The IGS Standard Operating Procedure for Automated Prokaryotic Annotation

por Galens, Kevin, Orvis, Joshua, Daugherty, Sean, Creasy, Heather H., Angiuoli, Sam, White, Owen, Wortman, Jennifer, Mahurkar, Anup, Giglio, Michelle Gwinn
Publicado 2011

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

por Haas, Brian J, Salzberg, Steven L, Zhu, Wei, Pertea, Mihaela, Allen, Jonathan E, Orvis, Joshua, White, Owen, Buell, C Robin, Wortman, Jennifer R
Publicado 2008

Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

por Martin, John, Sykes, Sean, Young, Sarah, Kota, Karthik, Sanka, Ravi, Sheth, Nihar, Orvis, Joshua, Sodergren, Erica, Wang, Zhengyuan, Weinstock, George M., Mitreva, Makedonka
Publicado 2012

Draft Genome Sequence of Mortierella alpina Isolate CDC-B6842

por Etienne, Kizee A., Chibucos, Marcus C., Su, Qi, Orvis, Joshua, Daugherty, Sean, Ott, Sandra, Sengamalay, Naomi A., Fraser, Claire M., Lockhart, Shawn R., Bruno, Vincent M.
Publicado 2014

HMPDACC: a Human Microbiome Project Multi-omic data resource

por Creasy, Heather Huot, Felix, Victor, Aluvathingal, Jain, Crabtree, Jonathan, Ifeonu, Olukemi, Matsumura, James, McCracken, Carrie, Nickel, Lance, Orvis, Joshua, Schor, Mike, Giglio, Michelle, Mahurkar, Anup, White, Owen
Publicado 2020

The TIGR Rice Genome Annotation Resource: improvements and new features

por Ouyang, Shu, Zhu, Wei, Hamilton, John, Lin, Haining, Campbell, Matthew, Childs, Kevin, Thibaud-Nissen, Françoise, Malek, Renae L., Lee, Yuandan, Zheng, Li, Orvis, Joshua, Haas, Brian, Wortman, Jennifer, Buell, C. Robin
Publicado 2007

The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations

por Cerqueira, Gustavo C., Arnaud, Martha B., Inglis, Diane O., Skrzypek, Marek S., Binkley, Gail, Simison, Matt, Miyasato, Stuart R., Binkley, Jonathan, Orvis, Joshua, Shah, Prachi, Wymore, Farrell, Sherlock, Gavin, Wortman, Jennifer R.
Publicado 2014

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

por Arnaud, Martha B., Chibucos, Marcus C., Costanzo, Maria C., Crabtree, Jonathan, Inglis, Diane O., Lotia, Adil, Orvis, Joshua, Shah, Prachi, Skrzypek, Marek S., Binkley, Gail, Miyasato, Stuart R., Wortman, Jennifer R., Sherlock, Gavin
Publicado 2010

Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys

por Ioannidis, Panagiotis, Lu, Yong, Kumar, Nikhil, Creasy, Todd, Daugherty, Sean, Chibucos, Marcus C, Orvis, Joshua, Shetty, Amol, Ott, Sandra, Flowers, Melissa, Sengamalay, Naomi, Tallon, Luke J, Pick, Leslie, Hotopp, Julie C Dunning
Publicado 2014

Ergatis: a web interface and scalable software system for bioinformatics workflows

por Orvis, Joshua, Crabtree, Jonathan, Galens, Kevin, Gussman, Aaron, Inman, Jason M., Lee, Eduardo, Nampally, Sreenath, Riley, David, Sundaram, Jaideep P., Felix, Victor, Whitty, Brett, Mahurkar, Anup, Wortman, Jennifer, White, Owen, Angiuoli, Samuel V.
Publicado 2010

Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms

por Tretina, Kyle, Pelle, Roger, Orvis, Joshua, Gotia, Hanzel T., Ifeonu, Olukemi O., Kumari, Priti, Palmateer, Nicholas C., Iqbal, Shaikh B. A., Fry, Lindsay M., Nene, Vishvanath M., Daubenberger, Claudia A., Bishop, Richard P., Silva, Joana C.
Publicado 2020

Characterization of the development of the mouse cochlear epithelium at the single cell level

por Kolla, Likhitha, Kelly, Michael C., Mann, Zoe F., Anaya-Rocha, Alejandro, Ellis, Kathryn, Lemons, Abigail, Palermo, Adam T., So, Kathy S., Mays, Joseph C., Orvis, Joshua, Burns, Joseph C., Hertzano, Ronna, Driver, Elizabeth C., Kelley, Matthew W.
Publicado 2020

Annotated draft genome sequences of three species of Cryptosporidium: Cryptosporidium meleagridis isolate UKMEL1, C. baileyi isolate TAMU-09Q1 and C. hominis isolates TU502_2012 an...

por Ifeonu, Olukemi O., Chibucos, Marcus C., Orvis, Joshua, Su, Qi, Elwin, Kristin, Guo, Fengguang, Zhang, Haili, Xiao, Lihua, Sun, Mingfei, Chalmers, Rachel M., Fraser, Claire M., Zhu, Guan, Kissinger, Jessica C., Widmer, Giovanni, Silva, Joana C.
Publicado 2016

Strains, functions and dynamics in the expanded Human Microbiome Project

por Lloyd-Price, Jason, Mahurkar, Anup, Rahnavard, Gholamali, Crabtree, Jonathan, Orvis, Joshua, Hall, A. Brantley, Brady, Arthur, Creasy, Heather H., McCracken, Carrie, Giglio, Michelle G., McDonald, Daniel, Franzosa, Eric A., Knight, Rob, White, Owen, Huttenhower, Curtis
Publicado 2017

Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project

por Lloyd-Price, Jason, Mahurkar, Anup, Rahnavard, Gholamali, Crabtree, Jonathan, Orvis, Joshua, Hall, A. Brantley, Brady, Arthur, Creasy, Heather H., McCracken, Carrie, Giglio, Michelle G., McDonald, Daniel, Franzosa, Eric A., Knight, Rob, White, Owen, Huttenhower, Curtis
Publicado 2017

The evolution of synaptic and cognitive capacity: Insights from the nervous system transcriptome of Aplysia

por Orvis, Joshua, Albertin, Caroline B., Shrestha, Pragya, Chen, Shuangshuang, Zheng, Melanie, Rodriguez, Cheyenne J., Tallon, Luke J., Mahurkar, Anup, Zimin, Aleksey V., Kim, Michelle, Liu, Kelvin, Kandel, Eric R., Fraser, Claire M., Sossin, Wayne, Abrams, Thomas W.
Publicado 2022

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

por Arnaud, Martha B., Cerqueira, Gustavo C., Inglis, Diane O., Skrzypek, Marek S., Binkley, Jonathan, Chibucos, Marcus C., Crabtree, Jonathan, Howarth, Clinton, Orvis, Joshua, Shah, Prachi, Wymore, Farrell, Binkley, Gail, Miyasato, Stuart R., Simison, Matt, Sherlock, Gavin, Wortman, Jennifer R.
Publicado 2012

A data analysis and coordination center for the human microbiome project

por Wortman, Jennifer, Giglio, Michelle, Creasy, Heather, Chen, Amy, Liolios, Konstantinos, Chu, Ken, Davidovics, Noam, Mazaitis, Mark, DeSantis, Todd, Singh, Navjeet, Orvis, Joshua, Crabtree, Jonathan, Felix, Victor, Jordan, Catherine, Mahurkar, Anup, Knight, Rob, Andersen, Gary, Kyrpides, Nikos, Markowitz, Victor, White, Owen
Publicado 2010

Horizontal gene transfer in Histophilus somni and its role in the evolution of pathogenic strain 2336, as determined by comparative genomic analyses

por Siddaramappa, Shivakumara, Challacombe, Jean F, Duncan, Alison J, Gillaspy, Allison F, Carson, Matthew, Gipson, Jenny, Orvis, Joshua, Zaitshik, Jeremy, Barnes, Gentry, Bruce, David, Chertkov, Olga, Detter, J Chris, Han, Cliff S, Tapia, Roxanne, Thompson, Linda S, Dyer, David W, Inzana, Thomas J
Publicado 2011

Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity

por Palmateer, Nicholas C., Tretina, Kyle, Orvis, Joshua, Ifeonu, Olukemi O., Crabtree, Jonathan, Drabék, Elliott, Pelle, Roger, Awino, Elias, Gotia, Hanzel T., Munro, James B., Tallon, Luke, Morrison, W. Ivan, Daubenberger, Claudia A., Nene, Vish, Knowles, Donald P., Bishop, Richard P., Silva, Joana C.
Publicado 2020