Drena Dobbs

41 papers B 2C 1Misc 3Journal 23Unranked 12
YearRankTypeTitle / Venue / Authors
2019 J jnl
The Gene Sculpt Suite: a set of tools for genome editing.
Nucleic Acids Res.
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
2017 J jnl
Template-based protein-protein docking exploiting pairwise interfacial residue restraints.
Briefings Bioinform.
Li C. Xue, João P. G. L. M. Rodrigues, Drena Dobbs, Vasant G. Honavar, Alexandre M. J. J. Bonvin
2016 Misc conf
A Motif-Based Method for Predicting Interfacial Residues in Both the RNA and Protein Components of Protein-RNA Complexes.
PSB
Usha Muppirala, Benjamin A. Lewis, Carla M. Mann, Drena Dobbs
2016 Misc conf
Session Introduction.
PSB
Drena Dobbs, Steven E. Brenner, Vasant G. Honavar, Robert L. Jernigan, Alain Laederach, Quaid Morris
2014 — conf
An analysis of conformational changes upon RNA-protein binding.
BCB
Kannan Sankar, Rasna R. Walia, Carla M. Mann, Robert L. Jernigan, Vasant G. Honavar, Drena Dobbs
2012 — conf
Predicting protective bacterial antigens using random forest classifiers.
BCB
Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
2012 J jnl
Predicting protein-protein interface residues using local surface structural similarity.
BMC Bioinform.
Rafael A. Jordan, Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
2012 J jnl
Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art.
BMC Bioinform.
Rasna R. Walia, Cornelia Caragea, Benjamin A. Lewis, Fadi Towfic, Michael Terribilini, Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
2011 J jnl
HomPPI: A Class of Sequence Homology Based Protein-Protein Interface Prediction Methods.
BMC Bioinform.
Li C. Xue, Drena Dobbs, Vasant G. Honavar
2011 — conf
Improving protein-RNA interface prediction by combining sequence homology based method with a naive Bayes classifier: preliminary results.
BCB
Li C. Xue, Rasna R. Walia, Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
2011 J jnl
PRIDB: a protein-RNA interface database.
Nucleic Acids Res.
Benjamin A. Lewis, Rasna R. Walia, Michael Terribilini, Jeff Ferguson, Charles Zheng, Vasant G. Honavar, Drena Dobbs
2011 J jnl
Predicting MHC-II Binding Affinity Using Multiple Instance Regression.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
2011 J jnl
Predicting RNA-Protein Interactions Using Only Sequence Information.
BMC Bioinform.
Usha Muppirala, Vasant G. Honavar, Drena Dobbs
2011 — conf
Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary study.
BCB
Li C. Xue, Rafael A. Jordan, Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
2010 J jnl
Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences.
BMC Bioinform.
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
2010 J jnl
Struct-NB: predicting protein-RNA binding sites using structural features.
Int. J. Data Min. Bioinform.
Fadi Towfic, Cornelia Caragea, David C. Gemperline, Drena Dobbs, Vasant G. Honavar
2010 J jnl
ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool.
Nucleic Acids Res.
Jeffry D. Sander, Morgan L. Maeder, Deepak Reyon, Daniel F. Voytas, J. Keith Joung, Drena Dobbs
2009 J jnl
Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling.
BMC Bioinform.
Cornelia Caragea, Jivko Sinapov, Drena Dobbs, Vasant G. Honavar
2009 J jnl
Zinc Finger Database (ZiFDB): a repository for information on C2H2 zinc fingers and engineered zinc-finger arrays.
Nucleic Acids Res.
Fengli Fu, Jeffry D. Sander, Morgan L. Maeder, Stacey Thibodeau-Beganny, J. Keith Joung, Drena Dobbs, Leslie L. Miller, Daniel F. Voytas
2008 — conf
Predicting Protective Linear B-Cell Epitopes Using Evolutionary Information.
BIBM
Yasser El-Manzalawy, Drena Dobbs, Vasant G. Honavar
2008 Misc conf
Striking Similarities in Diverse Telomerase Proteins Revealed by Combining Structure Prediction and Machine Learning Approaches.
Pacific Symposium on Biocomputing
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
2008 — conf
Using Global Sequence Similarity to Enhance Biological Sequence Labeling.
BIBM
Cornelia Caragea, Jivko Sinapov, Drena Dobbs, Vasant G. Honavar
2007 — conf
Analysis of Protein Protein Dimeric Interfaces.
BIBM
Feihong Wu, Fadi Towfic, Drena Dobbs, Vasant G. Honavar
2007 C conf
Assessing the Performance of Macromolecular Sequence Classifiers.
BIBE
Cornelia Caragea, Jivko Sinapov, Vasant G. Honavar, Drena Dobbs
2007 J jnl
Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach.
BMC Bioinform.
Carson M. Andorf, Drena Dobbs, Vasant G. Honavar
2007 J jnl
Glycosylation site prediction using ensembles of Support Vector Machine classifiers.
BMC Bioinform.
Cornelia Caragea, Jivko Sinapov, Adrian Silvescu, Drena Dobbs, Vasant G. Honavar
2007 J jnl
RNABindR: a server for analyzing and predicting RNA-binding sites in proteins.
Nucleic Acids Res.
Michael Terribilini, Jeffry D. Sander, Jae-Hyung Lee, Peter Zaback, Robert L. Jernigan, Vasant G. Honavar, Drena Dobbs
2007 J jnl
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool.
Nucleic Acids Res.
Jeffry D. Sander, Peter Zaback, J. Keith Joung, Daniel F. Voytas, Drena Dobbs
2006 J jnl
Predicting DNA-binding sites of proteins from amino acid sequence.
BMC Bioinform.
Changhui Yan, Michael Terribilini, Feihong Wu, Robert L. Jernigan, Drena Dobbs, Vasant G. Honavar
2005 J jnl
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
Michael Terribilini, Jae-Hyung Lee, Changhui Yan, Robert L. Jernigan, Susan Carpenter, Vasant G. Honavar, Drena Dobbs
2005 — conf
Information Integration and Knowledge Acquisition from Semantically Heterogeneous Biological Data Sources.
DILS
Doina Caragea, Jyotishman Pathak, Jie Bao, Adrian Silvescu, Carson M. Andorf, Drena Dobbs, Vasant G. Honavar
2005 — conf
Information Integration from Semantically Heterogeneous Biological Data Sources.
DEXA Workshops
Doina Caragea, Jie Bao, Jyotishman Pathak, Adrian Silvescu, Carson M. Andorf, Drena Dobbs, Vasant G. Honavar
2004 — conf
A two-stage classifier for identification of protein-protein interface residues.
ISMB/ECCB (Supplement of Bioinformatics)
Changhui Yan, Drena Dobbs, Vasant G. Honavar
2004 J jnl
Identification of interface residues in protease-inhibitor and antigen-antibody complexes: a support vector machine approach.
Neural Comput. Appl.
Changhui Yan, Vasant G. Honavar, Drena Dobbs
2004 J jnl
Predicting binding sites of hydrolase-inhibitor complexes by combining several methods.
BMC Bioinform.
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
2003 J jnl
Automated data-driven discovery of motif-based protein function classifiers.
Inf. Sci.
Xiangyun Wang, Diane Schroeder, Drena Dobbs, Vasant G. Honavar
2002 — conf
Data-Driven Discovery of Protein Function Classifiers: Decision Trees Based on MEME Motifs outperform PROSITE Patterns and Profiles on Peptidase Families.
JCIS
Xiangyun Wang, Diane Schroeder, Drena Dobbs, Vasant G. Honavar
2002 — conf
Discovering Protein Function Classification Rules from Reduced Alphabet Representations of Protein Sequences.
JCIS
Carson M. Andorf, Drena Dobbs, Vasant G. Honavar
1999 B conf
Data-Driven Theory Refinement Using
IDA
Jihoon Yang, Rajesh Parekh, Vasant G. Honavar, Drena Dobbs
1999 B conf
Data-driven theory refinement algorithms for bioinformatics.
IJCNN
Jihoon Yang, Rajesh Parekh, Vasant G. Honavar, Drena Dobbs
1994 J jnl
Modular sequence elements associated with origin regions in eukaryotic chromosomal DNA.
Nucleic Acids Res.
Drena Dobbs, Wen-Ling Shaiu, Robert M. Benbow