Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach

Global transcriptional responses of Acidithiobacillus ferrooxidans Wenelen under different sulfide minerals

(2016) Mauricio Latorre et al.   BIORESOURCE TECHNOLOGY

Metabolic dependencies drive species co-occurrence in diverse microbial communities

(2015) Aleksej Zelezniak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eukaryotic plankton diversity in the sunlit ocean

(2015) C. de Vargas et al.   SCIENCE

d-OptCom: Dynamic Multi-level and Multi-objective Metabolic Modeling of Microbial Communities

(2014) Ali R. Zomorrodi et al.   ACS Synthetic Biology

Simple topological properties predict functional misannotations in a metabolic network

(2013) Rodrigo Liberal et al.   BIOINFORMATICS

Natural Selection for Operons Depends on Genome Size

(2013) Pablo A. Nuñez et al.   Genome Biology and Evolution

Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes

(2013) Pascal Hingamp et al.   ISME Journal

Computational meta'omics for microbial community studies

(2013) N. Segata et al.   Molecular Systems Biology

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli

(2013) D. McCloskey et al.   Molecular Systems Biology

Turnover of soil bacterial diversity driven by wide-scale environmental heterogeneity

(2013) L. Ranjard et al.   Nature Communications

Draft Genome Sequence of the Sulfobacillus thermosulfidooxidans Cutipay Strain, an Indigenous Bacterium Isolated from a Naturally Extreme Mining Environment in Northern Chile

(2012) D. Travisany et al.   JOURNAL OF BACTERIOLOGY

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Robustness of metabolic networks: A review of existing definitions

(2011) Abdelhalim Larhlimi et al.   BIOSYSTEMS

A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities

(2011) Eleftheria Tzamali et al.   BMC Systems Biology

Ecosystems biology of microbial metabolism

(2011) Niels Klitgord et al.   CURRENT OPINION IN BIOTECHNOLOGY

Integrated analysis of the gene neighbouring impact on bacterial metabolic networks

(2011) P. Bordron et al.   IET Systems Biology

Draft Genome Sequence of the Extremely Acidophilic Biomining Bacterium Acidithiobacillus thiooxidans ATCC 19377 Provides Insights into the Evolution of the Acidithiobacillus Genus

(2011) J. Valdes et al.   JOURNAL OF BACTERIOLOGY

Complete genome of Leptospirillum ferriphilum ML-04 provides insight into its physiology and environmental adaptation

(2011) Shuang Mi et al.   JOURNAL OF MICROBIOLOGY

Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data

(2011) J. Raes et al.   Molecular Systems Biology

ProOpDB: Prokaryotic Operon DataBase

(2011) B. Taboada et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Combined phylogenetic and genomic approaches for the high-throughput study of microbial habitat adaptation

(2011) Jesse R.R. Zaneveld et al.   TRENDS IN MICROBIOLOGY

A Holistic Approach to Marine Eco-Systems Biology

(2011) Eric Karsenti et al.   PLOS BIOLOGY

Proteogenomic and functional analysis of chromate reduction in Acidiphilium cryptum JF-5, an Fe(III)-respiring acidophile

(2010) Timothy S. Magnuson et al.   BIOMETALS

A general co-expression network-based approach to gene expression analysis: comparison and applications

(2010) Jianhua Ruan et al.   BMC Systems Biology

Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families

(2010) P. V. Patel et al.   GENOME RESEARCH

A global network of coexisting microbes from environmental and whole-genome sequence data

(2010) S. Chaffron et al.   GENOME RESEARCH

Comparative genomics begins to unravel the ecophysiology of bioleaching

(2010) J. Valdés et al.   HYDROMETALLURGY

Acidithiobacillus ferrooxidans metabolism: from genome sequence to industrial applications

(2009) Jorge Valdés et al.   BMC GENOMICS

Extending the models for iron and sulfur oxidation in the extreme Acidophile Acidithiobacillus ferrooxidans

(2009) Raquel Quatrini et al.   BMC GENOMICS

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

Methods for unveiling cryptic microbial partnerships in nature

(2009) Victoria J Orphan   CURRENT OPINION IN MICROBIOLOGY

Microbial community structure in the North Pacific ocean

(2009) Mark V Brown et al.   ISME Journal

An integrative approach towards completing genome-scale metabolic networks

(2009) Nils Christian et al.   Molecular BioSystems

Impact of Genome Reduction on Bacterial Metabolism and Its Regulation

(2009) E. Yus et al.   SCIENCE

Estimating the size of the bacterial pan-genome

(2009) Pascal Lapierre et al.   TRENDS IN GENETICS

Comparative genomic analysis of carbon and nitrogen assimilation mechanisms in three indigenous bioleaching bacteria: predictions and validations

(2008) Gloria Levicán et al.   BMC GENOMICS

DOOR: a database for prokaryotic operons

(2008) Fenglou Mao et al.   NUCLEIC ACIDS RESEARCH

Large-scale reconstruction and phylogenetic analysis of metabolic environments

(2008) E. Borenstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial diversity based on 16S rRNA and gyrB genes at Yinshan mine, China

(2008) Huaqun Yin et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY