The CARLSBAD Database: A Confederated Database of Chemical Bioactivities. - Stephen L. Mathias; Jarrett Hines-Kay; Jeremy J. Yang; Gergely Zahoránszky-Köhalmi; Cristian Bologa; Oleg Ursu; Tudor I. Oprea (Database J. Biol. Databases Curation, 2013)

Badapple: promiscuity patterns from noisy evidence. - Jeremy J. Yang; Oleg Ursu; Christopher A. Lipinski; Larry A. Sklar; Tudor I. Oprea; Cristian Bologa (J. Cheminformatics, 2016)

TIN-X: target importance and novelty explorer. - Daniel Cannon; Jeremy J. Yang; Stephen L. Mathias; Oleg Ursu; Subramani Mani; Anna Waller; Stephan C. Schürer; Lars Juhl Jensen; Larry A. Sklar; Cristian Bologa; Tudor I. Oprea (Bioinform., 2017)

PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets. - Marija Djokic-Petrovic; Vladimir M. Cvjetkovic; Jeremy J. Yang; Marko Zivanovic; David J. Wild 001 (J. Biomed. Semant., 2017)

Drug target ontology to classify and integrate drug discovery data. - Yu Lin; Saurabh Mehta; Hande Küçük-McGinty; John Paul Turner; Dusica Vidovic; Michele Forlin; Amar Koleti; Dac-Trung Nguyen; Lars Juhl Jensen; Rajarshi Guha; Stephen L. Mathias; Oleg Ursu; et al. (J. Biomed. Semant., 2017)

Formalizing drug indications on the road to therapeutic intent. - Stuart J. Nelson; Tudor I. Oprea; Oleg Ursu; Cristian Bologa; Amrapali Zaveri; Jayme Holmes; Jeremy J. Yang; Stephen L. Mathias; Subramani Mani; Mark S. Tuttle; Michel Dumontier (J. Am. Medical Informatics Assoc., 2017)

Pharos: Collating protein information to shed light on the druggable genome. - Dac-Trung Nguyen; Stephen L. Mathias; Cristian Bologa; Søren Brunak; Nicolas F. Fernandez; Anna Gaulton; Anne Hersey; Jayme Holmes; Lars Juhl Jensen; Anneli Karlsson; Guixia Liu; Avi Ma'ayan; et al. (Nucleic Acids Res., 2017)

DrugCentral: online drug compendium. - Oleg Ursu; Jayme Holmes; Jeffrey Knockel; Cristian Bologa; Jeremy J. Yang; Stephen L. Mathias; Stuart J. Nelson; Tudor I. Oprea (Nucleic Acids Res., 2017)

edge2vec: Representation learning using edge semantics for biomedical knowledge discovery. - Zheng Gao 001; Gang Fu; Chunping Ouyang; Satoshi Tsutsui; Xiaozhong Liu; Jeremy J. Yang; Christopher Gessner; Brian Foote; David J. Wild 001; Ying Ding 001; Qi Yu 005 (BMC Bioinform., 2019)

DrugCentral 2018: an update. - Oleg Ursu; Jayme Holmes; Cristian Bologa; Jeremy J. Yang; Stephen L. Mathias; Vasileios Stathias; Dac-Trung Nguyen; Stephan C. Schürer; Tudor I. Oprea (Nucleic Acids Res., 2019)

TIGA: target illumination GWAS analytics. - Jeremy J. Yang; Dhouha Grissa; Christophe G. Lambert; Cristian Bologa; Stephen L. Mathias; Anna Waller; David J. Wild 001; Lars Juhl Jensen; Tudor I. Oprea (Bioinform., 2021)

DrugCentral 2021 supports drug discovery and repositioning. - Sorin I. Avram; Cristian Bologa; Jayme Holmes; Giovanni Bocci; Thomas B. Wilson; Dac-Trung Nguyen; Ramona Curpan; Liliana Halip; Alina Bora; Jeremy J. Yang; Jeffrey Knockel; Suman Sirimulla; et al. (Nucleic Acids Res., 2021)

TCRD and Pharos 2021: mining the human proteome for disease biology. - Timothy Sheils; Stephen L. Mathias; Keith J. Kelleher; Vishal B. Siramshetty; Dac-Trung Nguyen; Cristian Bologa; Lars Juhl Jensen; Dusica Vidovic; Amar Koleti; Stephan C. Schürer; Anna Waller; Jeremy J. Yang; et al. (Nucleic Acids Res., 2021)

A machine learning platform to estimate anti-SARS-CoV-2 activities. - Govinda B. Kc; Giovanni Bocci; Srijan Verma; Md Mahmudulla Hassan; Jayme Holmes; Jeremy J. Yang; Suman Sirimulla; Tudor I. Oprea (Nat. Mach. Intell., 2021)

Analyzing knowledge entities about COVID-19 using entitymetrics. - Qi Yu 005; Qi Wang 021; Yafei Zhang; Chongyan Chen; Hyeyoung Ryu; Namu Park; Jae-Eun Baek; Keyuan Li; Yifei Wu; Daifeng Li; Jian Xu 003; Meijun Liu; et al. (Scientometrics, 2021)

Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination. - Jeremy J. Yang; Christopher Gessner; Joel Duerksen; Daniel Biber; Jessica L. Binder; Murat Ozturk; Brian Foote; Robin McEntire; Kyle Stirling; Ying Ding 001; David J. Wild 001 (BMC Bioinform., 2022)

Reply to issues about entitymetrics and paper-entity citation network. - Qi Yu 005; Qi Wang 021; Yafei Zhang; Chongyan Chen; Hyeyoung Ryu; Namu Park; Jae-Eun Baek; Keyuan Li; Yifei Wu; Daifeng Li; Jian Xu 003; Meijun Liu; et al. (Scientometrics, 2022)

DrugCentral 2023 extends human clinical data and integrates veterinary drugs. - Sorin I. Avram; Thomas B. Wilson; Ramona Curpan; Liliana Halip; Ana Borota; Alina Bora; Cristian Bologa; Jayme Holmes; Jeffrey Knockel; Jeremy J. Yang; Tudor I. Oprea (Nucleic Acids Res., 2023)

Pharos 2023: an integrated resource for the understudied human proteome. - Keith J. Kelleher; Timothy Sheils; Stephen L. Mathias; Jeremy J. Yang; Vincent T. Metzger; Vishal B. Siramshetty; Dac-Trung Nguyen; Lars Juhl Jensen; Dusica Vidovic; Stephan C. Schürer; Jayme Holmes; Karlie R. Sharma; et al. (Nucleic Acids Res., 2023)

Detecting Opioid Use Disorder in Health Claims Data With Positive Unlabeled Learning. - Praveen Kumar; Fariha Moomtaheen; Scott A. Malec; Jeremy J. Yang; Cristian Bologa; Kristan Alexander Schneider; Yiliang Zhu 001; Mauricio Tohen; Gerardo Villarreal; Douglas J. Perkins; Elliot M. Fielstein; Sharon E. Davis; et al. (IEEE J. Biomed. Health Informatics, 2025)