Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation

Accounting for Experimental Noise Reveals That mRNA Levels, Amplified by Post-Transcriptional Processes, Largely Determine Steady-State Protein Levels in Yeast

(2015) Gábor Csárdi et al.   PLoS Genetics

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

Global Dynamics of the Escherichia coli Proteome and Phosphoproteome During Growth in Minimal Medium

(2013) Nelson C. Soares et al.   JOURNAL OF PROTEOME RESEARCH

Fortifying the barrier: the impact of lipid A remodelling on bacterial pathogenesis

(2013) Brittany D. Needham et al.   NATURE REVIEWS MICROBIOLOGY

The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum

(2013) William R. Harcombe et al.   PLoS Computational Biology

Improving metabolic flux predictions using absolute gene expression data

(2012) Dave Lee et al.   BMC Systems Biology

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

RNA snap ™: a rapid, quantitative and inexpensive, method for isolating total RNA from bacteria

(2012) Mark B. Stead et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Temporal Expression-based Analysis of Metabolism

(2012) Sara B. Collins et al.   PLoS Computational Biology

Modeling Phenotypic Metabolic Adaptations of Mycobacterium tuberculosis H37Rv under Hypoxia

(2012) Xin Fang et al.   PLoS Computational Biology

Comparative multi-omics systems analysis of Escherichia coli strains B and K-12

(2012) Sung Yoon et al.   GENOME BIOLOGY

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

The NumPy Array: A Structure for Efficient Numerical Computation

(2011) Stéfan van der Walt et al.   COMPUTING IN SCIENCE & ENGINEERING

Genome-wide detection of novel regulatory RNAs in E. coli

(2011) R. Raghavan et al.   GENOME RESEARCH

Quantification of mRNA and protein and integration with protein turnover in a bacterium

(2011) T. Maier et al.   Molecular Systems Biology

Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data

(2011) Christine Vogel et al.   Nature Protocols

Fundamental relationship between operon organization and gene expression

(2011) H. N. Lim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Remodelling of the Vibrio cholerae membrane by incorporation of exogenous fatty acids from host and aquatic environments

(2010) David K. Giles et al.   MOLECULAR MICROBIOLOGY

Sequence signatures and mRNA concentration can explain two-thirds of protein abundance variation in a human cell line

(2010) Christine Vogel et al.   Molecular Systems Biology

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models

(2010) Nathan E Lewis et al.   Molecular Systems Biology

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Predicting Metabolic Fluxes Using Gene Expression Differences As Constraints

(2009) Rogier J P van Berlo et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Gene Expression Profiling and the Use of Genome-Scale In Silico Models of Escherichia coli for Analysis: Providing Context for Content

(2009) N. E. Lewis et al.   JOURNAL OF BACTERIOLOGY

Genome Sequences of Escherichia coli B strains REL606 and BL21(DE3)

(2009) Haeyoung Jeong et al.   JOURNAL OF MOLECULAR BIOLOGY

13C-based metabolic flux analysis

(2009) Nicola Zamboni et al.   Nature Protocols

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

(2009) Pingzhao Hu et al.   PLOS BIOLOGY

Interpreting Expression Data with Metabolic Flux Models: Predicting Mycobacterium tuberculosis Mycolic Acid Production

(2009) Caroline Colijn et al.   PLoS Computational Biology

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli

(2008) Adam M Feist et al.   NATURE BIOTECHNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS