Publications

My publications in google scholar.

Selected recent publications:

• Ahmed Daoud and Asa Ben-Hur. Using large scale transfer learning to highlight the role of chromatin state in intron retention. bioRxiv 2024.01.26.577402, 2024.
• Fahad Ullah, Saira Jabeen, Maayan Salton, ASN Reddy, and Asa Ben-Hur. Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention. Genome Biology 24, 53, 2023.
• Fahad Ullah and Asa Ben-Hur. A self-attention model for inferring cooperativity between regulatory features. Nucleic Acids Research, 2021.
• Ameni Trabelsi, Mohamed Chaabane, and Asa Ben-Hur. Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities. Bioinformatics, 35(14), i269–i277, 2019 (ISMB 2019 special issue). (preprint)
• Alex Fout, Jonathon Byrd, Basir Shariat, and Asa Ben-Hur. Protein interface prediction using graph convolutional networks. In: Advances in Neural Information Processing Systems (NIPS), 2017. (code, data, poster)

2024

• Saira Jabeen and Asa Ben-Hur. A comprehensive evaluation of self attention for detecting feature interactions. bioRxiv 2024.08.23.609428, 2024.
• Ahmed Daoud and Asa Ben-Hur. Using large scale transfer learning to highlight the role of chromatin state in intron retention. bioRxiv 2024.01.26.577402, 2024.
• Zachary Burcham, Aeriel Belk, et al. A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables. Nature Microbiology, 2024.
• Eden Engal, Zhenwei Zhang, Ophir Geminder, Shiri Jaffe-Herman, Gillian Kay, Asa Ben-Hur, and Maayan Salton. The spectrum of pre-mRNA splicing in autism. WIREs RNA 15(2), 2024.

2023

• Fahad Ullah, Saira Jabeen, Maayan Salton, ASN Reddy, and Asa Ben-Hur. Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention. Genome Biology 24, 53, 2023.
• Soumyadip Roy and Asa Ben-Hur. Protein quality assessment with a loss function designed for high-quality decoys Frontiers in Bioinformatics 3, 2023.
• Muhammad Dawood, Mark Eastwood, Mostafa Jahanifar, Lawrence Young, Asa Ben-Hur, Kim Branson, Louise Jones, Nasir Rajpoot, and Fayyaz ul Amir Afsar Minhas. Cross-linking breast tumor transcriptomic states and tissue histology. Cell Reports Medicine, 4:12, 101313, 2023.
• Mik Hammers, Zachary J. Winn, Asa Ben-Hur, Dylan Larkin, Jamison Murry, and Richard Esten Mason. Phenotyping and predicting wheat spike characteristics using image analysis and machine learning The Plant Phenome Journal 6:1, e20087, 2023.

2022

• Don Neumann, ASN Reddy, and Asa Ben-Hur. RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data. BMC Bioinformatics 23, 142, 2022.
• Adiba Yaseen, Imran Amin, Naeem Akhter, Asa Ben-Hur, Fayyaz Minhas. Insights into performance evaluation of compound–protein interaction prediction methods. Bioinformatics 38(Supplement_2), ii75–ii81, 2022.
• Don Neumann, Soumyadip Roy, Fayyaz Ul Amir Afsar Minhas, and Asa Ben-Hur. On the choice of negative examples for prediction of host-pathogen protein interactions. Frontiers in Bioinformatics, 2, 2022.
• Runxuan Zhang et al. A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis. Genome biology 23(1), 1-37, 2022.

2021

• Fahad Ullah, Maayan Salton, Anireddy S.N. Reddy, Asa Ben-Hur. Evidence for the role of transcription factors in the co-transcriptional regulation of intron retention. bioRxiv 2021.11.18.469150.
• Fahad Ullah and Asa Ben-Hur. A self-attention model for inferring cooperativity between regulatory features. Nucleic Acids Research, 2021.
• Travis J. Sanders, Fahad Ullah, Alexandra M. Gehring, Brett W. Burkhart, Robert L. Vickerman, Sudili Fernando, Andrew F. Gardner, Asa Ben-Hur, and Thomas J. Santangelo. Extended archaeal histone-based chromatin structure regulates global gene expression in Thermococcus kodakarensis. Frontiers in microbiology, 2021.

2020

• Bryce C Asay, Blake Blue Edwards, Jenna Andrews, Michelle E Ramey, Jameson D Richard, Brendan K Podell, Juan F Muñoz Gutiérrez, Chad B Frank, Forgivemore Magunda, Gregory T Robertson, Michael Lyons, Asa Ben-Hur, and Anne J Lenaerts. Digital image Analysis of Heterogeneous tuberculosis pulmonary pathology in non-clinical Animal Models using Deep convolutional neural networks. Scientific Reports, 10(1), 1-14, 2020.
• A.S.N. Reddy, Jie Huang, Naeem H Syed, Asa Ben-Hur, Suomeng Dong, and Lianfeng Gu. Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. Biochemical Society Transactions, 48(6), 2399-2414, 2020.
• Salah E Abdel-Ghany, Fahad Ullah, Asa Ben-Hur, and A.S.N. Reddy. Transcriptome analysis of drought-resistant and drought-sensitive sorghum (Sorghum bicolor) genotypes in response to PEG-induced drought stress. International Journal of Molecular Sciences 21 (3), 772, 2020.

2019

• Ameni Trabelsi, Mohamed Chaabane, and Asa Ben-Hur. Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities. Bioinformatics, 35(14), i269–i277, 2019 (ISMB 2019 special issue). (preprint)
• Naihui Zhou et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology 20:244, 299. (preprint)
• Fayyaz Minhas, Amina Asif, and Asa Ben-Hur. Ten ways to fool the masses with machine learning. arXiv preprint arXiv:1901.01686, 2019.

2018

• Basir Shariat, Don Neumann, and Asa Ben-Hur. BLRM: A Basic Linear Ranking Model for protein interface prediction. In: IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2018.
• Wajid Arshad Abbasi, Amina Asif, Asa Ben-Hur, and Fayyaz ul Amir Afsar Minhas. Learning protein binding affinity using privileged information BMC Bioinformatics, 19:425, 2018.
• Amina Asif, Wajid Arshad Abbasi, Farzeen Munir, Asa Ben-Hur, and Fayyaz ul Amir Afsar Minhas. pyLEMMINGS: Large margin multiple instance classification and ranking for bioinformatics applications. arXiv:1711.04913. [cs.LG], 2018.
• Fahad Ullah, Michael Hamilton, A.S.N. Reddy, and Asa Ben-Hur. Exploring the relationship between intron retention and chromatin accessibility in plants. BMC Genomics 19:21, 2018.
• Sergei A Filichkin, Mike Hamilton, Palitha D Dharmawardhana, Sunil K Singh, Christopher Sullivan, Asa Ben-Hur, A.S.N. Reddy, and Pankaj Jaiswal. Abiotic stresses modulate landscape of poplar transcriptome via alternative splicing, differential intron retention, and isoform ratio switching. Frontiers in Plant Science 9, 2018.

2017

• Alex Fout, Jonathon Byrd, Basir Shariat, and Asa Ben-Hur. Protein interface prediction using graph convolutional networks. In: Advances in Neural Information Processing Systems (NIPS), 2017. (code, data, poster)
• Fayyaz ul Amir Afsar Minhas , Eric D. Ross and Asa Ben-Hur. Amino acid composition predicts prion activity. PLoS Computational Biology 13(4): e1005465.
• Indika Kahanda and Asa Ben-Hur. GOstruct 2.0: Automated Protein Function Prediction for Annotated Proteins. In: ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2017.

2016

• Salah E. Abdel-Ghany*, Michael Hamilton*, Jennifer L. Jacobi, Peter Ngam, Nicholas Devitt, Faye Schilkey, Asa Ben-Hur, and A.S.N. Reddy. A survey of the sorghum transcriptome using single-molecule long reads. Nature Communications 7, 2016. (*Joint first authors). Here’s a link to the TAPIS software.
• Yuxiang Jiang et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology 17:184, 2016. (preprint).
• Cameron Tolooee, Sangmi Lee Pallickara and Asa Ben-Hur. Mendel: A distributed storage framework for similarity searching over sequencing data. In: Proceedings of the 30th IEEE International Parallel & Distributed Processing Symposium (IPDPS), 2016.
• Thomas Harrison, Dan Sloan, Jaime Ruiz, Asa Ben-Hur, and Christina Boucher. aPPRove: an HMM-based method for accurate prediction of RNA-pentatricopeptide repeat protein binding events. PLOS ONE, 11(8), 2016.

2015

• Indika Kahanda, Chris Funk, Fahad Ullah, Karin Verspoor and Asa Ben-Hur. A close look at automated protein function prediction evaluation protocols.. GigaScience, 4(41), 2015.
• Indika Kahanda, Christopher Funk, Karin Verspoor, and Asa Ben-Hur. PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources. F1000Research, 4(259), 2015.
• Upulee Kanewala, James Bieman, and Asa Ben-Hur. Predicting Metamorphic Relations for Testing Scientific Software: A Machine Learning Approach Using Graph Kernels. Software Testing, Verification and Reliability, 2015.
• Christopher Funk, Indika Kahanda, Asa Ben-Hur and Karin Verspoor. Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct. Journal of Biomedical Semantics, 6(9), 2015.

2014

• Corey Broeckling, Fayyaz Afsar Minhas, Steffen Neumann, Asa Ben-Hur, and Jessica Prenni. RAMClust: a novel feature clustering method enables spectral-matching based annotation for metabolomics data. Analytical Chemistry, 86(14):6812–6817, 2014. Ramclust is available on github.

2013

• Fayyaz Afsar Minhas, Brian Geiss, and Asa Ben-Hur. PAIRpred: Partner-specific prediction of interacting residues from sequence and structure, PROTEINS: Structure, Function, and Bioinformatics, 2013. Links to a preprint and the PAIRpred software and data.
• Mark F. Rogers, Christina Boucher, and Asa Ben-Hur. SpliceGrapherXT: From Splice Graphs to Transcripts Using RNA-Seq. ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2013.
• Automated function prediction competition participants. A large-scale evaluation of computational protein function prediction. Nature Methods, 10:221–227, 2013.
• Artem Sokolov, Chris Funk, Kiley Graim, Karin Verspoor, and Asa Ben-Hur. Combining heterogeneous data sources for accurate functional annotation of proteins. Automated Function Prediction Meeting Proceedings (ISMB 2011). BMC Bioinformatics, 14(Suppl 3), 2013.

2012

• Fayyaz Afsar Minhas and Asa Ben-Hur. Multiple instance learning of Calmodulin binding sites. Bioinformatics 28(18): i416-i422, 2012 (special ECCB 2012 issue). An online version of the classifier is available.
• M.F. Rogers, J. Thomas, A.S.N. Reddy, and A. Ben-Hur. SpliceGrapher: Detecting patterns of alternative splicing from RNA-seq data in the context of gene models and EST data. Genome Biology 13:R4, 2012.
• J. Thomas, S.G. Palusa, K.V. Prasad, G.S. Ali, G.K. Surabhi, A. Ben-Hur A, S.E. Abdel-Ghany, and A.S.N. Reddy. Identification of an intronic splicing regulatory element involved in autoregulation of alternative splicing of the SCL33 pre-mRNA. Plant J. 2012.
• Milana Frenkel-Morgenstern, Alessandro Gorohovski, Vincent Lacroix, Mark Rogers, Kristina Ibanez, Cesar Boullosa, Eduardo Andres Leon, Asa Ben-Hur and Alfonso Valencia. ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.. Nucleic Acids Research, 2012.
• A.S.N. Reddy, Mark F. Rogers, Dale N. Richardson, Michael Hamilton, and Asa Ben-Hur. Deciphering the plant splicing code: Experimental and computational approaches for predicting alternative splicing and splicing regulatory elements. Frontiers in Plant Genetics and Genomics 3, 2012.
• James A. Toombs, Michelina Petri, Kacy R. Paul, Grace Y. Kan, Asa Ben-Hur, and Eric D. Ross. De novo design of synthetic prion domains. PNAS, 2012.

2011

• A. Sokolov and A. Ben-Hur. Multi-view prediction of protein function. In: ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2011. [ preprint ]
• M. Hamilton, A.S.N. Reddy, and A. Ben-Hur. Kernel methods for Calmodulin binding and binding site prediction. In: ACM Conference on Bioinformatics, Computational Biology and Biomedicine, 2011. [ preprint ]
• D.N. Richardson, M.F. Rogers, A. Labadorf, A. Ben-Hur, H. Guo, A.H. Paterson, and A.S.N. Reddy. Comparative analysis of Serine/Arginine-rich proteins across 27 eukaryotes: Insights into subfamily classification and extent of alternative splicing. PLoS ONE 6(9):e24542, 2011.
• A.S.N. Reddy, A. Ben-Hur, and I.S. Day. Experimental and computational approaches for the study of calmodulin interactions. Phytochemistry 72(11): 1007-1019, 2011.

2010

• A. Sokolov and A. Ben-Hur. Hierarchical classification of Gene Ontology terms using the GOstruct method. Journal of Bioinformatics and Computational Biology 8(2): 357-376, 2010. [ preprint ]
• T. Iverson, H. Iyer, and A. Ben-Hur. Predicting the Risk of Type 2 Diabetes Using Insurance Claims Data. In: NIPS 2010 workshop on predictive models in personalized medicine.
• Adam Labadorf, Alicia Link, Mark F Rogers, Julie Thomas, A.S.N. Reddy and Asa Ben-Hur. Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC Genomics 11:114, 2010.

2009

• A. Sokolov and A. Ben-Hur. GOstruct: utilizing the structure of the Gene Ontology for accurate prediction of protein function. 8th Annual International Conference on Computational System Bioinformatics (CSB2009). An extended version is available [ here ].
• C.D. Ross, B. McCarty, M. Hamilton, A. Ben-Hur, and E.D. Ross. A promiscuous prion: Efficient induction of [URE3] prion formation by heterologous prion domains. Genetics 183: 929-940, 2009.
• M. Rogers and A. Ben-Hur. The use of Gene Ontology evidence codes in preventing classifier assessment bias. Bioinformatics 25(9):1173-1177, 2009.
• A. Ben-Hur and J. Weston. A User’s guide to Support Vector Machines. In Data Mining Techniques for the Life Sciences. Oliviero Carugo and Frank Eisenhaber (eds.), 2009.

2008

• A. Ben-Hur, C-S. Ong, S. Sonnenburg, B. Schoelkopf, and G. Raetsch. Support vector machines and kernels for computational biology. PLoS Computational Biology 4(10): e1000173, 2008. [ web supplement ]

2007

• H. Wang, E. Segal, A. Ben-Hur, Q. Li, M. Vidal and D. Koller. InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. Genome Biology, 8(9): R192, 2007.
• J. Qiu, Martial Hue, A. Ben-Hur, J-P. Vert and W.S. Noble. An alignment kernel for protein structures. Bioinformatics 23(9): 1090-1098, 2007.
• W.S. Noble and A. Ben-Hur. Integrating information for protein function prediction. In: Bioinformatics - From Genomes to Therapies Vol. 3. Thomas Lengauer (ed.) 2007 pp. 1297-1314.

2006 and earlier

• S.Y. Rhee, J. Taylor, G. Wadhera, A. Ben-Hur, D. Brutlag, and R.W. Shafer. Genotypic predictors of human immonodeficiency virus type 1 drug resistance. PNAS 103(46): 17355-17360, 2006.
• A. Ben-Hur and W.S. Noble. Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinformatics 7(Suppl 1), 2006.
• A. Ben-Hur and D. Brutlag. Protein sequence motifs: Highly predictive features of protein function. In: Feature extraction, foundations and applications. I. Guyon, S. Gunn, M. Nikravesh, and L. Zadeh (eds.) Springer Verlag, 2006. [ preprint ]
• J.P. Miller, R.S. Lo, A. Ben-Hur, C. Desmarais, I. Stagljar, W.S. Noble and S. Fields. Large-scale identification of yeast integral membrane protein interactions PNAS 102(34): 12123-12128, 2005.
• A. Ben-Hur and W.S. Noble. Kernel methods for predicting protein-protein interactions. In: Proceedings, thirteenth international conference on intelligent systems for molecular biology. Bioinformatics 21(Suppl. 1): i38-i46, 2005.
• H. Wang, E. Segal, A. Ben-Hur, D. Brutlag and D. Koller. Identifying protein-protein interaction sites on a genome-wide scale. Advances in Neural Information Processing Systems 17, 2004.
• I. Guyon, S.R. Gunn, A. Ben-Hur and G. Dror. Results analysis of the NIPS 2003 feature selection challenge Advances in Neural Information Processing Systems 17, 2004.
• R. Sharan, A. Ben-Hur, G. Loots and I. Ovcharenko. CREME: cis-regulatory module explorer for the human genome. Nucleic Acids Research 32: W83-W88, 2004.
• A. Ben-Hur and D. Brutlag. Remote homology detection: a motif based approach. In: Proceedings, eleventh international conference on intelligent systems for molecular biology. Bioinformatics 19(Suppl. 1): i26-i33, 2003.
• R. Sharan, I. Ovcharenko, A. Ben-Hur and R.M. Karp. CREME: A framework for identifying cis-regulatory modules in human-mouse conserved segments In: Proceedings, eleventh international conference on intelligent systems for molecular biology. Bioinformatics 19(Suppl. 1): i283-i291, 2003.
• A. Ben-Hur and I. Guyon. Detecting stable clusters using principal component analysis. In Methods in Molecular Biology, M.J. Brownstein and A. Khodursky (eds.) Humana press, 2003 pp. 159-182.
• A. Ben-Hur, A. Elisseeff and I. Guyon. A stability based method for discovering structure in clustered data. Pacific Symposium on Biocomputing, 2002. There is an R implementation that is part of bioconductor.
• A. Ben-Hur, D. Horn, H.T. Siegelmann and V. Vapnik. Support vector clustering. Journal of Machine Learning Research 2:125-137, 2001.
• A. Ben-Hur, D. Horn, H.T. Siegelmann and V. Vapnik. A support vector method for clustering. Advances in Neural Information Processing Systems 13, 367-373, 2001.
• A. Ben-Hur, D. Horn, H.T. Siegelmann and V. Vapnik. A kernel clustering method. 15th International Conference on Pattern Recognition (ICPR), 728-731, 2000.

Work in analog computation and statistical physics:

• A. Ben-Hur, J. Feinberg, S. Fishman and H.T. Siegelmann. Probabilistic analysis of a differential equation for linear programming . Journal of Complexity 19(4) : 474-510, 2003.
• A. Roitershtein, A. Ben-Hur and H.T. Siegelmann. On probabilistic analog automata . Theoretical Computer Science 320(2-3):449-464, 2004.
• A. Ben-Hur, H.T. Siegelmann and S. Fishman. Complexity for continuous time systems. Journal of Complexity 18(1) : 51-86, 2002.
• H.T. Siegelmann, A. Ben-Hur and S. Fishman. Computational complexity for continuous time dynamics. Physical Review Letters, 83(7):1463-1466, 1999.
• A. Ben-Hur and H.T. Siegelmann. Computation in gene networks. In: M. Margenstern and Y. Rogozhin (Eds.): MCU 2001, LNCS 2055, pp. 11-24, 2001.
• H.T. Siegelmann, A. Roitershtein, and A. Ben-Hur. Noisy neural networks and generalizations. In Advances in Neural Information Processing Systems 12, Cambridge, MA, 2000. MIT Press.
• A. Ben-Hur, R. Hallgass and V. Loreto. A renormalization procedure for directed self-organized critical models. Physical Review E, 54:1426-1432, 1996.
• A. Ben-Hur and O. Biham. Universality in sandpile models. Physical Review E, 53:1317-1321, 1996.