A Theory of Complexity for Continuous Time Dynamics. - Hava T. Siegelmann; Asa Ben-Hur; Shmuel Fishman (MCU (1), 1998)

Noisy Neural Networks and Generalizations. - Hava T. Siegelmann; Alexander Roitershtein; Asa Ben-Hur (NIPS, 1999)

A Support Vector Clustering Method. - Asa Ben-Hur; Hava T. Siegelmann; David Horn 001; Vladimir Vapnik (ICPR, 2000)

A Support Vector Method for Clustering. - Asa Ben-Hur; David Horn 001; Hava T. Siegelmann; Vladimir Vapnik (NIPS, 2000)

Macroscopical Molecular Computation with Gene Networks. - Hava T. Siegelmann; Asa Ben-Hur (UMC, 2000)

Computation in Gene Networks. - Asa Ben-Hur; Hava T. Siegelmann (MCU, 2001)

Support Vector Clustering. - Asa Ben-Hur; David Horn 001; Hava T. Siegelmann; Vladimir Vapnik (J. Mach. Learn. Res., 2001)

A Stability Based Method for Discovering Structure in Clustered Data. - Asa Ben-Hur; André Elisseeff; Isabelle Guyon (Pacific Symposium on Biocomputing, 2002)

A Theory of Complexity for Continuous Time Systems. - Asa Ben-Hur; Hava T. Siegelmann; Shmuel Fishman (J. Complex., 2002)

Remote homology detection: a motif based approach. - Asa Ben-Hur; Douglas L. Brutlag (ISMB (Supplement of Bioinformatics), 2003)

CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. - Roded Sharan; Ivan Ovcharenko; Asa Ben-Hur; Richard M. Karp (ISMB (Supplement of Bioinformatics), 2003)

Probabilistic analysis of a differential equation for linear programming. - Asa Ben-Hur; Joshua Feinberg; Shmuel Fishman; Hava T. Siegelmann (J. Complex., 2003)

Result Analysis of the NIPS 2003 Feature Selection Challenge. - Isabelle Guyon; Steve R. Gunn; Asa Ben-Hur; Gideon Dror (NIPS, 2004)

Identifying Protein-Protein Interaction Sites on a Genome-Wide Scale. - Haidong Wang; Eran Segal; Asa Ben-Hur; Daphne Koller; Douglas L. Brutlag (NIPS, 2004)

CREME: Cis-Regulatory Module Explorer for the human genome. - Roded Sharan; Asa Ben-Hur; Gabriela G. Loots; Ivan Ovcharenko (Nucleic Acids Res., 2004)

On probabilistic analog automata. - Asa Ben-Hur; Alexander Roitershtein; Hava T. Siegelmann (Theor. Comput. Sci., 2004)

Kernel methods for predicting protein-protein interactions. - Asa Ben-Hur; William Stafford Noble (ISMB (Supplement of Bioinformatics), 2005)

Sequence Motifs: Highly Predictive Features of Protein Function. - Asa Ben-Hur; Douglas L. Brutlag (Feature Extraction, 2006)

Design and Analysis of the NIPS2003 Challenge. - Isabelle Guyon; Steve R. Gunn; Asa Ben-Hur; Gideon Dror (Feature Extraction, 2006)

Choosing negative examples for the prediction of protein-protein interactions. - Asa Ben-Hur; William Stafford Noble (BMC Bioinform., 2006)

A structural alignment kernel for protein structures. - Jian Qiu; Martial Hue; Asa Ben-Hur; Jean-Philippe Vert; William Stafford Noble (Bioinform., 2007)

Support Vector Machines and Kernels for Computational Biology. - Asa Ben-Hur; Cheng Soon Ong; Sören Sonnenburg; Bernhard Schölkopf; Gunnar Rätsch (PLoS Comput. Biol., 2008)

Support vector clustering. - Asa Ben-Hur (Scholarpedia, 2008)

Arcene. - Isabelle Guyon; Steve R. Gunn; Asa Ben-Hur; Gideon Dror (UCI Machine Learning Repository, 2008)

Dorothea. - Isabelle Guyon; Steve R. Gunn; Asa Ben-Hur; Gideon Dror (UCI Machine Learning Repository, 2008)

Gisette. - Isabelle Guyon; Steve R. Gunn; Asa Ben-Hur; Gideon Dror (UCI Machine Learning Repository, 2008)

Dexter. - Isabelle Guyon; Steve R. Gunn; Asa Ben-Hur; Gideon Dror (UCI Machine Learning Repository, 2008)

The use of gene ontology evidence codes in preventing classifier assessment bias. - Mark F. Rogers; Asa Ben-Hur (Bioinform., 2009)

Hierarchical Classification of Gene Ontology Terms Using the Gostruct Method. - Artem Sokolov; Asa Ben-Hur (J. Bioinform. Comput. Biol., 2010)

Kernel methods for Calmodulin binding and binding site prediction. - Michael Hamilton; A. S. N. Reddy; Asa Ben-Hur (BCB, 2011)

Multi-view prediction of protein function. - Artem Sokolov; Asa Ben-Hur (BCB, 2011)

Multiple instance learning of Calmodulin binding sites. - Fayyaz ul Amir Afsar Minhas; Asa Ben-Hur (Bioinform., 2012)

SpliceGrapherXT: From Splice Graphs to Transcripts Using RNA-Seq. - Mark F. Rogers; Christina Boucher 001; Asa Ben-Hur (BCB, 2013)

Combining heterogeneous data sources for accurate functional annotation of proteins. - Artem Sokolov; Christopher S. Funk; Kiley Graim; Karin Verspoor; Asa Ben-Hur (BMC Bioinform., 2013)

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. - Milana Frenkel-Morgenstern; Alessandro Gorohovski; Vincent Lacroix; Mark F. Rogers; Kristina Ibáñez; Cesar Boullosa; Eduardo Andrés León; Asa Ben-Hur; Alfonso Valencia (Nucleic Acids Res., 2013)

Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct. - Christopher S. Funk; Indika Kahanda; Asa Ben-Hur; Karin M. Verspoor (J. Biomed. Semant., 2015)

Mendel: A Distributed Storage Framework for Similarity Searching over Sequencing Data. - Cameron Tolooee; Sangmi Lee Pallickara; Asa Ben-Hur (IPDPS, 2016)

Predicting metamorphic relations for testing scientific software: a machine learning approach using graph kernels. - Upulee Kanewala; James M. Bieman; Asa Ben-Hur (Softw. Test. Verification Reliab., 2016)

GOstruct 2.0: Automated Protein Function Prediction for Annotated Proteins. - Indika Kahanda; Asa Ben-Hur (BCB, 2017)

Protein Interface Prediction using Graph Convolutional Networks. - Alex Fout; Jonathon Byrd; Basir Shariat; Asa Ben-Hur (NIPS, 2017)

pyLEMMINGS: Large Margin Multiple Instance Classification and Ranking for Bioinformatics Applications. - Amina Asif; Wajid Arshad Abbasi; Farzeen Munir; Asa Ben-Hur; Fayyaz ul Amir Afsar Minhas (CoRR, 2017)

Amino acid composition predicts prion activity. - Fayyaz ul Amir Afsar Minhas; Eric D. Ross; Asa Ben-Hur (PLoS Comput. Biol., 2017)

BLRM: A Basic Linear Ranking Model for Protein Interface Prediction. - Basir Shariat; Don Neumann; Asa Ben-Hur (BIBM, 2018)

Learning protein binding affinity using privileged information. - Wajid Arshad Abbasi; Amina Asif; Asa Ben-Hur; Fayyaz ul Amir Afsar Minhas (BMC Bioinform., 2018)

Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities. - Ameni Trabelsi; Mohamed Chaabane; Asa Ben-Hur (Bioinform., 2019)

Ten ways to fool the masses with machine learning. - Fayyaz ul Amir Afsar Minhas; Amina Asif; Asa Ben-Hur (CoRR, 2019)

Insights into performance evaluation of compound-protein interaction prediction methods. - Adiba Yaseen; Imran Amin; Naeem Akhter; Asa Ben-Hur; Fayyaz Minhas (Bioinform., 2022)

RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data. - Don Neumann; Anireddy S. N. Reddy; Asa Ben-Hur (BMC Bioinform., 2022)

Insights into performance evaluation of com-pound-protein interaction prediction methods. - Adiba Yaseen; Imran Amin; Naeem Akhter; Asa Ben-Hur; Fayyaz A. Minhas (CoRR, 2022)

On the choice of negative examples for prediction of host-pathogen protein interactions. - Don Neumann; Soumyadip Roy; Fayyaz ul Amir Afsar Minhas; Asa Ben-Hur (Frontiers Bioinform., 2022)

Protein quality assessment with a loss function designed for high-quality decoys. - Soumyadip Roy; Asa Ben-Hur (Frontiers Bioinform., 2023)

The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models. - Ahmed Daoud; Asa Ben-Hur (PLoS Comput. Biol., 2025)