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

Independent component analysis recovers consistent regulatory signals from disparate datasets

(2021) Anand V. Sastry et al.   PLoS Computational Biology

Response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius to solvent stress exemplified by 1-butanol exposure

(2021) Jens C. Benninghoff et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Propulsive nanomachines: the convergent evolution of archaella, flagella, and cilia

(2020) Morgan Beeby et al.   FEMS MICROBIOLOGY REVIEWS

Identification of XylR, the Activator of Arabinose/Xylose Inducible Regulon in Sulfolobus acidocaldarius and Its Application for Homologous Protein Expression

(2020) Nienke van der Kolk et al.   Frontiers in Microbiology

Defining heat shock response for the thermoacidophilic model crenarchaeon Sulfolobus acidocaldarius

(2020) Rani Baes et al.   EXTREMOPHILES

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

Sulfolobus acidocaldarius uses a complex trehalose metabolism for salt stress response involving a novel TPS/TPP pathway

(2020) Christina Stracke et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

iModulonDB: a knowledgebase of microbial transcriptional regulation derived from machine learning

(2020) Kevin Rychel et al.   NUCLEIC ACIDS RESEARCH

The biology of thermoacidophilic archaea from the order Sulfolobales

(2020) April M Lewis et al.   FEMS MICROBIOLOGY REVIEWS

Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

(2020) Kevin Rychel et al.   Nature Communications

Physical and Functional Compartmentalization of Archaeal Chromosomes

(2019) Naomichi Takemata et al.   CELL

Biochemical characterization of archaeal homocitrate synthase from Sulfolobus acidocaldarius

(2019) Tomohiro Suzuki et al.   FEBS LETTERS

Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets

(2019) Nicolas Sompairac et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A defined cultivation medium for Sulfolobus acidocaldarius

(2019) Julian Quehenberger et al.   JOURNAL OF BIOTECHNOLOGY

YtrASa, a GntR-Family Transcription Factor, Represses Two Genetic Loci Encoding Membrane Proteins in Sulfolobus acidocaldarius

(2019) Liesbeth Lemmens et al.   Frontiers in Microbiology

The Escherichia coli transcriptome mostly consists of independently regulated modules

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

The structure of the periplasmic FlaG–FlaF complex and its essential role for archaellar swimming motility

(2019) Chi-Lin Tsai et al.   Nature Microbiology

Profiling of glucose-induced transcription in Sulfolobus acidocaldarius DSM 639

(2018) Jungwook Park et al.   Genes & Genomics

Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in the early UV response

(2018) Frank Schult et al.   NUCLEIC ACIDS RESEARCH

Wing phosphorylation is a major functional determinant of the Lrs14-type biofilm and motility regulator AbfR1 in Sulfolobus acidocaldarius

(2017) Lingling Li et al.   MOLECULAR MICROBIOLOGY

Nextflow enables reproducible computational workflows

(2017) Paolo Di Tommaso et al.   NATURE BIOTECHNOLOGY

Sulfolobus – A Potential Key Organism in Future Biotechnology

(2017) Julian Quehenberger et al.   Frontiers in Microbiology

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

(2016) Philip Ewels et al.   BIOINFORMATICS

The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius

(2016) Han Liu et al.   BMC GENOMICS

Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes

(2016) Antoine Buetti-Dinh et al.   MICROBIOLOGY-SGM

ArnS, a kinase involved in starvation-induced archaellum expression

(2016) M. Florencia Haurat et al.   MOLECULAR MICROBIOLOGY

The archaeal Ced system imports DNA

(2016) Marleen van Wolferen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Processing Proteins Involved in the UV-Induced Stress Response of Sulfolobales

(2015) Marleen van Wolferen et al.   JOURNAL OF BACTERIOLOGY

Involvement of a eukaryotic-like ubiquitin-related modifier in the proteasome pathway of the archaeon Sulfolobus acidocaldarius

(2015) Rana S. Anjum et al.   Nature Communications

Archaeal Enzymes and Applications in Industrial Biocatalysts

(2015) Jennifer A. Littlechild   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Independent Component Analysis Uncovers the Landscape of the Bladder Tumor Transcriptome and Reveals Insights into Luminal and Basal Subtypes

(2014) Anne Biton et al.   Cell Reports

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

(2013) Y. Liao et al.   BIOINFORMATICS

Lrs14 transcriptional regulators influence biofilm formation and cell motility of Crenarchaea

(2013) Alvaro Orell et al.   ISME Journal

The one-component system ArnR: a membrane-bound activator of the crenarchaeal archaellum

(2013) Kerstin Lassak et al.   MOLECULAR MICROBIOLOGY

Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus

(2013) Takuya Ouchi et al.   Nature Chemical Biology

Expanded target and cofactor repertoire for the transcriptional activator LysM from Sulfolobus

(2013) Ningning Song et al.   NUCLEIC ACIDS RESEARCH

Alterations of the Transcriptome of Sulfolobus acidocaldarius by Exoribonuclease aCPSF2

(2013) Birgit Märtens et al.   PLoS One

Molecular analysis of the UV-inducible pili operon fromSulfolobus acidocaldarius

(2013) Marleen van Wolferen et al.   MicrobiologyOpen

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Regulation of archaella expression by the FHA and von Willebrand domain-containing proteins ArnA and ArnB inSulfolobus acidocaldarius

(2012) Julia Reimann et al.   MOLECULAR MICROBIOLOGY

Versatile Genetic Tool Box for the Crenarchaeote Sulfolobus acidocaldarius

(2012) Michaela Wagner et al.   Frontiers in Microbiology

Sa-Lrp fromSulfolobus acidocaldariusis a versatile, glutamine-responsive, and architectural transcriptional regulator

(2012) Amelia Vassart et al.   MicrobiologyOpen

Macromolecular Fingerprinting ofSulfolobusSpecies in Biofilm: A Transcriptomic and Proteomic Approach Combined with Spectroscopic Analysis

(2011) Andrea Koerdt et al.   JOURNAL OF PROTEOME RESEARCH

UV-inducible DNA exchange in hyperthermophilic archaea mediated by type IV pili

(2011) Małgorzata Ajon et al.   MOLECULAR MICROBIOLOGY

The archaeal cell envelope

(2011) Sonja-Verena Albers et al.   NATURE REVIEWS MICROBIOLOGY

The sequence read archive: explosive growth of sequencing data

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY