Ruth Dannenfelser

According to our database, Ruth Dannenfelser authored at least 14 papers between 2010 and 2026.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2026

Splitpea: a Python package for protein-protein interaction network rewiring analysis due to alternative splicing.

Jeffrey Zhong, Alyssa Cantu, Ruth Dannenfelser, Vicky Yao

Bioinform., 2026

2025

ALPINE: An Interpretable Approach for Decoding Phenotypes from Multi-condition Sequencing Data.

Wei-Hao Lee, Lechuan Li, Ruth Dannenfelser, Vicky Yao

Proceedings of the Research in Computational Molecular Biology, 2025

2024

Enhancing Gene Set Analysis in Embedding Spaces: A Novel Best-Match Approach.

Lechuan Li, Ruth Dannenfelser, Charlie Cruz, Vicky Yao

Proceedings of the Research in Computational Molecular Biology, 2024

2023

Joint embedding of biological networks for cross-species functional alignment.

Lechuan Li, Ruth Dannenfelser, Yu Zhu, Nathaniel Hejduk, Santiago Segarra, Vicky Yao

Bioinform., September, 2023

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

Proceedings of the Advances in Neural Information Processing Systems 36: Annual Conference on Neural Information Processing Systems 2023, 2023

2020

Data-Driven Approaches and Systems to Interrogate Complex Disease

Ruth Dannenfelser

PhD thesis, 2020

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

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

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

Genes2FANs: connecting genes through functional association networks.

Ruth Dannenfelser, Neil R. Clark, Avi Ma'ayan

BMC Bioinform., 2012

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

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

FNV: light-weight flash-based network and pathway viewer.

Ruth Dannenfelser, Alexander Lachmann, Mariola Szenk, Avi Ma'ayan

Bioinform., 2011

2010

JCoDA: a tool for detecting evolutionary selection.

Steven N. Steinway, Ruth Dannenfelser, Christopher D. Laucius, James E. Hayes, Sudhir Nayak

BMC Bioinform., 2010