Independent component analysis of Corynebacterium glutamicum transcriptomes reveals its transcriptional regulatory network

Biosynthesis of eriodictyol from tyrosine by Corynebacterium glutamicum

(2022) Xia Wu et al.   Microbial Cell Factories

Machine learning from Pseudomonas aeruginosa transcriptomes identifies independently modulated sets of genes associated with known transcriptional regulators

(2022) Akanksha Rajput et al.   NUCLEIC ACIDS RESEARCH

Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection

(2022) Reo Yoo et al.   mSphere

Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network

(2022) Hyun Gyu Lim et al.   METABOLIC ENGINEERING

Early Evolutionary Selection of NAD Biosynthesis Pathway in Bacteria

(2022) Suraj Sharma et al.   Metabolites

Machine Learning of Bacterial Transcriptomes Reveals Responses Underlying Differential Antibiotic Susceptibility

(2021) Anand V. Sastry et al.   mSphere

Optimal dimensionality selection for independent component analysis of transcriptomic data

(2021) John Luke McConn et al.   BMC BIOINFORMATICS

The Sequence Read Archive: a decade more of explosive growth

(2021) Kenneth Katz et al.   NUCLEIC ACIDS RESEARCH

Machine Learning Uncovers a Data-Driven Transcriptional Regulatory Network for the Crenarchaeal Thermoacidophile Sulfolobus acidocaldarius

(2021) Siddharth M. Chauhan et al.   Frontiers in Microbiology

Sulfur Administration in Fe–S Cluster Homeostasis

(2021) Leszek Rydz et al.   Antioxidants

Quantitative prediction of conditional vulnerabilities in regulatory and metabolic networks using PRIME

(2021) Selva Rupa Christinal Immanuel et al.   npj Systems Biology and Applications

CoryneRegNet 7, the reference database and analysis platform for corynebacterial gene regulatory networks

(2020) Mariana Teixeira Dornelles Parise et al.   Scientific Data

Revealing 29 sets of independently modulated genes inStaphylococcus aureus, their regulators, and role in key physiological response

(2020) Saugat Poudel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Database resources of the National Center for Biotechnology Information

(2020) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

(2020) Kevin Rychel et al.   Nature Communications

Identifying the Growth Modulon of Corynebacterium glutamicum

(2019) Thorsten Haas et al.   Frontiers in Microbiology

The Escherichia coli transcriptome mostly consists of independently regulated modules

(2019) Anand V. Sastry et al.   Nature Communications

A comprehensive evaluation of module detection methods for gene expression data

(2018) Wouter Saelens et al.   Nature Communications

Deciphering the Adaptation of Corynebacterium glutamicum in Transition from Aerobiosis via Microaerobiosis to Anaerobiosis

(2018) Julian Lange et al.   Genes

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Zero-growth bioprocesses: A challenge for microbial production strains and bioprocess engineering

(2016) Julian Lange et al.   ENGINEERING IN LIFE SCIENCES

Transcription of Sialic Acid Catabolism Genes in Corynebacterium glutamicum Is Subject to Catabolite Repression and Control by the Transcriptional Repressor NanR

(2016) Andreas Uhde et al.   JOURNAL OF BACTERIOLOGY

Metabolic engineering of Corynebacterium glutamicum for enhanced production of 5-aminovaleric acid

(2016) Jae Ho Shin et al.   Microbial Cell Factories

The extracytoplasmic function σ factor σCregulates expression of a branched quinol oxidation pathway inCorynebacterium glutamicum

(2016) Koichi Toyoda et al.   MOLECULAR MICROBIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Beyond growth rate 0.6: What drivesCorynebacterium glutamicumto higher growth rates in defined medium

(2013) Simon Unthan et al.   BIOTECHNOLOGY AND BIOENGINEERING

RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria

(2013) Pavel S Novichkov et al.   BMC GENOMICS

Complex Regulation of the Phosphoenolpyruvate Carboxykinase Gene pck and Characterization of Its GntR-Type Regulator IolR as a Repressor of myo-Inositol Utilization Genes in Corynebacterium glutamicum

(2013) S. Klaffl et al.   JOURNAL OF BACTERIOLOGY

Impact of different CO2/HCO3− levels on metabolism and regulation in Corynebacterium glutamicum

(2013) Bastian Blombach et al.   JOURNAL OF BIOTECHNOLOGY

Dynamic regulatory network controlling TH17 cell differentiation

(2013) Nir Yosef et al.   NATURE

The molecular mechanisms and physiological consequences of oxidative stress: lessons from a model bacterium

(2013) James A. Imlay   NATURE REVIEWS MICROBIOLOGY

Histidine biosynthesis, its regulation and biotechnological application inCorynebacterium glutamicum

(2013) Robert K. Kulis-Horn et al.   Microbial Biotechnology

Beyond growth rate 0.6:Corynebacterium glutamicumcultivated in highly diluted environments

(2012) Alexander Grünberger et al.   BIOTECHNOLOGY AND BIOENGINEERING

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Corynebacterium glutamicum Tailored for Efficient Isobutanol Production

(2011) Bastian Blombach et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effect of culture operating conditions on succinate production in a multiphase fed-batch bioreactor using an engineered Escherichia coli strain

(2011) Jiangfeng Zhu et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Molecular characterization of PrpR, the transcriptional activator of propionate catabolism in Corynebacterium glutamicum

(2011) Jens Plassmeier et al.   JOURNAL OF BIOTECHNOLOGY

Crosstalk in NF-κB signaling pathways

(2011) Andrea Oeckinghaus et al.   NATURE IMMUNOLOGY

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Regulation of the Expression of Genes Involved in NAD De Novo Biosynthesis in Corynebacterium glutamicum

(2010) H. Teramoto et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Zur regulon of Corynebacterium glutamicum ATCC 13032

(2010) Jasmin Schröder et al.   BMC GENOMICS

PcaO Positively Regulates pcaHG of the  -Ketoadipate Pathway in Corynebacterium glutamicum

(2010) K.-X. Zhao et al.   JOURNAL OF BACTERIOLOGY

Metabolic impact of the level of aeration during cell growth on anaerobic succinate production by an engineered Escherichia coli strain

(2010) Irene Martínez et al.   METABOLIC ENGINEERING

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Towards systems metabolic engineering of microorganisms for amino acid production

(2008) Jin Hwan Park et al.   CURRENT OPINION IN BIOTECHNOLOGY

Indole cell signaling occurs primarily at low temperatures in Escherichia coli

(2008) Jintae Lee et al.   ISME Journal

Regulation of the expression of phosphoenolpyruvate : carbohydrate phosphotransferase system (PTS) genes in Corynebacterium glutamicum R

(2008) Y. Tanaka et al.   MICROBIOLOGY-SGM

Identification of a novel α(1→6) mannopyranosyltransferase MptB fromCorynebacterium glutamicumby deletion of a conserved gene,NCgl1505, affords a lipomannan- and lipoarabinomannan-deficient mutant

(2008) Arun K. Mishra et al.   MOLECULAR MICROBIOLOGY