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2020 – today
- 2023
[j22]Soumyadip Roy, Asa Ben-Hur:
Protein quality assessment with a loss function designed for high-quality decoys. Frontiers Bioinform. 3 (2023)- 2022
- [j21]Don Neumann, Anireddy S. N. Reddy
, Asa Ben-Hur:
RODAN: a fully convolutional architecture for basecalling nanopore RNA sequencing data. BMC Bioinform. 23(1): 142 (2022) - [j20]Don Neumann, Soumyadip Roy, Fayyaz ul Amir Afsar Minhas, Asa Ben-Hur:
On the choice of negative examples for prediction of host-pathogen protein interactions. Frontiers Bioinform. 2 (2022) - [i6]Adiba Yaseen, Imran Amin, Naeem Akhter, Asa Ben-Hur, Fayyaz A. Minhas:
Insights into performance evaluation of com-pound-protein interaction prediction methods. CoRR abs/2202.00001 (2022)
2010 – 2019
- 2019
- [j19]Ameni Trabelsi, Mohamed Chaabane, Asa Ben-Hur:
Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities. Bioinform. 35(14): i269-i277 (2019) - [i5]Fayyaz ul Amir Afsar Minhas, Amina Asif, Asa Ben-Hur:
Ten ways to fool the masses with machine learning. CoRR abs/1901.01686 (2019) - [i4]Ameni Trabelsi, Mohamed Chaabane, Asa Ben-Hur:
Comprehensive Evaluation of Deep Learning Architectures for Prediction of DNA/RNA Sequence Binding Specificities. CoRR abs/1901.10526 (2019) - 2018
- [j18]Wajid Arshad Abbasi, Amina Asif, Asa Ben-Hur, Fayyaz ul Amir Afsar Minhas:
Learning protein binding affinity using privileged information. BMC Bioinform. 19(1): 425:1-425:12 (2018) - [c19]Basir Shariat, Don Neumann, Asa Ben-Hur:
BLRM: A Basic Linear Ranking Model for Protein Interface Prediction. BIBM 2018: 29-35 - 2017
- [j17]Fayyaz ul Amir Afsar Minhas, Eric D. Ross, Asa Ben-Hur:
Amino acid composition predicts prion activity. PLoS Comput. Biol. 13(4) (2017) - [c18]Indika Kahanda, Asa Ben-Hur:
GOstruct 2.0: Automated Protein Function Prediction for Annotated Proteins. BCB 2017: 60-66 - [c17]Alex Fout, Jonathon Byrd, Basir Shariat, Asa Ben-Hur:
Protein Interface Prediction using Graph Convolutional Networks. NIPS 2017: 6530-6539 - [i3]Amina Asif, Wajid Arshad Abbasi, Farzeen Munir, Asa Ben-Hur, Fayyaz ul Amir Afsar Minhas:
pyLEMMINGS: Large Margin Multiple Instance Classification and Ranking for Bioinformatics Applications. CoRR abs/1711.04913 (2017) - 2016
- [j16]Upulee Kanewala, James M. Bieman, Asa Ben-Hur:
Predicting metamorphic relations for testing scientific software: a machine learning approach using graph kernels. Softw. Test. Verification Reliab. 26(3): 245-269 (2016) - [c16]Cameron Tolooee, Sangmi Lee Pallickara, Asa Ben-Hur:
Mendel: A Distributed Storage Framework for Similarity Searching over Sequencing Data. IPDPS 2016: 790-799 - 2015
- [j15]Christopher S. Funk, Indika Kahanda, Asa Ben-Hur, Karin M. Verspoor:
Evaluating a variety of text-mined features for automatic protein function prediction with GOstruct. J. Biomed. Semant. 6: 9 (2015) - 2013
- [j14]Artem Sokolov, Christopher S. Funk, Kiley Graim, Karin Verspoor, Asa Ben-Hur:
Combining heterogeneous data sources for accurate functional annotation of proteins. BMC Bioinform. 14(S-3): S10 (2013) - [j13]Milana Frenkel-Morgenstern, Alessandro Gorohovski, Vincent Lacroix, Mark F. Rogers, Kristina Ibáñez, Cesar Boullosa, Eduardo Andrés León, Asa Ben-Hur, Alfonso Valencia:
ChiTaRS: a database of human, mouse and fruit fly chimeric transcripts and RNA-sequencing data. Nucleic Acids Res. 41(Database-Issue): 142-151 (2013) - [c15]Mark F. Rogers, Christina Boucher, Asa Ben-Hur:
SpliceGrapherXT: From Splice Graphs to Transcripts Using RNA-Seq. BCB 2013: 247 - 2012
- [j12]Fayyaz ul Amir Afsar Minhas, Asa Ben-Hur:
Multiple instance learning of Calmodulin binding sites. Bioinform. 28(18): 416-422 (2012) - 2011
- [c14]Artem Sokolov, Asa Ben-Hur:
Multi-view prediction of protein function. BCB 2011: 135-142 - [c13]Michael Hamilton, A. S. N. Reddy, Asa Ben-Hur:
Kernel methods for Calmodulin binding and binding site prediction. BCB 2011: 381-386 - 2010
- [j11]Artem Sokolov, Asa Ben-Hur:
Hierarchical Classification of Gene Ontology Terms Using the Gostruct Method. J. Bioinform. Comput. Biol. 8(2): 357-376 (2010)
2000 – 2009
- 2009
- [j10]Mark F. Rogers, Asa Ben-Hur:
The use of gene ontology evidence codes in preventing classifier assessment bias. Bioinform. 25(9): 1173-1177 (2009) - 2008
- [j9]Asa Ben-Hur, Cheng Soon Ong, Sören Sonnenburg, Bernhard Schölkopf, Gunnar Rätsch:
Support Vector Machines and Kernels for Computational Biology. PLoS Comput. Biol. 4(10) (2008) - [j8]Asa Ben-Hur:
Support vector clustering. Scholarpedia 3(6): 5187 (2008) - [d4]Isabelle Guyon, Steve R. Gunn, Asa Ben-Hur, Gideon Dror:
Arcene. UCI Machine Learning Repository, 2008
- [d3]Isabelle Guyon, Steve R. Gunn, Asa Ben-Hur, Gideon Dror:
Dorothea. UCI Machine Learning Repository, 2008 - [d2]Isabelle Guyon, Steve R. Gunn, Asa Ben-Hur, Gideon Dror:
Gisette. UCI Machine Learning Repository, 2008 - [d1]Isabelle Guyon, Steve R. Gunn, Asa Ben-Hur, Gideon Dror:
Dexter. UCI Machine Learning Repository, 2008 - 2007
- [j7]Jian Qiu, Martial Hue, Asa Ben-Hur, Jean-Philippe Vert, William Stafford Noble:
A structural alignment kernel for protein structures. Bioinform. 23(9): 1090-1098 (2007) - 2006
- [j6]Asa Ben-Hur, William Stafford Noble:
Choosing negative examples for the prediction of protein-protein interactions. BMC Bioinform. 7(S-1) (2006) - [p2]Isabelle Guyon, Steve R. Gunn, Asa Ben-Hur, Gideon Dror:
Design and Analysis of the NIPS2003 Challenge. Feature Extraction 2006: 237-263 - [p1]Asa Ben-Hur, Douglas L. Brutlag:
Sequence Motifs: Highly Predictive Features of Protein Function. Feature Extraction 2006: 625-645 - 2005
- [c12]Asa Ben-Hur, William Stafford Noble:
Kernel methods for predicting protein-protein interactions. ISMB (Supplement of Bioinformatics) 2005: 38-46 - 2004
- [j5]Roded Sharan, Asa Ben-Hur, Gabriela G. Loots, Ivan Ovcharenko:
CREME: Cis-Regulatory Module Explorer for the human genome. Nucleic Acids Res. 32(Web-Server-Issue): 253-256 (2004) - [j4]Asa Ben-Hur, Alexander Roitershtein, Hava T. Siegelmann:
On probabilistic analog automata. Theor. Comput. Sci. 320(2-3): 449-464 (2004) - [c11]Isabelle Guyon, Steve R. Gunn, Asa Ben-Hur, Gideon Dror:
Result Analysis of the NIPS 2003 Feature Selection Challenge. NIPS 2004: 545-552 - [c10]Haidong Wang, Eran Segal, Asa Ben-Hur, Daphne Koller, Douglas L. Brutlag:
Identifying Protein-Protein Interaction Sites on a Genome-Wide Scale. NIPS 2004: 1465-1472 - 2003
- [j3]Asa Ben-Hur, Joshua Feinberg, Shmuel Fishman, Hava T. Siegelmann:
Probabilistic analysis of a differential equation for linear programming. J. Complex. 19(4): 474-510 (2003) - [c9]Asa Ben-Hur, Douglas L. Brutlag:
Remote homology detection: a motif based approach. ISMB (Supplement of Bioinformatics) 2003: 26-33 - [c8]Roded Sharan, Ivan Ovcharenko, Asa Ben-Hur, Richard M. Karp:
CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. ISMB (Supplement of Bioinformatics) 2003: 283-291 - [i2]Asa Ben-Hur, Alexander Roitershtein, Hava T. Siegelmann:
On probabilistic analog automata. CoRR cs.OH/0304042 (2003) - 2002
- [j2]Asa Ben-Hur, Hava T. Siegelmann, Shmuel Fishman:
A Theory of Complexity for Continuous Time Systems. J. Complex. 18(1): 51-86 (2002) - [c7]Asa Ben-Hur, André Elisseeff, Isabelle Guyon:
A Stability Based Method for Discovering Structure in Clustered Data. Pacific Symposium on Biocomputing 2002: 6-17 - 2001
- [j1]Asa Ben-Hur, David Horn, Hava T. Siegelmann, Vladimir Vapnik:
Support Vector Clustering. J. Mach. Learn. Res. 2: 125-137 (2001) - [c6]Asa Ben-Hur, Hava T. Siegelmann:
Computation in Gene Networks. MCU 2001: 11-24 - [i1]Asa Ben-Hur, Joshua Feinberg, Shmuel Fishman, Hava T. Siegelmann:
Probabilistic analysis of a differential equation for linear programming. CoRR cs.CC/0110056 (2001) - 2000
- [c5]Asa Ben-Hur, Hava T. Siegelmann, David Horn, Vladimir Vapnik:
A Support Vector Clustering Method. ICPR 2000: 2724-2727 - [c4]Asa Ben-Hur, David Horn, Hava T. Siegelmann, Vladimir Vapnik:
A Support Vector Method for Clustering. NIPS 2000: 367-373 - [c3]Hava T. Siegelmann, Asa Ben-Hur:
Macroscopical Molecular Computation with Gene Networks. UMC 2000: 119-120
1990 – 1999
- 1999
- [c2]Hava T. Siegelmann, Alexander Roitershtein, Asa Ben-Hur:
Noisy Neural Networks and Generalizations. NIPS 1999: 335-341 - 1998
- [c1]Hava T. Siegelmann, Asa Ben-Hur, Shmuel Fishman:
A Theory of Complexity for Continuous Time Dynamics. MCU (1) 1998: 179-203
Coauthor Index
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