Transcriptional response of Escherichia coli to ammonia and glucose fluctuations

Construction of chromosomally encodedlacZandgfpreporter strains ofEscherichia colifor the study of global regulation of metabolism

(2016) Natalia Trachtmann et al.   ENGINEERING IN LIFE SCIENCES

Euler-Lagrange computational fluid dynamics for (bio)reactor scale down: An analysis of organism lifelines

(2016) Cees Haringa et al.   ENGINEERING IN LIFE SCIENCES

Engineering E. coli for large-scale production – Strategies considering ATP expenses and transcriptional responses

(2016) Michael Löffler et al.   METABOLIC ENGINEERING

Response ofCorynebacterium glutamicumexposed to oscillating cultivation conditions in a two- and a novel three-compartment scale-down bioreactor

(2015) Anja Lemoine et al.   BIOTECHNOLOGY AND BIOENGINEERING

An Iterative Leave-One-Out Approach to Outlier Detection in RNA-Seq Data

(2015) Nysia I. George et al.   PLoS One

CO2/HCO3 − perturbations of simulated large scale gradients in a scale-down device cause fast transcriptional responses in Corynebacterium glutamicum

(2014) Jens Buchholz et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Coordination of microbial metabolism

(2014) Victor Chubukov et al.   NATURE REVIEWS MICROBIOLOGY

Robustly detecting differential expression in RNA sequencing data using observation weights

(2014) Xiaobei Zhou et al.   NUCLEIC ACIDS RESEARCH

Nitrogen stress response and stringent response are coupled in Escherichia coli

(2014) Daniel R. Brown et al.   Nature Communications

Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

(2013) W. C. van Heeswijk et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Coordination of bacterial proteome with metabolism by cyclic AMP signalling

(2013) Conghui You et al.   NATURE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

An industrial perspective on bioreactor scale-down: What we can learn from combined large-scale bioprocess and model fluid studies

(2011) Henk Noorman   Biotechnology Journal

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Scale-up of microbial processes: Impacts, tools and open questions

(2011) R. Takors   JOURNAL OF BIOTECHNOLOGY

α-ketoglutarate coordinates carbon and nitrogen utilization via enzyme I inhibition

(2011) Christopher D Doucette et al.   Nature Chemical Biology

Novel Roles of cAMP Receptor Protein (CRP) in Regulation of Transport and Metabolism of Carbon Sources

(2011) Tomohiro Shimada et al.   PLoS One

Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the ‘feast to famine’ gradient in Escherichia coli

(2010) Matthew F. Traxler et al.   MOLECULAR MICROBIOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

GAGE: generally applicable gene set enrichment for pathway analysis

(2009) Weijun Luo et al.   BMC BIOINFORMATICS

DksA and ppGpp directly regulate transcription of the Escherichia coli flagellar cascade

(2009) Justin J. Lemke et al.   MOLECULAR MICROBIOLOGY

(p)ppGpp: Still Magical?

(2008) Katarzyna Potrykus et al.   Annual Review of Microbiology

The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli

(2008) Matthew F. Traxler et al.   MOLECULAR MICROBIOLOGY