Integrating multiple 'omics' analysis for microbial biology: application and methodologies

Proteomic and Transcriptomic Analyses Reveal Genes Upregulated by cis-Dichloroethene in Polaromonas sp. Strain JS666

(2009) L. K. Jennings et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Integrative analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: a non-linear model to predict abundance of undetected proteins

(2009) Wandaliz Torres-García et al.   BIOINFORMATICS

The era of 'omics unlimited

(2009) Raj P. Kandpal et al.   BIOTECHNIQUES

Sparse canonical methods for biological data integration: application to a cross-platform study

(2009) Kim-Anh Lê Cao et al.   BMC BIOINFORMATICS

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii

(2009) Patrick May et al.   BMC GENOMICS

Transcriptomic and metabolomic profiling of Zymomonas mobilis during aerobic and anaerobic fermentations

(2009) Shihui Yang et al.   BMC GENOMICS

The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti

(2009) Ignacio Rodriguez-Llorente et al.   BMC Systems Biology

Differential Binding Profiles of StpA in Wild-Type and hns Mutant Cells: a Comparative Analysis of Cooperative Partners by Chromatin Immunoprecipitation-Microarray Analysis

(2009) E. Uyar et al.   JOURNAL OF BACTERIOLOGY

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream

(2009) Nikos C Kyrpides   NATURE BIOTECHNOLOGY

Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation

(2009) Dwayne A. Elias et al.   NUCLEIC ACIDS RESEARCH

An Integrated Genomics Approach to Define Niche Establishment by Rhodococcus fascians

(2009) S. Depuydt et al.   PLANT PHYSIOLOGY

The proteome of Salmonella Typhimurium grown under in vivo-mimicking conditions

(2009) Kathleen A. J. Sonck et al.   PROTEOMICS

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

(2009) Pingzhao Hu et al.   PLOS BIOLOGY

Information Flow Analysis of Interactome Networks

(2009) Patrycja Vasilyev Missiuro et al.   PLoS Computational Biology

The Organization of the Bacterial Genome

(2008) Eduardo P.C. Rocha   Annual Review of Genetics

Development and Experimental Validation of a Predictive Threshold Cycle Equation for Quantification of Virulence and Marker Genes by High-Throughput Nanoliter-Volume PCR on the OpenArray Platform

(2008) R. D. Stedtfeld et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metabolic flux analysis ofShewanellaspp. reveals evolutionary robustness in central carbon metabolism

(2008) Yinjie J. Tang et al.   BIOTECHNOLOGY AND BIOENGINEERING

Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service

(2008) Jeong-Gu Kim et al.   BMC BIOINFORMATICS

Statistical Application and Challenges in Global Gel-Free Proteomic Analysis by Mass Spectrometry

(2008) Lei Nie et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

New tools for discovering and characterizing microbial diversity

(2008) Erick Cardenas et al.   CURRENT OPINION IN BIOTECHNOLOGY

Separation and mass spectrometry in microbial metabolomics

(2008) David E Garcia et al.   CURRENT OPINION IN MICROBIOLOGY

Metabolomics and fluxomics approaches

(2008) Marta Cascante et al.   Essays in Biochemistry

The Global Repressor SugR Controls Expression of Genes of Glycolysis and of the L-Lactate Dehydrogenase LdhA in Corynebacterium glutamicum

(2008) V. Engels et al.   JOURNAL OF BACTERIOLOGY

The Use of Chromatin Immunoprecipitation to Define PpsR Binding Activity in Rhodobacter sphaeroides 2.4.1

(2008) P. Bruscella et al.   JOURNAL OF BACTERIOLOGY

Correlating the Transcriptome, Proteome, and Metabolome in the Environmental Adaptation of a Hyperthermophile

(2008) Sunia A. Trauger et al.   JOURNAL OF PROTEOME RESEARCH

Advances in analysis of microbial metabolic fluxes via13C isotopic labeling

(2008) Yinjie J. Tang et al.   MASS SPECTROMETRY REVIEWS

Integration of Metabolomic and Proteomic Phenotypes

(2008) Stefanie Wienkoop et al.   MOLECULAR & CELLULAR PROTEOMICS

eSGA: E. coli synthetic genetic array analysis

(2008) Gareth Butland et al.   NATURE METHODS

High-throughput, quantitative analyses of genetic interactions in E. coli

(2008) Athanasios Typas et al.   NATURE METHODS

Microbiology in the post-genomic era

(2008) Duccio Medini et al.   NATURE REVIEWS MICROBIOLOGY

Uncovering Genes with Divergent mRNA-Protein Dynamics in Streptomyces coelicolor

(2008) Karthik P. Jayapal et al.   PLoS One

Detection of Large Numbers of Novel Sequences in the Metatranscriptomes of Complex Marine Microbial Communities

(2008) Jack A. Gilbert et al.   PLoS One

PhoP: A Missing Piece in the Intricate Puzzle of Mycobacterium tuberculosis Virulence

(2008) Jesús Gonzalo-Asensio et al.   PLoS One

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into environmental bioremediation by microorganisms through functional genomics and proteomics

(2008) Bing Zhao et al.   PROTEOMICS