Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles

An integrative, multi-scale, genome-wide model reveals the phenotypic landscape of Escherichia coli

(2014) J. Carrera et al.   Molecular Systems Biology

The Alternative Role of Enterobactin as an Oxidative Stress Protector Allows Escherichia coli Colony Development

(2014) Conrado Adler et al.   PLoS One

Linear Superposition and Prediction of Bacterial Promoter Activity Dynamics in Complex Conditions

(2014) Daphna Rothschild et al.   PLoS Computational Biology

Quantitative Genome-Wide Genetic Interaction Screens Reveal Global Epistatic Relationships of Protein Complexes in Escherichia coli

(2014) Mohan Babu et al.   PLoS Genetics

Ontology-aware classification of tissue and cell-type signals in gene expression profiles across platforms and technologies

(2013) Young-suk Lee et al.   BIOINFORMATICS

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Machine Learning Approaches Distinguish Multiple Stress Conditions using Stress-Responsive Genes and Identify Candidate Genes for Broad Resistance in Rice

(2013) R. Shaik et al.   PLANT PHYSIOLOGY

Global Transcriptome Analysis of Lactococcus garvieae Strains in Response to Temperature

(2013) Mónica Aguado-Urda et al.   PLoS One

High-Resolution Transcriptome Maps Reveal Strain-Specific Regulatory Features of Multiple Campylobacter jejuni Isolates

(2013) Gaurav Dugar et al.   PLoS Genetics

Batch effect removal methods for microarray gene expression data integration: a survey

(2012) C. Lazar et al.   BRIEFINGS IN BIOINFORMATICS

A gene ontology inferred from molecular networks

(2012) Janusz Dutkowski et al.   NATURE BIOTECHNOLOGY

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

How Hibernation Factors RMF, HPF, and YfiA Turn Off Protein Synthesis

(2012) Y. S. Polikanov et al.   SCIENCE

The Binding of Antibiotics in OmpF Porin

(2012) Brigitte K. Ziervogel et al.   STRUCTURE

Fitness Landscape Transformation through a Single Amino Acid Change in the Rho Terminator

(2012) Peter L. Freddolino et al.   PLoS Genetics

A mathematical model for adaptive prediction of environmental changes by microorganisms

(2011) A. Mitchell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries

(2010) Lukas Habegger et al.   BIOINFORMATICS

Predicting environmental chemical factors associated with disease-related gene expression data

(2010) Chirag J Patel et al.   BMC Medical Genomics

PpiD is a player in the network of periplasmic chaperones in Escherichia coli

(2010) Yvonne Matern et al.   BMC MICROBIOLOGY

Synthetic biology: applications come of age

(2010) Ahmad S. Khalil et al.   NATURE REVIEWS GENETICS

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

(2010) H. Parkinson et al.   NUCLEIC ACIDS RESEARCH

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Adaptive prediction of environmental changes by microorganisms

(2009) Amir Mitchell et al.   NATURE

Automated multidimensional phenotypic profiling using large public microarray repositories

(2009) M. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutual information and redundancy for categorical data

(2009) Chong Sun Hong et al.   STATISTICAL PAPERS

Predicting Cellular Growth from Gene Expression Signatures

(2009) Edoardo M. Airoldi et al.   PLoS Computational Biology

Genome-Wide Transcriptional Responses of Escherichia coli K-12 to Continuous Osmotic and Heat Stresses

(2008) T. S. Gunasekera et al.   JOURNAL OF BACTERIOLOGY

Control of RpoS in global gene expression of Escherichia coli in minimal media

(2008) Tao Dong et al.   MOLECULAR GENETICS AND GENOMICS

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation

(2008) Luis López-Maury et al.   NATURE REVIEWS GENETICS

SYSTEMS BIOLOGY: The Scale of Prediction

(2008) N. S. Baliga   SCIENCE

Predictive Behavior Within Microbial Genetic Networks

(2008) I. Tagkopoulos et al.   SCIENCE