A Regulatory Hierarchy Controls the Dynamic Transcriptional Response to Extreme Oxidative Stress in Archaea

Cis-regulatory logic in archaeal transcription

(2013) Eveline Peeters et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks

(2013) Alex Greenfield et al.   BIOINFORMATICS

The genome-wide binding profile of the Sulfolobus solfataricus transcription factor Ss-LrpB shows binding events beyond direct transcription regulation

(2013) Trong Nguyen-Duc et al.   BMC GENOMICS

Redox-sensitive DNA binding by homodimeric Methanosarcina acetivorans MsvR is modulated by cysteine residues

(2013) Catherine E Isom et al.   BMC MICROBIOLOGY

A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen

(2013) Sung Ho Yoon et al.   GENOME RESEARCH

Comparative study of SoxR activation by redox-active compounds

(2013) Atul K. Singh et al.   MOLECULAR MICROBIOLOGY

Studies of IscR reveal a unique mechanism for metal-dependent regulation of DNA binding specificity

(2013) Senapathy Rajagopalan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Protein-DNA binding dynamics predict transcriptional response to nutrients in archaea

(2013) H. Todor et al.   NUCLEIC ACIDS RESEARCH

The three-dimensional structure of TrmB, a transcriptional regulator of dual function in the hyperthermophilic archaeonPyrococcus furiosusin complex with sucrose

(2013) Michael Krug et al.   PROTEIN SCIENCE

Checkpoint Kinases Regulate a Global Network of Transcription Factors in Response to DNA Damage

(2013) Eric J. Jaehnig et al.   Cell Reports

Metallochaperones Regulate Intracellular Copper Levels

(2013) W. Lee Pang et al.   PLoS Computational Biology

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer

(2012) Yuri I Wolf et al.   Biology Direct

A Monte Carlo-based framework enhances the discovery and interpretation of regulatory sequence motifs

(2012) Phillip Seitzer et al.   BMC BIOINFORMATICS

The RosR transcription factor is required for gene expression dynamics in response to extreme oxidative stress in a hypersaline-adapted archaeon

(2012) Kriti Sharma et al.   BMC GENOMICS

Peroxide-Sensing Transcriptional Regulators in Bacteria

(2012) J. M. Dubbs et al.   JOURNAL OF BACTERIOLOGY

Genome-wide protein–DNA binding dynamics suggest a molecular clutch for transcription factor function

(2012) Colin R. Lickwar et al.   NATURE

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

(2012) Heladia Salgado et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Amelia Vassart et al.   MicrobiologyOpen

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

The Methanogen-Specific Transcription Factor MsvR Regulates the fpaA-rlp-rub Oxidative Stress Operon Adjacent to msvR in Methanothermobacter thermautotrophicus

(2010) E. A. Karr   JOURNAL OF BACTERIOLOGY

Identification and Genomic Analysis of Transcription Factors in Archaeal Genomes Exemplifies Their Functional Architecture and Evolutionary Origin

(2010) E. Perez-Rueda et al.   MOLECULAR BIOLOGY AND EVOLUTION

SurR regulates hydrogen production in Pyrococcus furiosus by a sulfur-dependent redox switch

(2010) Hua Yang et al.   MOLECULAR MICROBIOLOGY

Coordination of frontline defense mechanisms under severe oxidative stress

(2010) Amardeep Kaur et al.   Molecular Systems Biology

Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon

(2010) Amy K. Schmid et al.   NUCLEIC ACIDS RESEARCH

MutS and MutL Are Dispensable for Maintenance of the Genomic Mutation Rate in the Halophilic Archaeon Halobacterium salinarum NRC-1

(2010) Courtney R. Busch et al.   PLoS One

Management of Oxidative Stress inBacillus

(2009) Peter Zuber   Annual Review of Microbiology

Salt shield: intracellular salts provide cellular protection against ionizing radiation in the halophilic archaeon,Halobacterium salinarumNRC-1

(2009) A. Kish et al.   ENVIRONMENTAL MICROBIOLOGY

Hydrophobic carboxy-terminal residues dramatically reduce protein levels in the haloarchaeon Haloferax volcanii

(2009) C. J. Reuter et al.   MICROBIOLOGY-SGM

Prevalence of transcription promoters within archaeal operons and coding sequences

(2009) Tie Koide et al.   Molecular Systems Biology

A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability

(2009) Amy K Schmid et al.   Molecular Systems Biology

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

MEME SUITE: tools for motif discovery and searching

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

Cellular Defenses against Superoxide and Hydrogen Peroxide

(2008) James A. Imlay   Annual Review of Biochemistry

The role of TrmB and TrmB-like transcriptional regulators for sugar transport and metabolism in the hyperthermophilic archaeon Pyrococcus furiosus

(2008) Sung-Jae Lee et al.   ARCHIVES OF MICROBIOLOGY

Chromatin immunoprecipitation (ChIP) coupled to detection by quantitative real-time PCR to study transcription factor binding to DNA in Caenorhabditis elegans

(2008) Arnab Mukhopadhyay et al.   Nature Protocols

The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions

(2008) Tomohiro Shimada et al.   NUCLEIC ACIDS RESEARCH

A Novel OxyR Sensor and Regulator of Hydrogen Peroxide Stress with One Cysteine Residue in Deinococcus radiodurans

(2008) Huan Chen et al.   PLoS One