Publications

My publications on google scholar.

• CAFA competition participants. A large-scale evaluation of computational protein function prediction. Nature Methods, 2013.
• F.A. Minhas and A. 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.
• 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.
• 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 ]
• Adam Labadorf, Alicia Link, Mark F Rogers, Julie Thomas, Anireddy SN Reddy and Asa Ben-Hur. Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii. BMC Genomics 11:114, 2010.
• 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 Biological Data Mining. Oliviero Carugo and Frank Eisenhaber (eds.) Springer Protocols, 2009.
• 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 ]
• 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.
• 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.
• 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.

Analog computation

• 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.

Physics

• 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.