All Stories

  1. Deep-Plant: a supervised foundation model for plant regulatory genomics

    Article • April 2026, openRxiv

    Asa Ben-Hur

  2. A comprehensive evaluation of self-attention for detecting regulatory feature interactions

    Article • NAR Genomics and Bioinformatics, January 2026, Oxford University Press (OUP)

    Asa Ben-Hur

  3. The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models

    Article • PLoS Computational Biology, January 2025, PLOS

    Asa Ben-Hur

  4. A Comprehensive Evaluation of Self Attention for Detecting Regulatory Feature Interactions

    Article • August 2024, Cold Spring Harbor Laboratory Press

    Asa Ben-Hur

  5. The role of chromatin state in intron retention: a case study in leveraging large scale deep learning models

    Article • January 2024, Cold Spring Harbor Laboratory Press

    Asa Ben-Hur

  6. Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention

    Article • March 2023, Springer Science + Business Media

    Asa Ben-Hur

  7. Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention

    Article • November 2021, Cold Spring Harbor Laboratory Press

    Asa Ben-Hur

  8. A self-attention model for inferring cooperativity between regulatory features

    Article • Nucleic Acids Research, May 2021, Oxford University Press (OUP)

    Asa Ben-Hur

  9. Splicing Factor Transcript Abundance in Saliva as a Diagnostic Tool for Breast Cancer

    Article • Genes, August 2020, MDPI AG

    Asa Ben-Hur

  10. Transcriptome Analysis of Drought-Resistant and Drought-Sensitive Sorghum (Sorghum bicolor) Genotypes in Response to PEG-Induced Drought Stress

    Article • International Journal of Molecular Sciences, January 2020, MDPI AG

    Asa Ben-Hur

  11. Learning protein binding affinity using privileged information

    Article • BMC Bioinformatics, November 2018, Springer Science + Business Media

    Asa Ben-Hur

  12. Exploring the relationship between intron retention and chromatin accessibility in plants

    Article • BMC Genomics, January 2018, Springer Science + Business Media

    Asa Ben-Hur

  13. Amino acid composition predicts prion activity

    Article • PLoS Computational Biology, April 2017, PLOS

    Asa Ben-Hur

  14. Phenotype prediction incorporating literature mining

    Article • F1000Research, July 2015, Faculty of 1000, Ltd.

    Karin M Verspoor, Asa Ben-Hur, Indika Kahanda, Indika Kahanda

  15. Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct

    Article • Journal of Biomedical Semantics, January 2015, Springer Science + Business Media

    Karin M Verspoor, Asa Ben-Hur

  16. PAIRpred: Partner‐specific prediction of interacting residues from sequence and structure

    Article • Proteins Structure Function and Bioinformatics, December 2013, Wiley

    Asa Ben-Hur

  17. SpliceGrapherXT

    Article • September 2013, ACM (Association for Computing Machinery)

    Asa Ben-Hur

  18. A Bioinformatics Method for Identifying Q/N-Rich Prion-Like Domains in Proteins

    Article • January 2013, Springer Science + Business Media

    Asa Ben-Hur

  19. Identification of an intronic splicing regulatory element involved in auto-regulation of alternative splicing ofSCL33pre-mRNA

    Article • The Plant Journal, October 2012, Wiley

    Asa Ben-Hur

  20. Deciphering the Plant Splicing Code: Experimental and Computational Approaches for Predicting Alternative Splicing and Splicing Regulatory Elements

    Article • Frontiers in Plant Science, January 2012, Frontiers

    Asa Ben-Hur

  21. SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

    Article • Genome Biology, January 2012, Springer Science + Business Media

    Asa Ben-Hur

  22. Comparative Analysis of Serine/Arginine-Rich Proteins across 27 Eukaryotes: Insights into Sub-Family Classification and Extent of Alternative Splicing

    Article • PLOS One, September 2011, PLOS

    Asa Ben-Hur

  23. Kernel methods for Calmodulin binding and binding site prediction

    Article • August 2011, ACM (Association for Computing Machinery)

    Asa Ben-Hur

  24. Multi-view prediction of protein function

    Article • August 2011, ACM (Association for Computing Machinery)

    Asa Ben-Hur

  25. Experimental and computational approaches for the study of calmodulin interactions

    Article • Phytochemistry, July 2011, Elsevier

    Asa Ben-Hur

  26. HIERARCHICAL CLASSIFICATION OF GENE ONTOLOGY TERMS USING THE GOstruct METHOD

    Article • Journal of Bioinformatics and Computational Biology, April 2010, World Scientific Pub Co Pte Lt

    Asa Ben-Hur

  27. Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii

    Article • BMC Genomics, February 2010, Springer Science + Business Media

    Asa Ben-Hur

  28. A User’s Guide to Support Vector Machines

    Article • October 2009, Springer Science + Business Media

    Asa Ben-Hur

  29. Support Vector Machines and Kernels for Computational Biology

    Article • PLoS Computational Biology, October 2008, PLOS

    Asa Ben-Hur

  30. Support vector clustering

    Article • Scholarpedia, January 2008, Scholarpedia

    Asa Ben-Hur

  31. Integrating Information for Protein Function Prediction

    Article • January 2007, Wiley

    Asa Ben-Hur

  32. InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale

    Article • Genome Biology, January 2007, Springer Science + Business Media

    Asa Ben-Hur

  33. Choosing negative examples for the prediction of protein-protein interactions

    Article • BMC Bioinformatics, March 2006, Springer Science + Business Media

    Asa Ben-Hur

  34. On probabilistic analog automata

    Article • Theoretical Computer Science, June 2004, Elsevier

    Asa Ben-Hur

  35. Random matrix theory for the analysis of the performance of an analog computer: a scaling theory

    Article • Physics Letters A, March 2004, Elsevier

    Asa Ben-Hur

  36. Computation in gene networks

    Article • Chaos An Interdisciplinary Journal of Nonlinear Science, December 2003, American Institute of Physics

    Asa Ben-Hur

  37. Probabilistic analysis of a differential equation for linear programming

    Article • Journal of Complexity, August 2003, Elsevier

    Asa Ben-Hur

  38. A Theory of Complexity for Continuous Time Systems

    Article • Journal of Complexity, March 2002, Elsevier

    Asa Ben-Hur

  39. A stability based method for discovering structure in clustered data

    Article • December 2001, World Scientific Pub Co Pte Lt

    Asa Ben-Hur

  40. Computation in Gene Networks

    Article • January 2001, Springer Science + Business Media

    Asa Ben-Hur

  41. Macroscopic Molecular Computation with Gene Networks

    Article • January 2001, Springer Science + Business Media

    Asa Ben-Hur

  42. Computational Complexity for Continuous Time Dynamics

    Article • Physical Review Letters, August 1999, American Physical Society (APS)

    Asa Ben-Hur

  43. Universality in sandpile models

    Article • February 1996, American Physical Society (APS)

    Asa Ben-Hur

  44. Design and Analysis of the NIPS2003 Challenge

    Article • Springer Science + Business Media

    Asa Ben-Hur

  45. Sequence Motifs: Highly Predictive Features of Protein Function

    Article • Springer Science + Business Media

    Asa Ben-Hur

  46. Detecting Stable Clusters Using Principal Component Analysis

    Article • Springer Science + Business Media

    Asa Ben-Hur