A. Ben-Hur

发表

A large-scale evaluation of computational protein function prediction

Daniel W. A. Buchan, Thomas A. Hopf, Mark N. Wass, 2013, Nature Methods.

Result Analysis of the NIPS 2003 Feature Selection Challenge

Steve R. Gunn, Isabelle Guyon, Gideon Dror, 2004, NIPS.

Support Vector Clustering

Hava T. Siegelmann, David Horn, Asa Ben-Hur, 2002, J. Mach. Learn. Res..

Detecting stable clusters using principal component analysis.

I. Guyon, A. Ben-Hur, I. Ramadass Subramanian, 2003, Methods in molecular biology.

Design and Analysis of the NIPS2003 Challenge

Steve R. Gunn, Isabelle Guyon, Gideon Dror, 2006, Feature Extraction.

Integrating Information for Protein Function Prediction

William Stafford Noble, A. Ben-Hur, 2008 .

Support Vector Machines and Kernels for Computational Biology

Gunnar Rätsch, Bernhard Schölkopf, Cheng Soon Ong, 2008, PLoS Comput. Biol..

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

D. Koller, E. Segal, M. Vidal, 2007, Genome Biology.

Kernel methods for predicting protein-protein interactions

William Stafford Noble, Asa Ben-Hur, A. Ben-Hur, 2005, ISMB.

Genotypic predictors of human immunodeficiency virus type 1 drug resistance

R. Shafer, A. Ben-Hur, D. Brutlag, 2006, Proceedings of the National Academy of Sciences.

A user's guide to support vector machines.

Jason Weston, Asa Ben-Hur, J. Weston, 2010, Methods in molecular biology.

CREME: Cis-Regulatory Module Explorer for the human genome

Roded Sharan, Asa Ben-Hur, Ivan Ovcharenko, 2004, Nucleic Acids Res..

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

Dale N. Richardson, Mark F. Rogers, A. Ben-Hur, 2012, Front. Plant Sci..

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

A. Ben-Hur, B. Geiss, Fayyaz ul Amir Afsar Minhas, 2014, Proteins.

Large-scale identification of yeast integral membrane protein interactions.

William Stafford Noble, S. Fields, A. Ben-Hur, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Digital Image Analysis of Heterogeneous Tuberculosis Pulmonary Pathology in Non-Clinical Animal Models using Deep Convolutional Neural Networks

A. Ben-Hur, G. Robertson, Bryce C Asay, 2020, Scientific Reports.

METHOD Open Access

A. Ben-Hur, L. Maretty, J. Sibbesen, 2014 .

aPPRove: An HMM-Based Method for Accurate Prediction of RNA-Pentatricopeptide Repeat Protein Binding Events

Daniel B. Sloan, A. Ben-Hur, C. Boucher, 2016, PloS one.

Abiotic Stresses Modulate Landscape of Poplar Transcriptome via Alternative Splicing, Differential Intron Retention, and Isoform Ratio Switching

A. Ben-Hur, P. Jaiswal, S. Filichkin, 2018, Front. Plant Sci..

Thesis P300 Classification Using Deep Belief Nets Submitted By

A. Ben-Hur, C. Peterson, Charles Anderson, 2014 .

A survey of the sorghum transcriptome using single-molecule long reads

Faye D. Schilkey, A. Ben-Hur, A. Reddy, 2016, Nature Communications.

Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies.

A. Ben-Hur, A. Reddy, N. Syed, 2020, Biochemical Society transactions.

Identification of an intronic splicing regulatory element involved in auto-regulation of alternative splicing of SCL33 pre-mRNA.

A. Ben-Hur, A. Reddy, G. S. Ali, 2012, The Plant journal : for cell and molecular biology.

Transcriptome-Wide Identification of RNA Targets of Arabidopsis SERINE/ARGININE-RICH45 Uncovers the Unexpected Roles of This RNA Binding Protein in RNA Processing[OPEN]

A. Ben-Hur, A. Reddy, Michael Hamilton, 2015, Plant Cell.

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

Asa Ben-Hur, Dale N. Richardson, Anireddy S. N. Reddy, 2011, PloS one.

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Jari Björne, Tapio Salakoski, Giorgio Valentini, 2019, Genome Biology.

A structured outputs method for predicting protein binding sites

A. Ben-Hur, Michael Hamilton, 2008 .

DISSERTATION ACCURATE PREDICTION OF PROTEIN FUNCTION USING GOSTRUCT

A. Sokolov, A. Ben-Hur, R. McConnell, 2011 .

GOstruct: PREDICTION OF GENE ONTOLOGY TERMS USING METHODS FOR STRUCTURED OUTPUT SPACES

A. Sokolov, A. Ben-Hur, Artem Sokolov, 2009 .

Probabilistic analysis of the phase space flow for linear programming

H. Siegelmann, J. Feinberg, A. Ben-Hur, 2001, cond-mat/0110655.

Probabilistic analysis of a differential equation for linear programming

Hava T. Siegelmann, Shmuel Fishman, Asa Ben-Hur, 2001, J. Complex..

Development of the Automated Primer Design Workflow Uniqprimer and Diagnostic Primers for the Broad-Host-Range Plant Pathogen Dickeya dianthicola.

A. Ben-Hur, J. Leach, L. Triplett, 2019, Plant disease.

A user's guide to support vector machines.

J. Weston, A. Ben-Hur, Asa Ben-Hur, 2010, Methods in molecular biology.

Transcriptome-Wide Identification of RNA Targets of Arabidopsis SERINE/ARGININE-RICH45 Uncovers the Unexpected Roles of This RNA Binding Protein in RNA ProcessingOPEN

A. Ben-Hur, Michael Hamilton, Denghui Xing, 2015 .

RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data

A. Ben-Hur, A. Reddy, Don Neumann, 2022, BMC Bioinformatics.

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

A. Ben-Hur, A. Reddy, S. Abdel‐Ghany, 2020, International journal of molecular sciences.

On the choice of negative examples for prediction of host-pathogen protein interactions

A. Ben-Hur, F. Minhas, Don Neumann, 2022, Frontiers in Bioinformatics.

A close look at protein function prediction evaluation protocols

Karin M. Verspoor, Karin Verspoor, Indika Kahanda, 2015, GigaScience.

Data and software associated with PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources

Karin M. Verspoor, Karin Verspoor, Indika Kahanda, 2015 .

A Theory of Complexity for Continuous Time Dynamics

Hava T. Siegelmann, Asa Ben-Hur, Shmuel Fishman, 1998, MCU.

De novo design of synthetic prion domains

Asa Ben-Hur, Eric D Ross, A. Ben-Hur, 2012, Proceedings of the National Academy of Sciences.

Experimental and computational approaches for the study of calmodulin interactions.

Asa Ben-Hur, A. Ben-Hur, A. Reddy, 2011, Phytochemistry.

Exploring the relationship between intron retention and chromatin accessibility in plants

A. Ben-Hur, A. Reddy, Michael Hamilton, 2018, BMC Genomics.

Choosing negative examples for the prediction of protein-protein interactions

William Stafford Noble, Asa Ben-Hur, A. Ben-Hur, 2006, BMC Bioinformatics.

COMPARISON OF EEG PREPROCESSING METHODS TO IMPROVE THE CLASSIFICATION OF P 300 TRIALS Submitted

Asa Ben-Hur, Stuart Tobet, Zachary Cashero, 2011 .

A Stability Based Method for Discovering Structure in Clustered Data

Isabelle Guyon, André Elisseeff, Asa Ben-Hur, 2001, Pacific Symposium on Biocomputing.

Genome-wide analysis of alternative splicing in Chlamydomonas reinhardtii

Mark F. Rogers, A. Ben-Hur, A. Reddy, 2010, BMC Genomics.

A self-attention model for inferring cooperativity between regulatory features

Asa Ben-Hur, Fahad Ullah, A. Ben-Hur, 2020, bioRxiv.

Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities

Mohamed Chaabane, Asa Ben-Hur, Ameni Trabelsi, 2019, Bioinform..

RAMClust: a novel feature clustering method enables spectral-matching-based annotation for metabolomics data.

S Neumann, A. Ben-Hur, S. Neumann, 2014, Analytical chemistry.

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

A. Ben-Hur, T. Peretz, Mercedes Bentata, 2020, Genes.

ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data

Alfonso Valencia, Milana Frenkel-Morgenstern, Asa Ben-Hur, 2012, Nucleic Acids Res..

A Promiscuous Prion: Efficient Induction of [URE3] Prion Formation by Heterologous Prion Domains

A. Ben-Hur, Michael Hamilton, E. Ross, 2009, Genetics.

Mendel: A Distributed Storage Framework for Similarity Searching over Sequencing Data

Cameron Tolooee, Sangmi Lee Pallickara, Asa Ben-Hur, 2016, 2016 IEEE International Parallel and Distributed Processing Symposium (IPDPS).

Combining heterogeneous data sources for accurate functional annotation of proteins

Karin M. Verspoor, Asa Ben-Hur, Artem Sokolov, 2013, BMC Bioinformatics.

Multiple instance learning of Calmodulin binding sites

Asa Ben-Hur, Fayyaz ul Amir Afsar Minhas, A. Ben-Hur, 2012, Bioinform..

Kernel methods for Calmodulin binding and binding site prediction

Asa Ben-Hur, Michael Hamilton, A. S. N. Reddy, 2011, BCB '11.

Amino acid composition predicts prion activity

Asa Ben-Hur, Fayyaz ul Amir Afsar Minhas, Eric D. Ross, 2017, PLoS Comput. Biol..

A bioinformatics method for identifying Q/N-rich prion-like domains in proteins.

Charles Anderson, Asa Ben-Hur, Eric D Ross, 2013, Methods in molecular biology.

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

Karin M. Verspoor, Christopher S. Funk, A. Ben-Hur, 2015, J. Biomed. Semant..

Protein Interface Prediction using Graph Convolutional Networks

Alex Fout, Asa Ben-Hur, Basir Shariat, 2017, NIPS.

CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments

Roded Sharan, Richard M. Karp, Asa Ben-Hur, 2003, ISMB.

The use of gene ontology evidence codes in preventing classifier assessment bias

Asa Ben-Hur, Mark F. Rogers, A. Ben-Hur, 2009, Bioinform..

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens

Tapio Salakoski, Feng Zhang, Paolo Fontana, 2019, Genome Biology.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Tapio Salakoski, Paolo Fontana, Silvio C. E. Tosatto, 2016, Genome Biology.

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

A. Ben-Hur, A. Reddy, M. Salton, 2021, bioRxiv.

A close look at protein function prediction evaluation protocols

Karin M. Verspoor, Asa Ben-Hur, Indika Kahanda, 2015, GigaScience.

A Support Vector Method for Hierarchical Clustering

Asa Ben-Hur, A. Ben-Hur, 2007 .

A support vector clustering method

Hava T. Siegelmann, David Horn, Vladimir Vapnik, 2000, Proceedings 15th International Conference on Pattern Recognition. ICPR-2000.

A Support Vector Method for Clustering

Hava T. Siegelmann, David Horn, Vladimir Vapnik, 2000, NIPS.

BLRM: A Basic Linear Ranking Model for Protein Interface Prediction

Asa Ben-Hur, Basir Shariat, Don Neumann, 2018, 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).

Learning protein binding affinity using privileged information

Amina Asif, Asa Ben-Hur, Fayyaz ul Amir Afsar Minhas, 2017, BMC Bioinformatics.

On probabilistic analog automata

Hava T. Siegelmann, Asa Ben-Hur, Alexander Roitershtein, 2003, Theor. Comput. Sci..

Noisy Neural Networks and Generalizations

Hava T. Siegelmann, Alexander Roitershtein, Asa Ben-Hur, 1999, NIPS.

Computation in Gene Networks

Hava T. Siegelmann, Asa Ben-Hur, H. Siegelmann, 2001, MCU.

Remote homology detection: a motif based approach

Douglas L. Brutlag, Asa Ben-Hur, A. Ben-Hur, 2003, ISMB.

Digital Image Analysis of Heterogeneous Tuberculosis Pulmonary Pathology in Non-Clinical Animal Models using Deep Convolutional Neural Networks

A. Ben-Hur, G. Robertson, B. Edwards, 2020, Scientific Reports.

PHENOstruct: Prediction of human phenotype ontology terms using heterogeneous data sources

Karin M. Verspoor, Karin Verspoor, Indika Kahanda, 2015, F1000Research.

A Theory of Complexity for Continuous Time Systems

Hava T. Siegelmann, Shmuel Fishman, Asa Ben-Hur, 2002, J. Complex..

Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensis

A. Ben-Hur, T. Santangelo, A. F. Gardner, 2021, Frontiers in Microbiology.

Improving COVID-19 Testing Efficiency using Guided Agglomerative Sampling

Nasir Rajpoot, David Snead, Asa Ben-Hur, 2020, bioRxiv.

Hierarchical Classification of Gene Ontology Terms Using the Gostruct Method

Asa Ben-Hur, Artem Sokolov, A. Ben-Hur, 2010, J. Bioinform. Comput. Biol..

ISMB 2010 Organization

Roger L. Chang, S. Batzoglou, L. Cowen, 2010, Bioinformatics.

Generative Topographic Mapping of Electroencephalography ( EEG ) Data Submitted

A. Ben-Hur, Charles Anderson, P. Davies, 2014 .

Data-Driven Modelling of Gene Expression States in Breast Cancer and their Prediction from Routine Whole Slide Images

A. Ben-Hur, K. Branson, Muhammad Dawood, 2023, bioRxiv.

ISMB 2014 Proceedings Papers Committee

William Stafford Noble, Noah M. Daniels, D. Heckerman, 2014, Bioinformatics.

pyLEMMINGS: Large Margin Multiple Instance Classification and Ranking for Bioinformatics Applications pdf

Amina Asif, Farzeen Munir, Asa Ben-Hur, 2017, ArXiv.

Predicting metamorphic relations for testing scientific software: a machine learning approach using graph kernels

James M. Bieman, Upulee Kanewala, Asa Ben-Hur, 2016, Softw. Test. Verification Reliab..

Insights into performance evaluation of com-pound-protein interaction prediction methods

A. Ben-Hur, F. Minhas, I. Amin, 2022, Bioinformatics.

Learning protein binding affinity using privileged information

Wajid Arshad Abbasi, A. Ben-Hur, Amina Asif, 2018, BMC Bioinform..

Multi-view prediction of protein function

Artem Sokolov, Asa Ben-Hur, A. Ben-Hur, 2011, BCB '11.

Accurate prediction of protein function using gostruct

Asa Ben-Hur, Artem Sokolov, A. Ben-Hur, 2011 .

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

Hava T. Siegelmann, Asa Ben-Hur, Shmuel Fishman, 2004 .

GOstruct 2.0: Automated Protein Function Prediction for Annotated Proteins

Indika Kahanda, Asa Ben-Hur, A. Ben-Hur, 2017, BCB.

Identifying Protein-Protein Interaction Sites on a Genome-Wide Scale

Haidong Wang, Daphne Koller, Eran Segal, 2004, NIPS.

Exploring the relationship between intron retention and chromatin accessibility in plants

A. Ben-Hur, A. Reddy, Michael Hamilton, 2018, BMC Genomics.

SpliceGrapherXT: From Splice Graphs to Transcripts Using RNA-Seq

Christina Boucher, Asa Ben-Hur, Mark F. Rogers, 2013, BCB.

Computational complexity for continuous-time dynamics

Hava T. Siegelmann, Shmuel Fishman, Asa Ben-Hur, 2000, SPIE Optics + Photonics.

Computational Complexity for Continuous Time Dynamics

Hava T. Siegelmann, Asa Ben-Hur, Shmuel Fishman, 1999 .