Publications by authors named "Jeremy Yang"

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Badapple 2.0: An Empirical Predictor of Compound Promiscuity, Updated, Modernized, and Enhanced for Explainability.
John A Ringer, Christophe G Lambert, Steven B Bradfute, Cristian G Bologa, Jeremy J Yang

J Chem Inf Model· December 2025

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The Data Distillery: A Graph Framework for Semantic Integration and Querying of Biomedical Data.
Taha Mohseni Ahooyi, Benjamin Stear, J Alan Simmons, Vincent T Metzger, Praveen Kumar, Jeremy J Yang

bioRxiv· October 2025

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TICTAC: target illumination clinical trial analytics with cheminformatics.
Jeremiah I Abok, Jeremy S Edwards, Jeremy J Yang

Front Bioinform· June 2025

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KG2ML: Integrating Knowledge Graphs and Positive Unlabeled Learning for Identifying Disease-Associated Genes.
Praveen Kumar, Vincent T Metzger, Swastika T Purushotham, Priyansh Kedia, Cristian G Bologa, Jeremy J Yang

medRxiv· March 2025

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Deletion of murine astrocytic vesicular nucleotide transporter increases anxiety and depressive-like behavior and attenuates motivation for reward.
Qian Huang, Hiu Ham Lee, Bryan Volpe, Qingchen Zhang, Chang Xue, Jeremy S Yang

Mol Psychiatry· February 2025

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Detecting Opioid Use Disorder in Health Claims Data With Positive Unlabeled Learning.
Praveen Kumar, Fariha Moomtaheen, Scott A Malec, Jeremy J Yang, Cristian G Bologa

IEEE J Biomed Health Inform· February 2025

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The Impact of COVID-19 on Cholesteatoma Diagnosis and Treatment.
Courtney B Shires, Jeremy Yang, Mark Landry, Steven Conrad, Karuna Dewan

Cureus· November 2024

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TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets.
Vincent T Metzger, Daniel C Cannon, Jeremy J Yang, Stephen L Mathias, Cristian G Bologa

PeerJ· July 2024

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Computational drug repositioning identifies niclosamide and tribromsalan as inhibitors of Mycobacterium tuberculosis and Mycobacterium abscessus.
Jeremy J Yang, Aaron Goff, David J Wild, Ying Ding, Ayano Annis

Tuberculosis (Edinb)· May 2024

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Overview of the Knowledge Management Center for Illuminating the Druggable Genome.
Tudor I Oprea, Cristian Bologa, Jayme Holmes, Stephen Mathias, Vincent T Metzger, Jeremy J Yang

Drug Discov Today· March 2024

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Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning.
Luca Cappelletti, Lauren Rekerle, Tommaso Fontana, Peter Hansen, Elena Casiraghi, Jeremy J Yang

Bioinform Adv· March 2024

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User Centered Rare Disease Clinical Trial Knowledge Graph (RCTKG).
Jeremy Parker Yang, Devon Leadman, Richard M Ballew, Eric Sid, Yanji Xu

Stud Health Technol Inform· January 2024

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Toxicology knowledge graph for structural birth defects.
John Erol Evangelista, Daniel J B Clarke, Zhuorui Xie, Giacomo B Marino, Vivian Utti, Jeremy J Yang

Commun Med (Lond)· July 2023

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Concurrent Pediatric Lingual and Submental Dermoid Cysts: Case Report and Literature Review.
Natasha Gleichmann, Elizabeth Creighton, Austin Zhu, Nicholas Willard, Jeremy Yang

Cureus· July 2023

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DrugCentral 2023 extends human clinical data and integrates veterinary drugs.
Sorin Avram, Thomas B Wilson, Ramona Curpan, Liliana Halip, Ana Borota, Jeremy J Yang

Nucleic Acids Res· January 2023

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Pharos 2023: an integrated resource for the understudied human proteome.
Keith J Kelleher, Timothy K Sheils, Stephen L Mathias, Jeremy J Yang, Vincent T Metzger

Nucleic Acids Res· January 2023

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Machine learning prediction and tau-based screening identifies potential Alzheimer's disease genes relevant to immunity.
Jessica Binder, Oleg Ursu, Cristian Bologa, Shanya Jiang, Nicole Maphis, Jeremy J Yang

Commun Biol· February 2022

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Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination.
Jeremy J Yang, Christopher R Gessner, Joel L Duerksen, Daniel Biber, Jessica L Binder

BMC Bioinformatics· January 2022

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Getting Started with the IDG KMC Datasets and Tools.
Eryk Kropiwnicki, Jessica L Binder, Jeremy J Yang, Jayme Holmes, Alexander Lachmann

Curr Protoc· January 2022

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TIGA: target illumination GWAS analytics.
Jeremy J Yang, Dhouha Grissa, Christophe G Lambert, Cristian G Bologa, Stephen L Mathias

Bioinformatics· November 2021

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Analyzing knowledge entities about COVID-19 using entitymetrics.
Qi Yu, Qi Wang, Yafei Zhang, Chongyan Chen, Hyeyoung Ryu, Jeremy J Yang

Scientometrics· March 2021

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DrugCentral 2021 supports drug discovery and repositioning.
Sorin Avram, Cristian G Bologa, Jayme Holmes, Giovanni Bocci, Thomas B Wilson, Jeremy J Yang

Nucleic Acids Res· January 2021

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TCRD and Pharos 2021: mining the human proteome for disease biology.
Timothy K Sheils, Stephen L Mathias, Keith J Kelleher, Vishal B Siramshetty, Dac-Trung Nguyen, Jeremy J Yang

Nucleic Acids Res· January 2021

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REDIAL-2020: A suite of machine learning models to estimate Anti-SARS-CoV-2 activities.
K C Govinda, Giovanni Bocci, Srijan Verma, Mahmudulla Hassan, Jayme Holmes, Jeremy J Yang

ChemRxiv· September 2020

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Interdependence and the cost of uncoordinated responses to COVID-19.
David Holtz, Michael Zhao, Seth G Benzell, Cathy Y Cao, Mohammad Amin Rahimian, Jeremy Yang

Proc Natl Acad Sci U S A· August 2020

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