Modal Codon Usage: Assessing the Typical Codon Usage of a Genome

por Davis, James J., Olsen, Gary J.
Publicado 2010

Characterizing the Native Codon Usages of a Genome: An Axis Projection Approach

por Davis, James J., Olsen, Gary J.
Publicado 2011

Protein-coding gene promoters in Methanocaldococcus (Methanococcus) jannaschii

por Zhang, Jian, Li, Enhu, Olsen, Gary J.
Publicado 2009

Evolution of DNA Replication Protein Complexes in Eukaryotes and Archaea

por Chia, Nicholas, Cann, Isaac, Olsen, Gary J.
Publicado 2010

A whole-genome approach to identifying protein binding sites: promoters in Methanocaldococcus (Methanococcus) jannaschii

por Li, Enhu, Reich, Claudia I., Olsen, Gary J.
Publicado 2008

Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes

por Davis, James J., Xia, Fangfang, Overbeek, Ross A., Olsen, Gary J.
Publicado 2013

The repABC Plasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups

por Wetzel, Margaret E., Olsen, Gary J., Chakravartty, Vandana, Farrand, Stephen K.
Publicado 2015

In search of genome annotation consistency: solid gene clusters and how to use them

por Davis, James J., Olsen, Gary J., Overbeek, Ross, Vonstein, Veronika, Xia, Fangfang
Publicado 2013

The essential genome of the crenarchaeal model Sulfolobus islandicus

por Zhang, Changyi, Phillips, Alex P. R., Wipfler, Rebecca L., Olsen, Gary J., Whitaker, Rachel J.
Publicado 2018

PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database

por Davis, James J., Gerdes, Svetlana, Olsen, Gary J., Olson, Robert, Pusch, Gordon D., Shukla, Maulik, Vonstein, Veronika, Wattam, Alice R., Yoo, Hyunseung
Publicado 2016

SEED Servers: High-Performance Access to the SEED Genomes, Annotations, and Metabolic Models

por Aziz, Ramy K., Devoid, Scott, Disz, Terrence, Edwards, Robert A., Henry, Christopher S., Olsen, Gary J., Olson, Robert, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D., Stevens, Rick L., Vonstein, Veronika, Xia, Fangfang
Publicado 2012

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

por Overbeek, Ross, Olson, Robert, Pusch, Gordon D., Olsen, Gary J., Davis, James J., Disz, Terry, Edwards, Robert A., Gerdes, Svetlana, Parrello, Bruce, Shukla, Maulik, Vonstein, Veronika, Wattam, Alice R., Xia, Fangfang, Stevens, Rick
Publicado 2014

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

por Brettin, Thomas, Davis, James J., Disz, Terry, Edwards, Robert A., Gerdes, Svetlana, Olsen, Gary J., Olson, Robert, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D., Shukla, Maulik, Thomason, James A., Stevens, Rick, Vonstein, Veronika, Wattam, Alice R., Xia, Fangfang
Publicado 2015

Genomic Comparison of the Closely-Related Salmonella enterica Serovars Enteritidis, Dublin and Gallinarum

por Matthews, T. David, Schmieder, Robert, Silva, Genivaldo G. Z., Busch, Julia, Cassman, Noriko, Dutilh, Bas E., Green, Dawn, Matlock, Brian, Heffernan, Brian, Olsen, Gary J., Farris Hanna, Leigh, Schifferli, Dieter M., Maloy, Stanley, Dinsdale, Elizabeth A., Edwards, Robert A.
Publicado 2015

The RAST Server: Rapid Annotations using Subsystems Technology

por Aziz, Ramy K, Bartels, Daniela, Best, Aaron A, DeJongh, Matthew, Disz, Terrence, Edwards, Robert A, Formsma, Kevin, Gerdes, Svetlana, Glass, Elizabeth M, Kubal, Michael, Meyer, Folker, Olsen, Gary J, Olson, Robert, Osterman, Andrei L, Overbeek, Ross A, McNeil, Leslie K, Paarmann, Daniel, Paczian, Tobias, Parrello, Bruce, Pusch, Gordon D, Reich, Claudia, Stevens, Rick, Vassieva, Olga, Vonstein, Veronika, Wilke, Andreas, Zagnitko, Olga
Publicado 2008

The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation

por McNeil, Leslie Klis, Reich, Claudia, Aziz, Ramy K., Bartels, Daniela, Cohoon, Matthew, Disz, Terry, Edwards, Robert A., Gerdes, Svetlana, Hwang, Kaitlyn, Kubal, Michael, Margaryan, Gohar Rem, Meyer, Folker, Mihalo, William, Olsen, Gary J., Olson, Robert, Osterman, Andrei, Paarmann, Daniel, Paczian, Tobias, Parrello, Bruce, Pusch, Gordon D., Rodionov, Dmitry A., Shi, Xinghua, Vassieva, Olga, Vonstein, Veronika, Zagnitko, Olga, Xia, Fangfang, Zinner, Jenifer, Overbeek, Ross, Stevens, Rick
Publicado 2007

Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center

por Wattam, Alice R., Davis, James J., Assaf, Rida, Boisvert, Sébastien, Brettin, Thomas, Bun, Christopher, Conrad, Neal, Dietrich, Emily M., Disz, Terry, Gabbard, Joseph L., Gerdes, Svetlana, Henry, Christopher S., Kenyon, Ronald W., Machi, Dustin, Mao, Chunhong, Nordberg, Eric K., Olsen, Gary J., Murphy-Olson, Daniel E., Olson, Robert, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D., Shukla, Maulik, Vonstein, Veronika, Warren, Andrew, Xia, Fangfang, Yoo, Hyunseung, Stevens, Rick L.
Publicado 2017

PATRIC as a unique resource for studying antimicrobial resistance

por Antonopoulos, Dionysios A, Assaf, Rida, Aziz, Ramy Karam, Brettin, Thomas, Bun, Christopher, Conrad, Neal, Davis, James J, Dietrich, Emily M, Disz, Terry, Gerdes, Svetlana, Kenyon, Ronald W, Machi, Dustin, Mao, Chunhong, Murphy-Olson, Daniel E, Nordberg, Eric K, Olsen, Gary J, Olson, Robert, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D, Santerre, John, Shukla, Maulik, Stevens, Rick L, VanOeffelen, Margo, Vonstein, Veronika, Warren, Andrew S, Wattam, Alice R, Xia, Fangfang, Yoo, Hyunseung
Publicado 2017

Erratum: The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

por Klenk, Hans-Peter, Clayton, Rebecca A., Tomb, Jean-Francois, White, Owen, Nelson, Karen E., Ketchum, Karen A., Dodson, Robert J., Gwinn, Michelle, Hickey, Erin K., Peterson, Jeremy D., Richardson, Delwood L., Kerlavage, Anthony R., Graham, David E., Kyrpides, Nikos C., Fleischmann, Robert D., Quackenbush, John, Lee, Norman H., Sutton, Granger G., Gill, Steven, Kirkness, Ewen F., Dougherty, Brian A., McKenney, Keith, Adams, Mark D., Loftus, Brendan, Peterson, Scott, Reich, Claudia I., McNeil, Leslie K., Badger, Jonathan H., Glodek, Anna, Zhou, Lixin, Overbeek, Ross, Gocayne, Jeannine D., Weidman, Janice F., McDonald, Lisa, Utterback, Teresa, Cotton, Matthew D., Spriggs, Tracy, Artiach, Patricia, Kaine, Brian P., Sykes, Sean M., Sadow, Paul W., D'Andrea, Kurt P., Bowman, Cheryl, Fujii, Claire, Garland, Stacey A., Mason, Tanya M., Olsen, Gary J., Fraser, Claire M., Smith, Hamilton O., Woese, Carl R., Venter, J. Craig
Publicado 1998

KBase: The United States Department of Energy Systems Biology Knowledgebase

por Arkin, Adam P, Cottingham, Robert W, Henry, Christopher S, Harris, Nomi L, Stevens, Rick L, Maslov, Sergei, Dehal, Paramvir, Ware, Doreen, Perez, Fernando, Canon, Shane, Sneddon, Michael W, Henderson, Matthew L, Riehl, William J, Murphy-Olson, Dan, Chan, Stephen Y, Kamimura, Roy T, Kumari, Sunita, Drake, Meghan M, Brettin, Thomas S, Glass, Elizabeth M, Chivian, Dylan, Gunter, Dan, Weston, David J, Allen, Benjamin H, Baumohl, Jason, Best, Aaron A, Bowen, Ben, Brenner, Steven E, Bun, Christopher C, Chandonia, John-Marc, Chia, Jer-Ming, Colasanti, Ric, Conrad, Neal, Davis, James J, Davison, Brian H, DeJongh, Matthew, Devoid, Scott, Dietrich, Emily, Dubchak, Inna, Edirisinghe, Janaka N, Fang, Gang, Faria, José P, Frybarger, Paul M, Gerlach, Wolfgang, Gerstein, Mark, Greiner, Annette, Gurtowski, James, Haun, Holly L, He, Fei, Jain, Rashmi, Joachimiak, Marcin P, Keegan, Kevin P, Kondo, Shinnosuke, Kumar, Vivek, Land, Miriam L, Meyer, Folker, Mills, Marissa, Novichkov, Pavel S, Oh, Taeyun, Olsen, Gary J, Olson, Robert, Parrello, Bruce, Pasternak, Shiran, Pearson, Erik, Poon, Sarah S, Price, Gavin A, Ramakrishnan, Srividya, Ranjan, Priya, Ronald, Pamela C, Schatz, Michael C, Seaver, Samuel M D, Shukla, Maulik, Sutormin, Roman A, Syed, Mustafa H, Thomason, James, Tintle, Nathan L, Wang, Daifeng, Xia, Fangfang, Yoo, Hyunseung, Yoo, Shinjae, Yu, Dantong
Publicado 2018