Justin Reese - Publications, H-index & Citations

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Justin Reese

University Toronto Scarborough

36H-index

170Paper Count

1.1WCitation Count

Published Papers 47

Publication Date

Systematic benchmarking demonstrates large language models have not reached the diagnostic accuracy of traditional rare-disease decision support tools

European Journal of Human Genetics

IF4.6

2026-02-24

OAAI

Justin T. Reese; Leonardo Chimirri; Yasemin Bridges; Daniel Danis; J. Harry Caufield; Michael A. Gargano; Carlo Kroll; Andrew Schmeder; Fengchen Liu; Kyran Wissink; Julie A. McMurry; Adam S. L. Graefe; Enock Niyonkuru; Daniel R. Korn; Elena Casiraghi; Giorgio Valentini; Julius O. B. Jacobsen; Melissa Haendel; Damian Smedley; Christopher J. Mungall; Peter N. Robinson

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Ecolink: Towards a Knowledge Graph Schema for Complex Environmental Systems

NEW TRENDS IN THEORY AND PRACTICE OF DIGITAL LIBRARIES, TPDL 2025

IF0

2026-01-01

PREAI

Alamenciak, Tim; Arnillas, Carlos Alberto; Caufield, Harry; Compton, Katherine; Drew, Kian; Fruhstuckl, Robert; Heger, Tina; Koenig-Ries, Birgitta; Mungall, Chris; Moxon, Sierra; Reese, Justin; Tardif, Jordan; Vogt, Lars

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Consistent performance of large language models in rare disease diagnosis across ten languages and 4917 cases

eBioMedicine

IF10.8

2025-10-14

OAAI

Leonardo Chimirri; J. Harry Caufield; Yasemin Bridges; Nicolas Matentzoglu; Michael Gargano; Mario Cazalla; Shihan Chen; Daniel Danis; Alexander J.M. Dingemans; Klara Gehle; Petra Gehle; Adam S.L. Graefe; Weihong Gu; Markus S. Ladewig; Pablo Lapunzina; Julián Nevado; Enock Niyonkuru; Soichi Ogishima; Dominik Seelow; Jair A. Tenorio Castaño; Marek Turnovec; Bert B.A. de Vries; Kai Wang; Kyran Wissink; Zafer Yüksel; Gabriele Zucca; Melissa A. Haendel; Christopher J. Mungall; Justin Reese; Peter N. Robinson

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Chemical classification program synthesis using generative artificial intelligence

Journal of Cheminformatics

IF5.7

2025-10-04

OAAI

Christopher J. Mungall; Adnan Malik; Daniel R. Korn; Justin T. Reese; Noel M. O’Boyle; Janna Hastings

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Oncopacket: integration of cancer research data using GA4GH phenopackets

BIOINFORMATICS

IF5.4

2025-10-01

OAAI

Sierk, Michael; Danis, Daniel; Patil, Sujay; Kishor, Nobal; Mondal, Rajdeep; Jha, Abhishek; Chen, Qingrong; Yan, Chunhua; Munoz-Torres, Monica; Meerzaman, Daoud; Robinson, Peter N.; Reese, Justin T.

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Announcing the Biomedical Data Translator: Initial Public Release

cts clinical and translational science

IF0

2025-07-09

OAAI

Karamarie Fecho; Gwênlyn Glusman; Sergio E. Baranzini; Chris Bizon; Matthew Brush; William Byrd; Lawrence Chung; Andrew Crouse; Eric Deutsch; Michel Dumontier; Aleksandra Foksinska; Jennifer Hadlock; Kaiwen He; Sui Huang; Robert Hubal; Gregory M. Hyde; Sharat Israni; Kelyne Kenmogne; David Koslicki; Jana Dorfman Marcette; Ewy A. Mathe; Abrar Mesbah; Sierra A. T. Moxon; Christopher J. Mungall; John Osborne; Carrie Pasfield; Guangrong Qin; Stephen A. Ramsey; Justin Reese; Jared C. Roach; Reese Rose; Karthik Soman; Andrew I. Su; Casey Ta; Gaurav Vaidya; Rosina Weber; Qi Wei; Mark Williams; Chunlei Wu; Colleen Xu; Chase Yakaboski; The Biomedical Data Translator Consortium

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Replacing non-biomedical concepts improves embedding of biomedical concepts

PLOS ONE

IF2.6

2025-05-05

OAAI

Niyonkuru, Enock; Gomez, Mauricio Soto; Casarighi, Elena; Antogiovanni, Stephan; Blau, Hannah; Reese, Justin T.; Valentini, Giorgio; Robinson, Peter N.

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Intrinsic-dimension analysis for guiding dimensionality reduction and data fusion in multi-omics data processing

ARTIFICIAL INTELLIGENCE IN MEDICINE

IF6.2

2025-02-01

OAAI

Gliozzo, Jessica; Soto-Gomez, Mauricio; Guarino, Valentina; Bonometti, Arturo; Cabri, Alberto; Cavalleri, Emanuele; Reese, Justin; Robinson, Peter N.; Mesiti, Marco; Valentini, Giorgio; Casiraghi, Elena

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A corpus of GA4GH phenopackets: Case-level phenotyping for genomic diagnostics and discovery

HUMAN GENETICS AND GENOMICS ADVANCES

IF3.6

2025-01-01

OAAI

Danis, Daniel; Bamshad, Michael J.; Bridges, Yasemin; Caballero-Oteyza, Andres; 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, Allison J.; Mattina, Teresa; Mungall, Christopher J.; Munoz-Torres, Monica C.; Reese, Justin T.; Rehburg, Filip; Reis, Barbara 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.

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Predicting nutrition and environmental factors associated with female reproductive disorders using a knowledge graph and random forests

INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS

IF4.1

2024-07-01

OAAI

Chan, Lauren E.; Casiraghi, Elena; Reese, Justin; Harmon, Quaker E.; Schaper, Kevin; Hegde, Harshad; Valentini, Giorgio; Schmitt, Charles; Motsinger-Reif, Alison; Hall, Janet E.; Mungall, Christopher J.; Robinson, Peter N.; Haendel, Melissa A.

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Association of post-COVID phenotypic manifestations with new-onset psychiatric disease

TRANSLATIONAL PSYCHIATRY

IF6.2

2024-06-08

OAAI

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.

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An evaluation of GPT models for phenotype concept recognition

BMC MEDICAL INFORMATICS AND DECISION MAKING

IF3.8

2024-01-31

OAAI

Groza, Tudor; Caufield, Harry; Gration, Dylan; Baynam, Gareth; Haendel, Melissa A.; Robinson, Peter N.; Mungall, Christopher J.; Reese, Justin T.

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The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species

NUCLEIC ACIDS RESEARCH

IF13.1

2023-11-24

OAAI

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, Vinicius; 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.

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The Human Phenotype Ontology in 2024: phenotypes around the world

NUCLEIC ACIDS RESEARCH

IF13.1

2023-11-11

OAAI

Gargano, Michael A.; Matentzoglu, Nicolas; Coleman, Ben; Addo-Lartey, Eunice B.; Anagnostopoulos, Anna, V; Anderton, Joel; Avillach, Paul; Bagley, Anita M.; Bakstein, Eduard; Balhoff, James P.; Baynam, Gareth; Bello, Susan M.; Berk, Michael; Bertram, Holli; Bishop, Somer; Blau, Hannah; Bodenstein, David F.; Botas, Pablo; Boztug, Kaan; Cady, Jolana; Callahan, Tiffany J.; Cameron, Rhiannon; Carbon, Seth J.; Castellanos, Francisco; Caufield, J. Harry; Chan, Lauren E.; Chute, Christopher G.; Cruz-Rojo, Jaime; Dahan-Oliel, Noemi; Davids, Jon R.; de Dieuleveult, Maud; de Souza, Vinicius; de Vries, Bert B. A.; de Vries, Esther; DePaulo, J. Raymond; Derfalvi, Beata; Dhombres, Ferdinand; Diaz-Byrd, Claudia; Dingemans, Alexander J. M.; Donadille, Bruno; Duyzend, Michael; Elfeky, Reem; Essaid, Shahim; Fabrizzi, Carolina; Fico, Giovanna; Firth, Helen, V; Freudenberg-Hua, Yun; Fullerton, Janice M.; Gabriel, Davera L.; Gilmour, Kimberly; Giordano, Jessica; Goes, Fernando S.; Moses, Rachel Gore; Green, Ian; Griese, Matthias; Groza, Tudor; Gu, Weihong; Guthrie, Julia; Gyori, Benjamin; Hamosh, Ada; Hanauer, Marc; Hanusova, Katerina; He, Yongqun (Oliver); Hegde, Harshad; Helbig, Ingo; Holasova, Katerina; Hoyt, Charles Tapley; Huang, Shangzhi; Hurwitz, Eric; Jacobsen, Julius O. B.; Jiang, Xiaofeng; Joseph, Lisa; Keramatian, Kamyar; King, Bryan; Knoflach, Katrin; Koolen, David A.; Kraus, Megan L.; Kroll, Carlo; Kusters, Maaike; Ladewig, Markus S.; Lagorce, David; Lai, Meng-Chuan; Lapunzina, Pablo; Laraway, Bryan; Lewis-Smith, David; Li, Xiarong; Lucano, Caterina; Majd, Marzieh; Marazita, Mary L.; Martinez-Glez, Victor; McHenry, Toby H.; McInnis, Melvin G.; McMurry, Julie A.; Mihulova, Michaela; Millett, Caitlin E.; Mitchell, Philip B.; Moslerova, Veronika; Narutomi, Kenji; Nematollahi, Shahrzad; Nevado, Julian; Nierenberg, Andrew A.; Cajbikova, Nikola Novak; Nurnberger, John I., Jr.; Ogishima, Soichi; Olson, Daniel; Ortiz, Abigail; Pachajoa, Harry; Perez de Nanclares, Guiomar; Peters, Amy; Putman, Tim; Rapp, Christina K.; Rath, Ana; Reese, Justin; Rekerle, Lauren; Roberts, Angharad M.; Roy, Suzy; Sanders, Stephan J.; Schuetz, Catharina; Schulte, Eva C.; Schulze, Thomas G.; Schwarz, Martin; Scott, Katie; Seelow, Dominik; Seitz, Berthold; Shen, Yiping; Similuk, Morgan N.; Simon, Eric S.; Singh, Balwinder; Smedley, Damian; Smith, Cynthia L.; Smolinsky, Jake T.; Sperry, Sarah; Stafford, Elizabeth; Stefancsik, Ray; Steinhaus, Robin; Strawbridge, Rebecca; Sundaramurthi, Jagadish Chandrabose; Talapova, Polina; Tenorio Castano, Jair A.; Tesner, Pavel; Thomas, Rhys H.; Thurm, Audrey; Turnovec, Marek; van Gijn, Marielle E.; Vasilevsky, Nicole A.; Vlckova, Marketa; Walden, Anita; Wang, Kai; Wapner, Ron; Ware, James S.; Wiafe, Addo A.; Wiafe, Samuel A.; Wiggins, Lisa D.; Williams, Andrew E.; Wu, Chen; Wyrwoll, Margot J.; Xiong, Hui; Yalin, Nefize; Yamamoto, Yasunori; Yatham, Lakshmi N.; Yocum, Anastasia K.; Young, Allan H.; Yueksel, Zafer; Zandi, Peter P.; Zankl, Andreas; Zarante, Ignacio; Zvolsky, Miroslav; Toro, Sabrina; Carmody, Leigh C.; Harris, Nomi L.; Munoz-Torres, Monica C.; Danis, Daniel; Mungall, Christopher J.; Koehler, Sebastian; Haendel, Melissa A.; Robinson, Peter N.

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Predictive models of long COVID

EBIOMEDICINE

IF10.8

2023-10-01

OAAI

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.

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GRAPE for fast and scalable graph processing and random-walk-based embedding

NATURE COMPUTATIONAL SCIENCE

IF18.3

2023-06-26

OAAI

Cappelletti, Luca; Fontana, Tommaso; Casiraghi, Elena; Ravanmehr, Vida; Callahan, Tiffany J. J.; Cano, Carlos; Joachimiak, Marcin P. P.; Mungall, Christopher J. J.; Robinson, Peter N. N.; Reese, Justin; Valentini, Giorgio

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Using knowledge graphs to infer gene expression in plants

FRONTIERS IN ARTIFICIAL INTELLIGENCE

IF4.7

2023-06-13

OAAI

Thessen, Anne E.; Cooper, Laurel; Swetnam, Tyson L.; Hegde, Harshad; Reese, Justin; Elser, Justin; Jaiswal, Pankaj

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Ontologizing health systems data at scale: making translational discovery a reality

NPJ DIGITAL MEDICINE

IF15.1

2023-05-19

OAAI

Callahan, Tiffany J.; Stefanski, Adrianne L.; Wyrwa, Jordan M.; Zeng, Chenjie; Ostropolets, Anna; Banda, Juan M.; Baumgartner, William A., Jr.; Boyce, Richard D.; Casiraghi, Elena; Coleman, Ben D.; Collins, Janine H.; Davies, Sara J. Deakyne; Feinstein, James A.; Lin, Asiyah Y.; Martin, Blake; Matentzoglu, Nicolas A.; Meeker, Daniella; Reese, Justin; Sinclair, Jessica; Taneja, Sanya B.; Trinkley, Katy E.; Vasilevsky, Nicole A.; Williams, Andrew E.; Zhang, Xingmin A.; Denny, Joshua C.; Ryan, Patrick B.; Hripcsak, George; Bennett, Tellen D.; Haendel, Melissa A.; Robinson, Peter N.; Hunter, Lawrence E.; Kahn, Michael G.

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A method for comparing multiple imputation techniques: A case study on the US national COVID cohort collaborative

JOURNAL OF BIOMEDICAL INFORMATICS

IF4.5

2023-03-01

OAAI

Casiraghi, Elena; Wong, Rachel; Hall, Margaret; Coleman, Ben; Notaro, Marco; Evans, Michael D.; Tronieri, Jena S.; Blau, Hannah; Laraway, Bryan; Callahan, Tiffany J.; Chan, Lauren E.; Bramante, Carolyn T.; Buse, John B.; Moffitt, Richard A.; Sturmer, Til; Johnson, Steven G.; Shao, Yu Raymond; Reese, Justin; Robinson, Peter N.; Paccanaro, Alberto; Valentini, Giorgio; Huling, Jared D.; Wilkins, Kenneth J.

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Generalisable long COVID subtypes: Findings from the NIH N3C and RECOVER programmes

EBIOMEDICINE

IF10.8

2023-01-01

OAAI

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.

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Research Directions