List of works - Drena Dobbs

A Plasmodium-like virulence effector of the soybean cyst nematode suppresses plant innate immunity

scientific article published on 6 June 2016

A proteomic analysis of maize chloroplast biogenesis

scientific article published in February 2004

A two-stage classifier for identification of protein-protein interface residues

scientific article published in August 2004

An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins.

scientific article published on 04 December 2008

An analysis of conformational changes upon RNA-protein binding

article

Analysis of the EIAV Rev-responsive element (RRE) reveals a conserved RNA motif required for high affinity Rev binding in both HIV-1 and EIAV

scientific article

Assessing the Performance of Macromolecular Sequence Classifiers

scholarly article published October 2007

Automated data-driven discovery of motif-based protein function classifiers

article

Characterization of functional domains of equine infectious anemia virus Rev suggests a bipartite RNA-binding domain

scientific article

Characterization of protein-protein interfaces

scientific article

Computational Prediction of RNA-Protein Interactions.

scientific article published in January 2017

Computational modeling suggests dimerization of equine infectious anemia virus Rev is required for RNA binding.

scientific article

Computational prediction of protein interfaces: A review of data driven methods

scientific article

Data-Driven Theory Refinement Using KBDistAl

DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction

scientific article (publication date: 17 October 2013)

Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach

scientific article (publication date: 2007)

G-quadruplex (G4) motifs in the maize (Zea mays L.) genome are enriched at specific locations in thousands of genes coupled to energy status, hypoxia, low sugar, and nutrient deprivation

scientific article published on 4 November 2014

Glycosylation site prediction using ensembles of Support Vector Machine classifiers

scientific article

HomPPI: a class of sequence homology based protein-protein interface prediction methods

scientific article

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.

scientific article

Identification and characterization of a putative telomere end-binding protein from Tetrahymena thermophila.

scientific article published on March 1995

Identification of a homogenous structural basis for oligomerization by retroviral Rev-like proteins.

scientific article

Identification of interface residues in protease-inhibitor and antigen-antibody complexes: a support vector machine approach

scientific article

Improving protein-RNA interface prediction by combining sequence homology based method with a naive Bayes classifier

In Silico Prediction of Linear B-Cell Epitopes on Proteins

scientific article published in January 2017

Information Integration from Semantically Heterogeneous Biological Data Sources

article published in 2005

Mimosine Differentially Inhibits DNA Replication and Cell Cycle Progression in Somatic Cells Compared to Embryonic Cells of Xenopus laevis

scientific article published on 01 March 1995

Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling

scientific article (publication date: 2009)

On Evaluating MHC-II Binding Peptide Prediction Methods

scientific article (publication date: 24 September 2008)

PRIDB: a Protein-RNA interface database

scientific article

Partner‐specific Prediction of RNA‐binding Residues in Proteins: A Critical Assessment

scientific article published on 30 December 2018

Predicting DNA-binding sites of proteins from amino acid sequence

scientific article

Predicting MHC-II binding affinity using multiple instance regression

scientific article

Predicting Protective Linear B-Cell Epitopes Using Evolutionary Information

Predicting RNA-protein interactions using only sequence information

scientific article

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods

scientific article

Predicting flexible length linear B-cell epitopes.

scientific article

Predicting linear B-cell epitopes using string kernels

scientific article published on July 2008

Predicting protective bacterial antigens using random forest classifiers

Predicting protein-protein interface residues using local surface structural similarity

scientific article (publication date: 2012)

Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences ⬇️

scientific article published on November 2, 2010

Prediction of RNA binding sites in proteins from amino acid sequence

scientific article

Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art

scientific article

Proteomic differentiation between murine retinal and brain-derived progenitor cells.

scientific article published in February 2008

RNABindR: a server for analyzing and predicting RNA-binding sites in proteins

scientific article (publication date: 8 May 2007)

RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins

scientific article (publication date: 2014)

Ranking Docked Models of Protein-Protein Complexes Using Predicted Partner-Specific Protein-Protein Interfaces: A Preliminary Study

Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification

scientific article

Robust activation of microhomology-mediated end joining for precision gene editing applications

article

Sequence-Based Prediction of RNA-Binding Residues in Proteins.

scientific article published in January 2017

Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly.

scientific article

Struct-NB: predicting protein-RNA binding sites using structural features

scientific article

Structural characterization of RNA-binding sites of proteins: Preliminary results

Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases

scientific article

Template-based protein-protein docking exploiting pairwise interfacial residue restraints

scientific article

Using Global Sequence Similarity to Enhance Biological Sequence Labeling

Visualization of Nucleosomal Substructure in Native Chromatin by Atomic Force Microscopy

scientific article published on 01 April 1995

ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms.

scientific article

Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool.

scientific article

List of works by Drena Dobbs

A Plasmodium-like virulence effector of the soybean cyst nematode suppresses plant innate immunity

A proteomic analysis of maize chloroplast biogenesis

A two-stage classifier for identification of protein-protein interface residues

An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins.

An analysis of conformational changes upon RNA-protein binding

Analysis of the EIAV Rev-responsive element (RRE) reveals a conserved RNA motif required for high affinity Rev binding in both HIV-1 and EIAV

Assessing the Performance of Macromolecular Sequence Classifiers

Automated data-driven discovery of motif-based protein function classifiers

Characterization of functional domains of equine infectious anemia virus Rev suggests a bipartite RNA-binding domain

Characterization of protein-protein interfaces

Computational Prediction of RNA-Protein Interactions.

Computational modeling suggests dimerization of equine infectious anemia virus Rev is required for RNA binding.

Computational prediction of protein interfaces: A review of data driven methods

Data-Driven Theory Refinement Using KBDistAl

DockRank: Ranking docked conformations using partner-specific sequence homology-based protein interface prediction

Exploring inconsistencies in genome-wide protein function annotations: a machine learning approach

G-quadruplex (G4) motifs in the maize (Zea mays L.) genome are enriched at specific locations in thousands of genes coupled to energy status, hypoxia, low sugar, and nutrient deprivation

Glycosylation site prediction using ensembles of Support Vector Machine classifiers

HomPPI: a class of sequence homology based protein-protein interface prediction methods

Human telomerase model shows the role of the TEN domain in advancing the double helix for the next polymerization step.

Identification and characterization of a putative telomere end-binding protein from Tetrahymena thermophila.

Identification of a homogenous structural basis for oligomerization by retroviral Rev-like proteins.

Identification of interface residues in protease-inhibitor and antigen-antibody complexes: a support vector machine approach

Improving protein-RNA interface prediction by combining sequence homology based method with a naive Bayes classifier

In Silico Prediction of Linear B-Cell Epitopes on Proteins

Information Integration from Semantically Heterogeneous Biological Data Sources

Mimosine Differentially Inhibits DNA Replication and Cell Cycle Progression in Somatic Cells Compared to Embryonic Cells of Xenopus laevis

Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling

On Evaluating MHC-II Binding Peptide Prediction Methods

PRIDB: a Protein-RNA interface database

Partner‐specific Prediction of RNA‐binding Residues in Proteins: A Critical Assessment

Predicting DNA-binding sites of proteins from amino acid sequence

Predicting MHC-II binding affinity using multiple instance regression

Predicting Protective Linear B-Cell Epitopes Using Evolutionary Information

Predicting RNA-protein interactions using only sequence information

Predicting binding sites of hydrolase-inhibitor complexes by combining several methods

Predicting flexible length linear B-cell epitopes.

Predicting linear B-cell epitopes using string kernels

Predicting protective bacterial antigens using random forest classifiers

Predicting protein-protein interface residues using local surface structural similarity

Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences ⬇️

Prediction of RNA binding sites in proteins from amino acid sequence

Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art

Proteomic differentiation between murine retinal and brain-derived progenitor cells.

RNABindR: a server for analyzing and predicting RNA-binding sites in proteins

RNABindRPlus: a predictor that combines machine learning and sequence homology-based methods to improve the reliability of predicted RNA-binding residues in proteins

Ranking Docked Models of Protein-Protein Complexes Using Predicted Partner-Specific Protein-Protein Interfaces: A Preliminary Study

Rapid "open-source" engineering of customized zinc-finger nucleases for highly efficient gene modification

Robust activation of microhomology-mediated end joining for precision gene editing applications

Sequence-Based Prediction of RNA-Binding Residues in Proteins.

Standardized reagents and protocols for engineering zinc finger nucleases by modular assembly.

Struct-NB: predicting protein-RNA binding sites using structural features

Structural characterization of RNA-binding sites of proteins: Preliminary results

Targeted mutagenesis of duplicated genes in soybean with zinc-finger nucleases

Template-based protein-protein docking exploiting pairwise interfacial residue restraints

Using Global Sequence Similarity to Enhance Biological Sequence Labeling

Visualization of Nucleosomal Substructure in Native Chromatin by Atomic Force Microscopy

ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms.

Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool.