Greedily building protein networks with confidence. - Joel S. Bader (Bioinform., 2003)

Probabilistic inference of molecular networks from noisy data sources. - Ivan Iossifov; Michael Krauthammer; Carol Friedman; Vasileios Hatzivassiloglou; Joel S. Bader; Kevin P. White; Andrey Rzhetsky (Bioinform., 2004)

Genetic interaction motif finding by expectation maximization - a novel statistical model for inferring gene modules from synthetic lethality. - Yan Qi 003; Ping Ye; Joel S. Bader (BMC Bioinform., 2005)

Commensurate distances and similar motifs in genetic congruence and protein interaction networks in yeast. - Ping Ye; Brian D. Peyser; Forrest A. Spencer; Joel S. Bader (BMC Bioinform., 2005)

Probabilistic Paths for Protein Complex Inference. - Hailiang Huang; Lan V. Zhang; Frederick P. Roth; Joel S. Bader (Systems Biology and Computational Proteomics, 2006)

Ab initio Prediction of Transcription Factor Binding Sites. - L. Angela Liu; Joel S. Bader (Pacific Symposium on Biocomputing, 2007)

Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps. - Hailiang Huang; Bruno Jedynak; Joel S. Bader (PLoS Comput. Biol., 2007)

Automated Design of Assemblable, Modular, Synthetic Chromosomes. - Sarah M. Richardson; Brian S. Olson; Jessica S. Dymond; Randal C. Burns; Srinivasan Chandrasegaran; Jef D. Boeke; Amarda Shehu; Joel S. Bader (PPAM (2), 2009)

Precision and recall estimates for two-hybrid screens. - Hailiang Huang; Joel S. Bader (Bioinform., 2009)

Analytical approximations for the amplitude and period of a relaxation oscillator. - Carmen Kut; Vahid Golkhou; Joel S. Bader (BMC Syst. Biol., 2009)

Metabolic Flux Correlations, Genetic Interactions, and Disease. - Balaji Veeramani; Joel S. Bader (J. Comput. Biol., 2009)

NeMo: Network Module identification in Cytoscape. - Corban G. Rivera; Rachit Vakil; Joel S. Bader (BMC Bioinform., 2010)

Predicting functional associations from metabolism using bi-partite network algorithms. - Balaji Veeramani; Joel S. Bader (BMC Syst. Biol., 2010)

Resolving the structure of interactomes with hierarchical agglomerative clustering. - Yongjin Park; Joel S. Bader (BMC Bioinform., 2011)

Session Introduction. - Rachel Karchin; Michael F. Ochs; Joshua M. Stuart; Joel S. Bader (Pacific Symposium on Biocomputing, 2012)

Query-based Biclustering using Formal Concept Analysis. - Faris Alqadah; Joel S. Bader; Rajul Anand; Chandan K. Reddy (SDM, 2012)

How networks change with time. - Yongjin Park; Joel S. Bader (Bioinform., 2012)

Session Introduction. - Rachel Karchin; Michael F. Ochs; Joshua M. Stuart; Trey Ideker; Joel S. Bader (Pacific Symposium on Biocomputing, 2013)

BioPartsDB: a synthetic biology workflow web-application for education and research. - Giovanni Stracquadanio; Kun Yang 003; Jef D. Boeke; Joel S. Bader (Bioinform., 2016)

BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts. - Kun Yang 003; Giovanni Stracquadanio; Jingchuan Luo; Jef D. Boeke; Joel S. Bader (Bioinform., 2016)

OrgDyn: feature- and model-based characterization of spatial and temporal organoid dynamics. - Zaki Hasnain; Andrew K. Fraser; Dan Georgess; Alex Choi; Paul Macklin; Joel S. Bader; Shelly R. Peyton; Andrew J. Ewald; Paul K. Newton (Bioinform., 2020)

Between-tumor and within-tumor heterogeneity in invasive potential. - Veena Padmanaban; Yohannes Tsehay; Kevin J. Cheung; Andrew J. Ewald; Joel S. Bader (PLoS Comput. Biol., 2020)

Priors, population sizes, and power in genome-wide hypothesis tests. - Jitong Cai; Jianan Zhan; Dan E. Arking; Joel S. Bader (BMC Bioinform., 2023)

Prioritizing drug targets by perturbing biological network response functions. - Matthew C. Perrone; Michael G. Lerner; Matthew Dunworth; Andrew J. Ewald; Joel S. Bader (PLoS Comput. Biol., 2024)

Prioritization of causal genes from genome-wide association studies by Bayesian data integration across loci. - Zeinab Mousavi; Marios Arvanitis; Thuyvy Duong; Jennifer A. Brody; Alexis Battle; Nona Sotoodehnia; Ali Shojaie; Dan E. Arking; Joel S. Bader (PLoS Comput. Biol., 2025)