Modular sequence elements associated with origin regions in eukaryotic chromosomal DNA. - Drena Dobbs; Wen-Ling Shaiu; Robert M. Benbow (Nucleic Acids Res., 1994)

Data-Driven Theory Refinement Using KBDistAl. - Jihoon Yang; Rajesh Parekh; Vasant G. Honavar; Drena Dobbs (IDA, 1999)

Data-driven theory refinement algorithms for bioinformatics. - Jihoon Yang; Rajesh Parekh; Vasant G. Honavar; Drena Dobbs (IJCNN, 1999)

Discovering Protein Function Classification Rules from Reduced Alphabet Representations of Protein Sequences. - Carson M. Andorf; Drena Dobbs; Vasant G. Honavar (JCIS, 2002)

Data-Driven Discovery of Protein Function Classifiers: Decision Trees Based on MEME Motifs outperform PROSITE Patterns and Profiles on Peptidase Families. - Xiangyun Wang; Diane Schroeder; Drena Dobbs; Vasant G. Honavar (JCIS, 2002)

Automated data-driven discovery of motif-based protein function classifiers. - Xiangyun Wang; Diane Schroeder; Drena Dobbs; Vasant G. Honavar (Inf. Sci., 2003)

A two-stage classifier for identification of protein-protein interface residues. - Changhui Yan; Drena Dobbs; Vasant G. Honavar (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. - Taner Z. Sen; Andrzej Kloczkowski; Robert L. Jernigan; Changhui Yan; Vasant G. Honavar; Kai-Ming Ho; Cai-Zhuang Wang; Yungok Ihm; Haibo Cao; Xun Gu; Drena Dobbs (BMC Bioinform., 2004)

Identification of interface residues in protease-inhibitor and antigen-antibody complexes: a support vector machine approach. - Changhui Yan; Vasant G. Honavar; Drena Dobbs (Neural Comput. Appl., 2004)

Information Integration from Semantically Heterogeneous Biological Data Sources. - Doina Caragea; Jie Bao 001; Jyotishman Pathak; Adrian Silvescu; Carson M. Andorf; Drena Dobbs; Vasant G. Honavar (DEXA Workshops, 2005)

Information Integration and Knowledge Acquisition from Semantically Heterogeneous Biological Data Sources. - Doina Caragea; Jyotishman Pathak; Jie Bao 001; Adrian Silvescu; Carson M. Andorf; Drena Dobbs; Vasant G. Honavar (DILS, 2005)

Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and Rna Binding Sites in Rev Proteins of Hiv-1 and Eiav Agree with Experimental Data - Michael Terribilini; Jae-Hyung Lee; Changhui Yan; Robert L. Jernigan; Susan Carpenter; Vasant G. Honavar; Drena Dobbs (CoRR, 2005)

Predicting DNA-binding sites of proteins from amino acid sequence. - Changhui Yan; Michael Terribilini; Feihong Wu; Robert L. Jernigan; Drena Dobbs; Vasant G. Honavar (BMC Bioinform., 2006)

Assessing the Performance of Macromolecular Sequence Classifiers. - Cornelia Caragea; Jivko Sinapov; Vasant G. Honavar; Drena Dobbs (BIBE, 2007)

Analysis of Protein Protein Dimeric Interfaces. - Feihong Wu; Fadi Towfic; Drena Dobbs; Vasant G. Honavar (BIBM, 2007)

Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach. - Carson M. Andorf; Drena Dobbs; Vasant G. Honavar (BMC Bioinform., 2007)

Glycosylation site prediction using ensembles of Support Vector Machine classifiers. - Cornelia Caragea; Jivko Sinapov; Adrian Silvescu; Drena Dobbs; Vasant G. Honavar (BMC Bioinform., 2007)

Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. - Jeffry D. Sander; Peter Zaback; J. Keith Joung; Daniel F. Voytas; Drena Dobbs (Nucleic Acids Res., 2007)

RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. - Michael Terribilini; Jeffry D. Sander; Jae-Hyung Lee; Peter Zaback; Robert L. Jernigan; Vasant G. Honavar; Drena Dobbs (Nucleic Acids Res., 2007)

Using Global Sequence Similarity to Enhance Biological Sequence Labeling. - Cornelia Caragea; Jivko Sinapov; Drena Dobbs; Vasant G. Honavar (BIBM, 2008)

Predicting Protective Linear B-Cell Epitopes Using Evolutionary Information. - Yasser El-Manzalawy; Drena Dobbs; Vasant G. Honavar (BIBM, 2008)

Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches. - Jae-Hyung Lee; Michael Hamilton; Colin Gleeson; Cornelia Caragea; Peter Zaback; Jeffry D. Sander; Li C. Xue; Feihong Wu; Michael Terribilini; Vasant G. Honavar; Drena Dobbs (Pacific Symposium on Biocomputing, 2008)

Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling. - Cornelia Caragea; Jivko Sinapov; Drena Dobbs; Vasant G. Honavar (BMC Bioinform., 2009)

Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. - Fengli Fu; Jeffry D. Sander; Morgan L. Maeder; Stacey Thibodeau-Beganny; J. Keith Joung; Drena Dobbs; Leslie L. Miller; Daniel F. Voytas (Nucleic Acids Res., 2009)

Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences. - Jeffry D. Sander; Deepak Reyon; Morgan L. Maeder; Jonathan E. Foley; Stacey Thibodeau-Beganny; Xiaohong Li 018; Maureen R. Regan; Elizabeth Dahlborg; Mathew J. Goodwin; Fengli Fu; Daniel F. Voytas; J. Keith Joung; et al. (BMC Bioinform., 2010)

Struct-NB: predicting protein-RNA binding sites using structural features. - Fadi Towfic; Cornelia Caragea; David C. Gemperline; Drena Dobbs; Vasant G. Honavar (Int. J. Data Min. Bioinform., 2010)

ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. - Jeffry D. Sander; Morgan L. Maeder; Deepak Reyon; Daniel F. Voytas; J. Keith Joung; Drena Dobbs (Nucleic Acids Res., 2010)

Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary study. - Li C. Xue; Rafael A. Jordan; Yasser El-Manzalawy; Drena Dobbs; Vasant G. Honavar (BCB, 2011)

Improving protein-RNA interface prediction by combining sequence homology based method with a naive Bayes classifier: preliminary results. - Li C. Xue; Rasna R. Walia; Yasser El-Manzalawy; Drena Dobbs; Vasant G. Honavar (BCB, 2011)

Predicting RNA-Protein Interactions Using Only Sequence Information. - Usha Muppirala; Vasant G. Honavar; Drena Dobbs (BMC Bioinform., 2011)

HomPPI: A Class of Sequence Homology Based Protein-Protein Interface Prediction Methods. - Li C. Xue; Drena Dobbs; Vasant G. Honavar (BMC Bioinform., 2011)

PRIDB: a protein-RNA interface database. - Benjamin A. Lewis; Rasna R. Walia; Michael Terribilini; Jeff Ferguson; Charles Zheng 001; Vasant G. Honavar; Drena Dobbs (Nucleic Acids Res., 2011)

Predicting MHC-II Binding Affinity Using Multiple Instance Regression. - Yasser El-Manzalawy; Drena Dobbs; Vasant G. Honavar (IEEE ACM Trans. Comput. Biol. Bioinform., 2011)

Predicting protective bacterial antigens using random forest classifiers. - Yasser El-Manzalawy; Drena Dobbs; Vasant G. Honavar (BCB, 2012)

Predicting protein-protein interface residues using local surface structural similarity. - Rafael A. Jordan; Yasser El-Manzalawy; Drena Dobbs; Vasant G. Honavar (BMC Bioinform., 2012)

Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. - Rasna R. Walia; Cornelia Caragea; Benjamin A. Lewis; Fadi Towfic; Michael Terribilini; Yasser El-Manzalawy; Drena Dobbs; Vasant G. Honavar (BMC Bioinform., 2012)

An analysis of conformational changes upon RNA-protein binding. - Kannan Sankar; Rasna R. Walia; Carla M. Mann; Robert L. Jernigan; Vasant G. Honavar; Drena Dobbs (BCB, 2014)

Session Introduction. - Drena Dobbs; Steven E. Brenner; Vasant G. Honavar; Robert L. Jernigan; Alain Laederach; Quaid Morris (PSB, 2016)

A Motif-Based Method for Predicting Interfacial Residues in Both the RNA and Protein Components of Protein-RNA Complexes. - Usha Muppirala; Benjamin A. Lewis; Carla M. Mann; Drena Dobbs (PSB, 2016)

Template-based protein-protein docking exploiting pairwise interfacial residue restraints. - Li C. Xue; João P. G. L. M. Rodrigues; Drena Dobbs; Vasant G. Honavar; Alexandre M. J. J. Bonvin (Briefings Bioinform., 2017)

The Gene Sculpt Suite: a set of tools for genome editing. - Carla M. Mann; Gabriel Martínez-Gálvez; Jordan M. Welker; Wesley A. Wierson; Hirotaka Ata; Maira P. Almeida; Karl J. Clark; Jeffrey J. Essner; Maura McGrail; Stephen C. Ekker; Drena Dobbs (Nucleic Acids Res., 2019)