Search Results - Joshua Orvis

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  1. 1
    Identification of the Iron-Responsive Genes of <i>Neisseria gonorrhoeae</i> by Microarray Analysis in Defined Medium

    Identification of the Iron-Responsive Genes of <i>Neisseria gonorrhoeae</i> by Microarray Analysis in Defined Medium by Thomas F. Ducey, Matthew B. Carson, Joshua Orvis, Alain Stintzi, David W. Dyer

    Published 2005
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  2. 2
    Transcriptional and Functional Analysis of the <i>Neisseria gonorrhoeae</i> Fur Regulon

    Transcriptional and Functional Analysis of the <i>Neisseria gonorrhoeae</i> Fur Regulon by Lydgia Jackson, Thomas F. Ducey, Michael W. Day, Jeremy Zaitshik, Joshua Orvis, David W. Dyer

    Published 2009
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  3. 3
    Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

    Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments by Brian J. Haas, Steven L. Salzberg, Wei Zhu, Mihaela Pertea, Jonathan Allen, Joshua Orvis, Owen White, C. Robin Buell, Jennifer R. Wortman

    Published 2008
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  4. 4
    The IGS Standard Operating Procedure for Automated Prokaryotic Annotation

    The IGS Standard Operating Procedure for Automated Prokaryotic Annotation by Kevin Galens, Joshua Orvis, Sean C. Daugherty, Heather H. Creasy, Samuel V. Angiuoli, Owen White, Jennifer R. Wortman, Anup Mahurkar, Michelle Giglio

    Published 2011
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  5. 5
    Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

    Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities by John Martin, Sean M. Sykes, Sarah Young, Karthik Kota, Ravi Sanka, Nihar U. Sheth, Joshua Orvis, Erica Sodergren, Zhengyuan Wang, George M. Weinstock, Makedonka Mitreva

    Published 2012
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  6. 6
    The<i>Aspergillus</i>Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations

    The<i>Aspergillus</i>Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations by Gustavo Cerqueira, Martha B. Arnaud, Diane O. Inglis, Marek S. Skrzypek, Gail Binkley, Matt Simison, Stuart R. Miyasato, Jonathan Binkley, Joshua Orvis, Prachi Shah, Farrell Wymore, Gavin Sherlock, Jennifer R. Wortman

    Published 2013
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  7. 7
    The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community

    The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community by Martha B. Arnaud, Marcus C. Chibucos, Maria C. Costanzo, Jonathan Crabtree, Diane O. Inglis, Adil Lotia, Joshua Orvis, Prachi Shah, Marek S. Skrzypek, Gail Binkley, Stuart R. Miyasato, Jennifer R. Wortman, Gavin Sherlock

    Published 2009
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  8. 8
    Ergatis: a web interface and scalable software system for bioinformatics workflows

    Ergatis: a web interface and scalable software system for bioinformatics workflows by Joshua Orvis, Jonathan Crabtree, Kevin Galens, Aaron Gussman, Jason Inman, Eduardo Lee, Sreenath Nampally, David R. Riley, Jaideep P. Sundaram, Victor Felix, Brett R. Whitty, Anup Mahurkar, Jennifer R. Wortman, Owen White, Samuel V. Angiuoli

    Published 2010
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  9. 9
    The TIGR Rice Genome Annotation Resource: improvements and new features

    The TIGR Rice Genome Annotation Resource: improvements and new features by Shuai Ouyang, W. Zhu, John P. Hamilton, Haining Lin, Matthew A. Campbell, Kevin L. Childs, Françoise Thibaud‐Nissen, Renae L. Malek, Y. Lee, Li Zheng, Joshua Orvis, Brian J. Haas, Jennifer R. Wortman, C. Robin Buell

    Published 2006
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  10. 10
    Annotated draft genome sequences of three species of<i>Cryptosporidium</i>:<i>Cryptosporidium meleagridis</i>isolate UKMEL1,<i>C. baileyi</i>isolate TAMU-09Q1 and<i>C. hominis</i>isolates TU502_2012 and UKH1

    Annotated draft genome sequences of three species of<i>Cryptosporidium</i>:<i>Cryptosporidium meleagridis</i>isolate UKMEL1,<i>C. baileyi</i>isolate TAMU-09Q1 and<i>C. hominis</i>i... by Olukemi O. Ifeonu, Marcus C. Chibucos, Joshua Orvis, Qi Su, Kristin Elwin, Fengguang Guo, Haili Zhang, Lihua Xiao, Mingfei Sun, Rachel M. Chalmers, Claire M. Fraser, Guan Zhu, Jessica C. Kissinger, Giovanni Widmer, Joana C. Silva

    Published 2016
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  11. 11
    Strains, functions and dynamics in the expanded Human Microbiome Project

    Strains, functions and dynamics in the expanded Human Microbiome Project by Jason Lloyd‐Price, Anup Mahurkar, Ali Rahnavard, Jonathan Crabtree, Joshua Orvis, A. Brantley Hall, Arthur Brady, Heather H. Creasy, Carrie McCracken, Michelle Giglio, Daniel McDonald, Eric A. Franzosa, Rob Knight, Owen White, Curtis Huttenhower

    Published 2017
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  12. 12
    Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project

    Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project by Jason Lloyd‐Price, Anup Mahurkar, Ali Rahnavard, Jonathan Crabtree, Joshua Orvis, A. Brantley Hall, Arthur Brady, Heather H. Creasy, Carrie McCracken, Michelle Giglio, Daniel McDonald, Eric A. Franzosa, Rob Knight, Owen White, Curtis Huttenhower

    Published 2017
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  13. 13
    Characterization of the development of the mouse cochlear epithelium at the single cell level

    Characterization of the development of the mouse cochlear epithelium at the single cell level by Likhitha Kolla, Michael C. Kelly, Zoë F. Mann, Alejandro Anaya-Rocha, Kathryn A. Ellis, Abigail Lemons, Adam T. Palermo, Kathy S. So, Joseph C. Mays, Joshua Orvis, J. C. Burns, Ronna Hertzano, Elizabeth C. Driver, Matthew W. Kelley

    Published 2020
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  14. 14
    The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources

    The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources by M. B. Arnaud, Gustavo C. Cerqueira, Diane O. Inglis, Marek S. Skrzypek, Jill Binkley, Marcus C. Chibucos, Jonathan Crabtree, Catherine Howarth, Joshua Orvis, Prachi Shah, F. Wymore, Gail Binkley, Stuart R. Miyasato, Matt Simison, Gavin Sherlock, Jennifer R. Wortman

    Published 2011
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  15. 15
    Draft genome sequence of the oilseed species Ricinus communis

    Draft genome sequence of the oilseed species Ricinus communis by Agnes P. Chan, Jonathan Crabtree, Qi Zhao, Hernán Lorenzi, Joshua Orvis, Daniela Puiu, Admasu Melake‐Berhan, Kristine Jones, Julia C. Redman, Grace Chen, Edgar B. Cahoon, Melaku Gedil, Mario Stanke, Brian J. Haas, Jennifer R. Wortman, Claire M. Fraser, Jacques Ravel, Pablo D. Rabinowicz

    Published 2010
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  16. 16
    A cell-type-specific atlas of the inner ear transcriptional response to acoustic trauma

    A cell-type-specific atlas of the inner ear transcriptional response to acoustic trauma by Béatrice Milon, Eldad D. Shulman, Kathy S. So, Christopher R. Cederroth, Erika L. Lipford, Michal Sperber, Jonathan B. Sellon, Heela Sarlus, Gabriela Pregernig, Benjamin Shuster, Yang Song, Sunayana Mitra, Joshua Orvis, Zachary Margulies, Yoko Ogawa, Christopher Shults, Didier A. Depireux, Adam T. Palermo, Barbara Canlon, Joe Burns, Ran Elkon, Ronna Hertzano

    Published 2021
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  17. 17
    gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration

    gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration by Joshua Orvis, Brian Gottfried, Jayaram Kancherla, Ricky S. Adkins, Yang Song, Amiel A. Dror, Dustin Olley, Kevin Rose, Elena Chrysostomou, Michael C. Kelly, Béatrice Milon, Maggie S. Matern, Héla Azaiez, Brian R. Herb, Carlo Colantuoni, Robert Carter, Seth A. Ament, Matthew W. Kelley, Owen White, Héctor Corrada Bravo, Anup Mahurkar, Ronna Hertzano

    Published 2021
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  18. 18
    An integrated genomic and transcriptomic survey of mucormycosis-causing fungi

    An integrated genomic and transcriptomic survey of mucormycosis-causing fungi by Marcus C. Chibucos, Sameh S. M. Soliman, Teclegiorgis Gebremariam, Hong-Kyu Lee, Sean C. Daugherty, Joshua Orvis, Amol C. Shetty, Jonathan Crabtree, Tracy H. Hazen, Kizee A. Etienne, Priti Kumari, Timothy D. O’Connor, David A. Rasko, Scott G. Filler, Claire M. Fraser, Shawn R. Lockhart, Christopher D. Skory, Ashraf S. Ibrahim, Vincent M. Bruno

    Published 2016
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  19. 19
    De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

    De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis by Brian J. Haas, Alexie Papanicolaou, Moran Yassour, Manfred Grabherr, Philip D. Blood, Joshua C. Bowden, Matthew Brian Couger, David Eccles, Bo Li, Matthias Lieber, Matthew D. MacManes, Michael Ott, Joshua Orvis, Nathalie Pochet, Francesco Strozzi, Nathan T. Weeks, Rick Westerman, Thomas William, Colin N. Dewey, Robert Henschel, Richard D. LeDuc, Nir Friedman, Aviv Regev

    Published 2013
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  20. 20
    Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions

    Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions by Joana C. Silva, Emmanuel Cornillot, Carrie McCracken, Sahar Usmani‐Brown, Ankit Dwivedi, Olukemi O. Ifeonu, Jonathan Crabtree, Hanzel T. Gotia, Azan Z. Virji, Christelle Reynès, Jacques Colinge, Vidya P. Kumar, Lauren Lawres, Joseph E. Pazzi, Jozelyn Pablo, Chris Hung, Jana Brancato, Priti Kumari, Joshua Orvis, Kyle Tretina, Marcus C. Chibucos, Sandy Ott, Lisa Sadzewicz, Naomi Sengamalay, Amol C. Shetty, Qi Su, Luke J. Tallon, Claire M. Fraser, Roger Frutos, Douglas M. Molina, Peter J. Krause, Choukri Ben Mamoun

    Published 2016
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