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Showing 1 to 12 of 15 entries
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Pathogen metadata platform: software for accessing and analyzing pathogen strain information.

BMC bioinformatics

Chang WE, Peterson MW, Garay CD, Korves T.
PMID: 27634291
BMC Bioinformatics. 2016 Sep 15;17(1):379. doi: 10.1186/s12859-016-1231-2.

BACKGROUND: Pathogen metadata includes information about where and when a pathogen was collected and the type of environment it came from. Along with genomic nucleotide sequence data, this metadata is growing rapidly and becoming a valuable resource not only...

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Chang WE, Peterson MW, Garay CD, et al. Pathogen metadata platform: software for accessing and analyzing pathogen strain information. BMC Bioinformatics. 2016;17(1):379doi: 10.1186/s12859-016-1231-2.
Chang, W. E., Peterson, M. W., Garay, C. D., & Korves, T. (2016). Pathogen metadata platform: software for accessing and analyzing pathogen strain information. BMC bioinformatics, 17(1), 379. https://doi.org/10.1186/s12859-016-1231-2
Chang, Wenling E, et al. "Pathogen metadata platform: software for accessing and analyzing pathogen strain information." BMC bioinformatics vol. 17,1 (2016): 379. doi: https://doi.org/10.1186/s12859-016-1231-2
Chang WE, Peterson MW, Garay CD, Korves T. Pathogen metadata platform: software for accessing and analyzing pathogen strain information. BMC Bioinformatics. 2016 Sep 15;17(1):379. doi: 10.1186/s12859-016-1231-2. PMID: 27634291; PMCID: PMC5025631.
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[Omic technologies: Current situation and future challenges].

Revista Argentina de microbiologia

Quiroga C.
PMID: 28038716
Rev Argent Microbiol. 2016 Oct - Dec;48(4):265-266. doi: 10.1016/j.ram.2016.12.001.

No abstract available.

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Quiroga C. Las tecnologías «ómicas»: situación actual y desafíos futuros. [Omic technologies: Current situation and future challenges]. Rev Argent Microbiol. 2016;48(4):265-266doi: 10.1016/j.ram.2016.12.001.
Quiroga, C. (2016). Las tecnologías «ómicas»: situación actual y desafíos futuros. [Omic technologies: Current situation and future challenges]. Revista Argentina de microbiologia, 48(4), 265-266. https://doi.org/10.1016/j.ram.2016.12.001
Quiroga, Cecilia. "Las tecnologías «ómicas»: situación actual y desafíos futuros." [Omic technologies: Current situation and future challenges]. Revista Argentina de microbiologia vol. 48,4 (2016): 265-266. doi: https://doi.org/10.1016/j.ram.2016.12.001
Quiroga C. Las tecnologías «ómicas»: situación actual y desafíos futuros. [Omic technologies: Current situation and future challenges]. Rev Argent Microbiol. 2016 Oct - Dec;48(4):265-266. doi: 10.1016/j.ram.2016.12.001. Spanish. PMID: 28038716.
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Primary metabolites from overproducing microbial system using sustainable substrates.

Biotechnology and applied biochemistry

Srivastava RK, Akhtar N, Verma M, Imandi SB.
PMID: 32294277
Biotechnol Appl Biochem. 2020 Nov;67(6):852-874. doi: 10.1002/bab.1927. Epub 2020 May 21.

Primary (or secondary) metabolites are produced by animals, plants, or microbial cell systems either intracellularly or extracellularly. Production capabilities of microbial cell systems for many types of primary metabolites have been exploited at a commercial scale. But the high...

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Srivastava RK, Akhtar N, Verma M, et al. Primary metabolites from overproducing microbial system using sustainable substrates. Biotechnol Appl Biochem. 2020;67(6):852-874doi: 10.1002/bab.1927.
Srivastava, R. K., Akhtar, N., Verma, M., & Imandi, S. B. (2020). Primary metabolites from overproducing microbial system using sustainable substrates. Biotechnology and applied biochemistry, 67(6), 852-874. https://doi.org/10.1002/bab.1927
Srivastava, Rajesh K, et al. "Primary metabolites from overproducing microbial system using sustainable substrates." Biotechnology and applied biochemistry vol. 67,6 (2020): 852-874. doi: https://doi.org/10.1002/bab.1927
Srivastava RK, Akhtar N, Verma M, Imandi SB. Primary metabolites from overproducing microbial system using sustainable substrates. Biotechnol Appl Biochem. 2020 Nov;67(6):852-874. doi: 10.1002/bab.1927. Epub 2020 May 21. PMID: 32294277.
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The BioCyc collection of microbial genomes and metabolic pathways.

Briefings in bioinformatics

Karp PD, Billington R, Caspi R, Fulcher CA, Latendresse M, Kothari A, Keseler IM, Krummenacker M, Midford PE, Ong Q, Ong WK, Paley SM, Subhraveti P.
PMID: 29447345
Brief Bioinform. 2019 Jul 19;20(4):1085-1093. doi: 10.1093/bib/bbx085.

BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of...

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Karp PD, Billington R, Caspi R, et al. The BioCyc collection of microbial genomes and metabolic pathways. Brief Bioinform. 2019;20(4):1085-1093doi: 10.1093/bib/bbx085.
Karp, P. D., Billington, R., Caspi, R., Fulcher, C. A., Latendresse, M., Kothari, A., Keseler, I. M., Krummenacker, M., Midford, P. E., Ong, Q., Ong, W. K., Paley, S. M., & Subhraveti, P. (2019). The BioCyc collection of microbial genomes and metabolic pathways. Briefings in bioinformatics, 20(4), 1085-1093. https://doi.org/10.1093/bib/bbx085
Karp, Peter D, et al. "The BioCyc collection of microbial genomes and metabolic pathways." Briefings in bioinformatics vol. 20,4 (2019): 1085-1093. doi: https://doi.org/10.1093/bib/bbx085
Karp PD, Billington R, Caspi R, Fulcher CA, Latendresse M, Kothari A, Keseler IM, Krummenacker M, Midford PE, Ong Q, Ong WK, Paley SM, Subhraveti P. The BioCyc collection of microbial genomes and metabolic pathways. Brief Bioinform. 2019 Jul 19;20(4):1085-1093. doi: 10.1093/bib/bbx085. PMID: 29447345; PMCID: PMC6781571.
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A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems.

PloS one

Budinich M, Bourdon J, Larhlimi A, Eveillard D.
PMID: 28187207
PLoS One. 2017 Feb 10;12(2):e0171744. doi: 10.1371/journal.pone.0171744. eCollection 2017.

Interplay within microbial communities impacts ecosystems on several scales, and elucidation of the consequent effects is a difficult task in ecology. In particular, the integration of genome-scale data within quantitative models of microbial ecosystems remains elusive. This study advocates...

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Budinich M, Bourdon J, Larhlimi A, et al. A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems. PLoS One. 2017;12(2):e0171744doi: 10.1371/journal.pone.0171744.
Budinich, M., Bourdon, J., Larhlimi, A., & Eveillard, D. (2017). A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems. PloS one, 12(2), e0171744. https://doi.org/10.1371/journal.pone.0171744
Budinich, Marko, et al. "A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems." PloS one vol. 12,2 (2017): e0171744. doi: https://doi.org/10.1371/journal.pone.0171744
Budinich M, Bourdon J, Larhlimi A, Eveillard D. A multi-objective constraint-based approach for modeling genome-scale microbial ecosystems. PLoS One. 2017 Feb 10;12(2):e0171744. doi: 10.1371/journal.pone.0171744. eCollection 2017. PMID: 28187207; PMCID: PMC5302800.
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miComplete: weighted quality evaluation of assembled microbial genomes.

Bioinformatics (Oxford, England)

Hugoson E, Lam WT, Guy L.
PMID: 31504158
Bioinformatics. 2020 Feb 01;36(3):936-937. doi: 10.1093/bioinformatics/btz664.

SUMMARY: Metagenomics and single-cell genomics have revolutionized the study of microorganisms, increasing our knowledge of microbial genomic diversity by orders of magnitude. A major issue pertaining to metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) is to estimate their...

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Hugoson E, Lam WT, Guy L. miComplete: weighted quality evaluation of assembled microbial genomes. Bioinformatics. 2020;36(3):936-937doi: 10.1093/bioinformatics/btz664.
Hugoson, E., Lam, W. T., & Guy, L. (2020). miComplete: weighted quality evaluation of assembled microbial genomes. Bioinformatics (Oxford, England), 36(3), 936-937. https://doi.org/10.1093/bioinformatics/btz664
Hugoson, Eric, et al. "miComplete: weighted quality evaluation of assembled microbial genomes." Bioinformatics (Oxford, England) vol. 36,3 (2020): 936-937. doi: https://doi.org/10.1093/bioinformatics/btz664
Hugoson E, Lam WT, Guy L. miComplete: weighted quality evaluation of assembled microbial genomes. Bioinformatics. 2020 Feb 01;36(3):936-937. doi: 10.1093/bioinformatics/btz664. PMID: 31504158.
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Recovering Individual Genomes from Metagenomes Using MaxBin 2.0.

Current protocols

Wu YW, Singer SW.
PMID: 33961733
Curr Protoc. 2021 May;1(5):e128. doi: 10.1002/cpz1.128.

It is critical to identify individual genomes from microbiomic samples in order to carry out analysis of the microbes. Methods based on existing databases, however, may have limited capabilities in elucidating and quantifying the microbes due to the largely...

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Wu YW, Singer SW. Recovering Individual Genomes from Metagenomes Using MaxBin 2.0. Curr Protoc. 2021;1(5):e128doi: 10.1002/cpz1.128.
Wu, Y. W., & Singer, S. W. (2021). Recovering Individual Genomes from Metagenomes Using MaxBin 2.0. Current protocols, 1(5), e128. https://doi.org/10.1002/cpz1.128
Wu, Yu-Wei, and Singer, Steven W. "Recovering Individual Genomes from Metagenomes Using MaxBin 2.0." Current protocols vol. 1,5 (2021): e128. doi: https://doi.org/10.1002/cpz1.128
Wu YW, Singer SW. Recovering Individual Genomes from Metagenomes Using MaxBin 2.0. Curr Protoc. 2021 May;1(5):e128. doi: 10.1002/cpz1.128. PMID: 33961733.
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Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations.

Bioinformatics (Oxford, England)

Salazar AN, Abeel T.
PMID: 30423098
Bioinformatics. 2018 Sep 01;34(17):i732-i742. doi: 10.1093/bioinformatics/bty614.

MOTIVATION: A long-standing limitation in comparative genomic studies is the dependency on a reference genome, which hinders the spectrum of genetic diversity that can be identified across a population of organisms. This is especially true in the microbial world...

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Salazar AN, Abeel T. Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations. Bioinformatics. 2018;34(17):i732-i742doi: 10.1093/bioinformatics/bty614.
Salazar, A. N., & Abeel, T. (2018). Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations. Bioinformatics (Oxford, England), 34(17), i732-i742. https://doi.org/10.1093/bioinformatics/bty614
Salazar, Alex N, and Abeel, Thomas. "Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations." Bioinformatics (Oxford, England) vol. 34,17 (2018): i732-i742. doi: https://doi.org/10.1093/bioinformatics/bty614
Salazar AN, Abeel T. Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations. Bioinformatics. 2018 Sep 01;34(17):i732-i742. doi: 10.1093/bioinformatics/bty614. PMID: 30423098; PMCID: PMC6129293.
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PATRIC as a unique resource for studying antimicrobial resistance.

Briefings in bioinformatics

Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S, Kenyon RW, Machi D, Mao C, Murphy-Olson DE, Nordberg EK, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Santerre J, Shukla M, Stevens RL, VanOeffelen M, Vonstein V, Warren AS, Wattam AR, Xia F, Yoo H.
PMID: 28968762
Brief Bioinform. 2019 Jul 19;20(4):1094-1102. doi: 10.1093/bib/bbx083.

The Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org) is designed to provide researchers with the tools and services that they need to perform genomic and other 'omic' data analyses. In response to mounting concern over antimicrobial resistance (AMR), the PATRIC...

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Antonopoulos DA, Assaf R, Aziz RK, et al. PATRIC as a unique resource for studying antimicrobial resistance. Brief Bioinform. 2019;20(4):1094-1102doi: 10.1093/bib/bbx083.
Antonopoulos, D. A., Assaf, R., Aziz, R. K., Brettin, T., Bun, C., Conrad, N., Davis, J. J., Dietrich, E. M., Disz, T., Gerdes, S., Kenyon, R. W., Machi, D., Mao, C., Murphy-Olson, D. E., Nordberg, E. K., Olsen, G. J., Olson, R., Overbeek, R., Parrello, B., Pusch, G. D., Santerre, J., Shukla, M., Stevens, R. L., VanOeffelen, M., Vonstein, V., Warren, A. S., Wattam, A. R., Xia, F., & Yoo, H. (2019). PATRIC as a unique resource for studying antimicrobial resistance. Briefings in bioinformatics, 20(4), 1094-1102. https://doi.org/10.1093/bib/bbx083
Antonopoulos, Dionysios A, et al. "PATRIC as a unique resource for studying antimicrobial resistance." Briefings in bioinformatics vol. 20,4 (2019): 1094-1102. doi: https://doi.org/10.1093/bib/bbx083
Antonopoulos DA, Assaf R, Aziz RK, Brettin T, Bun C, Conrad N, Davis JJ, Dietrich EM, Disz T, Gerdes S, Kenyon RW, Machi D, Mao C, Murphy-Olson DE, Nordberg EK, Olsen GJ, Olson R, Overbeek R, Parrello B, Pusch GD, Santerre J, Shukla M, Stevens RL, VanOeffelen M, Vonstein V, Warren AS, Wattam AR, Xia F, Yoo H. PATRIC as a unique resource for studying antimicrobial resistance. Brief Bioinform. 2019 Jul 19;20(4):1094-1102. doi: 10.1093/bib/bbx083. PMID: 28968762; PMCID: PMC6781570.
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Microbial Base Editing: A Powerful Emerging Technology for Microbial Genome Engineering.

Trends in biotechnology

Wang Y, Liu Y, Zheng P, Sun J, Wang M.
PMID: 32680590
Trends Biotechnol. 2021 Feb;39(2):165-180. doi: 10.1016/j.tibtech.2020.06.010. Epub 2020 Jul 14.

Genome engineering is crucial for answering fundamental questions about, and exploring practical applications of, microorganisms. Various microbial genome-engineering tools, including CRISPR/Cas-enhanced homologous recombination (HR), have been developed, with ever-improving simplicity, efficiency, and applicability. Recently, a powerful emerging technology based...

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Wang Y, Liu Y, Zheng P, et al. Microbial Base Editing: A Powerful Emerging Technology for Microbial Genome Engineering. Trends Biotechnol. 2020;39(2):165-180doi: 10.1016/j.tibtech.2020.06.010.
Wang, Y., Liu, Y., Zheng, P., Sun, J., & Wang, M. (2021). Microbial Base Editing: A Powerful Emerging Technology for Microbial Genome Engineering. Trends in biotechnology, 39(2), 165-180. https://doi.org/10.1016/j.tibtech.2020.06.010
Wang, Yu, et al. "Microbial Base Editing: A Powerful Emerging Technology for Microbial Genome Engineering." Trends in biotechnology vol. 39,2 (2021): 165-180. doi: https://doi.org/10.1016/j.tibtech.2020.06.010
Wang Y, Liu Y, Zheng P, Sun J, Wang M. Microbial Base Editing: A Powerful Emerging Technology for Microbial Genome Engineering. Trends Biotechnol. 2021 Feb;39(2):165-180. doi: 10.1016/j.tibtech.2020.06.010. Epub 2020 Jul 14. PMID: 32680590.
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CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.

Genome research

Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW.
PMID: 25977477
Genome Res. 2015 Jul;25(7):1043-55. doi: 10.1101/gr.186072.114. Epub 2015 May 14.

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. Although this increasing breadth of draft genomes is providing key information regarding the...

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Parks DH, Imelfort M, Skennerton CT, et al. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043-55doi: 10.1101/gr.186072.114.
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome research, 25(7), 1043-55. https://doi.org/10.1101/gr.186072.114
Parks, Donovan H, et al. "CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes." Genome research vol. 25,7 (2015): 1043-55. doi: https://doi.org/10.1101/gr.186072.114
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015 Jul;25(7):1043-55. doi: 10.1101/gr.186072.114. Epub 2015 May 14. PMID: 25977477; PMCID: PMC4484387.
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COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

Greene CS, Foster JA, Stanton BA, Hogan DA, Bromberg Y.
PMID: 26776218
Pac Symp Biocomput. 2016;21:557-67.

Technological advances are making large-scale measurements of microbial communities commonplace. These newly acquired datasets are allowing researchers to ask and answer questions about the composition of microbial communities, the roles of members in these communities, and how genes and...

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Greene CS, Foster JA, Stanton BA, et al. COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES. Pac Symp Biocomput. 2016;21:557-67
Greene, C. S., Foster, J. A., Stanton, B. A., Hogan, D. A., & Bromberg, Y. (2016). COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 21557-67.
Greene, Casey S, et al. "COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES." Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing vol. 21 (2016): 557-67.
Greene CS, Foster JA, Stanton BA, Hogan DA, Bromberg Y. COMPUTATIONAL APPROACHES TO STUDY MICROBES AND MICROBIOMES. Pac Symp Biocomput. 2016;21:557-67. PMID: 26776218; PMCID: PMC4832978.
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Showing 1 to 12 of 15 entries