List of works - Taner Z Sen

A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence

scientific article

A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining

scientific article

A DNA-Centric Look at Protein-DNA Complexes

article

A Minimal Model for the Helix−Coil Transition of Wormlike Polymers. Insights from Monte Carlo Simulations and Theoretical Implications

article

A computational platform to maintain and migrate manual functional annotations for BioCyc databases

scientific article

A rigid network of long-range contacts increases thermostability in a mutant endoglucanase

scientific article

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

article

An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures

scientific article published on 22 April 2014

Application of Molecular Simulations Toward Understanding Cellulase Mechanisms

Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS)

Capturing Wheat Phenotypes at the Genome Level

scientific article published in 2022

Choosing a genome browser for a Model Organism Database: surveying the maize community.

scientific article

Co-expression pan-network reveals genes involved in complex traits within maize pan-genome

scientific article published in 2022

Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: combining GOR V and Fragment Database Mining (FDM)

scientific article

Data Mining for Protein Secondary Structure Prediction

Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium

scientific article published on 15 November 2023

Dynamics of Endoglucanase Catalytic Domains: Implications Towards Thermostability

article

Endoglucanases: insights into thermostability for biofuel applications

scientific article (publication date: 27 September 2013)

Experimental and computational studies of cellulases as bioethanol enzymes

FASSO: An AlphaFold based method to assign functional annotations by combining sequence and structure orthology

FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

scientific article published on 20 April 2021

Filler-induced deformations of amorphous polyethylene chains. The effects of the deformations on elastomeric properties, and some comparisons with experiments

Functional clustering of yeast proteins from the protein-protein interaction network

scientific article

G4Boost: a machine learning-based tool for quadruplex identification and stability prediction

scientific article published on 01 January 2022

GOR V server for protein secondary structure prediction

scientific article

Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices

article

Genome-Wide Discovery of G-quadruplexes in Wheat: Distribution and Putative Functional Roles

scientific article published on 15 April 2020

Genome-wide discovery of G-quadruplexes in barley

scientific article published on 12 April 2021

GrainGenes: Tools and Content to Assist Breeders Improving Oat Quality

GrainGenes: a data-rich repository for small grains genetics and genomics

GrainGenes: centralized small grain resources and digital platform for geneticists and breeders.

scientific article

JBrowse Connect: A server API to connect JBrowse instances and users

scientific article published on 18 August 2020

JBrowse Connect: A server API to connect JBrowse instances and users

LncMachine: a machine learning algorithm for long noncoding RNA annotation in plants

Maize Metabolic Network Construction and Transcriptome Analysis

MaizeGDB 2018: the maize multi-genome genetics and genomics database

article

MaizeGDB becomes 'sequence-centric'

scientific article

MaizeGDB update: new tools, data and interface for the maize model organism database

scientific article

MaizeGDB: The maize model organism database for basic, translational, and applied research

scientific article published on January 2008

MaizeGDB: curation and outreach go hand-in-hand ⬇️

scientific article

Modeling the deamidation of asparagine residues via succinimide intermediates

Modeling the elastomeric properties of stereoregular polypropylenes in nanocomposites with spherical fillers

Molecular Simulation of Fibronectin Adsorption onto Polyurethane Surfaces

scientific article published on 16 August 2012

Molecular modeling of matrix chain deformation in nanofiber filled composites

Monte Carlo Simulations on Nanoparticles in Elastomers. Effects of the Particles on the Dimensions of the Polymer Chains and the Mechanical Properties of the Networks

Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing

scientific article published in 2021

POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data

scientific article

PedigreeNet: a web-based pedigree viewer for biological databases

scientific article published on 01 October 2019

Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information

scientific article

Predicting Tissue-Specific mRNA and Protein Abundance in Maize: A Machine Learning Approach

scientific article published on 01 January 2022

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

scientific article

Predicting the Binding Patterns of Hub Proteins: A Study Using Yeast Protein Interaction Networks ⬇️

scientific article published on February 19, 2013

Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA.

scientific article published on 4 January 2008

Predicting the order in which contacts are broken during single molecule protein stretching experiments

scientific article

Prediction of protein secondary structure by mining structural fragment database

scientific article published on May 2005

Protein promiscuity: drug resistance and native functions--HIV-1 case

scientific article published in June 2005

SNPversity: a web-based tool for visualizing diversity.

scientific article published in January 2018

Sampling errors: Aristotle's suspect statistical skills

scientific article

Some simulations on filler reinforcement in elastomers

Structural dynamics of lytic polysaccharide monoxygenases reveals a highly flexible substrate binding region

scientific article published on 29 December 2018

Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation.

scientific article

The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models

scientific article published on January 2006

The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps

scientific article published in February 2010

The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video

scientific article

The art of curation at a biological database: Principles and application

scientific article published in 2017

The largest eigenvalue method for stereo-regular vinyl chains

The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize.

scientific article

The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

scientific article published on 24 November 2008

The transfer matrix method for lattice proteins—an application with cooperative interactions

Thermostability in endoglucanases is fold-specific

scientific article

Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize

scientific article published on 03 January 2020

List of works by Taner Z Sen

A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence

A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining

A DNA-Centric Look at Protein-DNA Complexes

A Minimal Model for the Helix−Coil Transition of Wormlike Polymers. Insights from Monte Carlo Simulations and Theoretical Implications

A computational platform to maintain and migrate manual functional annotations for BioCyc databases

A rigid network of long-range contacts increases thermostability in a mutant endoglucanase

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures

Application of Molecular Simulations Toward Understanding Cellulase Mechanisms

Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS)

Capturing Wheat Phenotypes at the Genome Level

Choosing a genome browser for a Model Organism Database: surveying the maize community.

Co-expression pan-network reveals genes involved in complex traits within maize pan-genome

Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: combining GOR V and Fragment Database Mining (FDM)

Data Mining for Protein Secondary Structure Prediction

Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium

Dynamics of Endoglucanase Catalytic Domains: Implications Towards Thermostability

Endoglucanases: insights into thermostability for biofuel applications

Experimental and computational studies of cellulases as bioethanol enzymes

FASSO: An AlphaFold based method to assign functional annotations by combining sequence and structure orthology

FINDER: An automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences

Filler-induced deformations of amorphous polyethylene chains. The effects of the deformations on elastomeric properties, and some comparisons with experiments

Functional clustering of yeast proteins from the protein-protein interaction network

G4Boost: a machine learning-based tool for quadruplex identification and stability prediction

GOR V server for protein secondary structure prediction

Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices

Genome-Wide Discovery of G-quadruplexes in Wheat: Distribution and Putative Functional Roles

Genome-wide discovery of G-quadruplexes in barley

GrainGenes: Tools and Content to Assist Breeders Improving Oat Quality

GrainGenes: a data-rich repository for small grains genetics and genomics

GrainGenes: centralized small grain resources and digital platform for geneticists and breeders.

JBrowse Connect: A server API to connect JBrowse instances and users

JBrowse Connect: A server API to connect JBrowse instances and users

LncMachine: a machine learning algorithm for long noncoding RNA annotation in plants

Maize Metabolic Network Construction and Transcriptome Analysis

MaizeGDB 2018: the maize multi-genome genetics and genomics database

MaizeGDB becomes 'sequence-centric'

MaizeGDB update: new tools, data and interface for the maize model organism database

MaizeGDB: The maize model organism database for basic, translational, and applied research

MaizeGDB: curation and outreach go hand-in-hand ⬇️

Modeling the deamidation of asparagine residues via succinimide intermediates

Modeling the elastomeric properties of stereoregular polypropylenes in nanocomposites with spherical fillers

Molecular Simulation of Fibronectin Adsorption onto Polyurethane Surfaces

Molecular modeling of matrix chain deformation in nanofiber filled composites

Monte Carlo Simulations on Nanoparticles in Elastomers. Effects of the Particles on the Dimensions of the Polymer Chains and the Mechanical Properties of the Networks

Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing

POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data

PedigreeNet: a web-based pedigree viewer for biological databases

Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information

Predicting Tissue-Specific mRNA and Protein Abundance in Maize: A Machine Learning Approach

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

Predicting the Binding Patterns of Hub Proteins: A Study Using Yeast Protein Interaction Networks ⬇️

Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA.

Predicting the order in which contacts are broken during single molecule protein stretching experiments

Prediction of protein secondary structure by mining structural fragment database

Protein promiscuity: drug resistance and native functions--HIV-1 case

SNPversity: a web-based tool for visualizing diversity.

Sampling errors: Aristotle's suspect statistical skills

Some simulations on filler reinforcement in elastomers

Structural dynamics of lytic polysaccharide monoxygenases reveals a highly flexible substrate binding region

Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation.

The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models

The Locus Lookup tool at MaizeGDB: identification of genomic regions in maize by integrating sequence information with physical and genetic maps

The MaizeGDB Genome Browser tutorial: one example of database outreach to biologists via video

The art of curation at a biological database: Principles and application

The largest eigenvalue method for stereo-regular vinyl chains

The quality of metabolic pathway resources depends on initial enzymatic function assignments: a case for maize.

The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

The transfer matrix method for lattice proteins—an application with cooperative interactions

Thermostability in endoglucanases is fold-specific

Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize

mirMachine: A One-Stop Shop for Plant miRNA Annotation