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For: Prakash T, Taylor TD. Functional assignment of metagenomic data: challenges and applications. Brief Bioinform 2012;13:711-27. [PMID: 22772835 PMCID: PMC3504928 DOI: 10.1093/bib/bbs033] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2012] [Accepted: 05/26/2012] [Indexed: 12/14/2022]  Open
Number Cited by Other Article(s)
1
Coskuner-Weber O, Alpsoy S, Yolcu O, Teber E, de Marco A, Shumka S. Metagenomics studies in aquaculture systems: Big data analysis, bioinformatics, machine learning and quantum computing. Comput Biol Chem 2025;118:108444. [PMID: 40187295 DOI: 10.1016/j.compbiolchem.2025.108444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2025] [Revised: 03/15/2025] [Accepted: 03/25/2025] [Indexed: 04/07/2025]
2
Abbà S, Valentini B, Stefanini I. Fungal Identifier (FId): An Updated Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Approach to Ease Ascomycetous Yeast Isolates' Identification in Ecological Studies. J Fungi (Basel) 2024;10:595. [PMID: 39330355 PMCID: PMC11433625 DOI: 10.3390/jof10090595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2024] [Revised: 08/13/2024] [Accepted: 08/21/2024] [Indexed: 09/28/2024]  Open
3
Wu J, Singleton SS, Bhuiyan U, Krammer L, Mazumder R. Multi-omics approaches to studying gastrointestinal microbiome in the context of precision medicine and machine learning. Front Mol Biosci 2024;10:1337373. [PMID: 38313584 PMCID: PMC10834744 DOI: 10.3389/fmolb.2023.1337373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 12/27/2023] [Indexed: 02/06/2024]  Open
4
Satari L, Torrent D, Ortega-Legarreta A, Latorre-Pérez A, Pascual J, Porcar M, Iglesias A. A laboratory ice machine as a cold oligotrophic artificial microbial niche for biodiscovery. Sci Rep 2023;13:22089. [PMID: 38086912 PMCID: PMC10716499 DOI: 10.1038/s41598-023-49017-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 12/03/2023] [Indexed: 12/18/2023]  Open
5
Montenegro J, Armet AM, Willing BP, Deehan EC, Fassini PG, Mota JF, Walter J, Prado CM. Exploring the Influence of Gut Microbiome on Energy Metabolism in Humans. Adv Nutr 2023;14:840-857. [PMID: 37031749 PMCID: PMC10334151 DOI: 10.1016/j.advnut.2023.03.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 03/13/2023] [Accepted: 03/30/2023] [Indexed: 04/11/2023]  Open
6
Chhiba V, Pillay P, Mtimka S, Moonsamy G, Kwezi L, Pooe OJ, Tsekoa TL. South Africa's indigenous microbial diversity for industrial applications: A review of the current status and opportunities. Heliyon 2023;9:e16723. [PMID: 37484259 PMCID: PMC10360602 DOI: 10.1016/j.heliyon.2023.e16723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 05/05/2023] [Accepted: 05/25/2023] [Indexed: 07/25/2023]  Open
7
Hallsworth JE, Udaondo Z, Pedrós‐Alió C, Höfer J, Benison KC, Lloyd KG, Cordero RJB, de Campos CBL, Yakimov MM, Amils R. Scientific novelty beyond the experiment. Microb Biotechnol 2023;16:1131-1173. [PMID: 36786388 PMCID: PMC10221578 DOI: 10.1111/1751-7915.14222] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 02/15/2023]  Open
8
Timmusk S, Pall T, Raz S, Fetsiukh A, Nevo E. The potential for plant growth-promoting bacteria to impact crop productivity in future agricultural systems is linked to understanding the principles of microbial ecology. Front Microbiol 2023;14:1141862. [PMID: 37275175 PMCID: PMC10235605 DOI: 10.3389/fmicb.2023.1141862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 03/28/2023] [Indexed: 06/07/2023]  Open
9
Falardeau J, Yildiz E, Yan Y, Castellarin SD, Wang S. Microbiome and Physicochemical Features Associated with Differential Listeria monocytogenes Growth in Soft, Surface-Ripened Cheeses. Appl Environ Microbiol 2023;89:e0200422. [PMID: 36975809 PMCID: PMC10132104 DOI: 10.1128/aem.02004-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 03/03/2023] [Indexed: 03/29/2023]  Open
10
Cao B, Wang B, Zhang Q. GCNSA: DNA storage encoding with a graph convolutional network and self-attention. iScience 2023;26:106231. [PMID: 36876131 PMCID: PMC9982308 DOI: 10.1016/j.isci.2023.106231] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 01/31/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023]  Open
11
Llinares-López F, Berthet Q, Blondel M, Teboul O, Vert JP. Deep embedding and alignment of protein sequences. Nat Methods 2023;20:104-111. [PMID: 36522501 DOI: 10.1038/s41592-022-01700-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 10/24/2022] [Indexed: 12/23/2022]
12
Zou X, Nguyen M, Overbeek J, Cao B, Davis JJ. Classification of bacterial plasmid and chromosome derived sequences using machine learning. PLoS One 2022;17:e0279280. [PMID: 36525447 PMCID: PMC9757591 DOI: 10.1371/journal.pone.0279280] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/02/2022] [Indexed: 12/23/2022]  Open
13
A simple method for the production of nano polyethylene particles for rapid assay of polyethylene biodegradation. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01225-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
14
Rodrigues CJC, de Carvalho CCCR. Marine Bioprospecting, Biocatalysis and Process Development. Microorganisms 2022;10:1965. [PMID: 36296241 PMCID: PMC9610463 DOI: 10.3390/microorganisms10101965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/22/2022] [Accepted: 09/30/2022] [Indexed: 11/22/2022]  Open
15
Escudeiro P, Henry CS, Dias RP. Functional characterization of prokaryotic dark matter: the road so far and what lies ahead. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022;3:100159. [PMID: 36561390 PMCID: PMC9764257 DOI: 10.1016/j.crmicr.2022.100159] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/18/2022] [Accepted: 08/05/2022] [Indexed: 12/25/2022]  Open
16
Sharma P, Singh SP, Iqbal HMN, Tong YW. Omics approaches in bioremediation of environmental contaminants: An integrated approach for environmental safety and sustainability. ENVIRONMENTAL RESEARCH 2022;211:113102. [PMID: 35300964 DOI: 10.1016/j.envres.2022.113102] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 02/05/2023]
17
Odrzywolek K, Karwowska Z, Majta J, Byrski A, Milanowska-Zabel K, Kosciolek T. Deep embeddings to comprehend and visualize microbiome protein space. Sci Rep 2022;12:10332. [PMID: 35725732 PMCID: PMC9209496 DOI: 10.1038/s41598-022-14055-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/31/2022] [Indexed: 12/13/2022]  Open
18
Karp PD, Paley S, Krummenacker M, Kothari A, Wannemuehler MJ, Phillips GJ. Pathway Tools Management of Pathway/Genome Data for Microbial Communities. FRONTIERS IN BIOINFORMATICS 2022;2:869150. [PMID: 36304298 PMCID: PMC9580912 DOI: 10.3389/fbinf.2022.869150] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/05/2022] [Indexed: 11/14/2022]  Open
19
Vicedomini R, Bouly JP, Laine E, Falciatore A, Carbone A. Multiple profile models extract features from protein sequence data and resolve functional diversity of very different protein families. Mol Biol Evol 2022;39:6556147. [PMID: 35353898 PMCID: PMC9016551 DOI: 10.1093/molbev/msac070] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
20
Tamang JP, Das S, Kharnaior P, Pariyar P, Thapa N, Jo SW, Yim EJ, Shin DH. Shotgun metagenomics of Cheonggukjang, a fermented soybean food of Korea: Community structure, predictive functionalities and amino acids profile. Food Res Int 2022;151:110904. [PMID: 34980421 DOI: 10.1016/j.foodres.2021.110904] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 09/10/2021] [Accepted: 12/13/2021] [Indexed: 12/11/2022]
21
Blakeley-Ruiz JA, Kleiner M. Considerations for Constructing a Protein Sequence Database for Metaproteomics. Comput Struct Biotechnol J 2022;20:937-952. [PMID: 35242286 PMCID: PMC8861567 DOI: 10.1016/j.csbj.2022.01.018] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 12/14/2022]  Open
22
How do green and black coffee brews and bioactive interaction with gut microbiome affect its health outcomes? Mining evidence from mechanistic studies, metagenomics and clinical trials. Trends Food Sci Technol 2021. [DOI: 10.1016/j.tifs.2021.11.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
23
Hill L, Sharma R, Hart L, Popov J, Moshkovich M, Pai N. The neonatal microbiome in utero and beyond: perinatal influences and long-term impacts. J LAB MED 2021. [DOI: 10.1515/labmed-2021-0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
24
Hesami Zokaei F, Gharavi S, Asgarani E, Zarrabi M, Soudi MR. A Comparative Taxonomic Profile of Microbial Polyethylene and Hydrocarbon-Degrading Communities in Diverse Environments. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021;19:e2955. [PMID: 34435063 PMCID: PMC8358170 DOI: 10.30498/ijb.2021.2955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
25
Lee CB, Chae SU, Jo SJ, Jerng UM, Bae SK. The Relationship between the Gut Microbiome and Metformin as a Key for Treating Type 2 Diabetes Mellitus. Int J Mol Sci 2021;22:ijms22073566. [PMID: 33808194 PMCID: PMC8037857 DOI: 10.3390/ijms22073566] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/22/2021] [Accepted: 03/27/2021] [Indexed: 02/08/2023]  Open
26
Joseph TA, Pe'er I. An Introduction to Whole-Metagenome Shotgun Sequencing Studies. Methods Mol Biol 2021;2243:107-122. [PMID: 33606255 DOI: 10.1007/978-1-0716-1103-6_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
27
Gut Microbiome: The Third Musketeer in the Cancer-Immune System Cross-Talk. JOURNAL OF PANCREATOLOGY 2020. [DOI: 10.1097/jp9.0000000000000057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
28
Brealey JC, Leitão HG, van der Valk T, Xu W, Bougiouri K, Dalén L, Guschanski K. Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome. Mol Biol Evol 2020;37:3003-3022. [PMID: 32467975 PMCID: PMC7530607 DOI: 10.1093/molbev/msaa135] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
29
Seyler L, Kujawinski EB, Azua-Bustos A, Lee MD, Marlow J, Perl SM, Cleaves II HJ. Metabolomics as an Emerging Tool in the Search for Astrobiologically Relevant Biomarkers. ASTROBIOLOGY 2020;20:1251-1261. [PMID: 32551936 PMCID: PMC7116171 DOI: 10.1089/ast.2019.2135] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
30
Tilocca B, Pieroni L, Soggiu A, Britti D, Bonizzi L, Roncada P, Greco V. Gut-Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization. Int J Mol Sci 2020;21:E4045. [PMID: 32516966 PMCID: PMC7312636 DOI: 10.3390/ijms21114045] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 05/31/2020] [Accepted: 06/04/2020] [Indexed: 12/12/2022]  Open
31
Valentine G, Prince A, Aagaard KM. The Neonatal Microbiome and Metagenomics: What Do We Know and What Is the Future? Neoreviews 2020;20:e258-e271. [PMID: 31261078 DOI: 10.1542/neo.20-5-e258] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
32
Treiber ML, Taft DH, Korf I, Mills DA, Lemay DG. Pre- and post-sequencing recommendations for functional annotation of human fecal metagenomes. BMC Bioinformatics 2020;21:74. [PMID: 32093654 PMCID: PMC7041091 DOI: 10.1186/s12859-020-3416-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 02/17/2020] [Indexed: 01/04/2023]  Open
33
Kiselev D, Matsvay A, Abramov I, Dedkov V, Shipulin G, Khafizov K. Current Trends in Diagnostics of Viral Infections of Unknown Etiology. Viruses 2020;12:E211. [PMID: 32074965 PMCID: PMC7077230 DOI: 10.3390/v12020211] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 02/10/2020] [Accepted: 02/12/2020] [Indexed: 12/27/2022]  Open
34
Why interindividual variation in response to consumption of plant food bioactives matters for future personalised nutrition. Proc Nutr Soc 2020;79:225-235. [PMID: 32014077 DOI: 10.1017/s0029665120000014] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
35
Novoa EM, Jungreis I, Jaillon O, Kellis M. Elucidation of Codon Usage Signatures across the Domains of Life. Mol Biol Evol 2020;36:2328-2339. [PMID: 31220870 PMCID: PMC6759073 DOI: 10.1093/molbev/msz124] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
36
Tilocca B, Costanzo N, Morittu VM, Spina AA, Soggiu A, Britti D, Roncada P, Piras C. Milk microbiota: Characterization methods and role in cheese production. J Proteomics 2019;210:103534. [PMID: 31629058 DOI: 10.1016/j.jprot.2019.103534] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/04/2019] [Accepted: 09/26/2019] [Indexed: 02/07/2023]
37
Haque MM, Mande SS. Decoding the microbiome for the development of translational applications: Overview, challenges and pitfalls. J Biosci 2019;44:118. [PMID: 31719227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
38
Haque MM, Mande SS. Decoding the microbiome for the development of translational applications: Overview, challenges and pitfalls. J Biosci 2019. [DOI: 10.1007/s12038-019-9932-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
39
Lakin SM, Kuhnle A, Alipanahi B, Noyes NR, Dean C, Muggli M, Raymond R, Abdo Z, Prosperi M, Belk KE, Morley PS, Boucher C. Hierarchical Hidden Markov models enable accurate and diverse detection of antimicrobial resistance sequences. Commun Biol 2019;2:294. [PMID: 31396574 PMCID: PMC6684577 DOI: 10.1038/s42003-019-0545-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/08/2019] [Indexed: 12/13/2022]  Open
40
Niu SY, Yang J, McDermaid A, Zhao J, Kang Y, Ma Q. Bioinformatics tools for quantitative and functional metagenome and metatranscriptome data analysis in microbes. Brief Bioinform 2019;19:1415-1429. [PMID: 28481971 DOI: 10.1093/bib/bbx051] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 12/12/2022]  Open
41
Nash MV, Anesio AM, Barker G, Tranter M, Varliero G, Eloe-Fadrosh EA, Nielsen T, Turpin-Jelfs T, Benning LG, Sánchez-Baracaldo P. Metagenomic insights into diazotrophic communities across Arctic glacier forefields. FEMS Microbiol Ecol 2019;94:5036517. [PMID: 29901729 PMCID: PMC6054269 DOI: 10.1093/femsec/fiy114] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 06/11/2018] [Indexed: 11/30/2022]  Open
42
Arango-Argoty GA, Dai D, Pruden A, Vikesland P, Heath LS, Zhang L. NanoARG: a web service for detecting and contextualizing antimicrobial resistance genes from nanopore-derived metagenomes. MICROBIOME 2019;7:88. [PMID: 31174603 PMCID: PMC6555988 DOI: 10.1186/s40168-019-0703-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 05/28/2019] [Indexed: 05/21/2023]
43
Fessler J, Matson V, Gajewski TF. Exploring the emerging role of the microbiome in cancer immunotherapy. J Immunother Cancer 2019;7:108. [PMID: 30995949 PMCID: PMC6471869 DOI: 10.1186/s40425-019-0574-4] [Citation(s) in RCA: 209] [Impact Index Per Article: 34.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Accepted: 03/22/2019] [Indexed: 12/24/2022]  Open
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Verce M, De Vuyst L, Weckx S. Shotgun Metagenomics of a Water Kefir Fermentation Ecosystem Reveals a Novel Oenococcus Species. Front Microbiol 2019;10:479. [PMID: 30918501 PMCID: PMC6424877 DOI: 10.3389/fmicb.2019.00479] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 02/25/2019] [Indexed: 12/29/2022]  Open
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Calderon D, Peña L, Suarez A, Villamil C, Ramirez-Rojas A, Anzola JM, García-Betancur JC, Cepeda ML, Uribe D, Del Portillo P, Mongui A. Recovery and functional validation of hidden soil enzymes in metagenomic libraries. Microbiologyopen 2019;8:e00572. [PMID: 30851083 PMCID: PMC6460280 DOI: 10.1002/mbo3.572] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Revised: 11/01/2017] [Accepted: 11/09/2017] [Indexed: 11/10/2022]  Open
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Sen P, Orešič M. Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview. Metabolites 2019;9:E22. [PMID: 30695998 PMCID: PMC6410263 DOI: 10.3390/metabo9020022] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/23/2019] [Accepted: 01/24/2019] [Indexed: 12/18/2022]  Open
47
Hamza IA, Bibby K. Critical issues in application of molecular methods to environmental virology. J Virol Methods 2019;266:11-24. [PMID: 30659861 DOI: 10.1016/j.jviromet.2019.01.008] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/16/2022]
48
Shotgun metagenomics offers novel insights into taxonomic compositions, metabolic pathways and antibiotic resistance genes in fish gut microbiome. Arch Microbiol 2019;201:295-303. [DOI: 10.1007/s00203-018-1615-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 11/28/2018] [Accepted: 12/20/2018] [Indexed: 12/18/2022]
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Kunath BJ, Minniti G, Skaugen M, Hagen LH, Vaaje-Kolstad G, Eijsink VGH, Pope PB, Arntzen MØ. Metaproteomics: Sample Preparation and Methodological Considerations. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019;1073:187-215. [DOI: 10.1007/978-3-030-12298-0_8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
50
Watson AK, Lannes R, Pathmanathan JS, Méheust R, Karkar S, Colson P, Corel E, Lopez P, Bapteste E. The Methodology Behind Network Thinking: Graphs to Analyze Microbial Complexity and Evolution. Methods Mol Biol 2019;1910:271-308. [PMID: 31278668 DOI: 10.1007/978-1-4939-9074-0_9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
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