Search Results - "Hufnagel, David E"

SequelTools: a suite of tools for working with PacBio Sequel raw sequence data by Hufnagel, David E, Hufford, Matthew B, Seetharam, Arun S

“…PacBio sequencing is an incredibly valuable third-generation DNA sequencing method due to very long read lengths, ability to detect methylated bases, and its…”
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MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations by Campbell, Michael S., Law, MeiYee, Holt, Carson, Stein, Joshua C., Moghe, Gaurav D., Hufnagel, David E., Lei, Jikai, Achawanantakun, Rujira, Jiao, Dian, Lawrence, Carolyn J., Ware, Doreen, Shiu, Shin-Han, Childs, Kevin L., Sun, Yanni, Jiang, Ning, Yandell, Mark

“…We have optimized and extended the widely used annotation engine MAKER in order to better support plant genome annotation efforts. New features include better…”
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Effect of sequence depth and length in long-read assembly of the maize inbred NC358 by Ou, Shujun, Liu, Jianing, Chougule, Kapeel M., Fungtammasan, Arkarachai, Seetharam, Arun S., Stein, Joshua C., Llaca, Victor, Manchanda, Nancy, Gilbert, Amanda M., Wei, Sharon, Chin, Chen-Shan, Hufnagel, David E., Pedersen, Sarah, Snodgrass, Samantha J., Fengler, Kevin, Woodhouse, Margaret, Walenz, Brian P., Koren, Sergey, Phillippy, Adam M., Hannigan, Brett T., Dawe, R. Kelly, Hirsch, Candice N., Hufford, Matthew B., Ware, Doreen

“…Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an…”
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A Chromosome-Level Genome of the Camphor Tree and the Underlying Genetic and Climatic Factors for Its Top-Geoherbalism by Jiang, Rihong, Chen, Xinlian, Liao, Xuezhu, Peng, Dan, Han, Xiaoxu, Zhu, Changsan, Wang, Ping, Hufnagel, David E, Wang, Li, Li, Kaixiang, Li, Cheng

“…Camphor tree [ (L.) J. Presl], a species in the magnoliid family Lauraceae, is known for its rich volatile oils and is used as a medical cardiotonic and as a…”
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Swine-to-Ferret Transmission of Antigenically Drifted Contemporary Swine H3N2 Influenza A Virus Is an Indicator of Zoonotic Risk to Humans by Souza, Carine K, Kimble, J Brian, Anderson, Tavis K, Arendsee, Zebulun W, Hufnagel, David E, Young, Katharine M, Gauger, Phillip C, Lewis, Nicola S, Davis, C Todd, Thor, Sharmi, Vincent Baker, Amy L

“…Human-to-swine transmission of influenza A (H3N2) virus occurs repeatedly and plays a critical role in swine influenza A virus (IAV) evolution and diversity…”
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The origin and evolution of maize in the Southwestern United States by da Fonseca, Rute R., Smith, Bruce D., Wales, Nathan, Cappellini, Enrico, Skoglund, Pontus, Fumagalli, Matteo, Samaniego, José Alfredo, Carøe, Christian, Ávila-Arcos, María C., Hufnagel, David E., Korneliussen, Thorfinn Sand, Vieira, Filipe Garrett, Jakobsson, Mattias, Arriaza, Bernardo, Willerslev, Eske, Nielsen, Rasmus, Hufford, Matthew B., Albrechtsen, Anders, Ross-Ibarra, Jeffrey, Gilbert, M. Thomas P.

“…The origin of maize ( Zea mays mays ) in the US Southwest remains contentious, with conflicting archaeological data supporting either coastal 1 – 4 or highland…”
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Interspecies Transmission from Pigs to Ferrets of Antigenically Distinct Swine H1 Influenza A Viruses with Reduced Reactivity to Candidate Vaccine Virus Antisera as Measures of Relative Zoonotic Risk by Kimble, J Brian, Souza, Carine K, Anderson, Tavis K, Arendsee, Zebulun W, Hufnagel, David E, Young, Katharine M, Lewis, Nicola S, Davis, C Todd, Thor, Sharmi, Vincent Baker, Amy L

“…During the last decade, endemic swine H1 influenza A viruses (IAV) from six different genetic clades of the hemagglutinin gene caused zoonotic infections in…”
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De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes by Hufford, Matthew B, Seetharam, Arun S, Woodhouse, Margaret R, Chougule, Kapeel M, Ou, Shujun, Liu, Jianing, Ricci, William A, Guo, Tingting, Olson, Andrew, Qiu, Yinjie, Della Coletta, Rafael, Tittes, Silas, Hudson, Asher I, Marand, Alexandre P, Wei, Sharon, Lu, Zhenyuan, Wang, Bo, Tello-Ruiz, Marcela K, Piri, Rebecca D, Wang, Na, Kim, Dong Won, Zeng, Yibing, O'Connor, Christine H, Li, Xianran, Gilbert, Amanda M, Baggs, Erin, Krasileva, Ksenia V, Portwood, 2nd, John L, Cannon, Ethalinda K S, Andorf, Carson M, Manchanda, Nancy, Snodgrass, Samantha J, Hufnagel, David E, Jiang, Qiuhan, Pedersen, Sarah, Syring, Michael L, Kudrna, David A, Llaca, Victor, Fengler, Kevin, Schmitz, Robert J, Ross-Ibarra, Jeffrey, Yu, Jianming, Gent, Jonathan I, Hirsch, Candice N, Ware, Doreen, Dawe, R Kelly

“…We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association…”
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Consequences of Whole-Genome Triplication as Revealed by Comparative Genomic Analyses of the Wild Radish Raphanus raphanistrum and Three Other Brassicaceae Species by Moghe, Gaurav D., Hufnagel, David E., Tang, Haibao, Xiao, Yongli, Dworkin, Ian, Town, Christopher D., Conner, Jeffrey K., Shiu, Shin-Han

“…Polyploidization events are frequent among flowering plants, and the duplicate genes produced via such events contribute significantly to plant evolution. We…”
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Evolution of TPS20‐related terpene synthases influences chemical diversity in the glandular trichomes of the wild tomato relative Solanum habrochaites by Gonzales‐Vigil, Eliana, Hufnagel, David E, Kim, Jeongwoon, Last, Robert L, Barry, Cornelius S

“…A systematic screen of volatile terpene production in the glandular trichomes of 79 accessions of Solanum habrochaites was conducted and revealed the presence…”
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Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidopsis thaliana by Lehti-Shiu, Melissa D, Uygun, Sahra, Moghe, Gaurav D, Panchy, Nicholas, Fang, Liang, Hufnagel, David E, Jasicki, Hannah L, Feig, Michael, Shiu, Shin-Han

“…Functional divergence between duplicate transcription factors (TFs) has been linked to critical events in the evolution of land plants and can result from…”
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Retained duplicate genes in green alga Chlamydomonas reinhardtii tend to be stress responsive and experience frequent response gains by Wu, Guangxi, Hufnagel, David E, Denton, Alisandra K, Shiu, Shin-Han

“…Green algae belong to a group of photosynthetic organisms that occupy diverse habitats, are closely related to land plants, and have been studied as sources of…”
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octoFLUshow: an Interactive Tool Describing Spatial and Temporal Trends in the Genetic Diversity of Influenza A Virus in U.S. Swine by Arendsee, Zebulun W, Chang, Jennifer, Hufnagel, David E, Markin, Alexey, Janas-Martindale, Alicia, Vincent, Amy L, Anderson, Tavis K

“…Influenza A virus (IAV) is passively surveilled in swine in the United States through a U.S. Department of Agriculture administered surveillance system. We…”
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The prevalence of deleterious mutations during the domestication and improvement of soybean by Sun, Shichao, Wang, Yumin, Wei, He, Hufnagel, David E., Wang, Ya, Guo, Shiyu, Li, Yinghui, Wang, Li, Qiu, Li-juan

“…Soybean (Glycine max L.) is a protein and oil crop grown worldwide. Its fitness may be reduced by deleterious mutations, whose identification and purging is…”
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Characterizing a century of genetic diversity and contemporary antigenic diversity of N1 neuraminidase in influenza A virus from North American swine by Hufnagel, David E, Young, Katharine M, Arendsee, Zebulun W, Gay, L Claire, Caceres, C Joaquin, Rajão, Daniela S, Perez, Daniel R, Vincent Baker, Amy L, Anderson, Tavis K

“…Abstract Influenza A viruses (IAVs) of the H1N1 classical swine lineage became endemic in North American swine following the 1918 pandemic. Additional…”
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Erratum: The origin and evolution of maize in the Southwestern United States by da Fonseca, Rute R., Smith, Bruce D., Wales, Nathan, Cappellini, Enrico, Skoglund, Pontus, Fumagalli, Matteo, Samaniego, José Alfredo, Carøe, Christian, Ávila-Arcos, María C., Hufnagel, David E., Korneliussen, Thorfinn Sand, Vieira, Filipe Garrett, Jakobsson, Mattias, Arriaza, Bernardo, Willerslev, Eske, Nielsen, Rasmus, Hufford, Matthew B., Albrechtsen, Anders, Ross-Ibarra, Jeffrey, Gilbert, M. Thomas P.

“…Nature Plants 1, 14003 (2015); published 8 January 2015; corrected 14 January 2015. In the version of the Supplementary Information originally posted online,…”
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Distinct Teosinte Hybrid Zones and Genomic Architectures of Hybridization by Hufnagel, David E

“…Hybridization is a major force of evolution and has profound consequences due to increased heterozygosity and the creation of novel allele combinations. Hybrid…”
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Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication inArabidopsis thaliana by Lehti-Shiu, Melissa D., Uygun, Sahra, Moghe, Gaurav D., Panchy, Nicholas, Fang, Liang, Hufnagel, David E., Jasicki, Hannah L., Feig, Michael, Shiu, Shin-Han

“…Functional divergence between duplicate transcription factors (TFs) has been linked to critical events in the evolution of land plants and can result from…”
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Molecular Evidence for Functional Divergence and Decay of a Transcription Factor Derived from Whole-Genome Duplication in Arabidopsis thaliana1[OPEN] by Lehti-Shiu, Melissa D., Uygun, Sahra, Moghe, Gaurav D., Panchy, Nicholas, Fang, Liang, Hufnagel, David E., Jasicki, Hannah L., Feig, Michael, Shiu, Shin-Han

“…Functional decay of a transcription factor retained after whole-genome duplication suggests that duplicate gene loss is a prolonged process occurring over tens…”
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MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations1[W][OPEN] by Campbell, Michael S., Law, MeiYee, Holt, Carson, Stein, Joshua C., Moghe, Gaurav D., Hufnagel, David E., Lei, Jikai, Achawanantakun, Rujira, Jiao, Dian, Lawrence, Carolyn J., Ware, Doreen, Shiu, Shin-Han, Childs, Kevin L., Sun, Yanni, Jiang, Ning, Yandell, Mark

“…MAKER-P annotates the entire Arabidopsis and maize genomes in less than 3 h with comparable quality to the current TAIR10 and maize V2 annotation builds . We…”
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