Search Results - "Reese, Justin T."

Web Apollo: a web-based genomic annotation editing platform by Lee, Eduardo, Helt, Gregg A, Reese, Justin T, Munoz-Torres, Monica C, Childers, Chris P, Buels, Robert M, Stein, Lincoln, Holmes, Ian H, Elsik, Christine G, Lewis, Suzanna E

“…Web Apollo is the first instantaneous, collaborative genomic annotation editor available on the web. One of the natural consequences following from current…”
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An evaluation of GPT models for phenotype concept recognition by Groza, Tudor, Caufield, Harry, Gration, Dylan, Baynam, Gareth, Haendel, Melissa A, Robinson, Peter N, Mungall, Christopher J, Reese, Justin T

“…Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building…”
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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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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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Association of post-COVID phenotypic manifestations with new-onset psychiatric disease by Coleman, Ben, Casiraghi, Elena, Callahan, Tiffany J., Blau, Hannah, Chan, Lauren E., Laraway, Bryan, Clark, Kevin B., Re’em, Yochai, Gersing, Ken R., Wilkins, Kenneth J., Harris, Nomi L., Valentini, Giorgio, Haendel, Melissa A., Reese, Justin T., Robinson, Peter N.

“…Acute COVID-19 infection can be followed by diverse clinical manifestations referred to as Post Acute Sequelae of SARS-CoV2 Infection (PASC). Studies have…”
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Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI) by Toro, Sabrina, Anagnostopoulos, Anna V, Bello, Susan M, Blumberg, Kai, Cameron, Rhiannon, Carmody, Leigh, Diehl, Alexander D, Dooley, Damion M, Duncan, William D, Fey, Petra, Gaudet, Pascale, Harris, Nomi L, Joachimiak, Marcin P, Kiani, Leila, Lubiana, Tiago, Munoz-Torres, Monica C, O'Neil, Shawn, Osumi-Sutherland, David, Puig-Barbe, Aleix, Reese, Justin T, Reiser, Leonore, Robb, Sofia Mc, Ruemping, Troy, Seager, James, Sid, Eric, Stefancsik, Ray, Weber, Magalie, Wood, Valerie, Haendel, Melissa A, Mungall, Christopher J

“…Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus…”
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A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery by Danis, Daniel, Bamshad, Michael J., Bridges, Yasemin, Caballero-Oteyza, Andrés, Cacheiro, Pilar, Carmody, Leigh C., Chimirri, Leonardo, Chong, Jessica X., Coleman, Ben, Dalgleish, Raymond, Freeman, Peter J., Graefe, Adam S.L., Groza, Tudor, Hansen, Peter, Jacobsen, Julius O.B., Klocperk, Adam, Kusters, Maaike, Ladewig, Markus S., Marcello, Anthony J., Mattina, Teresa, Mungall, Christopher J., Munoz-Torres, Monica C., Reese, Justin T., Rehburg, Filip, Reis, Bárbara C.S., Schuetz, Catharina, Smedley, Damian, Strauss, Timmy, Sundaramurthi, Jagadish Chandrabose, Thun, Sylvia, Wissink, Kyran, Wagstaff, John F., Zocche, David, Haendel, Melissa A., Robinson, Peter N.

“…The Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema was released in 2022 and approved by ISO as a standard for sharing clinical and genomic…”
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Computational and transcriptional evidence for microRNAs in the honey bee genome by Weaver, Daniel B, Anzola, Juan M, Evans, Jay D, Reid, Jeffrey G, Reese, Justin T, Childs, Kevin L, Zdobnov, Evgeny M, Samanta, Manoj P, Miller, Jonathan, Elsik, Christine G

“…BACKGROUND: Non-coding microRNAs (miRNAs) are key regulators of gene expression in eukaryotes. Insect miRNAs help regulate the levels of proteins involved with…”
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Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome by Reese, Justin T, Childers, Christopher P, Sundaram, Jaideep P, Dickens, C Michael, Childs, Kevin L, Vile, Donald C, Elsik, Christine G

“…A goal of the Bovine Genome Database (BGD; http://BovineGenome.org) has been to support the Bovine Genome Sequencing and Analysis Consortium (BGSAC) in the…”
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Molecular traces of alternative social organization in a termite genome by Terrapon, Nicolas, Li, Cai, Robertson, Hugh M., Ji, Lu, Meng, Xuehong, Booth, Warren, Chen, Zhensheng, Childers, Christopher P., Glastad, Karl M., Gokhale, Kaustubh, Gowin, Johannes, Gronenberg, Wulfila, Hermansen, Russell A., Hu, Haofu, Hunt, Brendan G., Huylmans, Ann Kathrin, Khalil, Sayed M. S., Mitchell, Robert D., Munoz-Torres, Monica C., Mustard, Julie A., Pan, Hailin, Reese, Justin T., Scharf, Michael E., Sun, Fengming, Vogel, Heiko, Xiao, Jin, Yang, Wei, Yang, Zhikai, Yang, Zuoquan, Zhou, Jiajian, Zhu, Jiwei, Brent, Colin S., Elsik, Christine G., Goodisman, Michael A. D., Liberles, David A., Roe, R. Michael, Vargo, Edward L., Vilcinskas, Andreas, Wang, Jun, Bornberg-Bauer, Erich, Korb, Judith, Zhang, Guojie, Liebig, Jürgen

“…Although eusociality evolved independently within several orders of insects, research into the molecular underpinnings of the transition towards social…”
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Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES): a method for populating knowledge bases using zero-shot learning by Caufield, J Harry, Hegde, Harshad, Emonet, Vincent, Harris, Nomi L, Joachimiak, Marcin P, Matentzoglu, Nicolas, Kim, HyeongSik, Moxon, Sierra, Reese, Justin T, Haendel, Melissa A, Robinson, Peter N, Mungall, Christopher J

“…Abstract Motivation Creating knowledge bases and ontologies is a time consuming task that relies on manual curation. AI/NLP approaches can assist expert…”
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Genome Sequence of Taurine Cattle: A Window to Ruminant Biology and Evolution by Elsik, Christine G, Tellam, Ross L, Worley, Kim C

“…To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of…”
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Generalisable long COVID subtypes: findings from the NIH N3C and RECOVER programmes by Reese, Justin T., Blau, Hannah, Casiraghi, Elena, Bergquist, Timothy, Loomba, Johanna J., Callahan, Tiffany J., Laraway, Bryan, Antonescu, Corneliu, Coleman, Ben, Gargano, Michael, Wilkins, Kenneth J., Cappelletti, Luca, Fontana, Tommaso, Ammar, Nariman, Antony, Blessy, Murali, T.M., Caufield, J. Harry, Karlebach, Guy, McMurry, Julie A., Williams, Andrew, Moffitt, Richard, Banerjee, Jineta, Solomonides, Anthony E., Davis, Hannah, Kostka, Kristin, Valentini, Giorgio, Sahner, David, Chute, Christopher G., Madlock-Brown, Charisse, Haendel, Melissa A., Robinson, Peter N., Spratt, Heidi, Visweswaran, Shyam, Flack, Joseph Eugene, Yoo, Yun Jae, Gabriel, Davera, Alexander, G. Caleb, Mehta, Hemalkumar B., Liu, Feifan, Miller, Robert T., Wong, Rachel, Hill, Elaine L., Thorpe, Lorna E., Divers, Jasmin

“…Stratification of patients with post-acute sequelae of SARS-CoV-2 infection (PASC, or long COVID) would allow precision clinical management strategies…”
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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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Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle by Kirkness, Ewen F., Haas, Brian J., Sun, Weilin, Braig, Henk R., Perotti, M. Alejandra, Clark, John M., Lee, Si Hyeock, Robertson, Hugh M., Kennedy, Ryan C., Elhaik, Eran, Gerlach, Daniel, Kriventseva, Evgenia V., Elsik, Christine G., Graur, Dan, Hill, Catherine A., Veenstra, Jan A., Walenz, Brian, Tubío, José Manuel C., Ribeiro, José M. C., Rozas, Julio, Johnston, J. Spencer, Reese, Justin T., Popadic, Aleksandar, Tojo, Marta, Raoult, Didier, Reed, David L., Tomoyasu, Yoshinori, Krause, Emily, Mittapalli, Omprakash, Margam, Venu M., Li, Hong-Mei, Meyer, Jason M., Johnson, Reed M., Romero-Severson, Jeanne, VanZee, Janice Pagel, Alvarez-Ponce, David, Vieira, Filipe G., Aguadé, Montserrat, Guirao-Rico, Sara, Anzola, Juan M., Yoon, Kyong S., Strycharz, Joseph P., Unger, Maria F., Christley, Scott, Lobo, Neil F., Seufferheld, Manfredo J., Wang, NaiKuan, Dasch, Gregory A., Struchiner, Claudio J., Madey, Greg, Hannick, Linda I., Bidwell, Shelby, Joardar, Vinita, Caler, Elisabet, Shao, Renfu, Barker, Stephen C., Cameron, Stephen, Bruggner, Robert V., Regier, Allison, Johnson, Justin, Viswanathan, Lakshmi, Utterback, Terry R., Sutton, Granger G., Lawson, Daniel, Waterhouse, Robert M., Venter, J. Craig, Strausberg, Robert L., Berenbaum, May R., Collins, Frank H., Zdobnov, Evgeny M., Pittendrigh, Barry R.

“…As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is an important vector for human diseases, including epidemic typhus, relapsing…”
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Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality by Simola, Daniel F, Wissler, Lothar, Donahue, Greg, Waterhouse, Robert M, Helmkampf, Martin, Roux, Julien, Nygaard, Sanne, Glastad, Karl M, Hagen, Darren E, Viljakainen, Lumi, Reese, Justin T, Hunt, Brendan G, Graur, Dan, Elhaik, Eran, Kriventseva, Evgenia V, Wen, Jiayu, Parker, Brian J, Cash, Elizabeth, Privman, Eyal, Childers, Christopher P, Muñoz-Torres, Monica C, Boomsma, Jacobus J, Bornberg-Bauer, Erich, Currie, Cameron R, Elsik, Christine G, Suen, Garret, Goodisman, Michael A D, Keller, Laurent, Liebig, Jürgen, Rawls, Alan, Reinberg, Danny, Smith, Chris D, Smith, Chris R, Tsutsui, Neil, Wurm, Yannick, Zdobnov, Evgeny M, Berger, Shelley L, Gadau, Jürgen

“…Genomes of eusocial insects code for dramatic examples of phenotypic plasticity and social organization. We compared the genomes of seven ants, the honeybee,…”
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The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle by Suen, Garret, Teiling, Clotilde, Li, Lewyn, Holt, Carson, Abouheif, Ehab, Bornberg-Bauer, Erich, Bouffard, Pascal, Caldera, Eric J, Cash, Elizabeth, Cavanaugh, Amy, Denas, Olgert, Elhaik, Eran, Favé, Marie-Julie, Gadau, Jürgen, Gibson, Joshua D, Graur, Dan, Grubbs, Kirk J, Hagen, Darren E, Harkins, Timothy T, Helmkampf, Martin, Hu, Hao, Johnson, Brian R, Kim, Jay, Marsh, Sarah E, Moeller, Joseph A, Muñoz-Torres, Mónica C, Murphy, Marguerite C, Naughton, Meredith C, Nigam, Surabhi, Overson, Rick, Rajakumar, Rajendhran, Reese, Justin T, Scott, Jarrod J, Smith, Chris R, Tao, Shu, Tsutsui, Neil D, Viljakainen, Lumi, Wissler, Lothar, Yandell, Mark D, Zimmer, Fabian, Taylor, James, Slater, Steven C, Clifton, Sandra W, Warren, Wesley C, Elsik, Christine G, Smith, Christopher D, Weinstock, George M, Gerardo, Nicole M, Currie, Cameron R

“…Leaf-cutter ants are one of the most important herbivorous insects in the Neotropics, harvesting vast quantities of fresh leaf material. The ants use leaves to…”
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Creating a honey bee consensus gene set by Elsik, Christine G, Mackey, Aaron J, Reese, Justin T, Milshina, Natalia V, Roos, David S, Weinstock, George M

“…We wished to produce a single reference gene set for honey bee (Apis mellifera). Our motivation was twofold. First, we wished to obtain an improved set of gene…”
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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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Predictive models of long COVID by Antony, Blessy, Blau, Hannah, Casiraghi, Elena, Loomba, Johanna J, Callahan, Tiffany J, Laraway, Bryan J, Wilkins, Kenneth J, Antonescu, Corneliu C, Valentini, Giorgio, Williams, Andrew E, Robinson, Peter N, Reese, Justin T, Murali, T M

“…The cause and symptoms of long COVID are poorly understood. It is challenging to predict whether a given COVID-19 patient will develop long COVID in the…”
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