相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Patterns of selection across gene regulatory networks
Jeanne M. C. McDonald et al.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY (2023)
Marginal specificity in protein interactions constrains evolution of a paralogous family
Dia A. Ghose et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2023)
Transcription factor expression levels and environmental signals constrain transcription factor innovation
Matthew J. Shepherd et al.
MICROBIOLOGY-SGM (2023)
Natural selection on crosstalk between gene regulatory networks facilitates bacterial adaptation to novel environments
Tiffany B. Taylor et al.
CURRENT OPINION IN MICROBIOLOGY (2022)
A Near-Deterministic Mutational Hotspot in Pseudomonas fluorescens Is Constructed by Multiple Interacting Genomic Features
M. J. Shepherd et al.
MOLECULAR BIOLOGY AND EVOLUTION (2022)
Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria
Satish Adhikari et al.
PLOS GENETICS (2021)
A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes
James S. Horton et al.
NATURE COMMUNICATIONS (2021)
Adaptation and compensation in a bacterial gene regulatory network evolving under antibiotic selection
Vishwa Patel et al.
ELIFE (2021)
The anti-sigma factor MucA is required for viability in Pseudomonas aeruginosa
Melissa C. Schofield et al.
MOLECULAR MICROBIOLOGY (2021)
Plastic Rewiring of Sef1 Transcriptional Networks and the Potential of Nonfunctional Transcription Factor Binding in Facilitating Adaptive Evolution
Po-Chen Hsu et al.
MOLECULAR BIOLOGY AND EVOLUTION (2021)
A computational system for identifying operons based on RNA-seq data
Brian Tjaden
METHODS (2020)
Dynamics of genetic variation in transcription factors and its implications for the evolution of regulatory networks in Bacteria
Farhan Ali et al.
NUCLEIC ACIDS RESEARCH (2020)
Gene Loss Predictably Drives Evolutionary Adaptation
Jana Helsen et al.
MOLECULAR BIOLOGY AND EVOLUTION (2020)
Rewiring of growth-dependent transcription regulation by a point mutation in region 1.1 of the housekeeping σ factor
Philipp Pletnev et al.
NUCLEIC ACIDS RESEARCH (2020)
RhoTermPredict: an algorithm for predicting Rho-dependent transcription terminators based on Escherichia coli, Bacillus subtilis and Salmonella enterica databases
Marco Di Salvo et al.
BMC BIOINFORMATICS (2019)
Plasticity of Promoter-Core Sequences Allows Bacteria to Compensate for the Loss of a Key Global Regulatory Gene
Otmane Lamrabet et al.
MOLECULAR BIOLOGY AND EVOLUTION (2019)
Enzyme promiscuity shapes adaptation to novel growth substrates
Gabriela Guzman et al.
MOLECULAR SYSTEMS BIOLOGY (2019)
Low-Affinity Binding Sites and the Transcription Factor Specificity Paradox in Eukaryotes
Judith F. Kribelbauer et al.
ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 35 (2019)
Role of network-mediated stochasticity in mammalian drug resistance
Kevin S. Farquhar et al.
NATURE COMMUNICATIONS (2019)
The Paradox Behind the Pattern of Rapid Adaptive Radiation: How Can the Speciation Process Sustain Itself Through an Early Burst?
Christopher H. Martin et al.
Annual Review of Ecology Evolution and Systematics (2019)
Population genomics of bacterial host adaptation
Samuel K. Sheppard et al.
NATURE REVIEWS GENETICS (2018)
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
Enis Afgan et al.
NUCLEIC ACIDS RESEARCH (2018)
Multi-component gene network design as a survival strategy in diverse environments
Xinyue Luo et al.
BMC SYSTEMS BIOLOGY (2018)
Gene regulation underlies environmental adaptation in house mice
Katya L. Mack et al.
GENOME RESEARCH (2018)
Dynamic Modeling of Streptococcus pneumoniae Competence Provides Regulatory Mechanistic Insights Into Its Tight Temporal Regulation
Mathias Weyder et al.
FRONTIERS IN MICROBIOLOGY (2018)
Evolutionary potential of transcription factors for gene regulatory rewiring
Claudia Igler et al.
NATURE ECOLOGY & EVOLUTION (2018)
Suppressor mutations reveal an NtrC-like response regulator, NmpR, for modulation of Type-IV Pili-dependent motility in Myxococcus xanthus
Daniel J. Bretl et al.
PLOS GENETICS (2018)
PhoU Allows Rapid Adaptation to High Phosphate Concentrations by Modulating PstSCAB Transport Rate in Sinorhizobium meliloti
George C. diCenzo et al.
JOURNAL OF BACTERIOLOGY (2017)
Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities
Xin Fang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
The rewiring of transcription circuits in evolution
Alexander D. Johnson
CURRENT OPINION IN GENETICS & DEVELOPMENT (2017)
The Escherichia coli rhaSR-PrhaBAD Inducible Promoter System Allows Tightly Controlled Gene Expression over a Wide Range in Pseudomonas aeruginosa
Jeffrey Meisner et al.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2016)
Growthcurver: an R package for obtaining interpretable metrics from microbial growth curves
Kathleen Sprouffske et al.
BMC BIOINFORMATICS (2016)
Rewiring of the Ppr1 Zinc Cluster Transcription Factor from Purine Catabolism to Pyrimidine Biogenesis in the Saccharomycetaceae
Walters Aji Tebung et al.
CURRENT BIOLOGY (2016)
Parallel Compensatory Evolution Stabilizes Plasmids across the Parasitism-Mutualism Continuum
Ellie Harrison et al.
CURRENT BIOLOGY (2015)
How do regulatory networks evolve and expand throughout evolution?
Karin Voordeckers et al.
CURRENT OPINION IN BIOTECHNOLOGY (2015)
Stress-response balance drives the evolution of a network module and its host genome
Caleb Gonzalez et al.
MOLECULAR SYSTEMS BIOLOGY (2015)
Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic exchange
Laura R. Hmelo et al.
NATURE PROTOCOLS (2015)
Comment on A promiscuous intermediate underlies the evolution of LEAFY DNA binding specificity
Jacob O. Brunkard et al.
SCIENCE (2015)
Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Tiffany B. Taylor et al.
SCIENCE (2015)
An evolutionary biochemist's perspective on promiscuity
Shelley D. Copley
TRENDS IN BIOCHEMICAL SCIENCES (2015)
The propagation of perturbations in rewired bacterial gene networks
Rebecca Baumstark et al.
NATURE COMMUNICATIONS (2015)
The biosurfactant viscosin produced by Pseudomonas fluorescens SBW25 aids spreading motility and plant growth promotion
Abdullah S. Alsohim et al.
ENVIRONMENTAL MICROBIOLOGY (2014)
Coherent feedforward transcriptional regulatory motifs enhance drug resistance
Daniel A. Charlebois et al.
PHYSICAL REVIEW E (2014)
Duplication of a promiscuous transcription factor drives the emergence of a new regulatory network
Ksenia Pougach et al.
NATURE COMMUNICATIONS (2014)
Extensive Rewiring and Complex Evolutionary Dynamics in a C. elegans Multiparameter Transcription Factor Network
John S. Reece-Hoyes et al.
MOLECULAR CELL (2013)
Evolutionary remodeling of global regulatory networks during long-term bacterial adaptation to human hosts
Soren Damkiaer et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Adaptive Mutations that Prevent Crosstalk Enable the Expansion of Paralogous Signaling Protein Families
Emily J. Capra et al.
CELL (2012)
Gene Overexpression: Uses, Mechanisms, and Interpretation
Gregory Prelich
GENETICS (2012)
Analysis of Cryptococcus neoformans Sexual Development Reveals Rewiring of the Pheromone-Response Network by a Change in Transcription Factor Identity
Emilia K. Kruzel et al.
GENETICS (2012)
Cooperative Binding of Transcription Factors Promotes Bimodal Gene Expression Response
Pablo S. Gutierrez et al.
PLOS ONE (2012)
Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression
Lesley T. MacNeil et al.
GENOME RESEARCH (2011)
Niche adaptation by expansion and reprogramming of general transcription factors
Serdar Turkarslan et al.
MOLECULAR SYSTEMS BIOLOGY (2011)
Integrative genomics viewer
James T. Robinson et al.
NATURE BIOTECHNOLOGY (2011)
Evolution and Adaptation in Pseudomonas aeruginosa Biofilms Driven by Mismatch Repair System-Deficient Mutators
Adela M. Lujan et al.
PLOS ONE (2011)
Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids
Anton V. Bryksin et al.
BIOTECHNIQUES (2010)
Two-component signaling circuit structure and properties
Mark Goulian
CURRENT OPINION IN MICROBIOLOGY (2010)
Regulation of glutamate dehydrogenase expression in Pseudomonas putida results from its direct repression by NtrC under nitrogen-limiting conditions
Ana B. Hervas et al.
MOLECULAR MICROBIOLOGY (2010)
Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation (vol 9, pg 583, 2008)
Luis Lopez-Maury et al.
NATURE REVIEWS GENETICS (2009)
Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens
Mark W. Silby et al.
GENOME BIOLOGY (2009)
Protein abundance profiling of the Escherichia coli cytosol
Yasushi Ishihama et al.
BMC GENOMICS (2008)
The Origins of Ecological Diversity in Prokaryotes
Frederick M. Cohan et al.
CURRENT BIOLOGY (2008)
Evolvability and hierarchy in rewired bacterial gene networks
Mark Isalan et al.
NATURE (2008)
Integrated bioinformatic and phenotypic analysis of RpoN-dependent traits in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25
Jacob Jones et al.
ENVIRONMENTAL MICROBIOLOGY (2007)
Transcriptional rewiring of fungal galactose-metabolism circuitry
Mikhail Martchenko et al.
CURRENT BIOLOGY (2007)
Evolution of global regulatory networks during a long-term experiment with Eisherichia coli
Nadege Philippe et al.
BIOESSAYS (2007)
Mini-Tn7 insertion in bacteria with single attTn7 sites: example Pseudomonas aeruginosa
Kyoung-Hee Choi et al.
NATURE PROTOCOLS (2006)
Structural classification of bacterial response regulators: Diversity of output domains and domain combinations
Michael Y. Galperin
JOURNAL OF BACTERIOLOGY (2006)
The 'evolvability' of promiscuous protein functions
A Aharoni et al.
NATURE GENETICS (2005)
Regulog analysis:: Detection of conserved regulatory networks across bacteria:: Application to Staphylococcus aureus
WBL Alkema et al.
GENOME RESEARCH (2004)
The evolution of a pleiotropic fitness tradeoff in Pseudomonas fluorescens
RC MacLean et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Optimization of specificity in a cellular protein interaction network by negative selection
A Zarrinpar et al.
NATURE (2003)
The mismatch repair system (mutS, mutL and uvrD genes) in Pseudomonas aeruginosa: molecular characterization of naturally occurring mutants
A Oliver et al.
MOLECULAR MICROBIOLOGY (2002)
Genomic analysis of the histidine kinase family in bacteria and archaea
D Kim et al.
MICROBIOLOGY-SGM (2001)
分享论文
