Sen, Taner Person

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- A uniform gene and chromosome nomenclature system for oat (Avena spp.). Crop & Pasture Science. 2024
- Harnessing the predicted maize pan-interactome for putative gene function prediction and prioritization of candidate genes for important traits. G3: Genes, Genomes, Genetics. 2024
- One hundred years of comparative genetic and physical mapping in cultivated oat (Avena sativa). Crop & Pasture Science. 2024
- PhosBoost: Improved phosphorylation prediction recall using gradient boosting and protein language models. Plant Direct. 2023
- Updated guidelines for gene nomenclature in wheat.. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2023
- Capturing Wheat Phenotypes at the Genome Level.. Frontiers in Plant Science. 2022
- Co-expression pan-network reveals genes involved in complex traits within maize pan-genome.. BMC Plant Biology. 2022
- Experimental and computational studies of cellulases as bioethanol enzymes. Bioengineered. 2022
- G4Boost: a machine learning-based tool for quadruplex identification and stability prediction.. BMC Bioinformatics. 2022
- GrainGenes: Tools and Content to Assist Breeders Improving Oat Quality. Foods. 2022
- GrainGenes: a data-rich repository for small grains genetics and genomics.. Database : the journal of biological databases and curation. 2022
- FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences.. BMC Bioinformatics. 2021
- Genome-wide discovery of G-quadruplexes in barley.. Scientific Reports. 2021
- LncMachine: a machine learning algorithm for long noncoding RNA annotation in plants. Functional & Integrative Genomics. 2021
- Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing. International Journal of Molecular Sciences. 2021
- mirMachine: A One-Stop Shop for Plant miRNA Annotation.. Journal of visualized experiments : JoVE. 2021
- Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS). F1000Research. 9:536. 2020
- Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles.. G3: Genes, Genomes, Genetics. 10:2021-2032. 2020
- Building a successful international research community through data sharing. F1000Research. 2020
- Genome-Wide Discovery of G-Quadruplexes in Wheat: Distribution and Putative Functional Roles. G3: Genes|Genomes|Genetics. 2020
- JBrowse Connect: A server API to connect JBrowse instances and users. PLOS Computational Biology. 2020
- Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize. BMC Plant Biology. 2020
- The Plant Trait Ontology Links Wheat Traits for Crop Improvement and Genomics (short paper). 2020
- GrainGenes: centralized small grain resources and digital platform for geneticists and breeders.. Database : the journal of biological databases and curation. 2019
- MaizeGDB 2018: the maize multi-genome genetics and genomics database. Nucleic Acids Research. 2019
- PedigreeNet: a web-based pedigree viewer for biological databases. Bioinformatics (Oxford, England). 2019
- Structural dynamics of lytic polysaccharide monoxygenases reveals a highly flexible substrate binding region. Journal of Molecular Graphics and Modelling. 2019
- AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database. 2018
- Application of Molecular Simulations Toward Understanding Cellulase Mechanisms. Bioenergy Research. 2018
- SNPversity: A web-based tool for visualizing diversity. Database. 2018
- Predicting Protein Secondary Structure Using Consensus Data Mining (CDM) Based on Empirical Statistics and Evolutionary Information.. Methods in Molecular Biology. 2017
- Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation. Database : the journal of biological databases and curation. 2017
- The art of curation at a biological database: Principles and application. Current Plant Biology. 2017
- A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence.. Frontiers in Plant Science. 2016
- MaizeGDB update: New tools, data and interface for the maize model organism database. Nucleic Acids Research. 2016
- The quality of metabolic pathway resources depends on initial enzymatic function assignments: A case for maize. BMC Systems Biology. 2016
- A computational platform to maintain and migrate manual functional annotations for BioCyc databases. BMC Systems Biology. 2014
- An adaptable pentaloop defines a robust neomycin-B RNA aptamer with conditional ligand-bound structures. RNA. 2014
- Sampling errors: Aristotle's suspect statistical skills. Nature. 2014
- Endoglucanases: Insights into thermostability for biofuel applications. Biotechnology for Biofuels. 2013
- Maize metabolic network construction and transcriptome analysis. Plant Genome. 2013
- Predicting the Binding Patterns of Hub Proteins: A Study Using Yeast Protein Interaction Networks. PLOS ONE. 2013
- A rigid network of long-range contacts increases thermostability in a mutant endoglucanase. Journal of Biomolecular Structure & Dynamics. 2012
- Molecular simulation of fibronectin adsorption onto polyurethane surfaces. Langmuir. 2012
- Dynamics of endoglucanase catalytic domains: Implications towards thermostability. Journal of Biomolecular Structure & Dynamics. 2011
- MaizeGDB: Curation and outreach go hand-in-hand. Database. 2011
- POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data.. International Journal of Plant Genomics. 2011
- The MaizeGDB Genome Browser tutorial: One example of database outreach to biologists via video. Database. 2011
- Thermostability in endoglucanases is fold-specific. BMC Structural Biology. 2011
- An international bioinformatics infrastructure to underpin the Arabidopsis community. 2010
- Choosing a genome browser for a Model Organism Database: surveying the maize community.. Database : the journal of biological databases and curation. 2010
- The Locus Lookup tool at MaizeGDB: Identification of genomic regions in maize by integrating sequence information with physical and genetic maps 2010
- MaizeGDB becomes 'sequence-centric'. Database. 2009
- MaizeGDB: The maize model organism database for basic, translational, and applied research. 2008
- Predicting the complex structure and functional motions of the outer membrane transporter and signal transducer FecA. Biophysical Journal. 2008
- Predicting the order in which contacts are broken during single molecule protein stretching experiments. Proteins: Structure, Function and Genetics. 2008
- The ribosome structure controls and directs mRNA entry, translocation and exit dynamics. Physical Biology. 2008
- Consensus Data Mining (CDM) Protein Secondary Structure Prediction Server: combining GOR V and Fragment Database Mining (FDM). 2007
- Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices. Journal of Chemical Physics. 2007
- 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. Macromolecular Symposia. 2007
- A Consensus Data Mining secondary structure prediction by combining GOR V and Fragment Database Mining.. Protein Science. 2006
- A DNA-Centric Look at Protein-DNA Complexes. Structure. 2006
- Filler-induced deformations of amorphous polyethylene chains. the effects of the deformations on elastomeric properties, and some comparisons with experiments. European Polymer Journal. 2006
- Functional clustering of yeast proteins from the protein-protein interaction network. BMC Bioinformatics. 2006
- Molecular modeling of matrix chain deformation in nanofiber filled composites. Colloid and Polymer Science. 2006
- The Extent of Cooperativity of Protein Motions Observed with Elastic Network Models Is Similar for Atomic and Coarser-Grained Models.. Journal of Chemical Theory and Computation. 2006
- GOR V server for protein secondary structure prediction 2005
- Modeling the elastomeric properties of stereoregular polypropylenes in nanocomposites with spherical fillers 2005
- Prediction of protein secondary structure by mining structural fragment database 2005
- Protein promiscuity: Drug resistance and native functions—hiv-1 case. Journal of Biomolecular Structure & Dynamics. 2005
- Some simulations on filler reinforcement in elastomers 2005
- The largest eigenvalue method for stereo-regular vinyl chains 2005
- A Minimal Model for the Helix−Coil Transition of Wormlike Polymers. Insights from Monte Carlo Simulations and Theoretical Implications 2004
- Predicting binding sites of hydrolase-inhibitor complexes by combining several methods. BMC Bioinformatics. 2004
- The transfer matrix method for lattice proteins - An application with cooperative interactions 2004
- The effect of natural rubber crosslink density on real time birefringence, true stress and true strain behavior. Macromolecular Symposia. 2002
- Modeling the deamidation of asparagine residues via succinimide intermediates. Journal of Molecular Modeling. 2001
- Local dynamics of cis-1,4-polybutadiene and cis-1,4-polyisoprene. A comparative study based on cooperative kinematics theory and NMR experiments 1999
book
chapter
- Wheat Data Integration and FAIRification: IWGSC, GrainGenes, Ensembl and Other Data Repositories. The Barley Genome. 2024
abstract
- GRAINGENES: VISUALIZATION, TOOLS, AND RESOURCES FOR WHEAT 2019
- WHEAT INFORMATION SYSTEM (WHEATIS): STANDARDIZED DATA DISCOVERY THROUGH A SINGLE PORTAL 2019
document