Sen, Taner Person

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- Delivering AI-Ready Genomics with MaizeGDB. Genetics. 2026
- Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data. Database. 2025
- Chromosome-level haplotype-resolved genome assembly of bread wheat's wild relative Aegilops mutica.. Scientific Data. 2025
- Oregon Wolfe barley genetic stocks – Research and teaching tools for next generation scientists. Journal of Plant Registrations. 2025
- Structural Variability of Pfam Domains Based on Alphafold2 Predictions. Proteins: Structure, Function, and Bioinformatics. 2025
- A uniform gene and chromosome nomenclature system for oat (Avena spp.). Crop & Pasture Science. 2024
- Chromosome-scale genome assembly of bread wheat's wild relative Triticum timopheevii.. Scientific Data. 2024
- Genome-wide association studies on resistance to powdery mildew in cultivated emmer wheat.. The Plant Genome. 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
- Fusarium Protein Toolkit: a web-based resource for structural and variant analysis of Fusarium species.. BMC Microbiology. 2024
- PhosBoost: Improved phosphorylation prediction recall using gradient boosting and protein language models. Plant direct. 2023
- Updated guidelines for gene nomenclature in wheat.. Theoretical and Applied Genetics. 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
- Predicting Tissue-Specific mRNA and Protein Abundance in Maize: A Machine Learning Approach.. Frontiers in artificial intelligence. 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. 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: The case of the Wheat Information System (WheatIS). 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. 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. The 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.. The Plant Cell. 2010
- Choosing a genome browser for a Model Organism Database: surveying the Maize community. Database: The Journal of Biological Databases and Curation.. 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.. Bioinformatics. 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). Bioinformatics. 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 DNA-centric look at protein-DNA complexes.. Structure. 2006
- A consensus data mining secondary structure prediction by combining GOR V and Fragment Database Mining. Protein Science. 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.. Bioinformatics. 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
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- Wheat Data Integration and FAIRification: IWGSC, GrainGenes, Ensembl and Other Data Repositories. The Barley Genome. 2024
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