, Chambers, Chip, Dawkins, Hugh J. S., Lewis, Janine, Della Rocca, Maria G., Snyder, Michelle, Boerkoel, Cornelius F., Rath, Ana, Terry, Sharon F., Kent, Alastair, Searle, Beverly, Baynam, Gareth, Jones, Erik, Gavin, Pam, Bamshad, Michael, Chong, Jessica, Groza, Tudor, Adams, David, Resnick, Adam C., Heath, Allison P., Mungall, Chris, Holm, Ingrid A., Rageth, Kayli, Brownstein, Catherine A., Shefchek, Kent, McMurry, Julie A., Robinson, Peter N., Köhler, Sebastian, Haendel, Melissa A.

“…For undiagnosed patients and those with rare diseases, the affected individuals themselves are an especially critical source of phenotyping information. These…”
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The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species by Mungall, Christopher J., McMurry, Julie A., Köhler, Sebastian, Balhoff, James P., Borromeo, Charles, Brush, Matthew, Carbon, Seth, Conlin, Tom, Dunn, Nathan, Engelstad, Mark, Foster, Erin, Gourdine, J. P., Jacobsen, Julius O. B., Keith, Dan, Laraway, Bryan, Lewis, Suzanna E., NguyenXuan, Jeremy, Shefchek, Kent, Vasilevsky, Nicole, Yuan, Zhou, Washington, Nicole, Hochheiser, Harry, Groza, Tudor, Smedley, Damian, Robinson, Peter N., Haendel, Melissa A.

“…The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges…”
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Genome Sequence of Enterobacter radicincitans DSM16656^sup T^, a Plant Growth-Promoting Endophyte by Witzel, Katja, Gwinn-Giglio, Michelle, Nadendla, Suvarna, Shefchek, Kent, Ruppel, Silke

“…Enterobacter radicincitans sp. nov. DSM16656... represents a new species of the genus Enterobacter which is a biological nitrogen-fixing endophytic bacterium…”
Get full text

Genome Sequence of Enterobacter radicincitans DSM16656 T , a Plant Growth-Promoting Endophyte by Witzel, Katja, Gwinn-Giglio, Michelle, Nadendla, Suvarna, Shefchek, Kent, Ruppel, Silke

“…ABSTRACT Enterobacter radicincitans sp. nov. DSM16656 T represents a new species of the genus Enterobacter which is a biological nitrogen-fixing endophytic…”
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Genome sequences of 65 Helicobacter pylori strains isolated from asymptomatic individuals and patients with gastric cancer, peptic ulcer disease, or gastritis by Blanchard, Thomas G., Czinn, Steven J., Correa, Pelayo, Nakazawa, Teruko, Keelan, Monika, Morningstar, Lindsay, Santana-Cruz, Ivette, Maroo, Ankit, McCracken, Carri, Shefchek, Kent, Daugherty, Sean, Song, Yang, Fraser, Claire M., Fricke, W. Florian

“…Abstract Helicobacter pylori , inhabitant of the gastric mucosa of over half of the world population, with decreasing prevalence in the U.S., has been…”
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The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species by Shefchek, Kent A, Harris, Nomi L, Gargano, Michael, Matentzoglu, Nicolas, Unni, Deepak, Brush, Matthew, Keith, Daniel, Conlin, Tom, Vasilevsky, Nicole, Zhang, Xingmin Aaron, Balhoff, James P, Babb, Larry, Bello, Susan M, Blau, Hannah, Bradford, Yvonne, Carbon, Seth, Carmody, Leigh, Chan, Lauren E, Cipriani, Valentina, Cuzick, Alayne, Della Rocca, Maria, Dunn, Nathan, Essaid, Shahim, Fey, Petra, Grove, Chris, Gourdine, Jean-Phillipe, Hamosh, Ada, Harris, Midori, Helbig, Ingo, Hoatlin, Maureen, Joachimiak, Marcin, Jupp, Simon, Lett, Kenneth B, Lewis, Suzanna E, McNamara, Craig, Pendlington, Zoë M, Pilgrim, Clare, Putman, Tim, Ravanmehr, Vida, Reese, Justin, Riggs, Erin, Robb, Sofia, Roncaglia, Paola, Seager, James, Segerdell, Erik, Similuk, Morgan, Storm, Andrea L, Thaxon, Courtney, Thessen, Anne, Jacobsen, Julius O B, McMurry, Julie A, Groza, Tudor, Köhler, Sebastian, Smedley, Damian, Robinson, Peter N, Mungall, Christopher J, Haendel, Melissa A, Munoz-Torres, Monica C, Osumi-Sutherland, David

“…Abstract In biology and biomedicine, relating phenotypic outcomes with genetic variation and environmental factors remains a challenge: patient phenotypes may…”
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Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science by Moxon, Sierra A. T., Bruskiewich, Richard, Dancik, Vlado, Dumontier, Michel, Fecho, Karamarie, Putman, Tim, Qin, Guangrong, Ramsey, Stephen A., Soman, Karthik, Thessen, Anne E., Haendel, Melissa A., Mungall, Christopher J., Ahalt, Stanley C., Alden, John, Alkanaq, Ahmed, Avila, Ricardo, Baumgartner, Andrew, Belhu, Basazin, Brandon, Namdi, Burtt, Noel, Byrd, William, Callaghan, Jackson, Cano, Marco Alvarado, Celebi, Remzi, Champion, James, Chen, Zhehuan, Chung, Lawrence, Cohen, Kevin, Costanzo, Maria, Dai, Cheng, Dančík, Vlado, Dougherty, Jennifer, Gardner, Vicki, Glen, Amy, Goel, Prateek, Gormley, Joseph, Greyber, Alon, Haaland, Perry, Hanspers, Kristina, He, Kaiwen, Hinderer, Eugene W., Hubal, Robert, Issabekova, Tursynay, Jarrell, Matthew, Jenkins, Lindsay, Kang, Jimin, Kim, Keum Joo, Knowles, Michael, Koesterer, Ryan, Korn, Daniel, Koslicki, David, Krishnamurthy, Ashok, Kvarfordt, Lindsey, Leigh, Margaret, Magis, Andrew, Mamidi, Tarun, Mantilla, Michelle, Massung, Jeffrey, Mauldin, Denise, McMurry, Julie, Mease, Philip, Mendoza, Luis, Mersmann, Marian, Muller, Sandrine, Muluka, Arun Teja, Osborne, John, Owen, Phil, Patton, Michael, Peden, David B., Peene, R. Carter, Pfaff, Emily, Price, Guthrie, Raj, Shruti, Reilly, Jason, Roach, Jared, Roper, Ryan T., Rosenblatt, Greg, Rubin, Irit, Scott, Erik, Sharma, Priya, Shrestha, Manil, Sinha, Meghamala, Southall, Noel, Stillwell, Lisa, Strasser, Michael " Michi", Tinglin, Jillian, Tropsha, Alexander, Vaidya, Gaurav, Viola, Adam, Wang, Max, Weber, Rosina, Wei, Qi, Whitlock, Jordan, Williams, Mark D., Xin, Jiwen Kevin, Xu, Hao, Xu, Colleen, Yao, Yao, Zhou, Eric, Zisk, Tom

“…Within clinical, biomedical, and translational science, an increasing number of projects are adopting graphs for knowledge representation. Graph‐based data…”
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