Search Results - "McMurry, A."

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease by Smedley, Damian, Schubach, Max, Jacobsen, Julius O.B., Köhler, Sebastian, Zemojtel, Tomasz, Spielmann, Malte, Jäger, Marten, Hochheiser, Harry, Washington, Nicole L., McMurry, Julie A., Haendel, Melissa A., Mungall, Christopher J., Lewis, Suzanna E., Groza, Tudor, Valentini, Giorgio, Robinson, Peter N.

“…The interpretation of non-coding variants still constitutes a major challenge in the application of whole-genome sequencing in Mendelian disease, especially…”
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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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Long COVID risk and pre-COVID vaccination in an EHR-based cohort study from the RECOVER program by Brannock, M. Daniel, Chew, Robert F., Preiss, Alexander J., Hadley, Emily C., Redfield, Signe, McMurry, Julie A., Leese, Peter J., Girvin, Andrew T., Crosskey, Miles, Zhou, Andrea G., Moffitt, Richard A., Funk, Michele Jonsson, Pfaff, Emily R., Haendel, Melissa A., Chute, Christopher G.

“…Long COVID, or complications arising from COVID-19 weeks after infection, has become a central concern for public health experts. The United States National…”
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Coding long COVID: characterizing a new disease through an ICD-10 lens by Pfaff, Emily R, Madlock-Brown, Charisse, Baratta, John M, Bhatia, Abhishek, Davis, Hannah, Girvin, Andrew, Hill, Elaine, Kelly, Elizabeth, Kostka, Kristin, Loomba, Johanna, McMurry, Julie A, Wong, Rachel, Bennett, Tellen D, Moffitt, Richard, Chute, Christopher G, Haendel, Melissa

“…Naming a newly discovered disease is a difficult process; in the context of the COVID-19 pandemic and the existence of post-acute sequelae of SARS-CoV-2…”
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Interpretable prioritization of splice variants in diagnostic next-generation sequencing by Danis, Daniel, Jacobsen, Julius O.B., Carmody, Leigh C., Gargano, Michael A., McMurry, Julie A., Hegde, Ayushi, Haendel, Melissa A., Valentini, Giorgio, Smedley, Damian, Robinson, Peter N.

“…A critical challenge in genetic diagnostics is the computational assessment of candidate splice variants, specifically the interpretation of nucleotide changes…”
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Risk factors associated with post-acute sequelae of SARS-CoV-2: an N3C and NIH RECOVER study by Hill, Elaine L, Mehta, Hemalkumar B, Sharma, Suchetha, Mane, Klint, Singh, Sharad Kumar, Xie, Catherine, Cathey, Emily, Loomba, Johanna, Russell, Seth, Spratt, Heidi, DeWitt, Peter E, Ammar, Nariman, Madlock-Brown, Charisse, Brown, Donald, McMurry, Julie A, Chute, Christopher G, Haendel, Melissa A, Moffitt, Richard, Pfaff, Emily R, Bennett, Tellen D

“…More than one-third of individuals experience post-acute sequelae of SARS-CoV-2 infection (PASC, which includes long-COVID). The objective is to identify risk…”
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Community risks for SARS-CoV-2 infection among fully vaccinated US adults by rurality: A retrospective cohort study from the National COVID Cohort Collaborative by Anzalone, Alfred Jerrod, Sun, Jing, Vinson, Amanda J, Beasley, William H, Hillegass, William B, Murray, Kimberly, Hendricks, Brian M, Haendel, Melissa, Geary, Carol Reynolds, Bailey, Kristina L, Hanson, Corrine K, Miele, Lucio, Horswell, Ronald, McMurry, Julie A, Porterfield, J Zachary, Vest, Michael T, Bunnell, H Timothy, Harper, Jeremy R, Price, Bradley S, Santangelo, Susan L, Rosen, Clifford J, McClay, James C, Hodder, Sally L

“…While COVID-19 vaccines reduce adverse outcomes, post-vaccination SARS-CoV-2 infection remains problematic. We sought to identify community factors impacting…”
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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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An analysis and metric of reusable data licensing practices for biomedical resources by Carbon, Seth, Champieux, Robin, McMurry, Julie A, Winfree, Lilly, Wyatt, Letisha R, Haendel, Melissa A

“…Data are the foundation of science, and there is an increasing focus on how data can be reused and enhanced to drive scientific discoveries. However, most…”
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NSAID use and clinical outcomes in COVID-19 patients: a 38-center retrospective cohort study by Reese, Justin T, Coleman, Ben, Chan, Lauren, Blau, Hannah, Callahan, Tiffany J, Cappelletti, Luca, Fontana, Tommaso, Bradwell, Katie R, Harris, Nomi L, Casiraghi, Elena, Valentini, Giorgio, Karlebach, Guy, Deer, Rachel, McMurry, Julie A, Haendel, Melissa A, Chute, Christopher G, Pfaff, Emily, Moffitt, Richard, Spratt, Heidi, Singh, Jasvinder A, Mungall, Christopher J, Williams, Andrew E, Robinson, Peter N

“…Non-steroidal anti-inflammatory drugs (NSAIDs) are commonly used to reduce pain, fever, and inflammation but have been associated with complications in…”
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The Human Phenotype Ontology in 2021 by Köhler, Sebastian, Gargano, Michael, Matentzoglu, Nicolas, Carmody, Leigh C, Lewis-Smith, David, Vasilevsky, Nicole A, Danis, Daniel, Balagura, Ganna, Baynam, Gareth, Brower, Amy M, Callahan, Tiffany J, Chute, Christopher G, Est, Johanna L, Galer, Peter D, Ganesan, Shiva, Griese, Matthias, Haimel, Matthias, Pazmandi, Julia, Hanauer, Marc, Harris, Nomi L, Hartnett, Michael J, Hastreiter, Maximilian, Hauck, Fabian, He, Yongqun, Jeske, Tim, Kearney, Hugh, Kindle, Gerhard, Klein, Christoph, Knoflach, Katrin, Krause, Roland, Lagorce, David, McMurry, Julie A, Miller, Jillian A, Munoz-Torres, Monica C, Peters, Rebecca L, Rapp, Christina K, Rath, Ana M, Rind, Shahmir A, Rosenberg, Avi Z, Segal, Michael M, Seidel, Markus G, Smedley, Damian, Talmy, Tomer, Thomas, Yarlalu, Wiafe, Samuel A, Xian, Julie, Yüksel, Zafer, Helbig, Ingo, Mungall, Christopher J, Haendel, Melissa A, Robinson, Peter N

“…Abstract The Human Phenotype Ontology (HPO, https://hpo.jax.org) was launched in 2008 to provide a comprehensive logical standard to describe and…”
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Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources by Köhler, Sebastian, Carmody, Leigh, Vasilevsky, Nicole, Jacobsen, Julius O B, Danis, Daniel, Gourdine, Jean-Philippe, Gargano, Michael, Harris, Nomi L, Matentzoglu, Nicolas, McMurry, Julie A, Osumi-Sutherland, David, Cipriani, Valentina, Balhoff, James P, Conlin, Tom, Blau, Hannah, Baynam, Gareth, Palmer, Richard, Gratian, Dylan, Dawkins, Hugh, Segal, Michael, Jansen, Anna C, Muaz, Ahmed, Chang, Willie H, Bergerson, Jenna, Laulederkind, Stanley J F, Yüksel, Zafer, Beltran, Sergi, Freeman, Alexandra F, Sergouniotis, Panagiotis I, Durkin, Daniel, Storm, Andrea L, Hanauer, Marc, Brudno, Michael, Bello, Susan M, Sincan, Murat, Rageth, Kayli, Wheeler, Matthew T, Oegema, Renske, Lourghi, Halima, Della Rocca, Maria G, Thompson, Rachel, Castellanos, Francisco, Priest, James, Cunningham-Rundles, Charlotte, Hegde, Ayushi, Lovering, Ruth C, Hajek, Catherine, Olry, Annie, Notarangelo, Luigi, Similuk, Morgan, Zhang, Xingmin A, Gómez-Andrés, David, Lochmüller, Hanns, Dollfus, Hélène, Rosenzweig, Sergio, Marwaha, Shruti, Rath, Ana, Sullivan, Kathleen, Smith, Cynthia, Milner, Joshua D, Leroux, Dorothée, Boerkoel, Cornelius F, Klion, Amy, Carter, Melody C, Groza, Tudor, Smedley, Damian, Haendel, Melissa A, Mungall, Chris, Robinson, Peter N

“…Abstract The Human Phenotype Ontology (HPO)—a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases—is used by thousands of…”
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Uniform resolution of compact identifiers for biomedical data by Wimalaratne, Sarala M., Juty, Nick, Kunze, John, Janée, Greg, McMurry, Julie A., Beard, Niall, Jimenez, Rafael, Grethe, Jeffrey S., Hermjakob, Henning, Martone, Maryann E., Clark, Tim

“…Most biomedical data repositories issue locally-unique accessions numbers, but do not provide globally unique, machine-resolvable, persistent identifiers for…”
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The Ontology of Biological Attributes (OBA)—computational traits for the life sciences by Stefancsik, Ray, Balhoff, James P., Balk, Meghan A., Ball, Robyn L., Bello, Susan M., Caron, Anita R., Chesler, Elissa J., de Souza, Vinicius, Gehrke, Sarah, Haendel, Melissa, Harris, Laura W., Harris, Nomi L., Ibrahim, Arwa, Koehler, Sebastian, Matentzoglu, Nicolas, McMurry, Julie A., Mungall, Christopher J., Munoz-Torres, Monica C., Putman, Tim, Robinson, Peter, Smedley, Damian, Sollis, Elliot, Thessen, Anne E., Vasilevsky, Nicole, Walton, David O., Osumi-Sutherland, David

“…Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other…”
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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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Waves in the Magnetized Solar Atmosphere. II. Waves from Localized Sources in Magnetic Flux Concentrations by Bogdan, T. J, Hansteen, M. Carlsson V, McMurry, A, Rosenthal, C. S, Johnson, M, Petty-Powell, S, Zita, E. J, Stein, R. F, McIntosh, S. W, Nordlund, Å

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The Environmental Conditions, Treatments, and Exposures Ontology (ECTO): connecting toxicology and exposure to human health and beyond by Chan, Lauren E, Thessen, Anne E, Duncan, William D, Matentzoglu, Nicolas, Schmitt, Charles, Grondin, Cynthia J, Vasilevsky, Nicole, McMurry, Julie A, Robinson, Peter N, Mungall, Christopher J, Haendel, Melissa A

“…Evaluating the impact of environmental exposures on organism health is a key goal of modern biomedicine and is critically important in an age of greater…”
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The case for open science: rare diseases by Rubinstein, Yaffa R, Robinson, Peter N, Gahl, William A, Avillach, Paul, Baynam, Gareth, Cederroth, Helene, Goodwin, Rebecca M, Groft, Stephen C, Hansson, Mats G, Harris, Nomi L, Huser, Vojtech, Mascalzoni, Deborah, McMurry, Julie A, Might, Matthew, Nellaker, Christoffer, Mons, Barend, Paltoo, Dina N, Pevsner, Jonathan, Posada, Manuel, Rockett-Frase, Alison P, Roos, Marco, Rubinstein, Tamar B, Taruscio, Domenica, van Enckevort, Esther, Haendel, Melissa A

“…The premise of Open Science is that research and medical management will progress faster if data and knowledge are openly shared. The value of Open Science is…”
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The GA4GH Phenopacket schema defines a computable representation of clinical data by Jacobsen, Julius O. B., Baudis, Michael, Baynam, Gareth S., Beckmann, Jacques S., Beltran, Sergi, Buske, Orion J., Callahan, Tiffany J., Chute, Christopher G., Courtot, Mélanie, Danis, Daniel, Elemento, Olivier, Essenwanger, Andrea, Freimuth, Robert R., Gargano, Michael A., Groza, Tudor, Hamosh, Ada, Harris, Nomi L., Kaliyaperumal, Rajaram, Lloyd, Kevin C. Kent, Khalifa, Aly, Krawitz, Peter M., Köhler, Sebastian, Laraway, Brian J., Lehväslaiho, Heikki, Matalonga, Leslie, McMurry, Julie A., Metke-Jimenez, Alejandro, Mungall, Christopher J., Munoz-Torres, Monica C., Ogishima, Soichi, Papakonstantinou, Anastasios, Piscia, Davide, Pontikos, Nikolas, Queralt-Rosinach, Núria, Roos, Marco, Sass, Julian, Schofield, Paul N., Seelow, Dominik, Siapos, Anastasios, Smedley, Damian, Smith, Lindsay D., Steinhaus, Robin, Sundaramurthi, Jagadish Chandrabose, Swietlik, Emilia M., Thun, Sylvia, Vasilevsky, Nicole A., Wagner, Alex H., Warner, Jeremy L., Weiland, Claus, Haendel, Melissa A., Robinson, Peter N.

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Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data by McMurry, Julie A, Juty, Nick, Blomberg, Niklas, Burdett, Tony, Conlin, Tom, Conte, Nathalie, Courtot, Mélanie, Deck, John, Dumontier, Michel, Fellows, Donal K, Gonzalez-Beltran, Alejandra, Gormanns, Philipp, Grethe, Jeffrey, Hastings, Janna, Hériché, Jean-Karim, Hermjakob, Henning, Ison, Jon C, Jimenez, Rafael C, Jupp, Simon, Kunze, John, Laibe, Camille, Le Novère, Nicolas, Malone, James, Martin, Maria Jesus, McEntyre, Johanna R, Morris, Chris, Muilu, Juha, Müller, Wolfgang, Rocca-Serra, Philippe, Sansone, Susanna-Assunta, Sariyar, Murat, Snoep, Jacky L, Soiland-Reyes, Stian, Stanford, Natalie J, Swainston, Neil, Washington, Nicole, Williams, Alan R, Wimalaratne, Sarala M, Winfree, Lilly M, Wolstencroft, Katherine, Goble, Carole, Mungall, Christopher J, Haendel, Melissa A, Parkinson, Helen

“…In many disciplines, data are highly decentralized across thousands of online databases (repositories, registries, and knowledgebases). Wringing value from…”
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