IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes
Abstract
The Integrated Microbial Genomes & Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source datasets include those generated by the DOE's Joint Genome Institute (JGI), submitted by external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed through the IMG annotation pipeline and then loaded into the IMG data warehouse. IMG's web user interface provides a variety of analytical and visualization tools for comparative analysis of isolate genomes and metagenomes in IMG. IMG/M allows open access to all public genomes in the IMG data warehouse, while its expert review (ER) system (IMG/MER: https://img.jgi.doe.gov/mer/) enabled registered users to access their private genomes and to store their private datasets in workspace for sharing and for further analysis. IMG/M data content has increased by 60% since the last report published in the 2017 NAR Database Issue. IMG/M v.5.0 has a new and more powerful genome search feature, new statistical tools, and supports metagenome binning.
- Authors:
-
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Resphera Biosciences, Baltimore, MD (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER); National Energy Research Scientific Computing Center (NERSC)
- OSTI Identifier:
- 1542357
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Volume: 47; Journal Issue: D1; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Chen, I-Min A., Chu, Ken, Palaniappan, Krishna, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Varghese, Neha, White, James R., Seshadri, Rekha, Smirnova, Tatyana, Kirton, Edward, Jungbluth, Sean P., Woyke, Tanja, Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., and Kyrpides, Nikos C. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. United States: N. p., 2018.
Web. doi:10.1093/nar/gky901.
Chen, I-Min A., Chu, Ken, Palaniappan, Krishna, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Varghese, Neha, White, James R., Seshadri, Rekha, Smirnova, Tatyana, Kirton, Edward, Jungbluth, Sean P., Woyke, Tanja, Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., & Kyrpides, Nikos C. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. United States. doi:10.1093/nar/gky901.
Chen, I-Min A., Chu, Ken, Palaniappan, Krishna, Pillay, Manoj, Ratner, Anna, Huang, Jinghua, Huntemann, Marcel, Varghese, Neha, White, James R., Seshadri, Rekha, Smirnova, Tatyana, Kirton, Edward, Jungbluth, Sean P., Woyke, Tanja, Eloe-Fadrosh, Emiley A., Ivanova, Natalia N., and Kyrpides, Nikos C. Fri .
"IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes". United States. doi:10.1093/nar/gky901. https://www.osti.gov/servlets/purl/1542357.
@article{osti_1542357,
title = {IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes},
author = {Chen, I-Min A. and Chu, Ken and Palaniappan, Krishna and Pillay, Manoj and Ratner, Anna and Huang, Jinghua and Huntemann, Marcel and Varghese, Neha and White, James R. and Seshadri, Rekha and Smirnova, Tatyana and Kirton, Edward and Jungbluth, Sean P. and Woyke, Tanja and Eloe-Fadrosh, Emiley A. and Ivanova, Natalia N. and Kyrpides, Nikos C.},
abstractNote = {The Integrated Microbial Genomes & Microbiomes system v.5.0 (IMG/M: https://img.jgi.doe.gov/m/) contains annotated datasets categorized into: archaea, bacteria, eukarya, plasmids, viruses, genome fragments, metagenomes, cell enrichments, single particle sorts, and metatranscriptomes. Source datasets include those generated by the DOE's Joint Genome Institute (JGI), submitted by external scientists, or collected from public sequence data archives such as NCBI. All submissions are typically processed through the IMG annotation pipeline and then loaded into the IMG data warehouse. IMG's web user interface provides a variety of analytical and visualization tools for comparative analysis of isolate genomes and metagenomes in IMG. IMG/M allows open access to all public genomes in the IMG data warehouse, while its expert review (ER) system (IMG/MER: https://img.jgi.doe.gov/mer/) enabled registered users to access their private genomes and to store their private datasets in workspace for sharing and for further analysis. IMG/M data content has increased by 60% since the last report published in the 2017 NAR Database Issue. IMG/M v.5.0 has a new and more powerful genome search feature, new statistical tools, and supports metagenome binning.},
doi = {10.1093/nar/gky901},
journal = {Nucleic Acids Research},
number = D1,
volume = 47,
place = {United States},
year = {2018},
month = {10}
}
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Works referenced in this record:
InterProScan 5: genome-scale protein function classification
journal, January 2014
- Jones, P.; Binns, D.; Chang, H. -Y.
- Bioinformatics, Vol. 30, Issue 9
Adaptive seeds tame genomic sequence comparison
journal, January 2011
- Kielbasa, S. M.; Wan, R.; Sato, K.
- Genome Research, Vol. 21, Issue 3
Expanded microbial genome coverage and improved protein family annotation in the COG database
journal, November 2014
- Galperin, Michael Y.; Makarova, Kira S.; Wolf, Yuri I.
- Nucleic Acids Research, Vol. 43, Issue D1
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses
journal, October 2016
- Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna
- Nucleic Acids Research, Vol. 45, Issue D1
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families
journal, November 2017
- Kalvari, Ioanna; Argasinska, Joanna; Quinones-Olvera, Natalia
- Nucleic Acids Research, Vol. 46, Issue D1
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system
journal, April 2016
- Chen, I-Min A.; Markowitz, Victor M.; Palaniappan, Krishna
- BMC Genomics, Vol. 17, Issue 1
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements
journal, October 2016
- Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon
- Nucleic Acids Research, Vol. 45, Issue D1
On a Test of Whether one of Two Random Variables is Stochastically Larger than the Other
journal, March 1947
- Mann, H. B.; Whitney, D. R.
- The Annals of Mathematical Statistics, Vol. 18, Issue 1
CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
journal, June 2007
- Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah
- BMC Bioinformatics, Vol. 8, Issue 1
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4)
journal, October 2015
- Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
- Standards in Genomic Sciences, Vol. 10, Issue 1
The Pfam protein families database: towards a more sustainable future
journal, December 2015
- Finn, Robert D.; Coggill, Penelope; Eberhardt, Ruth Y.
- Nucleic Acids Research, Vol. 44, Issue D1
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
journal, August 2017
- Bowers, Robert M.; Kyrpides, Nikos C.; Stepanauskas, Ramunas
- Nature Biotechnology, Vol. 35, Issue 8
Guidelines to Statistical Analysis of Microbial Composition Data Inferred from Metagenomic Sequencing
journal, January 2017
- Odintsova, Vera; Tyakht, Alexander; Alexeev, Dmitry
- Current Issues in Molecular Biology
Recovering complete and draft population genomes from metagenome datasets
journal, March 2016
- Sangwan, Naseer; Xia, Fangfang; Gilbert, Jack A.
- Microbiome, Vol. 4, Issue 1
Improving Microbial Genome Annotations in an Integrated Database Context
journal, February 2013
- Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
- PLoS ONE, Vol. 8, Issue 2
The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4)
journal, February 2016
- Huntemann, Marcel; Ivanova, Natalia N.; Mavromatis, Konstantinos
- Standards in Genomic Sciences, Vol. 11, Issue 1
Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software
journal, October 2017
- Sczyrba, Alexander; Hofmann, Peter; Belmann, Peter
- Nature Methods, Vol. 14, Issue 11
Locating proteins in the cell using TargetP, SignalP and related tools
journal, April 2007
- Emanuelsson, Olof; Brunak, Søren; von Heijne, Gunnar
- Nature Protocols, Vol. 2, Issue 4
GenBank
journal, November 2012
- Benson, Dennis A.; Cavanaugh, Mark; Clark, Karen
- Nucleic Acids Research, Vol. 41, Issue D1
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
journal, November 2015
- Caspi, Ron; Billington, Richard; Ferrer, Luciana
- Nucleic Acids Research, Vol. 44, Issue D1
Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management System
journal, November 2009
- Mavromatis, Konstantinos; Chu, Ken; Ivanova, Natalia
- PLoS ONE, Vol. 4, Issue 11
TIGRFAMs and Genome Properties in 2013
journal, November 2012
- Haft, Daniel H.; Selengut, Jeremy D.; Richter, Roland A.
- Nucleic Acids Research, Vol. 41, Issue D1
Genomic Standards Consortium Projects
journal, February 2014
- Field, Dawn; Sterk, Peter; Kottmann, Renzo
- Standards in Genomic Sciences, Vol. 9, Issue 3
Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life
journal, September 2017
- Parks, Donovan H.; Rinke, Christian; Chuvochina, Maria
- Nature Microbiology, Vol. 2, Issue 11
HMMER web server: 2015 update
journal, May 2015
- Finn, Robert D.; Clements, Jody; Arndt, William
- Nucleic Acids Research, Vol. 43, Issue W1
Prodigal: prokaryotic gene recognition and translation initiation site identification
journal, March 2010
- Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F.
- BMC Bioinformatics, Vol. 11, Issue 1
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
journal, January 2015
- Kang, Dongwan D.; Froula, Jeff; Egan, Rob
- PeerJ, Vol. 3
Microbial species delineation using whole genome sequences
journal, July 2015
- Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia
- Nucleic Acids Research, Vol. 43, Issue 14
antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification
journal, April 2017
- Blin, Kai; Wolf, Thomas; Chevrette, Marc G.
- Nucleic Acids Research, Vol. 45, Issue W1
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
journal, May 2015
- Parks, Donovan H.; Imelfort, Michael; Skennerton, Connor T.
- Genome Research, Vol. 25, Issue 7
Maintaining a microbial genome & metagenome data analysis system in an academic setting
conference, January 2014
- Chen, I-Min A.; Markowitz, Victor M.; Szeto, Ernest
- Proceedings of the 26th International Conference on Scientific and Statistical Database Management - SSDBM '14
Infernal 1.1: 100-fold faster RNA homology searches
journal, September 2013
- Nawrocki, E. P.; Eddy, S. R.
- Bioinformatics, Vol. 29, Issue 22
The reconstruction of 2,631 draft metagenome-assembled genomes from the global oceans
journal, January 2018
- Tully, Benjamin J.; Graham, Elaina D.; Heidelberg, John F.
- Scientific Data, Vol. 5, Issue 1
Infernal 1.0: inference of RNA alignments
journal, March 2009
- Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R.
- Bioinformatics, Vol. 25, Issue 10
Shotgun metagenomics, from sampling to analysis
journal, September 2017
- Quince, Christopher; Walker, Alan W.; Simpson, Jared T.
- Nature Biotechnology, Vol. 35, Issue 9
IMG/M: integrated genome and metagenome comparative data analysis system
journal, October 2016
- Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
- Nucleic Acids Research, Vol. 45, Issue D1
Protein interaction maps for complete genomes based on gene fusion events
journal, November 1999
- Enright, Anton J.; Iliopoulos, Ioannis; Kyrpides, Nikos C.
- Nature, Vol. 402, Issue 6757
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
journal, January 1995
- Benjamini, Yoav; Hochberg, Yosef
- Journal of the Royal Statistical Society: Series B (Methodological), Vol. 57, Issue 1
IMG-ABC: new features for bacterial secondary metabolism analysis and targeted biosynthetic gene cluster discovery in thousands of microbial genomes
journal, November 2016
- Hadjithomas, Michalis; Chen, I-Min A.; Chu, Ken
- Nucleic Acids Research, Vol. 45, Issue D1
KEGG as a reference resource for gene and protein annotation
journal, October 2015
- Kanehisa, Minoru; Sato, Yoko; Kawashima, Masayuki
- Nucleic Acids Research, Vol. 44, Issue D1
Evaluation of methods for the prediction of membrane spanning regions
journal, July 2001
- Moller, S.; Croning, M. D. R.; Apweiler, R.
- Bioinformatics, Vol. 17, Issue 7
Infernal 1.0: inference of RNA alignments
journal, June 2009
- Nawrocki, E. P.; Kolbe, D. L.; Eddy, S. R.
- Bioinformatics, Vol. 25, Issue 13
Works referencing / citing this record:
Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2
journal, May 2019
- Gonnella, Giorgio; Adam, Nicole; Perner, Mirjam
- BMC Genomics, Vol. 20, Issue 1
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journal, July 2019
- Thomas, Scott C.; Tamadonfar, Kevin O.; Seymour, Cale O.
- Frontiers in Microbiology, Vol. 10
Complete genome sequence analysis of the thermoacidophilic verrucomicrobial methanotroph “Candidatus Methylacidiphilum kamchatkense” strain Kam1 and comparison with its closest relatives
journal, August 2019
- Kruse, Thomas; Ratnadevi, Chandini Murarilal; Erikstad, Helge-André
- BMC Genomics, Vol. 20, Issue 1
Thermophilic methanotrophs: in hot pursuit
journal, August 2019
- Houghton, Karen M.; Carere, Carlo R.; Stott, Matthew B.
- FEMS Microbiology Ecology, Vol. 95, Issue 9
IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase
journal, October 2019
- Palaniappan, Krishnaveni; Chen, I-Min A.; Chu, Ken
- Nucleic Acids Research
Aquirufa antheringensis gen. nov., sp. nov. and Aquirufa nivalisilvae sp. nov., representing a new genus of widespread freshwater bacteria
journal, September 2019
- Pitt, Alexandra; Schmidt, Johanna; Koll, Ulrike
- International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 9
Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families
journal, November 2019
- Wang, Yan; Shi, Qiang; Yang, Pengshuo
- Genome Biology, Vol. 20, Issue 1
Chemotaxis Towards Aromatic Compounds: Insights from Comamonas testosteroni
journal, June 2019
- Wang, Yun-Hao; Huang, Zhou; Liu, Shuang-Jiang
- International Journal of Molecular Sciences, Vol. 20, Issue 11
Marine Natural Products from Microalgae: An -Omics Overview
journal, May 2019
- Lauritano, Chiara; Ferrante, Maria Immacolata; Rogato, Alessandra
- Marine Drugs, Vol. 17, Issue 5
Thermophilic methanotrophs: in hot pursuit
journal, August 2019
- Houghton, Karen M.; Carere, Carlo R.; Stott, Matthew B.
- FEMS Microbiology Ecology, Vol. 95, Issue 9
IMG-ABC v.5.0: an update to the IMG/Atlas of Biosynthetic Gene Clusters Knowledgebase
journal, October 2019
- Palaniappan, Krishnaveni; Chen, I-Min A.; Chu, Ken
- Nucleic Acids Research
Aquirufa antheringensis gen. nov., sp. nov. and Aquirufa nivalisilvae sp. nov., representing a new genus of widespread freshwater bacteria
journal, September 2019
- Pitt, Alexandra; Schmidt, Johanna; Koll, Ulrike
- International Journal of Systematic and Evolutionary Microbiology, Vol. 69, Issue 9
Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2
journal, May 2019
- Gonnella, Giorgio; Adam, Nicole; Perner, Mirjam
- BMC Genomics, Vol. 20, Issue 1
Complete genome sequence analysis of the thermoacidophilic verrucomicrobial methanotroph “Candidatus Methylacidiphilum kamchatkense” strain Kam1 and comparison with its closest relatives
journal, August 2019
- Kruse, Thomas; Ratnadevi, Chandini Murarilal; Erikstad, Helge-André
- BMC Genomics, Vol. 20, Issue 1
Fueling ab initio folding with marine metagenomics enables structure and function predictions of new protein families
journal, November 2019
- Wang, Yan; Shi, Qiang; Yang, Pengshuo
- Genome Biology, Vol. 20, Issue 1
Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures
journal, July 2019
- Thomas, Scott C.; Tamadonfar, Kevin O.; Seymour, Cale O.
- Frontiers in Microbiology, Vol. 10
Chemotaxis Towards Aromatic Compounds: Insights from Comamonas testosteroni
journal, June 2019
- Wang, Yun-Hao; Huang, Zhou; Liu, Shuang-Jiang
- International Journal of Molecular Sciences, Vol. 20, Issue 11
Marine Natural Products from Microalgae: An -Omics Overview
journal, May 2019
- Lauritano, Chiara; Ferrante, Maria Immacolata; Rogato, Alessandra
- Marine Drugs, Vol. 17, Issue 5
Discovery of 20 novel ribosomal leader candidates in bacteria and archaea
journal, May 2020
- Eckert, Iris; Weinberg, Zasha
- BMC Microbiology, Vol. 20, Issue 1
Different roles of two groEL homologues in methylotrophic utiliser of dichloromethane Methylorubrum extorquens DM4
journal, August 2019
- Firsova, Yulia E.; Torgonskaya, Maria L.
- Antonie van Leeuwenhoek, Vol. 113, Issue 1
Microbial community analysis using high-throughput sequencing technology: a beginner’s guide for microbiologists
journal, February 2020
- Jo, Jihoon; Oh, Jooseong; Park, Chungoo
- Journal of Microbiology, Vol. 58, Issue 3
Data mining of metagenomes to find novel enzymes: a non-computationally intensive method
journal, January 2020
- Góngora-Castillo, Elsa; López-Ochoa, Luisa A.; Apolinar-Hernández, Max M.
- 3 Biotech, Vol. 10, Issue 2
Active subseafloor microbial communities from Mariana back-arc venting fluids share metabolic strategies across different thermal niches and taxa
journal, May 2019
- Trembath-Reichert, Elizabeth; Butterfield, David A.; Huber, Julie A.
- The ISME Journal, Vol. 13, Issue 9
High proportions of bacteria and archaea across most biomes remain uncultured
journal, August 2019
- Steen, Andrew D.; Crits-Christoph, Alexander; Carini, Paul
- The ISME Journal, Vol. 13, Issue 12
Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere
journal, November 2019
- Doud, Devin F. R.; Bowers, Robert M.; Schulz, Frederik
- The ISME Journal, Vol. 14, Issue 3
MpsAB is important for Staphylococcus aureus virulence and growth at atmospheric CO2 levels
journal, August 2019
- Fan, Sook-Ha; Ebner, Patrick; Reichert, Sebastian
- Nature Communications, Vol. 10, Issue 1
A predator-prey interaction between a marine Pseudoalteromonas sp. and Gram-positive bacteria
journal, January 2020
- Tang, Bai-Lu; Yang, Jie; Chen, Xiu-Lan
- Nature Communications, Vol. 11, Issue 1
Cyclic GMP–AMP signalling protects bacteria against viral infection
journal, September 2019
- Cohen, Daniel; Melamed, Sarah; Millman, Adi
- Nature, Vol. 574, Issue 7780
Giant virus diversity and host interactions through global metagenomics
journal, January 2020
- Schulz, Frederik; Roux, Simon; Paez-Espino, David
- Nature, Vol. 578, Issue 7795
Microbial metagenomes and metatranscriptomes during a coastal phytoplankton bloom
journal, July 2019
- Nowinski, Brent; Smith, Christa B.; Thomas, Courtney M.
- Scientific Data, Vol. 6, Issue 1
Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot
journal, July 2019
- Camargo, Antonio Pedro; de Souza, Rafael Soares Correa; de Britto Costa, Patrícia
- Scientific Data, Vol. 6, Issue 1
Manipulating nitrogen regulation in diazotrophic bacteria for agronomic benefit
journal, April 2019
- Bueno Batista, Marcelo; Dixon, Ray
- Biochemical Society Transactions, Vol. 47, Issue 2
Large-scale identification of pathogen essential genes during coinfection with sympatric and allopatric microbes
journal, August 2019
- Lewin, Gina R.; Stacy, Apollo; Michie, Kelly L.
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 39
Genome-wide identification of Pseudomonas syringae genes required for fitness during colonization of the leaf surface and apoplast
journal, September 2019
- Helmann, Tyler C.; Deutschbauer, Adam M.; Lindow, Steven E.
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 38
GDGT cyclization proteins identify the dominant archaeal sources of tetraether lipids in the ocean
journal, October 2019
- Zeng, Zhirui; Liu, Xiao-Lei; Farley, Kristen R.
- Proceedings of the National Academy of Sciences, Vol. 116, Issue 45
Insights into the mechanism and regulation of the CbbQO-type Rubisco activase, a MoxR AAA+ ATPase
journal, December 2019
- Tsai, Yi-Chin Candace; Ye, Fuzhou; Liew, Lynette
- Proceedings of the National Academy of Sciences, Vol. 117, Issue 1
Energy conservation involving 2 respiratory circuits
journal, December 2019
- Schoelmerich, Marie Charlotte; Katsyv, Alexander; Dönig, Judith
- Proceedings of the National Academy of Sciences, Vol. 117, Issue 2
DeePaC: predicting pathogenic potential of novel DNA with reverse-complement neural networks
journal, July 2019
- Bartoszewicz, Jakub M.; Seidel, Anja; Rentzsch, Robert
- Bioinformatics
AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences
journal, January 2019
- Singh, Abhijeet; Müller, Bettina; Fuxelius, Hans-Henrik
- Database, Vol. 2019
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
journal, October 2019
- Mende, Daniel R.; Letunic, Ivica; Maistrenko, Oleksandr M.
- Nucleic Acids Research
MGnify: the microbiome analysis resource in 2020
journal, November 2019
- Mitchell, Alex L.; Almeida, Alexandre; Beracochea, Martin
- Nucleic Acids Research
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis
journal, October 2019
- Vallenet, David; Calteau, Alexandra; Dubois, Mathieu
- Nucleic Acids Research
High-quality draft genome sequences of Pseudomonas monteilii DSM 14164T, Pseudomonas mosselii DSM 17497T, Pseudomonas plecoglossicida DSM 15088T, Pseudomonas taiwanensis DSM 21245T and Pseudomonas vranovensis DSM 16006T: taxonomic considerations
journal, December 2019
- Peña, Arantxa; Busquets, Antonio; Gomila, Margarita
- Access Microbiology, Vol. 1, Issue 10
Fluviispira multicolorata gen. nov., sp. nov. and Silvanigrella paludirubra sp. nov., isolated from freshwater habitats
journal, March 2020
- Pitt, Alexandra; Koll, Ulrike; Schmidt, Johanna
- International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 3
AzeR, a transcriptional regulator that responds to azelaic acid in Pseudomonas nitroreducens
journal, January 2020
- Bez, Cristina; Javvadi, Sree Gowrinadh; Bertani, Iris
- Microbiology, Vol. 166, Issue 1
Geologic legacy spanning >90 years explains unique Yellowstone hot spring geochemistry and biodiversity
journal, August 2019
- Payne, Devon; Dunham, Eric C.; Mohr, Elizabeth
- Environmental Microbiology, Vol. 21, Issue 11
Symbiosis of a P2‐family phage and deep‐sea Shewanella putrefaciens
journal, August 2019
- Liu, Xiaoxiao; Tang, Kaihao; Zhang, Dali
- Environmental Microbiology, Vol. 21, Issue 11
l ‐Rhamnose catabolism in archaea
journal, February 2019
- Reinhardt, Andreas; Johnsen, Ulrike; Schönheit, Peter
- Molecular Microbiology, Vol. 111, Issue 4
Genome Sequences of Four Vibrio parahaemolyticus Strains Isolated from the English Channel and the River Thames
journal, June 2019
- Witherall, Lucy; Wagley, Sariqa; Butler, Clive
- Microbiology Resource Announcements, Vol. 8, Issue 24
Draft Genome Sequence of Mn(II)-Oxidizing Bacterium Oxalobacteraceae sp. Strain AB_14
journal, October 2019
- Bushman, Timothy J.; Akob, Denise M.; Bohu, Tsing
- Microbiology Resource Announcements, Vol. 8, Issue 43
Metatranscriptomic Sequencing of a Cyanobacterial Soil-Surface Consortium with and without a Diverse Underlying Soil Microbiome
journal, January 2020
- Bell, Terrence H.; Trexler, Ryan V.; Peng, Xin
- Microbiology Resource Announcements, Vol. 9, Issue 1
Complete Genome Sequence for Asinibacterium sp. Strain OR53 and Draft Genome Sequence for Asinibacterium sp. Strain OR43, Two Bacteria Tolerant to Uranium
journal, April 2019
- Brzoska, Ryann M.; Huntemann, Marcel; Clum, Alicia
- Microbiology Resource Announcements, Vol. 8, Issue 14
Curated BLAST for Genomes
journal, March 2019
- Price, Morgan N.; Arkin, Adam P.
- mSystems, Vol. 4, Issue 2
Genome Sequence of Colistin-Resistant Bacteremic Shewanella algae Carrying the Beta-Lactamase Gene bla OXA-55
journal, June 2019
- Chen, Ying-Ju; Tung, Kwong-Chung; Hong, Yu-Kai
- Canadian Journal of Infectious Diseases and Medical Microbiology, Vol. 2019
Direct pathway cloning of the sodorifen biosynthetic gene cluster and recombinant generation of its product in E. coli
journal, February 2019
- Duell, Elke R.; D’Agostino, Paul M.; Shapiro, Nicole
- Microbial Cell Factories, Vol. 18, Issue 1
Challenges in the construction of knowledge bases for human microbiome-disease associations
journal, September 2019
- Badal, Varsha Dave; Wright, Dustin; Katsis, Yannis
- Microbiome, Vol. 7, Issue 1
A pipeline for targeted metagenomics of environmental bacteria
journal, February 2020
- Grieb, Anissa; Bowers, Robert M.; Oggerin, Monike
- Microbiome, Vol. 8, Issue 1
Shotgun metagenomic analysis of microbial communities from the Loxahatchee nature preserve in the Florida Everglades
journal, January 2020
- Abraham, Briana S.; Caglayan, Deniz; Carrillo, Natalie V.
- Environmental Microbiome, Vol. 15, Issue 1
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journal, August 2019
- de Souza, Rafael Soares Correa; Armanhi, Jaderson Silveira Leite; Damasceno, Natália de Brito
- Frontiers in Microbiology, Vol. 10
Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes
journal, September 2019
- García-López, Marina; Meier-Kolthoff, Jan P.; Tindall, Brian J.
- Frontiers in Microbiology, Vol. 10
Genomic Insights into the Carbon and Energy Metabolism of a Thermophilic Deep-Sea Bacterium Deferribacter autotrophicus Revealed New Metabolic Traits in the Phylum Deferribacteres
journal, October 2019
- Slobodkin, Alexander; Slobodkina, Galina; Allioux, Maxime
- Genes, Vol. 10, Issue 11
Cytochrome P450 Monooxygenase CYP139 Family Involved in the Synthesis of Secondary Metabolites in 824 Mycobacterial Species
journal, May 2019
- Syed, Puleng Rosinah; Chen, Wanping; Nelson, David R.
- International Journal of Molecular Sciences, Vol. 20, Issue 11
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives
journal, October 2019
- Ambrosino, Luca; Tangherlini, Michael; Colantuono, Chiara
- Marine Drugs, Vol. 17, Issue 10
Broad Environmental Tolerance for a Salicola Host-Phage Pair Isolated from the Cargill Solar Saltworks, Newark, CA, USA
journal, April 2019
- Rodela, Meghan L.; Sabet, Shereen; Peterson, Allison
- Microorganisms, Vol. 7, Issue 4
Structural elucidation and environmental distributions of butanetriol and pentanetriol dialkyl glycerol tetraethers (BDGTs and PDGTs)
journal, January 2020
- Coffinet, Sarah; Meador, Travis B.; Mühlena, Lukas
- Biogeosciences, Vol. 17, Issue 2
Enterococcus faecium secreted antigen A generates muropeptides to enhance host immunity and limit bacterial pathogenesis
journal, April 2019
- Kim, Byungchul; Wang, Yen-Chih; Hespen, Charles W.
- eLife, Vol. 8
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
journal, January 2019
- Kang, Dongwan D.; Li, Feng; Kirton, Edward
- PeerJ, Vol. 7