Works matching Microbial genomes

Results: 2456

A Comparison of Microbial Genome Web Portals.

Published in:

Frontiers in Microbiology, 2019, p. 1, doi. 10.3389/fmicb.2019.00208

By:

Karp, Peter D.;
Ivanova, Natalia;
Krummenacker, Markus;
Kyrpides, Nikos;
Latendresse, Mario;
Midford, Peter;
Ong, Wai Kit;
Paley, Suzanne;
Seshadri, Rekha

Publication type:

Article

The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4).

Published in:

Standards in Genomic Sciences, 2015, v. 10, n. 1, p. 1, doi. 10.1186/s40793-015-0077-y

By:

Huntemann, Marcel;
Ivanova, Natalia;
Mavromatis, Konstantinos;
Tripp, H.;
Paez-Espino, David;
Palaniappan, Krishnaveni;
Szeto, Ernest;
Pillay, Manoj;
Chen, I-Min;
Pati, Amrita;
Nielsen, Torben;
Markowitz, Victor;
Kyrpides, Nikos

Publication type:

Article

Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls.

Published in:

Frontiers in Microbiology, 2020, p. 1, doi. 10.3389/fmicb.2019.03119

By:

San, James Emmanuel;
Baichoo, Shakuntala;
Kanzi, Aquillah;
Moosa, Yumna;
Lessells, Richard;
Fonseca, Vagner;
Mogaka, John;
Power, Robert;
de Oliveira, Tulio

Publication type:

Article

Mismatch Intolerance of 5′-Truncated sgRNAs in CRISPR/Cas9 Enables Efficient Microbial Single-Base Genome Editing.

Published in:

International Journal of Molecular Sciences, 2021, v. 22, n. 12, p. 6457, doi. 10.3390/ijms22126457

By:

Lee, Ho Joung;
Kim, Hyun Ju;
Lee, Sang Jun

Publication type:

Article

The BioCyc collection of microbial genomes and metabolic pathways.

Published in:

Briefings in Bioinformatics, 2019, p. 1085, doi. 10.1093/bib/bbx085

By:

Karp, Peter D;
Billington, Richard;
Caspi, Ron;
Fulcher, Carol A;
Latendresse, Mario;
Kothari, Anamika;
Keseler, Ingrid M;
Krummenacker, Markus;
Midford, Peter E;
Ong, Quang;
Ong, Wai Kit;
Paley, Suzanne M;
Subhraveti, Pallavi

Publication type:

Article

Antimicrobial Peptide Screening from Microbial Genomes in Sludge Based on Deep Learning.

Published in:

Applied Sciences (2076-3417), 2024, v. 14, n. 5, p. 1936, doi. 10.3390/app14051936

By:

Liu, Yin-Xuan;
Jin, Xue-Bo;
Xu, Chun-Ming;
Ma, Hui-Jun;
Wu, Qi;
Liu, Hao-Si;
Li, Zi-Meng

Publication type:

Article

DeepCheck: multitask learning aids in assessing microbial genome quality.

Published in:

Briefings in Bioinformatics, 2024, v. 25, n. 6, p. 1, doi. 10.1093/bib/bbae539

By:

Wei, Guo;
Wu, Nannan;
Zhao, Kunyang;
Yang, Sihai;
Wang, Long;
Liu, Yan

Publication type:

Article

Editorial: Computational predictions, dynamic tracking, and evolutionary analysis of antibiotic resistance through the mining of microbial genomes and metagenomic data, volume II.

Published in:

Frontiers in Microbiology, 2023, p. 1, doi. 10.3389/fmicb.2023.1203297

By:

Qi Zhao;
Jian Li;
Tay, Alfred;
Liang Wang

Publication type:

Article

Robust Inference of Genetic Exchange Communities from Microbial Genomes Using TF-IDF.

Published in:

Frontiers in Microbiology, 2017, v. 8, p. 1, doi. 10.3389/fmicb.2017.00021

By:

Yingnan Cong;
Yao-ban Chan;
Phillips, Charles A.;
Langston, Michael A.;
Ragan, Mark A.

Publication type:

Article

NanoForms: an integrated server for processing, analysis and assembly of raw sequencing data of microbial genomes, from Oxford Nanopore technology.

Published in:

PeerJ, 2022, p. 1, doi. 10.7717/peerj.13056

By:

Czmil, Anna;
Wronski, Michal;
Czmil, Sylwester;
Sochacka-Pieta, Marta;
Cmil, Michal;
Gawor, Jan;
Wołkowicz, Tomasz;
Plewczynski, Dariusz;
Strzalka, Dominik;
Pietal, Michal

Publication type:

Article

Editorial: Computational Predictions, Dynamic Tracking, and Evolutionary Analysis of Antibiotic Resistance Through the Mining of Microbial Genomes and Metagenomic Data.

Published in:

2022

By:

Wang, Liang;
Tay, Alfred Chin Yen;
Li, Jian;
Zhao, Qi

Publication type:

Editorial

Microbial genome mining for accelerated natural products discovery: is a renaissance in the making?

Published in:

Journal of Industrial Microbiology & Biotechnology, 2014, v. 41, n. 2, p. 175, doi. 10.1007/s10295-013-1389-9

By:

Bachmann, Brian;
Lanen, Steven;
Baltz, Richard

Publication type:

Article

Large-scale contamination of microbial isolate genomes by Illumina PhiX control.

Published in:

Standards in Genomic Sciences, 2015, v. 10, n. 1, p. 1, doi. 10.1186/1944-3277-10-18

By:

Mukherjee, Supratim;
Huntemann, Marcel;
Ivanova, Natalia;
Kyrpides, Nikos C.;
Pati, Amrita

Publication type:

Article

Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads.

Published in:

GigaScience, 2022, v. 11, p. 1, doi. 10.1093/gigascience/giac116

By:

Zhang, Yan;
Jiang, Fan;
Yang, Boyuan;
Wang, Sen;
Wang, Hengchao;
Wang, Anqi;
Xu, Dong;
Fan, Wei

Publication type:

Article

CAMITAX: Taxon labels for microbial genomes.

Published in:

GigaScience, 2020, v. 9, n. 1, p. N.PAG, doi. 10.1093/gigascience/giz154

By:

Bremges, Andreas;
Fritz, Adrian;
McHardy, Alice C

Publication type:

Article

Exploring high-quality microbial genomes by assembling short-reads with long-range connectivity.

Published in:

Nature Communications, 2024, v. 15, n. 1, p. 1, doi. 10.1038/s41467-024-49060-z

By:

Zhang, Zhenmiao;
Xiao, Jin;
Wang, Hongbo;
Yang, Chao;
Huang, Yufen;
Yue, Zhen;
Chen, Yang;
Han, Lijuan;
Yin, Kejing;
Lyu, Aiping;
Fang, Xiaodong;
Zhang, Lu

Publication type:

Article

Insights into rumen microbial biosynthetic gene cluster diversity through genome-resolved metagenomics.

Published in:

Communications Biology, 2021, v. 4, p. 1, doi. 10.1038/s42003-021-02331-7

By:

Anderson, Christopher L.;
Fernando, Samodha C.

Publication type:

Article

Sampling of microbial diversity by complete genomes.

Published in:

2006

By:

Galperin, Michael Y.

Publication type:

Other

Epigenetic Segregation of Microbial Genomes from Complex Samples Using Restriction Endonucleases HpaII and McrB.

Published in:

PLoS ONE, 2016, v. 11, n. 1, p. 1, doi. 10.1371/journal.pone.0146064

By:

Liu, Guohong;
Weston, Christopher Q.;
Pham, Long K.;
Waltz, Shannon;
Barnes, Helen;
King, Paula;
Sphar, Dan;
Yamamoto, Robert T.;
Forsyth, R. Allyn

Publication type:

Article

Exploring the Capabilities of the Geobiosphere's Microbial Genome.

Published in:

AIChE Journal, 2013, v. 59, n. 3, p. 688, doi. 10.1002/aic.14032

By:

Papoutsakis, Eleftherios T.

Publication type:

Article

Microbial genome analysis: the COG approach.

Published in:

Briefings in Bioinformatics, 2019, p. 1063, doi. 10.1093/bib/bbx117

By:

Galperin, Michael Y;
Kristensen, David M;
Makarova, Kira S;
Wolf, Yuri I;
Koonin, Eugene V

Publication type:

Article

MetaSanity: an integrated microbial genome evaluation and annotation pipeline.

Published in:

Bioinformatics, 2020, v. 36, n. 15, p. 4341, doi. 10.1093/bioinformatics/btaa512

By:

Neely, Christopher J;
Graham, Elaina D;
Tully, Benjamin J

Publication type:

Article

Approximate, simultaneous comparison of microbial genome architectures via syntenic anchoring of quiver representations.

Published in:

Bioinformatics, 2018, v. 34, n. 17, p. i732, doi. 10.1093/bioinformatics/bty614

By:

Salazar, Alex N;
Abeel, Thomas

Publication type:

Article

Prediction of translation initiation site for microbial genomes with TriTISA.

Published in:

Bioinformatics, 2009, v. 25, n. 1, p. 123, doi. 10.1093/bioinformatics/btn576

By:

Gang-Qing Hu;
Xiaobin Zheng;
Huai-Qiu Zhu;
Zhen-Su She

Publication type:

Article

METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks.

Published in:

Microbiome, 2022, v. 10, n. 1, p. 1, doi. 10.1186/s40168-021-01213-8

By:

Zhou, Zhichao;
Tran, Patricia Q.;
Breister, Adam M.;
Liu, Yang;
Kieft, Kristopher;
Cowley, Elise S.;
Karaoz, Ulas;
Anantharaman, Karthik

Publication type:

Article

Metagenome-assembled genomes provide insight into the microbial taxonomy and ecology of the Buhera soda pans, Zimbabwe.

Published in:

PLoS ONE, 2024, v. 19, n. 12, p. 1, doi. 10.1371/journal.pone.0299620

By:

Mangoma, Ngonidzashe;
Zhou, Nerve;
Ncube, Thembekile

Publication type:

Article

ContigScape: a Cytoscape plugin facilitating microbial genome gap closing.

Published in:

BMC Genomics, 2013, v. 14, n. 1, p. 1, doi. 10.1186/1471-2164-14-289

By:

Biao Tang;
Qi Wang;
Minjun Yang;
Feng Xie;
Yongqiang Zhu;
Ying Zhuo;
Shengyue Wang;
Hong Gao;
Xiaoming Ding;
Lixin Zhang;
Guoping Zhao;
Huajun Zheng

Publication type:

Article

GenomeViz: visualizing microbial genomes.

Published in:

BMC Bioinformatics, 2004, v. 5, p. 198, doi. 10.1186/1471-2105-5-198

By:

Ghai, Rohit;
Hain, Torsten;
Chakraborty, Trinad

Publication type:

Article

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size in Four Major Biomes.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 12, p. 1, doi. 10.1371/journal.pcbi.1000593

By:

Angly, Florent E.;
Willner, Dana;
Prieto-Davó, Alejandra;
Edwards, Robert A.;
Schmieder, Robert;
Vega-Thurber, Rebecca;
Antonopoulos, Dionysios A.;
Barott, Katie;
Cottrell, Matthew T.;
Desnues, Christelle;
Dinsdale, Elizabeth A.;
Furlan, Mike;
Haynes, Matthew;
Henn, Matthew R.;
Yongfei Hu;
Kirchman, David L.;
McDole, Tracey;
McPherson, John D.;
Meyer, Folker;
Miller, R. Michael

Publication type:

Article

Comprehensive prediction of secondary metabolite structure and biological activity from microbial genome sequences.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. N.PAG, doi. 10.1038/s41467-020-19986-1

By:

Skinnider, Michael A.;
Johnston, Chad W.;
Gunabalasingam, Mathusan;
Merwin, Nishanth J.;
Kieliszek, Agata M.;
MacLellan, Robyn J.;
Li, Haoxin;
Ranieri, Michael R. M.;
Webster, Andrew L. H.;
Cao, My P. T.;
Pfeifle, Annabelle;
Spencer, Norman;
To, Q. Huy;
Wallace, Dan Peter;
Dejong, Chris A.;
Magarvey, Nathan A.

Publication type:

Article

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0.

Published in:

Nature Communications, 2020, v. 11, n. 1, p. 1, doi. 10.1038/s41467-020-16366-7

By:

Asnicar, Francesco;
Thomas, Andrew Maltez;
Beghini, Francesco;
Mengoni, Claudia;
Manara, Serena;
Manghi, Paolo;
Zhu, Qiyun;
Bolzan, Mattia;
Cumbo, Fabio;
May, Uyen;
Sanders, Jon G.;
Zolfo, Moreno;
Kopylova, Evguenia;
Pasolli, Edoardo;
Knight, Rob;
Mirarab, Siavash;
Huttenhower, Curtis;
Segata, Nicola

Publication type:

Article

MicroScope: a platform for microbial genome annotation and comparative genomics.

Published in:

Database: The Journal of Biological Databases & Curation, 2009, v. 2009, p. 1, doi. 10.1093/database/bap021

By:

Vallenet, D.;
Engelen, S.;
Mornico, D.;
Cruveiller, S.;
Fleury, L.;
Lajus, A.;
Rouy, Z.;
Roche, D.;
Salvignol, G.;
Scarpelli, C.;
Médigue, C.

Publication type:

Article

Evaluation and Validation of Assembling Corrected PacBio Long Reads for Microbial Genome Completion via Hybrid Approaches.

Published in:

PLoS ONE, 2015, v. 10, n. 12, p. 1, doi. 10.1371/journal.pone.0144305

By:

Lin, Hsin-Hung;
Liao, Yu-Chieh

Publication type:

Article

γ-PGA Hydrolases of Phage Origin in Bacillus subtilis and Other Microbial Genomes.

Published in:

PLoS ONE, 2015, v. 10, n. 7, p. 1, doi. 10.1371/journal.pone.0130810

By:

Mamberti, Stefania;
Prati, Paola;
Cremaschi, Paolo;
Seppi, Claudio;
Morelli, Carlo F.;
Galizzi, Alessandro;
Fabbi, Massimo;
Calvio, Cinzia

Publication type:

Article

INDIGO – INtegrated Data Warehouse of MIcrobial GenOmes with Examples from the Red Sea Extremophiles.

Published in:

PLoS ONE, 2013, v. 8, n. 12, p. 1, doi. 10.1371/journal.pone.0082210

By:

Alam, Intikhab;
Antunes, André;
Kamau, Allan Anthony;
Ba alawi, Wail;
Kalkatawi, Manal;
Stingl, Ulrich;
Bajic, Vladimir B.

Publication type:

Article

Improving Microbial Genome Annotations in an Integrated Database Context.

Published in:

PLoS ONE, 2013, v. 8, n. 2, p. 1, doi. 10.1371/journal.pone.0054859

By:

Chen, I-Min A.;
Markowitz, Victor M.;
Chu, Ken;
Anderson, Iain;
Mavromatis, Konstantinos;
Kyrpides, Nikos C.;
Ivanova, Natalia N.

Publication type:

Article

The Fast Changing Landscape of Sequencing Technologies and Their Impact on Microbial Genome Assemblies and Annotation.

Published in:

PLoS ONE, 2012, v. 7, n. 12, p. 1, doi. 10.1371/journal.pone.0048837

By:

Mavromatis, Konstantinos;
Land, Miriam L.;
Brettin, Thomas S.;
Quest, Daniel J.;
Copeland, Alex;
Clum, Alicia;
Goodwin, Lynne;
Woyke, Tanja;
Lapidus, Alla;
Klenk, Hans Peter;
Cottingham, Robert W.;
Kyrpides, Nikos C.

Publication type:

Article

The Catalog of Microbial Genes and Metagenome-Assembled Genomes from the Gut Microbiomes of Five Typical Crow Species on the Qinghai–Tibetan Plateau.

Published in:

Microorganisms, 2024, v. 12, n. 10, p. 2033, doi. 10.3390/microorganisms12102033

By:

Tang, Boyu;
Wang, You;
Dong, Yonggang;
Cui, Quanchao;
Zeng, Zhanhao;
He, Shunfu;
Zhao, Wenxin;
Lancuo, Zhuoma;
Li, Shaobin;
Wang, Wen

Publication type:

Article

Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential.

Published in:

Microorganisms, 2024, v. 12, n. 4, p. 791, doi. 10.3390/microorganisms12040791

By:

Isokpehi, Raphael D.;
Kim, Yungkul;
Krejci, Sarah E.;
Trivedi, Vishwa D.

Publication type:

Article

Selective Whole Genome Amplification for Resequencing Target Microbial Species from Complex Natural Samples.

Published in:

Genetics, 2014, v. 198, n. 2, p. 473, doi. 10.1534/genetics.114.165498

By:

Leichty, Aaron R.;
Brisson, Dustin

Publication type:

Article

Comparative evaluation of Nanopore polishing tools for microbial genome assembly and polishing strategies for downstream analysis.

Published in:

Scientific Reports, 2021, v. 11, n. 1, p. 1, doi. 10.1038/s41598-021-00178-w

By:

Lee, Jin Young;
Kong, Minyoung;
Oh, Jinjoo;
Lim, JinSoo;
Chung, Sung Hee;
Kim, Jung-Min;
Kim, Jae-Seok;
Kim, Ki-Hwan;
Yoo, Jae-Chan;
Kwak, Woori

Publication type:

Article

Removal of sequencing adapter contamination improves microbial genome databases.

Published in:

BMC Genomics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12864-024-10956-1

By:

Moeller, Andrew H.;
Dillard, Brian A.;
Goldman, Samantha L.;
Real, Madalena V. F.;
Sprockett, Daniel D.

Publication type:

Article

MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes.

Published in:

BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-020-03940-5

By:

Ruiz-Perez, Carlos A.;
Conrad, Roth E.;
Konstantinidis, Konstantinos T.

Publication type:

Article

Statistical prediction of microbial metabolic traits from genomes.

Published in:

PLoS Computational Biology, 2023, v. 19, n. 12, p. 1, doi. 10.1371/journal.pcbi.1011705

By:

Li, Zeqian;
Selim, Ahmed;
Kuehn, Seppe

Publication type:

Article

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project.

Published in:

Standards in Genomic Sciences, 2014, v. 9, n. 3, p. 1278, doi. 10.4056/sigs.5068949

By:

Kyrpides, Nikos;
Woyke, Tanja;
Eisen, Jonathan;
Garrity, George;
Lilburn, Timothy;
Beck, Brian;
Whitman, William;
Hugenholtz, Phil;
Klenk, Hans-Peter

Publication type:

Article

AMRomics: a scalable workflow to analyze large microbial genome collections.

Published in:

BMC Genomics, 2024, v. 25, n. 1, p. 1, doi. 10.1186/s12864-024-10620-8

By:

Le, Duc Quang;
Nguyen, Tam Thi;
Nguyen, Canh Hao;
Ho, Tho Huu;
Vo, Nam S.;
Nguyen, Trang;
Nguyen, Hoang Anh;
Vinh, Le Sy;
Dang, Thanh Hai;
Cao, Minh Duc;
Nguyen, Son Hoang

Publication type:

Article

Metagenome sequencing and 768 microbial genomes from cold seep in South China Sea.

Published in:

Scientific Data, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41597-022-01586-x

By:

Zhang, Huan;
Wang, Minxiao;
Wang, Hao;
Chen, Hao;
Cao, Lei;
Zhong, Zhaoshan;
Lian, Chao;
Zhou, Li;
Li, Chaolun

Publication type:

Article

MicroGMT: A Mutation Tracker for SARS-CoV-2 and Other Microbial Genome Sequences.

Published in:

Frontiers in Microbiology, 2020, v. 11, p. 1, doi. 10.3389/fmicb.2020.01502

By:

Xing, Yue;
Li, Xiao;
Gao, Xiang;
Dong, Qunfeng

Publication type:

Article

The importance of genome sequence quality to microbial comparative genomics.

Published in:

2019

By:

Smits, Theo H. M.

Publication type:

Editorial

Microbial population genomes from the Amazon River reveal possible modulation of the organic matter degradation process in tropical freshwaters.

Published in:

Molecular Ecology, 2022, v. 31, n. 1, p. 206, doi. 10.1111/mec.16222

By:

Santos‐Júnior, Célio Dias;
Logares, Ramiro;
Henrique‐Silva, Flávio

Publication type:

Article