Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR
Olson, Robert D, Assaf, Rida, Brettin, Thomas, Conrad, Neal, Cucinell, Clark, Davis, James J, Dempsey, Donald M, Dickerman, Allan, Dietrich, Emily M, Kenyon, Ronald W, Kuscuoglu, Mehmet, Lefkowitz, Elliot J, Lu, Jian, Machi, Dustin, Macken, Catherine, Mao, Chunhong, Niewiadomska, Anna, Nguyen, Marcus, Olsen, Gary J, Overbeek, Jamie C, Parrello, Bruce, Parrello, Victoria, Porter, Jacob S, Pusch, Gordon D, Shukla, Maulik, Singh, Indresh, Stewart, Lucy, Tan, Gene, Thomas, Chris, VanOeffelen, Margo, Vonstein, Veronika, Wallace, Zachary S, Warren, Andrew S, Wattam, Alice R, Xia, Fangfang, Yoo, Hyunseung, Zhang, Yun, Zmasek, Christian M, Scheuermann, Richard H, Stevens, Rick L
Published in Nucleic acids research (06.01.2023)
Published in Nucleic acids research (06.01.2023)
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Journal Article
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
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
Published in Nucleic acids research (01.01.2014)
Published in Nucleic acids research (01.01.2014)
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Journal Article
RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
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, 3rd, James A, Stevens, Rick, Vonstein, Veronika, Wattam, Alice R, Xia, Fangfang
Published in Scientific reports (10.02.2015)
Published in Scientific reports (10.02.2015)
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Journal Article
Supervised extraction of near-complete genomes from metagenomic samples: A new service in PATRIC
Parrello, Bruce, Butler, Rory, Chlenski, Philippe, Pusch, Gordon D, Overbeek, Ross
Published in PloS one (15.04.2021)
Published in PloS one (15.04.2021)
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Journal Article
SEED servers: high-performance access to the SEED genomes, annotations, and metabolic models
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
Published in PloS one (24.10.2012)
Published in PloS one (24.10.2012)
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Journal Article
Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
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
Published in Nucleic acids research (04.01.2017)
Published in Nucleic acids research (04.01.2017)
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Journal Article
PATRIC, the bacterial bioinformatics database and analysis resource
Wattam, Alice R, Abraham, David, Dalay, Oral, Disz, Terry L, Driscoll, Timothy, Gabbard, Joseph L, Gillespie, Joseph J, Gough, Roger, Hix, Deborah, Kenyon, Ronald, Machi, Dustin, Mao, Chunhong, Nordberg, Eric K, Olson, Robert, Overbeek, Ross, Pusch, Gordon D, Shukla, Maulik, Schulman, Julie, Stevens, Rick L, Sullivan, Daniel E, Vonstein, Veronika, Warren, Andrew, Will, Rebecca, Wilson, Meredith J C, Yoo, Hyun Seung, Zhang, Chengdong, Zhang, Yan, Sobral, Bruno W
Published in Nucleic acids research (01.01.2014)
Published in Nucleic acids research (01.01.2014)
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Journal Article
The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities
Davis, James J, Wattam, Alice R, Aziz, Ramy K, Brettin, Thomas, Butler, Ralph, Butler, Rory M, Chlenski, Philippe, Conrad, Neal, Dickerman, Allan, Dietrich, Emily M, Gabbard, Joseph L, Gerdes, Svetlana, Guard, Andrew, Kenyon, Ronald W, Machi, Dustin, Mao, Chunhong, Murphy-Olson, Dan, Nguyen, Marcus, Nordberg, Eric K, Olsen, Gary J, Olson, Robert D, Overbeek, Jamie C, Overbeek, Ross, Parrello, Bruce, Pusch, Gordon D, Shukla, Maulik, Thomas, Chris, VanOeffelen, Margo, Vonstein, Veronika, Warren, Andrew S, Xia, Fangfang, Xie, Dawen, Yoo, Hyunseung, Stevens, Rick
Published in Nucleic acids research (08.01.2020)
Published in Nucleic acids research (08.01.2020)
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Journal Article
PATtyFams: Protein Families for the Microbial Genomes in the PATRIC Database
Davis, James J, Gerdes, Svetlana, Olsen, Gary J, Olson, Robert, Pusch, Gordon D, Shukla, Maulik, Vonstein, Veronika, Wattam, Alice R, Yoo, Hyunseung
Published in Frontiers in microbiology (08.02.2016)
Published in Frontiers in microbiology (08.02.2016)
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Journal Article
The RAST Server: rapid annotations using subsystems technology
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
Published in BMC genomics (08.02.2008)
Published in BMC genomics (08.02.2008)
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Journal Article
A machine learning-based service for estimating quality of genomes using PATRIC
Parrello, Bruce, Butler, Rory, Chlenski, Philippe, Olson, Robert, Overbeek, Jamie, Pusch, Gordon D, Vonstein, Veronika, Overbeek, Ross
Published in BMC bioinformatics (03.10.2019)
Published in BMC bioinformatics (03.10.2019)
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Journal Article
Assembly, Annotation, and Comparative Genomics in PATRIC, the All Bacterial Bioinformatics Resource Center
Wattam, Alice R, Brettin, Thomas, Davis, James J, Gerdes, Svetlana, Kenyon, Ronald, Machi, Dustin, Mao, Chunhong, Olson, Robert, Overbeek, Ross, Pusch, Gordon D, Shukla, Maulik P, Stevens, Rick, Vonstein, Veronika, Warren, Andrew, Xia, Fangfang, Yoo, Hyunseung
Published in Methods in molecular biology (Clifton, N.J.) (01.01.2018)
Published in Methods in molecular biology (Clifton, N.J.) (01.01.2018)
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Journal Article
PATRIC as a unique resource for studying antimicrobial resistance
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
Published in Briefings in bioinformatics (19.07.2019)
Published in Briefings in bioinformatics (19.07.2019)
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Journal Article
A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes
VanOeffelen, Margo, Nguyen, Marcus, Aytan-Aktug, Derya, Brettin, Thomas, Dietrich, Emily M, Kenyon, Ronald W, Machi, Dustin, Mao, Chunhong, Olson, Robert, Pusch, Gordon D, Shukla, Maulik, Stevens, Rick, Vonstein, Veronika, Warren, Andrew S, Wattam, Alice R, Yoo, Hyunseung, Davis, James J
Published in Briefings in bioinformatics (05.11.2021)
Published in Briefings in bioinformatics (05.11.2021)
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Journal Article
Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus
Bolotin, A, Quinquis, B, Renault, P, Sorokin, A, Ehrlich, S.D, Kulakauskas, S, Lapidus, A, Goltsman, E, Mazur, M, Pusch, G.D
Published in Nature biotechnology (01.12.2004)
Published in Nature biotechnology (01.12.2004)
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Journal Article
The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes
Overbeek, Ross, Begley, Tadhg, Butler, Ralph M., Choudhuri, Jomuna V., Chuang, Han-Yu, Cohoon, Matthew, de Crécy-Lagard, Valérie, Diaz, Naryttza, Disz, Terry, Edwards, Robert, Fonstein, Michael, Frank, Ed D., Gerdes, Svetlana, Glass, Elizabeth M., Goesmann, Alexander, Hanson, Andrew, Iwata-Reuyl, Dirk, Jensen, Roy, Jamshidi, Neema, Krause, Lutz, Kubal, Michael, Larsen, Niels, Linke, Burkhard, McHardy, Alice C., Meyer, Folker, Neuweger, Heiko, Olsen, Gary, Olson, Robert, Osterman, Andrei, Portnoy, Vasiliy, Pusch, Gordon D., Rodionov, Dmitry A., Rückert, Christian, Steiner, Jason, Stevens, Rick, Thiele, Ines, Vassieva, Olga, Ye, Yuzhen, Zagnitko, Olga, Vonstein, Veronika
Published in Nucleic acids research (01.01.2005)
Published in Nucleic acids research (01.01.2005)
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Journal Article
Real Time Metagenomics: Using k-mers to annotate metagenomes
EDWARDS, Robert A, OLSON, Robert, DISZ, Terry, PUSCH, Gordon D, VONSTEIN, Veronika, STEVENS, Rick, OVERBEEK, Ross
Published in Bioinformatics (01.12.2012)
Published in Bioinformatics (01.12.2012)
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Journal Article
Comparative supragenomic analyses among the pathogens Staphylococcus aureus, Streptococcus pneumoniae, and Haemophilus influenzae using a modification of the finite supragenome model
Boissy, Robert, Ahmed, Azad, Janto, Benjamin, Earl, Josh, Hall, Barry G, Hogg, Justin S, Pusch, Gordon D, Hiller, Luisa N, Powell, Evan, Hayes, Jay, Yu, Susan, Kathju, Sandeep, Stoodley, Paul, Post, J Christopher, Ehrlich, Garth D, Hu, Fen Z
Published in BMC genomics (13.04.2011)
Published in BMC genomics (13.04.2011)
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