Drena Dobbs

Publication Activity (10 Years)

Years Active: 1994-2019
Publications (10 Years): 4

Top Topics

Predicting Protein

Structural Motifs

Top Venues

Briefings Bioinform.

Publications

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
The Gene Sculpt Suite: a set of tools for genome editing. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Li C. Xue, João P. G. L. M. Rodrigues, Drena Dobbs, Vasant G. Honavar, Alexandre M. J. J. Bonvin
Template-based protein-protein docking exploiting pairwise interfacial residue restraints. Briefings Bioinform. 18 (3) (2017)
Usha Muppirala, Benjamin A. Lewis, Carla M. Mann, Drena Dobbs
A Motif-Based Method for Predicting Interfacial Residues in Both the RNA and Protein Components of Protein-RNA Complexes. PSB (2016)
Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris
Session Introduction. PSB (2016)
Kannan Sankar, Rasna R. Walia, Carla M. Mann, Robert L. Jernigan, Vasant G. Honavar, Drena Dobbs
An analysis of conformational changes upon RNA-protein binding. BCB (2014)
Rasna R. Walia, Cornelia Caragea, Benjamin A. Lewis, Fadi Towfic, Michael Terribilini, Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. BMC Bioinform. 13 (2012)
Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
Predicting protective bacterial antigens using random forest classifiers. BCB (2012)
Rafael A. Jordan, Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
Predicting protein-protein interface residues using local surface structural similarity. BMC Bioinform. 13 (2012)
Usha Muppirala, Vasant G. Honavar, Drena Dobbs
Predicting RNA-Protein Interactions Using Only Sequence Information. BMC Bioinform. 12 (2011)
Li C. Xue, Rafael A. Jordan, Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary study. BCB (2011)
Li C. Xue, Rasna R. Walia, Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
Improving protein-RNA interface prediction by combining sequence homology based method with a naive Bayes classifier: preliminary results. BCB (2011)
Li C. Xue, Drena Dobbs, Vasant G. Honavar
HomPPI: A Class of Sequence Homology Based Protein-Protein Interface Prediction Methods. BMC Bioinform. 12 (2011)
Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
Predicting MHC-II Binding Affinity Using Multiple Instance Regression. IEEE ACM Trans. Comput. Biol. Bioinform. 8 (4) (2011)
Benjamin A. Lewis, Rasna R. Walia, Michael Terribilini, Jeff Ferguson, Charles Zheng, Vasant G. Honavar, Drena Dobbs
PRIDB: a protein-RNA interface database. Nucleic Acids Res. 39 (Database-Issue) (2011)
Jeffry D. Sander, Morgan L. Maeder, Deepak Reyon, Daniel F. Voytas, J. Keith Joung, Drena Dobbs
ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)
Fadi Towfic, Cornelia Caragea, David C. Gemperline, Drena Dobbs, Vasant G. Honavar
Struct-NB: predicting protein-RNA binding sites using structural features. Int. J. Data Min. Bioinform. 4 (1) (2010)
Jeffry D. Sander, Deepak Reyon, Morgan L. Maeder, Jonathan E. Foley, Stacey Thibodeau-Beganny, Xiaohong Li, Maureen R. Regan, Elizabeth Dahlborg, Mathew J. Goodwin, Fengli Fu, Daniel F. Voytas, J. Keith Joung, Drena Dobbs
Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences. BMC Bioinform. 11 (2010)
Fengli Fu, Jeffry D. Sander, Morgan L. Maeder, Stacey Thibodeau-Beganny, J. Keith Joung, Drena Dobbs, Leslie L. Miller, Daniel F. Voytas
Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays. Nucleic Acids Res. 37 (Database-Issue) (2009)
Cornelia Caragea, Jivko Sinapov, Drena Dobbs, Vasant G. Honavar
Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling. BMC Bioinform. 10 (S-4) (2009)
Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
Predicting Protective Linear B-Cell Epitopes Using Evolutionary Information. BIBM (2008)
Cornelia Caragea, Jivko Sinapov, Drena Dobbs, Vasant G. Honavar
Using Global Sequence Similarity to Enhance Biological Sequence Labeling. BIBM (2008)
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
Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches. Pacific Symposium on Biocomputing (2008)
Cornelia Caragea, Jivko Sinapov, Vasant G. Honavar, Drena Dobbs
Assessing the Performance of Macromolecular Sequence Classifiers. BIBE (2007)
Cornelia Caragea, Jivko Sinapov, Adrian Silvescu, Drena Dobbs, Vasant G. Honavar
Glycosylation site prediction using ensembles of Support Vector Machine classifiers. BMC Bioinform. 8 (2007)
Michael Terribilini, Jeffry D. Sander, Jae-Hyung Lee, Peter Zaback, Robert L. Jernigan, Vasant G. Honavar, Drena Dobbs
RNABindR: a server for analyzing and predicting RNA-binding sites in proteins. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Carson M. Andorf, Drena Dobbs, Vasant G. Honavar
Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach. BMC Bioinform. 8 (2007)
Jeffry D. Sander, Peter Zaback, J. Keith Joung, Daniel F. Voytas, Drena Dobbs
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Feihong Wu, Fadi Towfic, Drena Dobbs, Vasant G. Honavar
Analysis of Protein Protein Dimeric Interfaces. BIBM (2007)
Changhui Yan, Michael Terribilini, Feihong Wu, Robert L. Jernigan, Drena Dobbs, Vasant G. Honavar
Predicting DNA-binding sites of proteins from amino acid sequence. BMC Bioinform. 7 (2006)
Michael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, Susan Carpenter, Vasant G. Honavar, Drena Dobbs
Identifying Interaction Sites in "Recalcitrant" Proteins: Predicted Protein and Rna Binding Sites in Rev Proteins of Hiv-1 and Eiav Agree with Experimental Data CoRR (2005)
Doina Caragea, Jyotishman Pathak, Jie Bao, Adrian Silvescu, Carson M. Andorf, Drena Dobbs, Vasant G. Honavar
Information Integration and Knowledge Acquisition from Semantically Heterogeneous Biological Data Sources. DILS (2005)
Doina Caragea, Jie Bao, Jyotishman Pathak, Adrian Silvescu, Carson M. Andorf, Drena Dobbs, Vasant G. Honavar
Information Integration from Semantically Heterogeneous Biological Data Sources. DEXA Workshops (2005)
Changhui Yan, Vasant G. Honavar, Drena Dobbs
Identification of interface residues in protease-inhibitor and antigen-antibody complexes: a support vector machine approach. Neural Comput. Appl. 13 (2) (2004)
Changhui Yan, Drena Dobbs, Vasant G. Honavar
A two-stage classifier for identification of protein-protein interface residues. ISMB/ECCB (Supplement of Bioinformatics) (2004)
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
Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. BMC Bioinform. 5 (2004)
Xiangyun Wang, Diane Schroeder, Drena Dobbs, Vasant G. Honavar
Automated data-driven discovery of motif-based protein function classifiers. Inf. Sci. 155 (1-2) (2003)
Xiangyun Wang, Diane Schroeder, Drena Dobbs, Vasant G. Honavar
Data-Driven Discovery of Protein Function Classifiers: Decision Trees Based on MEME Motifs outperform PROSITE Patterns and Profiles on Peptidase Families. JCIS (2002)
Carson M. Andorf, Drena Dobbs, Vasant G. Honavar
Discovering Protein Function Classification Rules from Reduced Alphabet Representations of Protein Sequences. JCIS (2002)
Jihoon Yang, Rajesh Parekh, Vasant G. Honavar, Drena Dobbs
. IDA (1999)
Jihoon Yang, Rajesh Parekh, Vasant G. Honavar, Drena Dobbs
Data-driven theory refinement algorithms for bioinformatics. IJCNN (1999)
Drena Dobbs, Wen-Ling Shaiu, Robert M. Benbow
Modular sequence elements associated with origin regions in eukaryotic chromosomal DNA. Nucleic Acids Res. 22 (13) (1994)