Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform
Abstract
Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. As a result, this bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.
- Authors:
-
- Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
- Defense Threat Reduction Agency, Fort Belvoir, VA (United States); Naval Medical Research Center-Frederick, Fort Detrick, MD (United States)
- Naval Medical Research Center-Frederick, Fort Detrick, MD (United States); Henry M. Jackson Foundation, Bethesda, MD (United States)
- Naval Medical Research Center-Frederick, Fort Detrick, MD (United States)
- Publication Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOD; USDOE
- OSTI Identifier:
- 1342855
- Report Number(s):
- LA-UR-15-27035; LA-UR-15-22467
Journal ID: ISSN 0305-1048; TRN: US1701210
- Grant/Contract Number:
- AC52-06NA25396
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nucleic Acids Research
- Additional Journal Information:
- Journal Volume: 45; Journal Issue: 1; Conference: DHS Biodetection strategy meeting, Los Alamos, NM (United States), 15-16 Apr 2015; Journal ID: ISSN 0305-1048
- Publisher:
- Oxford University Press
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 97 MATHEMATICS AND COMPUTING; Biological Science; Computer Science; cloud compatible bioinformatics pipelines and workflows; integrated web-based genome analysis; isolate and metagenome NGS data analysis and visualization; next generation sequencing genomics and metagenome
Citation Formats
Li, Po-E, Lo, Chien -Chi, Anderson, Joseph J., Davenport, Karen W., Bishop-Lilly, Kimberly A., Xu, Yan, Ahmed, Sanaa, Feng, Shihai, Mokashi, Vishwesh P., and Chain, Patrick S. G. Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. United States: N. p., 2016.
Web. doi:10.1093/nar/gkw1027.
Li, Po-E, Lo, Chien -Chi, Anderson, Joseph J., Davenport, Karen W., Bishop-Lilly, Kimberly A., Xu, Yan, Ahmed, Sanaa, Feng, Shihai, Mokashi, Vishwesh P., & Chain, Patrick S. G. Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform. United States. https://doi.org/10.1093/nar/gkw1027
Li, Po-E, Lo, Chien -Chi, Anderson, Joseph J., Davenport, Karen W., Bishop-Lilly, Kimberly A., Xu, Yan, Ahmed, Sanaa, Feng, Shihai, Mokashi, Vishwesh P., and Chain, Patrick S. G. Thu .
"Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform". United States. https://doi.org/10.1093/nar/gkw1027. https://www.osti.gov/servlets/purl/1342855.
@article{osti_1342855,
title = {Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform},
author = {Li, Po-E and Lo, Chien -Chi and Anderson, Joseph J. and Davenport, Karen W. and Bishop-Lilly, Kimberly A. and Xu, Yan and Ahmed, Sanaa and Feng, Shihai and Mokashi, Vishwesh P. and Chain, Patrick S. G.},
abstractNote = {Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. As a result, this bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.},
doi = {10.1093/nar/gkw1027},
journal = {Nucleic Acids Research},
number = 1,
volume = 45,
place = {United States},
year = {Thu Nov 24 00:00:00 EST 2016},
month = {Thu Nov 24 00:00:00 EST 2016}
}
Web of Science
Works referenced in this record:
Accurate read-based metagenome characterization using a hierarchical suite of unique signatures
journal, March 2015
- Freitas, Tracey Allen K.; Li, Po-E; Scholz, Matthew B.
- Nucleic Acids Research, Vol. 43, Issue 10
RNA-seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803
journal, January 2012
- Wang, Jiangxin; Chen, Lei; Huang, Siqiang
- Biotechnology for Biofuels, Vol. 5, Issue 1
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
IMG/M 4 version of the integrated metagenome comparative analysis system
journal, October 2013
- Markowitz, Victor M.; Chen, I-Min A.; Chu, Ken
- Nucleic Acids Research, Vol. 42, Issue D1, p. D568-D573
Ralstonia pickettii—innocent bystander or a potential threat?
journal, February 2006
- Stelzmueller, I.; Biebl, M.; Wiesmayr, S.
- Clinical Microbiology and Infection, Vol. 12, Issue 2
Versatile and open software for comparing large genomes
journal, January 2004
- Kurtz, Stefan; Phillippy, Adam; Delcher, Arthur L.
- Genome Biology, Vol. 5, Issue 2, R12
Next-generation sequencing diagnostics of bacteremia in septic patients
journal, July 2016
- Grumaz, Silke; Stevens, Philip; Grumaz, Christian
- Genome Medicine, Vol. 8, Issue 1
GenePattern 2.0
journal, May 2006
- Reich, Michael; Liefeld, Ted; Gould, Joshua
- Nature Genetics, Vol. 38, Issue 5
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
journal, October 2011
- Kircher, Martin; Sawyer, Susanna; Meyer, Matthias
- Nucleic Acids Research, Vol. 40, Issue 1
RATT: Rapid Annotation Transfer Tool
journal, February 2011
- Otto, Thomas D.; Dillon, Gary P.; Degrave, Wim S.
- Nucleic Acids Research, Vol. 39, Issue 9
Novel Bacteriophages Containing a Genome of Another Bacteriophage within Their Genomes
journal, July 2012
- Swanson, Maud M.; Reavy, Brian; Makarova, Kira S.
- PLoS ONE, Vol. 7, Issue 7
Basic Local Alignment Search Tool
journal, October 1990
- Altschul, S.
- Journal of Molecular Biology, Vol. 215, Issue 3
Next generation sequencing technology: Advances and applications
journal, October 2014
- Buermans, H. P. J.; den Dunnen, J. T.
- Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Vol. 1842, Issue 10
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010
- Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.
- PLoS ONE, Vol. 5, Issue 3
Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production
journal, September 2014
- Wohlbach, Dana J.; Rovinskiy, Nikolay; Lewis, Jeffrey A.
- Genome Biology and Evolution, Vol. 6, Issue 9
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
journal, November 2014
- Salter, Susannah J.; Cox, Michael J.; Turek, Elena M.
- BMC Biology, Vol. 12, Issue 1
Pneumonic Plague Cluster, Uganda, 2004
journal, March 2006
- Begier, Elizabeth M.; Asiki, Gershim; Anywaine, Zaccheus
- Emerging Infectious Diseases, Vol. 12, Issue 3
Genomic characterization of the Yersinia genus
journal, January 2010
- Chen, Peter E.; Cook, Christopher; Stewart, Andrew C.
- Genome Biology, Vol. 11, Issue 1
Primer3—new capabilities and interfaces
journal, June 2012
- Untergasser, Andreas; Cutcutache, Ioana; Koressaar, Triinu
- Nucleic Acids Research, Vol. 40, Issue 15
Interactive metagenomic visualization in a Web browser
journal, September 2011
- Ondov, Brian D.; Bergman, Nicholas H.; Phillippy, Adam M.
- BMC Bioinformatics, Vol. 12, Issue 1
Kraken: ultrafast metagenomic sequence classification using exact alignments
journal, January 2014
- Wood, Derrick E.; Salzberg, Steven L.
- Genome Biology, Vol. 15, Issue 3
Complete Genome Sequences for 35 Biothreat Assay-Relevant Bacillus Species: TABLE 1
journal, April 2015
- Johnson, Shannon L.; Daligault, Hajnalka E.; Davenport, Karen W.
- Genome Announcements, Vol. 3, Issue 2
The microbiome of New World vultures
journal, November 2014
- Roggenbuck, Michael; Bærholm Schnell, Ida; Blom, Nikolaj
- Nature Communications, Vol. 5, Issue 1
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014
- Stamatakis, Alexandros
- Bioinformatics, Vol. 30, Issue 9
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012
- Peng, Y.; Leung, H. C. M.; Yiu, S. M.
- Bioinformatics, Vol. 28, Issue 11
Prokka: rapid prokaryotic genome annotation
journal, March 2014
- Seemann, T.
- Bioinformatics, Vol. 30, Issue 14
Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences
journal, October 2006
- Fouts, Derrick E.
- Nucleic Acids Research, Vol. 34, Issue 20
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
journal, May 2012
- Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry
- Journal of Computational Biology, Vol. 19, Issue 5
Single-molecule sequencing to track plasmid diversity of hospital-associated carbapenemase-producing Enterobacteriaceae
journal, September 2014
- Conlan, S.; Thomas, P. J.; Deming, C.
- Science Translational Medicine, Vol. 6, Issue 254
Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists
journal, January 2010
- Blankenberg, Daniel; Kuster, Gregory Von; Coraor, Nathaniel
- Current Protocols in Molecular Biology, Vol. 89, Issue 1
JBrowse: A next-generation genome browser
journal, July 2009
- Skinner, M. E.; Uzilov, A. V.; Stein, L. D.
- Genome Research, Vol. 19, Issue 9
Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia
journal, March 2013
- Watson-Haigh, N. S.; Shang, C. A.; Haimel, M.
- Briefings in Bioinformatics, Vol. 14, Issue 5
Automated ensemble assembly and validation of microbial genomes
journal, May 2014
- Koren, Sergey; Treangen, Todd J.; Hill, Christopher M.
- BMC Bioinformatics, Vol. 15, Issue 1
PATRIC, the bacterial bioinformatics database and analysis resource
journal, November 2013
- Wattam, Alice R.; Abraham, David; Dalay, Oral
- Nucleic Acids Research, Vol. 42, Issue D1
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
Rapid Whole-Genome Sequencing for Surveillance of Salmonella enterica Serovar Enteritidis
journal, August 2014
- den Bakker, Henk C.; Allard, Marc W.; Bopp, Dianna
- Emerging Infectious Diseases, Vol. 20, Issue 8
jsPhyloSVG: A Javascript Library for Visualizing Interactive and Vector-Based Phylogenetic Trees on the Web
journal, August 2010
- Smits, Samuel A.; Ouverney, Cleber C.
- PLoS ONE, Vol. 5, Issue 8
DNA sequencing with chain-terminating inhibitors
journal, December 1977
- Sanger, F.; Nicklen, S.; Coulson, A. R.
- Proceedings of the National Academy of Sciences, Vol. 74, Issue 12
Bacterial Pathogens in the Nasopharynx, Nasal Cavity, and Osteomeatal Complex during Wellness and Viral Infection
journal, January 2013
- Rawlings, Brad A.; Higgins, Thomas S.; Han, Joseph K.
- American Journal of Rhinology & Allergy, Vol. 27, Issue 1
Genome sequencing in microfabricated high-density picolitre reactors
journal, July 2005
- Margulies, Marcel; Egholm, Michael; Altman, William E.
- Nature, Vol. 437, Issue 7057, p. 376-380
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
journal, November 2013
- Overbeek, Ross; Olson, Robert; Pusch, Gordon D.
- Nucleic Acids Research, Vol. 42, Issue D1
Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry
journal, April 2009
- Scott, L. J.; Muglia, P.; Kong, X. Q.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 18
Metagenomic microbial community profiling using unique clade-specific marker genes
journal, June 2012
- Segata, Nicola; Waldron, Levi; Ballarini, Annalisa
- Nature Methods, Vol. 9, Issue 8
A new method for sequencing DNA.
journal, February 1977
- Maxam, A. M.; Gilbert, W.
- Proceedings of the National Academy of Sciences, Vol. 74, Issue 2
Understanding the limitations of next generation sequencing informatics, an approach to clinical pipeline validation using artificial data sets
journal, December 2013
- Daber, Robert; Sukhadia, Shrey; Morrissette, Jennifer J. D.
- Cancer Genetics, Vol. 206, Issue 12
Rapid evaluation and quality control of next generation sequencing data with FaQCs
journal, November 2014
- Lo, Chien-Chi; Chain, Patrick S. G.
- BMC Bioinformatics, Vol. 15, Issue 1
Bacillus weihenstephanensis characteristics are present in Bacillus cereus and Bacillus mycoides strains
journal, March 2013
- Soufiane, Brahim; Côté, Jean-Charles
- FEMS Microbiology Letters, Vol. 341, Issue 2
DNA extraction approaches substantially influence the assessment of the human breast milk microbiome
journal, January 2020
- Douglas, Chloe A.; Ivey, Kerry L.; Papanicolas, Lito E.
- Scientific Reports, Vol. 10, Issue 1
Chemogenomic profiling of breast cancer patient-derived xenografts reveals targetable vulnerabilities for difficult-to-treat tumors
journal, June 2020
- Savage, Paul; Pacis, Alain; Kuasne, Hellen
- Communications Biology, Vol. 3, Issue 1
Automated ensemble assembly and validation of microbial genomes
journal, February 2014
- Koren, Sergey; Treangen, Todd J.; Hill, Christopher M.
- BMC Bioinformatics
Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea
journal, February 2021
- Kangale, Luis Johnson; Levasseur, Anthony; Raoult, Didier
- Microbiology Resource Announcements, Vol. 10, Issue 5
Draft Genome Sequence of Medusavirus Stheno, Isolated from the Tatakai River of Uji, Japan
journal, January 2021
- Yoshida, Koki; Zhang, Ruixuan; Garcia, Kimberly G.
- Microbiology Resource Announcements, Vol. 10, Issue 1
An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities.
text, January 2021
- O'Sullivan, Denise M.; Doyle, Ronan M.; Temisak, Sasithon
- Apollo - University of Cambridge Repository
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses.
text, January 2014
- Salter, Susannah; Cox, Michael J.; Turek, Elena M.
- Apollo - University of Cambridge Repository
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
text, January 2014
- Stamatakis, A.
- Karlsruhe
Automated ensemble assembly and validation of microbial genomes
text, January 2014
- Koren, Sergey; Treangen, Todd J.; Hill, Christopher M.
- Springer Nature
Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists
journal, January 2010
- Blankenberg, Daniel; Kuster, Gregory Von; Coraor, Nathaniel
- Current Protocols in Molecular Biology, Vol. 89, Issue 1
Understanding the limitations of next generation sequencing informatics, an approach to clinical pipeline validation using artificial data sets
journal, December 2013
- Daber, Robert; Sukhadia, Shrey; Morrissette, Jennifer J. D.
- Cancer Genetics, Vol. 206, Issue 12
Genome sequencing in microfabricated high-density picolitre reactors
journal, July 2005
- Margulies, Marcel; Egholm, Michael; Altman, William E.
- Nature, Vol. 437, Issue 7057, p. 376-380
The microbiome of New World vultures
journal, November 2014
- Roggenbuck, Michael; Bærholm Schnell, Ida; Blom, Nikolaj
- Nature Communications, Vol. 5, Issue 1
GenePattern 2.0
journal, May 2006
- Reich, Michael; Liefeld, Ted; Gould, Joshua
- Nature Genetics, Vol. 38, Issue 5
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
Metagenomic microbial community profiling using unique clade-specific marker genes
journal, June 2012
- Segata, Nicola; Waldron, Levi; Ballarini, Annalisa
- Nature Methods, Vol. 9, Issue 8
Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry
journal, April 2009
- Scott, L. J.; Muglia, P.; Kong, X. Q.
- Proceedings of the National Academy of Sciences, Vol. 106, Issue 18
DNA sequencing with chain-terminating inhibitors
journal, December 1977
- Sanger, F.; Nicklen, S.; Coulson, A. R.
- Proceedings of the National Academy of Sciences, Vol. 74, Issue 12
SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
journal, May 2012
- Bankevich, Anton; Nurk, Sergey; Antipov, Dmitry
- Journal of Computational Biology, Vol. 19, Issue 5
Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia
journal, March 2013
- Watson-Haigh, N. S.; Shang, C. A.; Haimel, M.
- Briefings in Bioinformatics, Vol. 14, Issue 5
IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth
journal, April 2012
- Peng, Y.; Leung, H. C. M.; Yiu, S. M.
- Bioinformatics, Vol. 28, Issue 11
Prokka: rapid prokaryotic genome annotation
journal, March 2014
- Seemann, T.
- Bioinformatics, Vol. 30, Issue 14
Comparative Genomics of Saccharomyces cerevisiae Natural Isolates for Bioenergy Production
journal, September 2014
- Wohlbach, Dana J.; Rovinskiy, Nikolay; Lewis, Jeffrey A.
- Genome Biology and Evolution, Vol. 6, Issue 9
Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences
journal, October 2006
- Fouts, Derrick E.
- Nucleic Acids Research, Vol. 34, Issue 20
Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform
journal, October 2011
- Kircher, Martin; Sawyer, Susanna; Meyer, Matthias
- Nucleic Acids Research, Vol. 40, Issue 1
Primer3—new capabilities and interfaces
journal, June 2012
- Untergasser, Andreas; Cutcutache, Ioana; Koressaar, Triinu
- Nucleic Acids Research, Vol. 40, Issue 15
PATRIC, the bacterial bioinformatics database and analysis resource
journal, November 2013
- Wattam, Alice R.; Abraham, David; Dalay, Oral
- Nucleic Acids Research, Vol. 42, Issue D1
IMG/M 4 version of the integrated metagenome comparative analysis system
journal, October 2013
- Markowitz, Victor M.; Chen, I-Min A.; Chu, Ken
- Nucleic Acids Research, Vol. 42, Issue D1, p. D568-D573
JBrowse: A next-generation genome browser
journal, July 2009
- Skinner, M. E.; Uzilov, A. V.; Stein, L. D.
- Genome Research, Vol. 19, Issue 9
Bacillus weihenstephanensis characteristics are present in Bacillus cereus and Bacillus mycoides strains
journal, March 2013
- Soufiane, Brahim; Côté, Jean-Charles
- FEMS Microbiology Letters, Vol. 341, Issue 2
Ralstonia pickettii—innocent bystander or a potential threat?
journal, February 2006
- Stelzmueller, I.; Biebl, M.; Wiesmayr, S.
- Clinical Microbiology and Infection, Vol. 12, Issue 2
Thirty-Two Complete Genome Assemblies of Nine Yersinia Species, Including Y. pestis , Y. pseudotuberculosis , and Y. enterocolitica : TABLE 1
journal, April 2015
- Johnson, Shannon L.; Daligault, Hajnalka E.; Davenport, Karen W.
- Genome Announcements, Vol. 3, Issue 2
New method for plague surveillance using polymerase chain reaction to detect Yersinia pestis in fleas.
journal, January 1993
- Hinnebusch, J.; Schwan, T. G.
- Journal of Clinical Microbiology, Vol. 31, Issue 6
PCR Assay To Detect Bacillus anthracis Spores in Heat-Treated Specimens
journal, February 2003
- Fasanella, A.; Losito, S.; Adone, R.
- Journal of Clinical Microbiology, Vol. 41, Issue 2
Analysis of the Upper Respiratory Tract Microbiotas as the Source of the Lung and Gastric Microbiotas in Healthy Individuals
journal, March 2015
- Bassis, Christine M.; Erb-Downward, John R.; Dickson, Robert P.
- mBio, Vol. 6, Issue 2
Interactive metagenomic visualization in a Web browser
journal, September 2011
- Ondov, Brian D.; Bergman, Nicholas H.; Phillippy, Adam M.
- BMC Bioinformatics, Vol. 12, Issue 1
RNA-seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803
journal, January 2012
- Wang, Jiangxin; Chen, Lei; Huang, Siqiang
- Biotechnology for Biofuels, Vol. 5, Issue 1
Genomic characterization of the Yersinia genus
journal, January 2010
- Chen, Peter E.; Cook, Christopher; Stewart, Andrew C.
- Genome Biology, Vol. 11, Issue 1
Kraken: ultrafast metagenomic sequence classification using exact alignments
journal, January 2014
- Wood, Derrick E.; Salzberg, Steven L.
- Genome Biology, Vol. 15, Issue 3
Rapid evaluation and quality control of next generation sequencing data with FaQCs
journal, November 2014
- Lo, Chien-Chi; Chain, Patrick S. G.
- BMC Bioinformatics, Vol. 15, Issue 1
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
Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
journal, November 2014
- Salter, Susannah J.; Cox, Michael J.; Turek, Elena M.
- BMC Biology, Vol. 12, Issue 1
Next-generation sequencing diagnostics of bacteremia in septic patients
journal, July 2016
- Grumaz, Silke; Stevens, Philip; Grumaz, Christian
- Genome Medicine, Vol. 8, Issue 1
Automated ensemble assembly and validation of microbial genomes
text, January 2014
- Koren, Sergey; Treangen, Todd J.; Hill, Christopher M.
- Springer Nature
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010
- Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.
- PLoS ONE, Vol. 5, Issue 3
Bacterial Pathogens in the Nasopharynx, Nasal Cavity, and Osteomeatal Complex during Wellness and Viral Infection
journal, January 2013
- Rawlings, Brad A.; Higgins, Thomas S.; Han, Joseph K.
- American Journal of Rhinology & Allergy, Vol. 27, Issue 1
Pneumonic Plague Cluster, Uganda, 2004
journal, March 2006
- Begier, Elizabeth M.; Asiki, Gershim; Anywaine, Zaccheus
- Emerging Infectious Diseases, Vol. 12, Issue 3
Rapid Whole-Genome Sequencing for Surveillance of Salmonella enterica Serovar Enteritidis
journal, August 2014
- den Bakker, Henk C.; Allard, Marc W.; Bopp, Dianna
- Emerging Infectious Diseases, Vol. 20, Issue 8
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
text, January 2014
- Stamatakis, A.
- Karlsruhe
Works referencing / citing this record:
Microbial Diversity in Bushmeat Samples Recovered from the Serengeti Ecosystem in Tanzania
journal, December 2019
- Katani, Robab; Schilling, Megan A.; Lyimo, Beatus
- Scientific Reports, Vol. 9, Issue 1
Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life
journal, February 2020
- Shakya, Migun; Ahmed, Sanaa A.; Davenport, Karen W.
- Scientific Reports, Vol. 10, Issue 1
Systematic processing of ribosomal RNA gene amplicon sequencing data
journal, December 2019
- Tremblay, Julien; Yergeau, Etienne
- GigaScience, Vol. 8, Issue 12
Next Generation Sequencing and Bioinformatics Methodologies for Infectious Disease Research and Public Health: Approaches, Applications, and Considerations for Development of Laboratory Capacity
journal, October 2019
- Maljkovic Berry, Irina; Melendrez, Melanie C.; Bishop-Lilly, Kimberly A.
- The Journal of Infectious Diseases
Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes
journal, July 2019
- Weiser, Rebecca; Green, Angharad E.; Bull, Matthew J.
- Microbial Genomics, Vol. 5, Issue 7
Nasal and gut microbiota for sows of different health status within six commercial swine farms from one swine production system
posted_content, April 2019
- Arruda, Andréia Gonçalves; Deblais, Loic; Hale, Vanessa
- BioRxiv
Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009‐2017
journal, January 2020
- Owuor, D. Collins; Ngoi, Joyce M.; Otieno, James R.
- Influenza and Other Respiratory Viruses, Vol. 14, Issue 3
Vampirovibrio chlorellavorus draft genome sequence, annotation, and preliminary characterization of pathogenicity determinants
journal, July 2019
- Hovde, Blake T.; Steichen, Seth A.; Starkenburg, Shawn R.
- Phycological Research, Vol. 68, Issue 1
“ Candidatus Nitrosotenuis aquarius,” an Ammonia-Oxidizing Archaeon from a Freshwater Aquarium Biofilter
journal, June 2018
- Sauder, Laura A.; Engel, Katja; Lo, Chien-Chi
- Applied and Environmental Microbiology, Vol. 84, Issue 19
Characterization of Novel Reoviruses Wad Medani Virus (Orbivirus) and Kundal Virus (Coltivirus) Collected from Hyalomma anatolicum Ticks in India during Surveillance for Crimean Congo Hemorrhagic Fever
journal, April 2019
- Yadav, Pragya D.; Whitmer, Shannon L. M.; Sarkale, Prasad
- Journal of Virology, Vol. 93, Issue 13
Complete Genome Sequence of a Parabacteroides distasonis Strain (CavFT hAR46) Isolated from a Gut Wall-Cavitating Microlesion in a Patient with Severe Crohn’s Disease
journal, September 2019
- Yang, Falong; Kumar, Anand; Davenport, Karen Walston
- Microbiology Resource Announcements, Vol. 8, Issue 36
Complete Genome Sequences of Historic Clostridioides difficile Food-Dwelling Ribotype 078 Strains in Canada Identical to That of the Historic Human Clinical Strain M120 in the United Kingdom
journal, September 2018
- Kumar, Anand; Davenport, Karen Walston; Vuyisich, Grace
- Microbiology Resource Announcements, Vol. 7, Issue 12
Draft Genome Sequence of the Industrially Significant Bacterium Bacillus amyloliquefaciens NRRL 942
journal, November 2018
- Meier, Matthew J.; Dodge, Annette; Beaudette, Lee A.
- Microbiology Resource Announcements, Vol. 7, Issue 18
Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples
journal, February 2019
- Paskey, Adrian C.; Frey, Kenneth G.; Schroth, Gary
- BMC Genomics, Vol. 20, Issue 1
Direct-from-blood RNA sequencing identifies the cause of post-bronchoscopy fever
journal, October 2019
- Ko, Emily R.; Philipson, Casandra W.; Burke, Thomas W.
- BMC Infectious Diseases, Vol. 19, Issue 1
Complete genome sequences of Clostridium perfringens Del1 strain isolated from chickens affected by necrotic enteritis
journal, November 2017
- Li, Charles; Yan, Xianghe; Lillehoj, Hyun S.
- Gut Pathogens, Vol. 9, Issue 1
Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
journal, March 2019
- Clarke, Erik L.; Taylor, Louis J.; Zhao, Chunyu
- Microbiome, Vol. 7, Issue 1
Effects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil
journal, May 2020
- Salam, Lateef B.; Obayori, Oluwafemi S.; Ilori, Mathew O.
- Bioresources and Bioprocessing, Vol. 7, Issue 1
Next-Generation Sequencing for Biodefense: Biothreat Detection, Forensics, and the Clinic
journal, March 2019
- Minogue, Timothy D.; Koehler, Jeffrey W.; Stefan, Christopher P.
- Clinical Chemistry, Vol. 65, Issue 3
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data
journal, March 2017
- Roumpeka, Despoina D.; Wallace, R. John; Escalettes, Frank
- Frontiers in Genetics, Vol. 8
Advances and Challenges in Metatranscriptomic Analysis
journal, September 2019
- Shakya, Migun; Lo, Chien-Chi; Chain, Patrick S. G.
- Frontiers in Genetics, Vol. 10
Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS)
journal, January 2019
- Deshpande, Samir V.; Reed, Timothy M.; Sullivan, Raymond F.
- MDPI
Characterizing Phage Genomes for Therapeutic Applications
journal, April 2018
- Philipson, Casandra; Voegtly, Logan; Lueder, Matthew
- Viruses, Vol. 10, Issue 4
Morphology and chemical behavior of model CsO x /Cu 2 O/Cu(111) nanocatalysts for methanol synthesis: Reaction with CO 2 and H 2
journal, January 2020
- Hamlyn, Rebecca; Mahapatra, Mausumi; Orozco, Ivan
- The Journal of Chemical Physics, Vol. 152, Issue 4
Microbial Diversity in Bushmeat Samples Recovered from the Serengeti Ecosystem in Tanzania
journal, December 2019
- Katani, Robab; Schilling, Megan A.; Lyimo, Beatus
- Scientific Reports, Vol. 9, Issue 1
Standardized phylogenetic and molecular evolutionary analysis applied to species across the microbial tree of life
journal, February 2020
- Shakya, Migun; Ahmed, Sanaa A.; Davenport, Karen W.
- Scientific Reports, Vol. 10, Issue 1
Systematic processing of ribosomal RNA gene amplicon sequencing data
journal, December 2019
- Tremblay, Julien; Yergeau, Etienne
- GigaScience, Vol. 8, Issue 12
Ten Genome Sequences of Human and Livestock Isolates of Bacillus anthracis from the Country of Georgia
journal, May 2017
- Khmaladze, Ekaterine; Dzavashvili, Giorgi; Chanturia, Gvantsa
- Genome Announcements, Vol. 5, Issue 19
Complete Genome Sequence of a Parabacteroides distasonis Strain (CavFT hAR46) Isolated from a Gut Wall-Cavitating Microlesion in a Patient with Severe Crohn’s Disease
journal, September 2019
- Yang, Falong; Kumar, Anand; Davenport, Karen Walston
- Microbiology Resource Announcements, Vol. 8, Issue 36
Complete Genome Sequences of Historic Clostridioides difficile Food-Dwelling Ribotype 078 Strains in Canada Identical to That of the Historic Human Clinical Strain M120 in the United Kingdom
journal, September 2018
- Kumar, Anand; Davenport, Karen Walston; Vuyisich, Grace
- Microbiology Resource Announcements, Vol. 7, Issue 12
Draft Genome Sequence of the Industrially Significant Bacterium Pseudomonas fluorescens ATCC 13525
journal, November 2018
- Meier, M. J.; Subasinghe, R. M.; Beaudette, L. A.
- Microbiology Resource Announcements, Vol. 7, Issue 17
Draft Genome Sequence of the Industrially Significant Bacterium Bacillus amyloliquefaciens NRRL 942
journal, November 2018
- Meier, Matthew J.; Dodge, Annette; Beaudette, Lee A.
- Microbiology Resource Announcements, Vol. 7, Issue 18
High-Quality Draft Genome Sequence of Pseudomonas aeruginosa 268 Isolated from a Patient with a Left Ventricular Assist Device
journal, January 2019
- Voegtly, Logan J.; Rice, Gregory K.; Cer, Regina Z.
- Microbiology Resource Announcements, Vol. 8, Issue 1
Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples
journal, February 2019
- Paskey, Adrian C.; Frey, Kenneth G.; Schroth, Gary
- BMC Genomics, Vol. 20, Issue 1
Complete genome sequences of Clostridium perfringens Del1 strain isolated from chickens affected by necrotic enteritis
journal, November 2017
- Li, Charles; Yan, Xianghe; Lillehoj, Hyun S.
- Gut Pathogens, Vol. 9, Issue 1
Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
journal, March 2019
- Clarke, Erik L.; Taylor, Louis J.; Zhao, Chunyu
- Microbiome, Vol. 7, Issue 1
Multiplex PCR−Based Next-Generation Sequencing and Global Diversity of Seoul Virus in Humans and Rats
journal, February 2018
- Kim, Won-Keun; No, Jin Sun; Lee, Seung-Ho
- Emerging Infectious Diseases, Vol. 24, Issue 2
Advances and Challenges in Metatranscriptomic Analysis
journal, September 2019
- Shakya, Migun; Lo, Chien-Chi; Chain, Patrick S. G.
- Frontiers in Genetics, Vol. 10
An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs
journal, October 2019
- Dong, Xiaoli; Strous, Marc
- Frontiers in Genetics, Vol. 10
Constructing and Characterizing Bacteriophage Libraries for Phage Therapy of Human Infections
journal, November 2019
- Gibson, Shelley B.; Green, Sabrina I.; Liu, Carmen Gu
- Frontiers in Microbiology, Vol. 10
Offline Next Generation Metagenomics Sequence Analysis Using MinION Detection Software (MINDS)
journal, January 2019
- Deshpande, Samir V.; Reed, Timothy M.; Sullivan, Raymond F.
- MDPI
Characterization of Unknown Orthobunya-Like Viruses from India
journal, August 2018
- Whitmer, Shannon; Yadav, Pragya; Sarkale, Prasad
- Viruses, Vol. 10, Issue 9