JCoDA: a tool for detecting evolutionary selection. - Steven N. Steinway; Ruth Dannenfelser; Christopher D. Laucius; James E. Hayes; Sudhir Nayak (BMC Bioinform., 2010)

FNV: light-weight flash-based network and pathway viewer. - Ruth Dannenfelser; Alexander Lachmann; Mariola Szenk; Avi Ma'ayan (Bioinform., 2011)

Recovering Protein-Protein and Domain-Domain Interactions from Aggregation of IP-MS Proteomics of Coregulator Complexes. - Amin R. Mazloom; Ruth Dannenfelser; Neil R. Clark; Arsen V. Grigoryan; Kathryn M. Linder; Timothy Cardozo; Julia C. Bond; Aislyn D. W. Boran; Ravi Iyengar; Anna Malovannaya; Rainer B. Lanz; Avi Ma'ayan (PLoS Comput. Biol., 2011)

Genes2WordCloud: a quick way to identify biological themes from gene lists and free text. - Caroline Baroukh; Sherry L. Jenkins; Ruth Dannenfelser; Avi Ma'ayan (Source Code Biol. Medicine, 2011)

Genes2FANs: connecting genes through functional association networks. - Ruth Dannenfelser; Neil R. Clark; Avi Ma'ayan (BMC Bioinform., 2012)

Sets2Networks: network inference from repeated observations of sets. - Neil R. Clark; Ruth Dannenfelser; Christopher M. Tan; Michael E. Komosinski; Avi Ma'ayan (BMC Syst. Biol., 2012)

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells. - Huilei Xu; Caroline Baroukh; Ruth Dannenfelser; Edward Y. Chen; Christopher M. Tan; Yan Kou; Yujin E. Kim; Ihor Lemischka; Avi Ma'ayan (Database J. Biol. Databases Curation, 2013)

Network2Canvas: network visualization on a canvas with enrichment analysis. - Christopher M. Tan; Edward Y. Chen; Ruth Dannenfelser; Neil R. Clark; Avi Ma'ayan (Bioinform., 2013)

Data-Driven Approaches and Systems to Interrogate Complex Disease - Ruth Dannenfelser (2020)

Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts. - Ruth Dannenfelser; Jeffrey Zhong; Ran Zhang; Vicky Yao (NeurIPS, 2023)

Joint embedding of biological networks for cross-species functional alignment. - Lechuan Li; Ruth Dannenfelser; Yu Zhu 003; Nathaniel Hejduk; Santiago Segarra; Vicky Yao (Bioinform., 2023)

Enhancing Gene Set Analysis in Embedding Spaces: A Novel Best-Match Approach. - Lechuan Li; Ruth Dannenfelser; Charlie Cruz; Vicky Yao (RECOMB, 2024)

ALPINE: An Interpretable Approach for Decoding Phenotypes from Multi-condition Sequencing Data. - Wei-Hao Lee; Lechuan Li; Ruth Dannenfelser; Vicky Yao (RECOMB, 2025)