Literature DB >> 22219204

NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment.

Rogan Carr1, Elhanan Borenstein.   

Abstract

UNLABELLED: NetSeed is a web tool and Perl module for analyzing the topology of metabolic networks and calculating the set of exogenously acquired compounds. NetSeed is based on the seed detection algorithm, developed and validated in previous studies. AVAILABILITY: The NetSeed web-based tool, open-source Perl module, examples and documentation are freely available online at: http://depts.washington.edu/elbogs/NetSeed.

Mesh：

Year:  2012        PMID： 22219204     DOI： 10.1093/bioinformatics/btr721

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  14 in total

Review 1.  Community metabolic modeling approaches to understanding the gut microbiome: Bridging biochemistry and ecology.

Authors:  Helena Mendes-Soares; Nicholas Chia
Journal:  Free Radic Biol Med       Date:  2016-12-15       Impact factor: 7.376

2.  Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome.

Authors:  David B Bernstein; Floyd E Dewhirst; Daniel Segrè
Journal:  Elife       Date:  2019-06-13       Impact factor: 8.140

Review 3.  Towards a predictive systems-level model of the human microbiome: progress, challenges, and opportunities.

Authors:  Sharon Greenblum; Hsuan-Chao Chiu; Roie Levy; Rogan Carr; Elhanan Borenstein
Journal:  Curr Opin Biotechnol       Date:  2013-04-23       Impact factor: 9.740

4.  Global genomic and proteomic analysis indicates co-evolution of Neisseria species and with their human host.

Authors:  Indrani Sarkar; Prateek Dey; Saurabh Singh Rathore; Gyan Dev Singh; Ram Pratap Singh
Journal:  World J Microbiol Biotechnol       Date:  2022-07-01       Impact factor: 3.312

Review 5.  Mass spectrometry-based metabolomics in microbiome investigations.

Authors:  Anelize Bauermeister; Helena Mannochio-Russo; Letícia V Costa-Lotufo; Alan K Jarmusch; Pieter C Dorrestein
Journal:  Nat Rev Microbiol       Date:  2021-09-22       Impact factor: 78.297

6.  NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation.

Authors:  Roie Levy; Rogan Carr; Anat Kreimer; Shiri Freilich; Elhanan Borenstein
Journal:  BMC Bioinformatics       Date:  2015-05-17       Impact factor: 3.169

7.  RevEcoR: an R package for the reverse ecology analysis of microbiomes.

Authors:  Yang Cao; Yuanyuan Wang; Xiaofei Zheng; Fei Li; Xiaochen Bo
Journal:  BMC Bioinformatics       Date:  2016-07-29       Impact factor: 3.169

8.  Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation.

Authors:  Shany Ofaim; Maya Ofek-Lalzar; Noa Sela; Jiandong Jinag; Yechezkel Kashi; Dror Minz; Shiri Freilich
Journal:  Front Microbiol       Date:  2017-08-23       Impact factor: 5.640

9.  Genome composition and phylogeny of microbes predict their co-occurrence in the environment.

Authors:  Olga K Kamneva
Journal:  PLoS Comput Biol       Date:  2017-02-02       Impact factor: 4.475

10.  Modeling trophic dependencies and exchanges among insects' bacterial symbionts in a host-simulated environment.

Authors:  Itai Opatovsky; Diego Santos-Garcia; Zhepu Ruan; Tamar Lahav; Shany Ofaim; Laurence Mouton; Valérie Barbe; Jiandong Jiang; Einat Zchori-Fein; Shiri Freilich
Journal:  BMC Genomics       Date:  2018-05-25       Impact factor: 3.969
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