Analyzing networks of phenotypes in complex diseases: methodology and applications in COPD. - Jen-hwa Chu; Craig P. Hersh; Peter J. Castaldi; Michael H. Cho; Benjamin A. Raby; Nan M. Laird; Russell Bowler; Stephen I. Rennard; Joseph Loscalzo; John Quackenbush; Edwin K. Silverman (BMC Syst. Biol., 2014)

DiseaseConnect: a comprehensive web server for mechanism-based disease-disease connections. - Chun-Chi Liu; Yu-Ting Tseng; Wenyuan Li 006; Chia-Yu Wu; Ilya Mayzus; Andrey Rzhetsky; Fengzhu Sun; Michael S. Waterman; Jeremy J. W. Chen; Preet M. Chaudhary; Joseph Loscalzo; Edward Crandall; et al. (Nucleic Acids Res., 2014)

Systems Pharmacology and Rational Polypharmacy: Nitric Oxide-Cyclic GMP Signaling Pathway as an Illustrative Example and Derivation of the General Case. - Farshid S. Garmaroudi; Diane E. Handy; Yang-Yu Liu; Joseph Loscalzo (PLoS Comput. Biol., 2016)

Determinants of drug-target interactions at the single cell level. - Vlad Elgart; Jia-Ren Lin; Joseph Loscalzo (PLoS Comput. Biol., 2018)

Network Medicine Framework for Identifying Drug Repurposing Opportunities for COVID-19. - Deisy Morselli Gysi; Ítalo Do Valle; Marinka Zitnik; Asher Ameli; Xiao Gan; Onur Varol; Helia Sanchez; Rebecca Marlene Baron; Dina Ghiassian; Joseph Loscalzo; Albert-László Barabási (CoRR, 2020)

Disease Gene Prioritization With Quantum Walks. - Harto Saarinen; Mark Goldsmith; Rui-Sheng Wang; Joseph Loscalzo; Sabrina Maniscalco (CoRR, 2023)

Enriched phenotypes in rare variant carriers suggest pathogenic mechanisms in rare disease patients. - Lane Fitzsimmons; Maria T. Acosta; David R. Adams; Ben Afzali; Ali Al-Beshri; Eric Allenspach; Aimee Allworth; Raquel L. Alvarez; Justin Alvey; Ashley Andrews; Euan A. Ashley; Carlos A. Bacino; et al. (BioData Min., 2025)

Patient agency and large language models in worldwide encoding of equity. - Antonis A. Armoundas; Joseph Loscalzo (npj Digit. Medicine, 2025)

One Patient, Many Contexts: Scaling Medical AI Through Contextual Intelligence. - Michelle M. Li; Ben Y. Reis; Adam Rodman; Tianxi Cai; Noa Dagan; Ran D. Balicer; Joseph Loscalzo; Isaac S. Kohane; Marinka Zitnik (CoRR, 2025)

Prediction of Protein Three-dimensional Structures via a Hardware-Executable Quantum Computing Framework. - Yuqi Zhang; Yuxin Yang; William Martin 011; Kingsten Lin; Zixu Wang; Cheng-Chang Lu; Weiwen Jiang; Ruth Nussinov; Joseph Loscalzo; Qiang Guan; Feixiong Cheng (CoRR, 2025)