FNTM: a server for predicting functional networks of tissues in mouse. - Jonathan Goya; Aaron K. Wong; Victoria Yao; Arjun Krishnan; Max Homilius; Olga G. Troyanskaya (Nucleic Acids Res., 2015)

IMP 2.0: a multi-species functional genomics portal for integration, visualization and prediction of protein functions and networks. - Aaron K. Wong; Arjun Krishnan; Victoria Yao; Alicja Tadych; Olga G. Troyanskaya (Nucleic Acids Res., 2015)

A loop-counting method for covariate-corrected low-rank biclustering of gene-expression and genome-wide association study data. - Aaditya V. Rangan; Caroline C. McGrouther; John Kelsoe; Nicholas J. Schork; Eli Stahl; Qian Zhu 005; Arjun Krishnan; Vicky Yao; Olga G. Troyanskaya; Seda Bilaloglu; Preeti Raghavan; Sarah Bergen; et al. (PLoS Comput. Biol., 2018)

Integrative network-based approaches to analyze genomics data - Victoria Yao (2018)

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)