Search Results - "Sen, Taner Z."

MaizeGDB 2018: the maize multi-genome genetics and genomics database by Portwood, John L, Woodhouse, Margaret R, Cannon, Ethalinda K, Gardiner, Jack M, Harper, Lisa C, Schaeffer, Mary L, Walsh, Jesse R, Sen, Taner Z, Cho, Kyoung Tak, Schott, David A, Braun, Bremen L, Dietze, Miranda, Dunfee, Brittney, Elsik, Christine G, Manchanda, Nancy, Coe, Ed, Sachs, Marty, Stinard, Philip, Tolbert, Josh, Zimmerman, Shane, Andorf, Carson M

“…Abstract Since its 2015 update, MaizeGDB, the Maize Genetics and Genomics database, has expanded to support the sequenced genomes of many maize inbred lines in…”
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G4Boost: a machine learning-based tool for quadruplex identification and stability prediction by Cagirici, H. Busra, Budak, Hikmet, Sen, Taner Z

“…Abstract Background G-quadruplexes (G4s), formed within guanine-rich nucleic acids, are secondary structures involved in important biological processes…”
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Genome-wide discovery of G-quadruplexes in barley by Cagirici, H. Busra, Budak, Hikmet, Sen, Taner Z.

“…G-quadruplexes (G4s) are four-stranded nucleic acid structures with closely spaced guanine bases forming square planar G-quartets. Aberrant formation of G4…”
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Co-expression pan-network reveals genes involved in complex traits within maize pan-genome by Cagirici, H Busra, Andorf, Carson M, Sen, Taner Z

“…With the advances in the high throughput next generation sequencing technologies, genome-wide association studies (GWAS) have identified a large set of…”
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FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences by Banerjee, Sagnik, Bhandary, Priyanka, Woodhouse, Margaret, Sen, Taner Z, Wise, Roger P, Andorf, Carson M

“…Gene annotation in eukaryotes is a non-trivial task that requires meticulous analysis of accumulated transcript data. Challenges include transcriptionally…”
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MaizeGDB update: new tools, data and interface for the maize model organism database by Andorf, Carson M, Cannon, Ethalinda K, Portwood, 2nd, John L, Gardiner, Jack M, Harper, Lisa C, Schaeffer, Mary L, Braun, Bremen L, Campbell, Darwin A, Vinnakota, Abhinav G, Sribalusu, Venktanaga V, Huerta, Miranda, Cho, Kyoung Tak, Wimalanathan, Kokulapalan, Richter, Jacqueline D, Mauch, Emily D, Rao, Bhavani S, Birkett, Scott M, Sen, Taner Z, Lawrence-Dill, Carolyn J

“…MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant and model organism Zea mays ssp…”
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Genome-Wide Discovery of G-quadruplexes in Wheat: Distribution and Putative Functional Roles by Cagirici, H Busra, Sen, Taner Z

“…G-quadruplexes are nucleic acid secondary structures formed by a stack of square planar G-quartets. G-quadruplexes were implicated in many biological functions…”
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JBrowse Connect: A server API to connect JBrowse instances and users by Yao, Eric, Buels, Robert, Stein, Lincoln, Sen, Taner Z, Holmes, Ian

“…We describe JBrowse Connect, an optional expansion to the JBrowse genome browser, targeted at developers. JBrowse Connect allows live messaging, notifications…”
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Fusarium Protein Toolkit: a web-based resource for structural and variant analysis of Fusarium species by Kim, Hye-Seon, Haley, Olivia C, Portwood Ii, John L, Harding, Stephen, Proctor, Robert H, Woodhouse, Margaret R, Sen, Taner Z, Andorf, Carson M

“…​​The genus Fusarium poses significant threats to food security and safety worldwide because numerous species of the fungus cause destructive diseases and/or…”
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Multiple Variant Calling Pipelines in Wheat Whole Exome Sequencing by Cagirici, H., Akpinar, Bala, Sen, Taner, Budak, Hikmet

“…The highly challenging hexaploid wheat (Triticum aestivum) genome is becoming ever more accessible due to the continued development of multiple reference…”
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Tissue-specific gene expression and protein abundance patterns are associated with fractionation bias in maize by Walsh, Jesse R, Woodhouse, Margaret R, Andorf, Carson M, Sen, Taner Z

“…Maize experienced a whole-genome duplication event approximately 5 to 12 million years ago. Because this event occurred after speciation from sorghum, the…”
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PhosBoost: Improved phosphorylation prediction recall using gradient boosting and protein language models by Poretsky, Elly, Andorf, Carson M., Sen, Taner Z.

“…Protein phosphorylation is a dynamic and reversible post‐translational modification that regulates a variety of essential biological processes. The regulatory…”
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PedigreeNet: a web-based pedigree viewer for biological databases by Braun, Bremen L, Schott, David A, Portwood, John L, Andorf, Carson M, Sen, Taner Z

“…Abstract Motivation Plant breeding aims to improve current germplasm that can tolerate a wide range of biotic and abiotic stresses. To accomplish this goal,…”
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Chromosome-scale genome assembly of bread wheat’s wild relative Triticum timopheevii by Grewal, Surbhi, Yang, Cai-yun, Scholefield, Duncan, Ashling, Stephen, Ghosh, Sreya, Swarbreck, David, Collins, Joanna, Yao, Eric, Sen, Taner Z., Wilson, Michael, Yant, Levi, King, Ian P., King, Julie

“…Wheat ( Triticum aestivum ) is one of the most important food crops with an urgent need for increase in its production to feed the growing world. Triticum…”
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Predicting Tissue-Specific mRNA and Protein Abundance in Maize: A Machine Learning Approach by Cho, Kyoung Tak, Sen, Taner Z., Andorf, Carson M.

“…Machine learning and modeling approaches have been used to classify protein sequences for a broad set of tasks including predicting protein function,…”
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Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium by Clarke, Jennifer L, Cooper, Laurel D, Poelchau, Monica F, Berardini, Tanya Z, Elser, Justin, Farmer, Andrew D, Ficklin, Stephen, Kumari, Sunita, Laporte, Marie-Angélique, Nelson, Rex T, Sadohara, Rie, Selby, Peter, Thessen, Anne E, Whitehead, Brandon, Sen, Taner Z

“…Abstract Over the last couple of decades, there has been a rapid growth in the number and scope of agricultural genetics, genomics and breeding databases and…”
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Building a successful international research community through data sharing: The case of the Wheat Information System (WheatIS) [version 1; peer review: 2 approved, 1 approved with reservations] by Sen, Taner Z, Caccamo, Mario, Edwards, David, Quesneville, Hadi

“…The International Wheat Information System (WheatIS) Expert Working Group (EWG) was initiated in 2012 under the Wheat Initiative with a broad range of…”
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Predicting the Binding Patterns of Hub Proteins: A Study Using Yeast Protein Interaction Networks by Andorf, Carson M, Honavar, Vasant, Sen, Taner Z, Porollo, Aleksey

“…Protein-protein interactions are critical to elucidating the role played by individual proteins in important biological pathways. Of particular interest are…”
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GrainGenes: Tools and Content to Assist Breeders Improving Oat Quality by Blake, Victoria C, Wight, Charlene P, Yao, Eric, Sen, Taner Z

“…GrainGenes is the USDA-ARS database and Web resource for wheat, barley, oat, rye, and their relatives. As a community Web hub and database for small grains,…”
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A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence by Jones, Dallas C, Zheng, Wenguang, Huang, Sheng, Du, Chuanlong, Zhao, Xuefeng, Yennamalli, Ragothaman M, Sen, Taner Z, Nettleton, Dan, Wurtele, Eve S, Li, Ling

“…Nearly immobile, plants have evolved new components to be able to respond to changing environments. One example is Qua Quine Starch (QQS, AT3G30720), an…”
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