Towards Biomedical Problem Solving in a Game Environment. - Yang Cai 002; Ingo Snel; B. Suman Bharathi; Clementine Klein; Judith Klein-Seetharaman (International Conference on Computational Science, 2003)

Ambient intelligence for scientific discovery. - Yang Cai 002; Judith Klein-Seetharaman (CHI Extended Abstracts, 2004)

Computational Biology and Language. - Madhavi Ganapathiraju; Narayanas Balakrishnan; Raj Reddy; Judith Klein-Seetharaman (Ambient Intelligence for Scientific Discovery, 2004)

Identification of fundamental building blocks in protein sequences using statistical association measures. - Deborah K. Weisser; Judith Klein-Seetharaman (SAC, 2004)

Context sensitive vocabulary and its application in protein secondary structure prediction. - Yan Liu 002; Jaime G. Carbonell; Judith Klein-Seetharaman; Vanathi Gopalakrishnan (SIGIR, 2004)

Comparison of probabilistic combination methods for protein secondary structure prediction. - Yan Liu 002; Jaime G. Carbonell; Judith Klein-Seetharaman; Vanathi Gopalakrishnan (Bioinform., 2004)

Characterization of protein secondary structure. - Madhavi K. Ganapathiraju; Judith Klein-Seetharaman; Narayanaswamy Balakrishnan 001; Raj Reddy (IEEE Signal Process. Mag., 2004)

A Machine Text-Inspired Machine Learning Approach for Identification of Transmembrane Helix Boundaries. - Betty Yee Man Cheng; Jaime G. Carbonell; Judith Klein-Seetharaman (ISMIS, 2005)

Random Forest Similarity for Protein-Protein Interaction Prediction from Multiple Sources. - Yanjun Qi; Judith Klein-Seetharaman; Ziv Bar-Joseph (Pacific Symposium on Biocomputing, 2005)

BioSim–a biomedical character-based problem solving environment. - Yang Cai 002; Ingo Snel; Betty Cheng; B. Suman Bharathi; Clementine Klein; Judith Klein-Seetharaman (Future Gener. Comput. Syst., 2005)

Collaborative Discovery Through Biological Language Modeling Interface. - Madhavi Ganapathiraju; Vijayalaxmi Manoharan; Raj Reddy; Judith Klein-Seetharaman (Ambient Intelligence in Everyday, 2006)

TMpro web server and web service: transmembrane helix prediction through amino acid property analysis. - Madhavi Ganapathiraju; Christopher Jon Jursa; Hassan A. Karimi; Judith Klein-Seetharaman (Bioinform., 2007)

A mixture of feature experts approach for protein-protein interaction prediction. - Yanjun Qi; Judith Klein-Seetharaman; Ziv Bar-Joseph (BMC Bioinform., 2007)

Protein complex identification by supervised graph local clustering. - Yanjun Qi; Fernanda Balem; Christos Faloutsos; Judith Klein-Seetharaman; Ziv Bar-Joseph (ISMB, 2008)

Transmembrane helix prediction using amino acid property features and latent semantic analysis. - Madhavi Ganapathiraju; Narayanaswamy Balakrishnan 001; Raj Reddy; Judith Klein-Seetharaman (BMC Bioinform., 2008)

Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors. - Naveena Yanamala; Kalyan C. Tirupula; Judith Klein-Seetharaman (BMC Bioinform., 2008)

Communication interception of human signal transduction pathways by Human Immunodeficiency Virus-1. - Sivaraman Balakrishnan; Öznur Tastan; Jaime G. Carbonell; Judith Klein-Seetharaman (GENSiPS, 2009)

Prediction of Interactions Between HIV-1 and Human Proteins by Information Integration. - Öznur Tastan; Yanjun Qi; Jaime G. Carbonell; Judith Klein-Seetharaman (Pacific Symposium on Biocomputing, 2009)

Comparison of virus interactions with human signal transduction pathways. - Irtisha Singh; Öznur Tastan; Judith Klein-Seetharaman (BCB, 2010)

Analogies between structural and systems biology and systems-of-systems engineering in dynamic environments. - Subhodeep Moitra; Naveena Yanamala; Öznur Tastan; Irtisha Singh; Christopher James Langmead; Judith Klein-Seetharaman (SoSE, 2010)

Semi-supervised multi-task learning for predicting interactions between HIV-1 and human proteins. - Yanjun Qi; Öznur Tastan; Jaime G. Carbonell; Judith Klein-Seetharaman; Jason Weston (Bioinform., 2010)

Virus interactions with human signal transduction pathways. - Zhongming Zhao; Junfeng Xia; Öznur Tastan; Irtisha Singh; Meghana Kshirsagar 001; Jaime G. Carbonell; Judith Klein-Seetharaman (Int. J. Comput. Biol. Drug Des., 2011)

Determining Confidence of Predicted Interactions Between HIV-1 and Human Proteins Using Conformal Method. - Ilia Nouretdinov; Alex Gammerman; Yanjun Qi; Judith Klein-Seetharaman (Pacific Symposium on Biocomputing, 2012)

Techniques to cope with missing data in host-pathogen protein interaction prediction. - Meghana Kshirsagar 001; Jaime G. Carbonell; Judith Klein-Seetharaman (Bioinform., 2012)

BIPS: BIANA Interolog Prediction Server. A tool for protein-protein interaction inference. - Javier García-García 002; Sylvia Schleker; Judith Klein-Seetharaman; Baldo Oliva (Nucleic Acids Res., 2012)

Signal Processing in Genomics and Proteomics: Defining Its Role [From the Guest Editors]. - Nevenka Dimitrova; Judith Klein-Seetharaman; Peter Beyerlein; Ahmed H. Tewfik (IEEE Signal Process. Mag., 2012)

Multitask learning for host-pathogen protein interactions. - Meghana Kshirsagar 001; Jaime G. Carbonell; Judith Klein-Seetharaman (Bioinform., 2013)

Refining Literature Curated Protein Interactions Using Expert Opinions. - Öznur Tastan; Yanjun Qi; Jaime G. Carbonell; Judith Klein-Seetharaman (Pacific Symposium on Biocomputing, 2015)

Multitask Matrix Completion for Learning Protein Interactions Across Diseases. - Meghana Kshirsagar 001; Keerthiram Murugesan; Jaime G. Carbonell; Judith Klein-Seetharaman (J. Comput. Biol., 2017)

Insulin biosensor development: a case study. - Narinder Sanghera; Alexander Anderson; Nick Nuar; Can Xie; Daniel Mitchell; Judith Klein-Seetharaman (Int. J. Parallel Emergent Distributed Syst., 2017)

Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 - human interactome. - Meghana Kshirsagar 001; Nure Tasnina; Michael D. Ward; Jeffrey N. Law; T. M. Murali 001; Juan M. Lavista Ferres; Gregory R. Bowman; Judith Klein-Seetharaman (PSB, 2021)

Bioinformatics of corals: Investigating heterogeneous omics data from coral holobionts for insight into reef health and resillience. - Lenore J. Cowen; Judith Klein-Seetharaman; Hollie Putnam (PSB, 2021)

Building a Quantum Engineering Undergraduate Program. - Abraham T. Asfaw; Alexandre Blais; Kenneth R. Brown; Jonathan Candelaria; Christopher Cantwell; Lincoln D. Carr; Joshua Combes; Dripto M. Debroy; John M. Donohue; Sophia E. Economou; Emily Edwards; Michael F. J. Fox; et al. (IEEE Trans. Educ., 2022)

Neonatal Risk Modeling and Prediction. - Abdullah Mamun; Chia-Cheng Kuo; David W. Britt; Lawrence D. Devoe; Mark I. Evans; Hassan Ghasemzadeh 001; Judith Klein-Seetharaman (BSN, 2023)

Trimming of AlphaFold Predicted Protein Structures for Functional Characterization. - Roshan Klein-Seetharaman; Thomas Jennewein; Chase Harms; Punarvash Mitta; Gil Speyer; Judith Klein-Seetharaman (ICCBB, 2024)

Use of What-if Scenarios to Help Explain Artificial Intelligence Models for Neonatal Health. - Abdullah Mamun; Lawrence D. Devoe; Mark I. Evans; David W. Britt; Judith Klein-Seetharaman; Hassan Ghasemzadeh 001 (CoRR, 2024)

Decoding the Functional Interactome of Non-model Organisms with PHILHARMONIC. - Samuel Sledzieski; Charlotte Versavel; Rohit Singh 001; Faith Ocitti; Kapil Devkota; Lokender Kumar; Polina Shpilker; Liza Roger; Jinkyu Yang; Nastassja Lewinski; Hollie Putnam; Bonnie Berger; et al. (RECOMB, 2025)