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Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing|December 31, 2023
Splitpea: quantifying protein interaction network rewiring changes due to alternative splicing in cancerRuth Dannenfelser, Vicky YaoBioinformatics (Oxford, England)|April 11, 2026
Splitpea: a Python package for protein-protein interaction network rewiring analysis due to alternative splicingJeffrey Zhong, Alyssa Cantu, Ruth Dannenfelser, et al.Genome Research|September 4, 2024
A best-match approach for gene set analyses in embedding spacesLechuan Li, Ruth Dannenfelser, Charlie Cruz, et al.Nature Communications|October 1, 2025
Disentangling associations between complex traits and cell types with seismicQiliang Lai, Ruth Dannenfelser, Jean-Pierre Roussarie, et al.Genome Research|October 22, 2025
Interpretable phenotype decoding from multicondition sequencing data with ALPINEWei-Hao Lee, Lechuan Li, Ruth Dannenfelser, et al.Biorxiv : the Preprint Server for Biology|May 20, 2024
Disentangling associations between complex traits and cell types with <i>seismic</i>Qiliang Lai, Ruth Dannenfelser, Jean-Pierre Roussarie, et al.Cell Reports Methods|March 13, 2026
Ontology-aware DNA methylation classification with a curated atlas of human tissues and cell typesMirae Kim, Ruth Dannenfelser, Yufei Cui, et al.Bioinformatics (Oxford, England)|August 26, 2023
Joint embedding of biological networks for cross-species functional alignmentLechuan Li, Ruth Dannenfelser, Yu Zhu, et al.BMC Bioinformatics|July 4, 2012
Genes2FANs: connecting genes through functional association networksRuth Dannenfelser, Neil R Clark, Avi Ma'ayanBioinformatics (Oxford, England)|February 26, 2011
FNV: light-weight flash-based network and pathway viewerRuth Dannenfelser, Alexander Lachmann, Mariola Szenk, et al.Pageof 4