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Asa Ben-Hur - Publications

Affiliations: 
Computer Science Colorado State University, Fort Collins, CO 
Area:
Computer Science, Bioinformatics Biology
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42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Neumann D, Roy S, Minhas FUAA, Ben-Hur A. On the choice of negative examples for prediction of host-pathogen protein interactions. Frontiers in Bioinformatics. 2: 1083292. PMID 36591335 DOI: 10.3389/fbinf.2022.1083292  0.352
2022 Yaseen A, Amin I, Akhter N, Ben-Hur A, Minhas F. Insights into performance evaluation of compound-protein interaction prediction methods. Bioinformatics (Oxford, England). 38: ii75-ii81. PMID 36124806 DOI: 10.1093/bioinformatics/btac496  0.685
2019 Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, ... ... Ben-Hur A, 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. PMID 31744546 DOI: 10.1186/S13059-019-1835-8  0.422
2019 Trabelsi A, Chaabane M, Ben-Hur A. Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities. Bioinformatics (Oxford, England). 35: i269-i277. PMID 31510640 DOI: 10.1093/Bioinformatics/Btz339  0.354
2018 Abbasi WA, Asif A, Ben-Hur A, Minhas FUAA. Learning protein binding affinity using privileged information. Bmc Bioinformatics. 19: 425. PMID 30442086 DOI: 10.1186/S12859-018-2448-Z  0.491
2017 Afsar Minhas FU, Ross ED, Ben-Hur A. Amino acid composition predicts prion activity. Plos Computational Biology. 13: e1005465. PMID 28394888 DOI: 10.1371/Journal.Pcbi.1005465  0.393
2016 Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/S13059-016-1037-6  0.481
2016 Harrison T, Ruiz J, Sloan DB, Ben-Hur A, Boucher C. aPPRove: An HMM-Based Method for Accurate Prediction of RNA-Pentatricopeptide Repeat Protein Binding Events. Plos One. 11: e0160645. PMID 27560805 DOI: 10.1371/Journal.Pone.0160645  0.423
2016 Abdel-Ghany SE, Hamilton M, Jacobi JL, Ngam P, Devitt N, Schilkey F, Ben-Hur A, Reddy AS. A survey of the sorghum transcriptome using single-molecule long reads. Nature Communications. 7: 11706. PMID 27339290 DOI: 10.1038/Ncomms11706  0.341
2016 Kanewala U, Bieman JM, Ben-Hur A. Predicting metamorphic relations for testing scientific software: A machine learning approach using graph kernels Software Testing Verification and Reliability. 26: 245-269. DOI: 10.1002/Stvr.1594  0.336
2015 Kahanda I, Funk C, Verspoor K, Ben-Hur A. PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources. F1000research. 4: 259. PMID 26834980 DOI: 10.12688/F1000Research.6670.1  0.389
2015 Xing D, Wang Y, Hamilton M, Ben-Hur A, Reddy AS. Transcriptome-Wide Identification of RNA Targets of Arabidopsis SERINE/ARGININE-RICH45 Uncovers the Unexpected Roles of This RNA Binding Protein in RNA Processing. The Plant Cell. PMID 26603559 DOI: 10.1105/Tpc.15.00641  0.312
2015 Kahanda I, Funk CS, Ullah F, Verspoor KM, Ben-Hur A. A close look at protein function prediction evaluation protocols. Gigascience. 4: 41. PMID 26380075 DOI: 10.1186/S13742-015-0082-5  0.446
2015 Funk CS, Kahanda I, Ben-Hur A, Verspoor KM. Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct. Journal of Biomedical Semantics. 6: 9. PMID 26005564 DOI: 10.1186/S13326-015-0006-4  0.48
2014 Minhas Fu, Geiss BJ, Ben-Hur A. PAIRpred: partner-specific prediction of interacting residues from sequence and structure. Proteins. 82: 1142-55. PMID 24243399 DOI: 10.1002/Prot.24479  0.722
2013 Ross ED, Maclea KS, Anderson C, Ben-Hur A. A bioinformatics method for identifying Q/N-rich prion-like domains in proteins. Methods in Molecular Biology (Clifton, N.J.). 1017: 219-28. PMID 23719919 DOI: 10.1007/978-1-62703-438-8_16  0.413
2013 Sokolov A, Funk C, Graim K, Verspoor K, Ben-Hur A. Combining heterogeneous data sources for accurate functional annotation of proteins. Bmc Bioinformatics. 14: S10. PMID 23514123 DOI: 10.1186/1471-2105-14-S3-S10  0.615
2013 Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, et al. A large-scale evaluation of computational protein function prediction. Nature Methods. 10: 221-7. PMID 23353650 DOI: 10.1038/Nmeth.2340  0.657
2013 Frenkel-Morgenstern M, Gorohovski A, Lacroix V, Rogers M, Ibanez K, Boullosa C, Andres Leon E, Ben-Hur A, Valencia A. ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. Nucleic Acids Research. 41: D142-51. PMID 23143107 DOI: 10.1093/Nar/Gks1041  0.304
2012 Minhas Fu, Ben-Hur A. Multiple instance learning of Calmodulin binding sites. Bioinformatics (Oxford, England). 28: i416-i422. PMID 22962461 DOI: 10.1093/Bioinformatics/Bts416  0.693
2012 Thomas J, Palusa SG, Prasad KV, Ali GS, Surabhi GK, Ben-Hur A, Abdel-Ghany SE, Reddy AS. Identification of an intronic splicing regulatory element involved in auto-regulation of alternative splicing of SCL33 pre-mRNA. The Plant Journal : For Cell and Molecular Biology. 72: 935-46. PMID 22913769 DOI: 10.1111/Tpj.12004  0.353
2012 Reddy AS, Rogers MF, Richardson DN, Hamilton M, Ben-Hur A. Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements. Frontiers in Plant Science. 3: 18. PMID 22645572 DOI: 10.3389/Fpls.2012.00018  0.329
2012 Toombs JA, Petri M, Paul KR, Kan GY, Ben-Hur A, Ross ED. De novo design of synthetic prion domains. Proceedings of the National Academy of Sciences of the United States of America. 109: 6519-24. PMID 22474356 DOI: 10.1073/Pnas.1119366109  0.371
2012 Rogers MF, Thomas J, Reddy AS, Ben-Hur A. SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome Biology. 13: R4. PMID 22293517 DOI: 10.1186/Gb-2012-13-1-R4  0.387
2012 Funk C, Sokolov A, Graim K, Ben-Hur A, Verspoor K. Improving automated protein function prediction by integrating natural language processing and machine learning F1000research. 3. DOI: 10.7490/F1000Research.1089821.1  0.604
2011 Richardson DN, Rogers MF, Labadorf A, Ben-Hur A, Guo H, Paterson AH, Reddy AS. Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing. Plos One. 6: e24542. PMID 21935421 DOI: 10.1371/Journal.Pone.0024542  0.307
2011 Reddy AS, Ben-Hur A, Day IS. Experimental and computational approaches for the study of calmodulin interactions. Phytochemistry. 72: 1007-19. PMID 21338992 DOI: 10.1016/J.Phytochem.2010.12.022  0.415
2011 Hamilton M, Reddy ASN, Ben-Hur A. Kernel methods for Calmodulin binding and binding site prediction 2011 Acm Conference On Bioinformatics, Computational Biology and Biomedicine, Bcb 2011. 381-386. DOI: 10.1145/2147805.2147855  0.311
2011 Sokolov A, Ben-Hur A. Multi-view prediction of protein function 2011 Acm Conference On Bioinformatics, Computational Biology and Biomedicine, Bcb 2011. 135-142. DOI: 10.1145/2147805.2147820  0.629
2010 Sokolov A, Ben-Hur A. Hierarchical classification of gene ontology terms using the GOstruct method. Journal of Bioinformatics and Computational Biology. 8: 357-76. PMID 20401950 DOI: 10.1142/S0219720010004744  0.65
2009 Ross CD, McCarty BR, Hamilton M, Ben-Hur A, Ross ED. A promiscuous prion: efficient induction of [URE3] prion formation by heterologous prion domains. Genetics. 183: 929-40. PMID 19752212 DOI: 10.1534/Genetics.109.109322  0.309
2009 Rogers MF, Ben-Hur A. The use of gene ontology evidence codes in preventing classifier assessment bias. Bioinformatics (Oxford, England). 25: 1173-7. PMID 19254922 DOI: 10.1093/Bioinformatics/Btp122  0.45
2008 Ben-Hur A, Ong CS, Sonnenburg S, Schölkopf B, Rätsch G. Support vector machines and kernels for computational biology. Plos Computational Biology. 4: e1000173. PMID 18974822 DOI: 10.1371/Journal.Pcbi.1000173  0.386
2008 Noble WS, Ben-Hur A. Integrating Information for Protein Function Prediction Bioinformatics-From Genomes to Therapies. 3: 1297-1314. DOI: 10.1002/9783527619368.ch35  0.31
2007 Wang H, Segal E, Ben-Hur A, Li QR, Vidal M, Koller D. InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale. Genome Biology. 8: R192. PMID 17868464 DOI: 10.1186/Gb-2007-8-9-R192  0.477
2007 Qiu J, Hue M, Ben-Hur A, Vert JP, Noble WS. A structural alignment kernel for protein structures. Bioinformatics (Oxford, England). 23: 1090-8. PMID 17234638 DOI: 10.1093/Bioinformatics/Btl642  0.383
2006 Ben-Hur A, Noble WS. Choosing negative examples for the prediction of protein-protein interactions. Bmc Bioinformatics. 7: S2. PMID 16723005 DOI: 10.1186/1471-2105-7-S1-S2  0.498
2006 Ben-Hur A, Brutlag D. Sequence motifs: Highly predictive features of protein function Studies in Fuzziness and Soft Computing. 207: 625-645.  0.366
2005 Miller JP, Lo RS, Ben-Hur A, Desmarais C, Stagljar I, Noble WS, Fields S. Large-scale identification of yeast integral membrane protein interactions. Proceedings of the National Academy of Sciences of the United States of America. 102: 12123-8. PMID 16093310 DOI: 10.1073/Pnas.0505482102  0.417
2005 Ben-Hur A, Noble WS. Kernel methods for predicting protein-protein interactions. Bioinformatics (Oxford, England). 21: i38-46. PMID 15961482 DOI: 10.1093/Bioinformatics/Bti1016  0.524
2004 Sharan R, Ben-Hur A, Loots GG, Ovcharenko I. CREME: Cis-Regulatory Module Explorer for the human genome. Nucleic Acids Research. 32: W253-6. PMID 15215390 DOI: 10.1093/Nar/Gkh385  0.321
2003 Sharan R, Ovcharenko I, Ben-Hur A, Karp RM. CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics (Oxford, England). 19: i283-91. PMID 12855471 DOI: 10.1093/Bioinformatics/Btg1039  0.304
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