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Author Details

Asa Ben-Hur
Colorado State University
1996
56
33
PMIDPaper TitleJournal TitlePublished Year
36124806Insights into performance evaluation of compound-protein interaction prediction methods.Bioinformatics2022
35443610RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data.BMC Bioinformatics2022
36591335On the choice of negative examples for prediction of host-pathogen protein interactions.Front Bioinform2022
33950192A self-attention model for inferring cooperativity between regulatory features.Nucleic Acids Res2021
34054788Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensis.Front Microbiol2021
32269234Digital Image Analysis of Heterogeneous Tuberculosis Pulmonary Pathology in Non-Clinical Animal Models using Deep Convolutional Neural Networks.Sci Rep2020
31991584Transcriptome Analysis of Drought-Resistant and Drought-Sensitive Sorghum (<i>Sorghum bicolor</i>) Genotypes in Response to PEG-Induced Drought Stress.Int J Mol Sci2020
33196096Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies.Biochem Soc Trans2020
32756364Splicing Factor Transcript Abundance in Saliva as a Diagnostic Tool for Breast Cancer.Genes (Basel)2020
31510640Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities.Bioinformatics2019
31744546The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.Genome Biol2019
31436473Development of the Automated Primer Design Workflow Uniqprimer and Diagnostic Primers for the Broad-Host-Range Plant Pathogen <i>Dickeya dianthicola</i>.Plant Dis2019
29304739Exploring the relationship between intron retention and chromatin accessibility in plants.BMC Genomics2018
30442086Learning protein binding affinity using privileged information.BMC Bioinformatics2018
29483921Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching.Front Plant Sci2018
28394888Amino acid composition predicts prion activity.PLoS Comput Biol2017
27339290A survey of the sorghum transcriptome using single-molecule long reads.Nat Commun2016
27604469An expanded evaluation of protein function prediction methods shows an improvement in accuracy.Genome Biol2016
27560805aPPRove: An HMM-Based Method for Accurate Prediction of RNA-Pentatricopeptide Repeat Protein Binding Events.PLoS One2016
26005564Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct.J Biomed Semantics2015
26603559Transcriptome-Wide Identification of RNA Targets of Arabidopsis SERINE/ARGININE-RICH45 Uncovers the Unexpected Roles of This RNA Binding Protein in RNA Processing.Plant Cell2015
26380075A close look at protein function prediction evaluation protocols.Gigascience2015
26834980PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources.F1000Res2015
24243399PAIRpred: partner-specific prediction of interacting residues from sequence and structure.Proteins2014
24927477RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data.Anal Chem2014
23143107ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data.Nucleic Acids Res2013
23719919A bioinformatics method for identifying Q/N-rich prion-like domains in proteins.Methods Mol Biol2013
23514123Combining heterogeneous data sources for accurate functional annotation of proteins.BMC Bioinformatics2013
23353650A large-scale evaluation of computational protein function prediction.Nat Methods2013
22293517SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data.Genome Biol2012
22962461Multiple instance learning of Calmodulin binding sites.Bioinformatics2012
22913769Identification of an intronic splicing regulatory element involved in auto-regulation of alternative splicing of SCL33 pre-mRNA.Plant J2012
22474356De novo design of synthetic prion domains.Proc Natl Acad Sci U S A2012
22645572Deciphering the plant splicing code: experimental and computational approaches for predicting alternative splicing and splicing regulatory elements.Front Plant Sci2012
21338992Experimental and computational approaches for the study of calmodulin interactions.Phytochemistry2011
21935421Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing.PLoS One2011
20401950Hierarchical classification of gene ontology terms using the GOstruct method.J Bioinform Comput Biol2010
20221922A user's guide to support vector machines.Methods Mol Biol2010
20163725Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii.BMC Genomics2010
19254922The use of gene ontology evidence codes in preventing classifier assessment bias.Bioinformatics2009
19752212A promiscuous prion: efficient induction of [URE3] prion formation by heterologous prion domains.Genetics2009
18974822Support vector machines and kernels for computational biology.PLoS Comput Biol2008
17234638A structural alignment kernel for protein structures.Bioinformatics2007
17868464InSite: a computational method for identifying protein-protein interaction binding sites on a proteome-wide scale.Genome Biol2007
16723005Choosing negative examples for the prediction of protein-protein interactions.BMC Bioinformatics2006
17065321Genotypic predictors of human immunodeficiency virus type 1 drug resistance.Proc Natl Acad Sci U S A2006
15961482Kernel methods for predicting protein-protein interactions.Bioinformatics2005
16093310Large-scale identification of yeast integral membrane protein interactions.Proc Natl Acad Sci U S A2005
15003055Computation in gene networks.Chaos2004
15215390CREME: Cis-Regulatory Module Explorer for the human genome.Nucleic Acids Res2004
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Collaborators

Christopher Funk
University of Colorado School of Medicine
Co-authored papers 6
Karin Verspoor
National Centre for Infections in Cancer, 5Peter MacCallum Cancer Centre
Co-authored papers 6
Indika Kahanda
University of North Florida
Co-authored papers 5
William Stafford Noble
Co-authored papers 4
Prajwal Bhat
Royal Holloway University of London
Co-authored papers 3
Mark N Wass
University of Kent
Co-authored papers 3
Alberto Paccanaro
University of London
Co-authored papers 3
Julian Gough
Medical Research Council Laboratory of Molecular Biology
Co-authored papers 3
Christine Orengo
University College London, Institute of Structural and Molecular Biology
Co-authored papers 3
Jianlin Cheng
University of Missouri
Co-authored papers 3
Marco Falda
University of Padova
Co-authored papers 3
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Harvard Medical School
Co-authored papers 3
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University of Miami
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University of Padova
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San Pio Hospital
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Indiana University
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Catalan Institution for Research and Advanced Studies (ICREA)
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University of Galway
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University of Bristol
Co-authored papers 3
Stefano Toppo
University of Padova
Co-authored papers 3
Patricia C Babbitt
University of California san francisco
Co-authored papers 3
Michal Linial
Institute of Life Sciences, The Hebrew University of Jerusalem
Co-authored papers 3
Daisuke Kihara
Purdue University
Co-authored papers 3
Iddo Friedberg
Iowa State University
Co-authored papers 3
David T Jones
University College London
Co-authored papers 3
Steven E Brenner
University of California berkeley
Co-authored papers 3
Rita Casadio
Department of Pharmacy and Biotechnology, University of Bologna
Co-authored papers 3
Burkhard Rost
Technical University of Munich (TUM)
Co-authored papers 3
Domenico Cozzetto
Imperial College London
Co-authored papers 3
Release 1.2