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Select item 100259351.

Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim

Chen Yang, Theodora Lo, Ka Ming Nip, Saber Hafezqorani, René L Warren, Inanc Birol

Gigascience. 2023; 12: giad013. Published online 2023 Mar 20. doi: 10.1093/gigascience/giad013

PMCID:: PMC10025935

Abstract Article PDF–2.2M

Select item 99944722.

FunFun: ITS‐based functional annotator of fungal communities

Danil V. Krivonos, Dmitry N. Konanov, Elena N. Ilina

Ecol Evol. 2023 Mar; 13(3): e9874. Published online 2023 Mar 8. doi: 10.1002/ece3.9874

PMCID:: PMC9994472

Abstract Article PDF–3.1M

Select item 99602873.

Enhanced Viral Metagenomics with Lazypipe 2

Ilya Plyusnin, Olli Vapalahti, Tarja Sironen, Ravi Kant, Teemu Smura

Viruses. 2023 Feb; 15(2): 431. Published online 2023 Feb 4. doi: 10.3390/v15020431

PMCID:: PMC9960287

Abstract Article PDF–932K

Select item 99029114.

Evaluation of computational phage detection tools for metagenomic datasets

Kenneth E. Schackart, III, Jessica B. Graham, Alise J. Ponsero, Bonnie L. Hurwitz

Front Microbiol. 2023; 14: 1078760. Published online 2023 Jan 25. doi: 10.3389/fmicb.2023.1078760

PMCID:: PMC9902911

Abstract Article PDF–5.1M

Select item 89176885.

SprayNPray: user-friendly taxonomic profiling of genome and metagenome contigs

Arkadiy I. Garber, Catherine R. Armbruster, Stella E. Lee, Vaughn S. Cooper, Jennifer M. Bomberger, Sean M. McAllister

BMC Genomics. 2022; 23: 202. Published online 2022 Mar 12. doi: 10.1186/s12864-022-08382-2

PMCID:: PMC8917688

Abstract Article PDF–1.2M

Select item 88984586.

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics

Gleb Goussarov, Jürgen Claesen, Mohamed Mysara, Ilse Cleenwerck, Natalie Leys, Peter Vandamme, Rob Van Houdt

Environ Microbiome. 2022; 17: 9. Published online 2022 Mar 5. doi: 10.1186/s40793-022-00403-7

PMCID:: PMC8898458

Abstract Article PDF–4.2M

Select item 85317317.

Application of Deep Learning in Plant–Microbiota Association Analysis

Zhiyu Deng, Jinming Zhang, Junya Li, Xiujun Zhang

Front Genet. 2021; 12: 697090. Published online 2021 Oct 8. doi: 10.3389/fgene.2021.697090

PMCID:: PMC8531731

Abstract Article PDF–916K

Select item 82289408.

SCAPP: an algorithm for improved plasmid assembly in metagenomes

David Pellow, Alvah Zorea, Maraike Probst, Ori Furman, Arik Segal, Itzhak Mizrahi, Ron Shamir

Microbiome. 2021; 9: 144. Published online 2021 Jun 25. doi: 10.1186/s40168-021-01068-z

PMCID:: PMC8228940

Abstract Article PDF–1.5M

Select item 81756359.

Reads Binning Improves the Assembly of Viral Genome Sequences From Metagenomic Samples

Kai Song

Front Microbiol. 2021; 12: 664560. Published online 2021 May 21. doi: 10.3389/fmicb.2021.664560

PMCID:: PMC8175635

Abstract Article PDF–3.4M

Select item 789081710.

PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data

Laura de Nies, Sara Lopes, Susheel Bhanu Busi, Valentina Galata, Anna Heintz-Buschart, Cedric Christian Laczny, Patrick May, Paul Wilmes

Microbiome. 2021; 9: 49. Published online 2021 Feb 17. doi: 10.1186/s40168-020-00993-9

PMCID:: PMC7890817

Abstract Article PDF–2.2M

Select item 791324011.

Information Theoretic Metagenome Assembly Allows the Discovery of Disease Biomarkers in Human Microbiome

O. Ufuk Nalbantoglu

Entropy (Basel) 2021 Feb; 23(2): 187. Published online 2021 Feb 2. doi: 10.3390/e23020187

PMCID:: PMC7913240

Abstract Article PDF–1.9M

Select item 777247112.

Novel NGS pipeline for virus discovery from a wide spectrum of hosts and sample types

Ilya Plyusnin, Ravi Kant, Anne J Jääskeläinen, Tarja Sironen, Liisa Holm, Olli Vapalahti, Teemu Smura

Virus Evol. 2020 Jul; 6(2): veaa091. Published online 2020 Dec 2. doi: 10.1093/ve/veaa091

PMCID:: PMC7772471

Abstract Article PDF–294K

Select item 759359113.

phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes

Harald R. Gruber-Vodicka, Brandon K. B. Seah, Elmar Pruesse

mSystems. 2020 Sep-Oct; 5(5): e00920-20. Published online 2020 Oct 27. doi: 10.1128/mSystems.00920-20

PMCID:: PMC7593591

Abstract Article PDF–1.0M

Select item 755917314.

In silico benchmarking of metagenomic tools for coding sequence detection reveals the limits of sensitivity and precision

Jonathan Louis Golob, Samuel Schwartz Minot

BMC Bioinformatics. 2020; 21: 459. Published online 2020 Oct 15. doi: 10.1186/s12859-020-03802-0

PMCID:: PMC7559173

Abstract Article PDF–1.1M

Select item 742754315.

Evaluation of computational methods for human microbiome analysis using simulated data

Matthieu J. Miossec, Sandro L. Valenzuela, Marcos Pérez-Losada, W. Evan Johnson, Keith A. Crandall, Eduardo Castro-Nallar

PeerJ. 2020; 8: e9688. Published online 2020 Aug 11. doi: 10.7717/peerj.9688

PMCID:: PMC7427543

Abstract Article PDF–1.8M

Select item 735442116.

Toxin-Antitoxin Systems: A Tool for Taxonomic Analysis of Human Intestinal Microbiota

Ksenia M. Klimina, Viktoriya N. Voroshilova, Elena U. Poluektova, Vladimir A. Veselovsky, Roman A. Yunes, Aleksey S. Kovtun, Anna V. Kudryavtseva, Artem S. Kasianov, Valery N. Danilenko

Toxins (Basel) 2020 Jun; 12(6): 388. Published online 2020 Jun 12. doi: 10.3390/toxins12060388

PMCID:: PMC7354421

Abstract Article PDF–653K

Select item 718943917.

CCMetagen: comprehensive and accurate identification of eukaryotes and prokaryotes in metagenomic data

Vanessa R. Marcelino, Philip T. L. C. Clausen, Jan P. Buchmann, Michelle Wille, Jonathan R. Iredell, Wieland Meyer, Ole Lund, Tania C. Sorrell, Edward C. Holmes

Genome Biol. 2020; 21: 103. Published online 2020 Apr 28. doi: 10.1186/s13059-020-02014-2

PMCID:: PMC7189439

Abstract Article PDF–1.1M

Select item 730512218.

Targeted assemblies of cas1 suggest CRISPR-Cas’s response to soil warming

Ruonan Wu, Benli Chai, James R. Cole, Santosh K. Gunturu, Xue Guo, Renmao Tian, Ji-Dong Gu, Jizhong Zhou, James M. Tiedje

ISME J. 2020 Jul; 14(7): 1651–1662. Published online 2020 Mar 27. doi: 10.1038/s41396-020-0635-1

PMCID:: PMC7305122

Abstract Article PDF–5.8M

Select item 695206919.

MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

Liu Cao, Alexey Gurevich, Kelsey L. Alexander, C. Benjamin Naman, Tiago Leão, Evgenia Glukhov, Tal Luzzatto-Knaan, Fernando Vargas, Robby Quinn, Amina Bouslimani, Louis Felix Nothias, Nitin K. Singh, Jon G. Sanders, Rodolfo A. S. Benitez, Luke R. Thompson, Md-Nafiz Hamid, James T. Morton, Alla Mikheenko, Alexander Shlemov, Anton Korobeynikov, Iddo Friedberg, Rob Knight, Kasthuri Venkateswaran, William H. Gerwick, Lena Gerwick, Pieter C. Dorrestein, Pavel A. Pevzner, Hosein Mohimani

Cell Syst. Author manuscript; available in PMC 2020 Dec 18.

Published in final edited form as: Cell Syst. 2019 Dec 18; 9(6): 600–608.e4. Published online 2019 Oct 16. doi: 10.1016/j.cels.2019.09.004

PMCID:: PMC6952069

Abstract Article PDF–1.3M

Select item 670041820.

The Human Gut Microbiome is Structured to Optimize Molecular Interaction Networks

Yiwei Ling, Yu Watanabe, Shujiro Okuda

Comput Struct Biotechnol J. 2019; 17: 1040–1046. Published online 2019 Jul 29. doi: 10.1016/j.csbj.2019.07.011

PMCID:: PMC6700418

Abstract Article PDF–1.7M

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