Interplay between gene expression noise and regulatory network architecture.

PubWeight™: 1.61‹?› | Rank: Top 4%

🔗 View Article (PMC 3340541)

Published in Trends Genet on February 25, 2012

Authors

Guilhem Chalancon1, Charles N J Ravarani, S Balaji, Alfonso Martinez-Arias, L Aravind, Raja Jothi, M Madan Babu

Author Affiliations

1: MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK. guilhem@mrc-lmb.cam.ac.uk

Articles citing this

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation. Nature (2014) 3.86

Bursty gene expression in the intact mammalian liver. Mol Cell (2015) 1.72

Interplay of microRNAs, transcription factors and target genes: linking dynamic expression changes to function. Nucleic Acids Res (2013) 1.38

Temperature-induced variation in gene expression burst size in metazoan cells. BMC Mol Biol (2015) 1.38

Genetic variants contribute to gene expression variability in humans. Genetics (2012) 1.20

Noise in biology. Rep Prog Phys (2014) 1.09

Navigating the transcriptional roadmap regulating plant secondary cell wall deposition. Front Plant Sci (2013) 1.01

Nuclear Retention of mRNA in Mammalian Tissues. Cell Rep (2015) 1.01

A Paradoxical Evolutionary Mechanism in Stochastically Switching Environments. Sci Rep (2016) 1.00

The role of dimerisation and nuclear transport in the Hes1 gene regulatory network. Bull Math Biol (2013) 0.94

The interplay of intrinsic and extrinsic bounded noises in biomolecular networks. PLoS One (2013) 0.90

Temporal dynamics and transcriptional control using single-cell gene expression analysis. Genome Biol (2013) 0.89

Determinants of expression variability. Nucleic Acids Res (2014) 0.89

FliZ is a global regulatory protein affecting the expression of flagellar and virulence genes in individual Xenorhabdus nematophila bacterial cells. PLoS Genet (2013) 0.84

Genome-wide and single-cell analyses reveal a context dependent relationship between CBP recruitment and gene expression. Nucleic Acids Res (2014) 0.83

Variability of Gene Expression Identifies Transcriptional Regulators of Early Human Embryonic Development. PLoS Genet (2015) 0.82

Optimal Design of Non-equilibrium Experiments for Genetic Network Interrogation. Appl Math Lett (2015) 0.80

A Bayesian Framework for the Classification of Microbial Gene Activity States. Front Microbiol (2016) 0.79

Heterogeneity of cellular circadian clocks in intact plants and its correction under light-dark cycles. Sci Adv (2016) 0.79

Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells. Appl Microbiol Biotechnol (2013) 0.78

Natural yeast promoter variants reveal epistasis in the generation of transcriptional-mediated noise and its potential benefit in stressful conditions. Genome Biol Evol (2015) 0.78

Recognition of multiple imbalanced cancer types based on DNA microarray data using ensemble classifiers. Biomed Res Int (2013) 0.78

Effects of Collective Histone State Dynamics on Epigenetic Landscape and Kinetics of Cell Reprogramming. Sci Rep (2015) 0.77

Differential Masking of Natural Genetic Variation by miR-9a in Drosophila. Genetics (2015) 0.77

Modeling heterogeneous responsiveness of intrinsic apoptosis pathway. BMC Syst Biol (2013) 0.77

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering. J R Soc Interface (2016) 0.76

Are transcriptional responses to inbreeding a functional response to alleviate inbreeding depression? Fly (Austin) (2013) 0.76

Autoregulation and heterogeneity in expression of human Cripto-1. PLoS One (2015) 0.76

Chromatin states modify network motifs contributing to cell-specific functions. Sci Rep (2015) 0.76

Single-Cell and Single-Molecule Analysis of Gene Expression Regulation. Annu Rev Genet (2016) 0.76

Spatially coordinated replication and minimization of expression noise constrain three-dimensional organization of yeast genome. DNA Res (2016) 0.76

Evidence for a sexual dimorphism in gene expression noise in metazoan species. PeerJ (2015) 0.76

Over-expression of Arabidopsis AtCHR23 chromatin remodeling ATPase results in increased variability of growth and gene expression. BMC Plant Biol (2014) 0.76

Increased gene expression noise in human cancers is correlated with low p53 and immune activities as well as late stage cancer. Oncotarget (2016) 0.75

A mathematical model of mechanotransduction reveals how mechanical memory regulates mesenchymal stem cell fate decisions. BMC Syst Biol (2017) 0.75

Intracellular Information Processing through Encoding and Decoding of Dynamic Signaling Features. PLoS Comput Biol (2015) 0.75

Effect of transcription factor resource sharing on gene expression noise. PLoS Comput Biol (2017) 0.75

Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis. Nucleic Acids Res (2016) 0.75

A structured population modeling framework for quantifying and predicting gene expression noise in flow cytometry data. Appl Math Lett (2013) 0.75

Ecophenotypic Variation and Developmental Instability in the Late Cretaceous Echinoid Micraster brevis (Irregularia; Spatangoida). PLoS One (2016) 0.75

Potential unsatisfiability of cyclic constraints on stochastic biological networks biases selection towards hierarchical architectures. J R Soc Interface (2015) 0.75

Engineering of a synthetic quadrastable gene network to approach Waddington landscape and cell fate determination. Elife (2017) 0.75

A homozygous FITM2 mutation causes a deafness-dystonia syndrome with motor regression and signs of ichthyosis and sensory neuropathy. Dis Model Mech (2016) 0.75

Physiologically Shrinking the Solution Space of a Saccharomyces cerevisiae Genome-Scale Model Suggests the Role of the Metabolic Network in Shaping Gene Expression Noise. PLoS One (2015) 0.75

Modeling heterogeneity in the pluripotent state: A promising strategy for improving the efficiency and fidelity of stem cell differentiation. Bioessays (2016) 0.75

Molecular profiling of single organelles for quantitative analysis of cellular heterogeneity. Sci Rep (2017) 0.75

pathVar: a new method for pathway-based interpretation of gene expression variability. PeerJ (2017) 0.75

Articles cited by this

(truncated to the top 100)

Stochastic gene expression in a single cell. Science (2002) 34.54

A synthetic oscillatory network of transcriptional regulators. Nature (2000) 24.58

Global quantification of mammalian gene expression control. Nature (2011) 22.36

A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell (1991) 18.19

Bacterial persistence as a phenotypic switch. Science (2004) 15.80

Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science (2011) 15.45

Network motifs: theory and experimental approaches. Nat Rev Genet (2007) 15.04

ENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON. Proc Natl Acad Sci U S A (1957) 14.34

Noise in eukaryotic gene expression. Nature (2003) 13.01

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise. Nature (2006) 12.92

Engineering stability in gene networks by autoregulation. Nature (2000) 12.88

Control of stochasticity in eukaryotic gene expression. Science (2004) 12.85

Nature, nurture, or chance: stochastic gene expression and its consequences. Cell (2008) 12.13

Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci U S A (2002) 11.46

Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science (2010) 11.37

A chromatin-mediated reversible drug-tolerant state in cancer cell subpopulations. Cell (2010) 11.20

Noise in gene expression: origins, consequences, and control. Science (2005) 9.64

Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32

Direct cell reprogramming is a stochastic process amenable to acceleration. Nature (2009) 8.71

Persister cells, dormancy and infectious disease. Nat Rev Microbiol (2006) 8.35

Phenotypic diversity, population growth, and information in fluctuating environments. Science (2005) 8.21

Noise propagation in gene networks. Science (2005) 8.19

Stochastic protein expression in individual cells at the single molecule level. Nature (2006) 8.00

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature (2008) 7.60

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis. Nature (2009) 7.24

Functional roles for noise in genetic circuits. Nature (2010) 6.96

Negative autoregulation speeds the response times of transcription networks. J Mol Biol (2002) 6.32

An excitable gene regulatory circuit induces transient cellular differentiation. Nature (2006) 6.03

Stochastic switching as a survival strategy in fluctuating environments. Nat Genet (2008) 5.87

Variability in gene expression underlies incomplete penetrance. Nature (2010) 5.85

Non-genetic individuality: chance in the single cell. Nature (1976) 5.52

A synchronized quorum of genetic clocks. Nature (2010) 5.47

Dynamic proteomics of individual cancer cells in response to a drug. Science (2008) 5.43

Single-cell NF-kappaB dynamics reveal digital activation and analogue information processing. Nature (2010) 5.27

Tunability and noise dependence in differentiation dynamics. Science (2007) 5.23

Regulated fluctuations in nanog expression mediate cell fate decisions in embryonic stem cells. PLoS Biol (2009) 4.60

Global signatures of protein and mRNA expression levels. Mol Biosyst (2009) 4.43

Stochasticity and cell fate. Science (2008) 4.39

Correlation of mRNA and protein in complex biological samples. FEBS Lett (2009) 4.38

Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc Natl Acad Sci U S A (2005) 4.11

Contributions of low molecule number and chromosomal positioning to stochastic gene expression. Nat Genet (2005) 4.07

Probing cellular protein complexes using single-molecule pull-down. Nature (2011) 3.92

Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat Rev Genet (2008) 3.84

Real-time observation of transcription initiation and elongation on an endogenous yeast gene. Science (2011) 3.67

Population context determines cell-to-cell variability in endocytosis and virus infection. Nature (2009) 3.37

Filtering transcriptional noise during development: concepts and mechanisms. Nat Rev Genet (2006) 3.26

Chromatin decouples promoter threshold from dynamic range. Nature (2008) 3.24

Modular cell biology: retroactivity and insulation. Mol Syst Biol (2008) 3.11

Stochastic spineless expression creates the retinal mosaic for colour vision. Nature (2006) 3.09

Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell (2009) 3.05

Information transduction capacity of noisy biochemical signaling networks. Science (2011) 2.95

Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci U S A (2005) 2.84

Stochastic gene expression: from single molecules to the proteome. Curr Opin Genet Dev (2007) 2.81

General properties of transcriptional time series in Escherichia coli. Nat Genet (2011) 2.76

Myeloid lineage commitment from the hematopoietic stem cell. Immunity (2007) 2.76

Fundamental limits on the suppression of molecular fluctuations. Nature (2010) 2.75

Single-molecule approaches to stochastic gene expression. Annu Rev Biophys (2009) 2.75

Temporal competition between differentiation programs determines cell fate choice. Mol Syst Biol (2011) 2.61

Predicting mutation outcome from early stochastic variation in genetic interaction partners. Nature (2011) 2.56

Evolution of chromosome organization driven by selection for reduced gene expression noise. Nat Genet (2007) 2.55

Information flow and optimization in transcriptional regulation. Proc Natl Acad Sci U S A (2008) 2.55

Measurement of single-cell dynamics. Nature (2010) 2.55

Microfluidic devices for measuring gene network dynamics in single cells. Nat Rev Genet (2009) 2.52

Molecular titration and ultrasensitivity in regulatory networks. J Mol Biol (2008) 2.48

Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription. Cell (2008) 2.47

Noncooperative interactions between transcription factors and clustered DNA binding sites enable graded transcriptional responses to environmental inputs. Mol Cell (2010) 2.43

Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network. BMC Bioinformatics (2004) 2.41

Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J Mol Biol (2006) 2.36

Dissecting timing variability in yeast meiosis. Cell (2007) 2.35

Non-genetic heterogeneity from stochastic partitioning at cell division. Nat Genet (2010) 2.32

A multistep epigenetic switch enables the stable inheritance of DNA methylation states. Nat Genet (2007) 2.14

Protein sequestration generates a flexible ultrasensitive response in a genetic network. Mol Syst Biol (2009) 2.09

Individual histories and selection in heterogeneous populations. Proc Natl Acad Sci U S A (2010) 2.01

Noise propagation and signaling sensitivity in biological networks: a role for positive feedback. PLoS Comput Biol (2007) 1.94

Selection to minimise noise in living systems and its implications for the evolution of gene expression. Mol Syst Biol (2008) 1.88

PhoU is a persistence switch involved in persister formation and tolerance to multiple antibiotics and stresses in Escherichia coli. Antimicrob Agents Chemother (2007) 1.85

Spatial and temporal specification of neural fates by transcription factor codes. Development (2007) 1.76

Genomic analysis reveals a tight link between transcription factor dynamics and regulatory network architecture. Mol Syst Biol (2009) 1.73

Intrinsic variability of gene expression encoded in nucleosome positioning sequences. Nat Genet (2009) 1.71

Partial penetrance facilitates developmental evolution in bacteria. Nature (2009) 1.66

Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression. Genome Res (2011) 1.62

Variability and robustness in biomolecular systems. Mol Cell (2007) 1.61

Hsp90 selectively modulates phenotype in vertebrate development. PLoS Genet (2007) 1.60

Tuning and controlling gene expression noise in synthetic gene networks. Nucleic Acids Res (2010) 1.52

Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks. J Mol Biol (2006) 1.52

Impact of gene expression noise on organismal fitness and the efficacy of natural selection. Proc Natl Acad Sci U S A (2011) 1.46

Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. PLoS Genet (2009) 1.46

Behavior-specific changes in transcriptional modules lead to distinct and predictable neurogenomic states. Proc Natl Acad Sci U S A (2011) 1.43

Information capacity of genetic regulatory elements. Phys Rev E Stat Nonlin Soft Matter Phys (2008) 1.40

Positive selection for elevated gene expression noise in yeast. Mol Syst Biol (2009) 1.30

Microfluidics for synthetic biology: from design to execution. Methods Enzymol (2011) 1.30

The genetic requirements for fast and slow growth in mycobacteria. PLoS One (2009) 1.29

Mechanisms of non-Mendelian inheritance in genetic disease. Hum Mol Genet (2004) 1.29

Systems biology. Attractors and democratic dynamics. Science (2009) 1.27

Stochastic receptor expression determines cell fate upon interferon treatment. Mol Cell Biol (2011) 1.26

Biological role of noise encoded in a genetic network motif. Proc Natl Acad Sci U S A (2010) 1.25

Analysis of diverse regulatory networks in a hierarchical context shows consistent tendencies for collaboration in the middle levels. Proc Natl Acad Sci U S A (2010) 1.24

A genomic model of condition-specific nucleosome behavior explains transcriptional activity in yeast. Genome Res (2011) 1.23

Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway. Nat Cell Biol (2010) 1.22

Persistence: mechanisms for triggering and enhancing phenotypic variability. Curr Opin Genet Dev (2011) 1.22

Articles by these authors

Initial sequencing and analysis of the human genome. Nature (2001) 212.86

Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science (2009) 32.97

Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements. Nucleic Acids Res (2001) 22.33

Genome sequence of an obligate intracellular pathogen of humans: Chlamydia trachomatis. Science (1998) 13.64

De-ubiquitination and ubiquitin ligase domains of A20 downregulate NF-kappaB signalling. Nature (2004) 12.41

AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res (1999) 11.30

Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science (2000) 10.82

Genomic analysis of regulatory network dynamics reveals large topological changes. Nature (2004) 9.32

Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature (2010) 8.87

Horizontal gene transfer in prokaryotes: quantification and classification. Annu Rev Microbiol (2001) 8.14

Genome sequence of the radioresistant bacterium Deinococcus radiodurans R1. Science (1999) 8.01

Role of Rpn11 metalloprotease in deubiquitination and degradation by the 26S proteasome. Science (2002) 7.49

Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res (2008) 7.41

IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics (1999) 6.91

Classification and evolution of P-loop GTPases and related ATPases. J Mol Biol (2002) 6.85

Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). Genome Biol (2000) 6.50

Comparison of the complete protein sets of worm and yeast: orthology and divergence. Science (1998) 6.28

Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science (2004) 5.64

Molecular signatures of G-protein-coupled receptors. Nature (2013) 5.19

Role of predicted metalloprotease motif of Jab1/Csn5 in cleavage of Nedd8 from Cul1. Science (2002) 4.95

Genome of the extremely radiation-resistant bacterium Deinococcus radiodurans viewed from the perspective of comparative genomics. Microbiol Mol Biol Rev (2001) 4.75

Risk factors for arrhythmia and sudden cardiac death late after repair of tetralogy of Fallot: a multicentre study. Lancet (2000) 4.75

Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol (2004) 4.68

Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res (2006) 4.49

Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48

A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis. Nucleic Acids Res (2002) 4.39

Common origin of four diverse families of large eukaryotic DNA viruses. J Virol (2001) 4.28

The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res (2002) 4.28

Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids. Cell Cycle (2009) 4.14

Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet (1998) 4.10

An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network. Proc Natl Acad Sci U S A (2009) 4.07

Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res (2002) 4.00

Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol (2000) 3.99

Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems. Biol Direct (2011) 3.92

Chromosome 2 sequence of the human malaria parasite Plasmodium falciparum. Science (1998) 3.83

Gene regulatory network growth by duplication. Nat Genet (2004) 3.79

The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens. Proc Natl Acad Sci U S A (2002) 3.72

Randomized clinical trial of routine on-table cholangiography during laparoscopic cholecystectomy. Br J Surg (2010) 3.63

Comparative genomics of the Archaea (Euryarchaeota): evolution of conserved protein families, the stable core, and the variable shell. Genome Res (1999) 3.62

An expanded Oct4 interaction network: implications for stem cell biology, development, and disease. Cell Stem Cell (2010) 3.60

Tight regulation of unstructured proteins: from transcript synthesis to protein degradation. Science (2008) 3.48

Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res (1999) 3.44

Discovery of the principal specific transcription factors of Apicomplexa and their implication for the evolution of the AP2-integrase DNA binding domains. Nucleic Acids Res (2005) 3.36

Eukaryotic signalling domain homologues in archaea and bacteria. Ancient ancestry and horizontal gene transfer. J Mol Biol (1999) 3.28

Multiple transporters associated with malaria parasite responses to chloroquine and quinine. Mol Microbiol (2003) 3.26

The impact of comparative genomics on our understanding of evolution. Cell (2000) 3.25

PAS: a multifunctional domain family comes to light. Curr Biol (1997) 3.20

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription. Nat Rev Mol Cell Biol (2013) 3.18

Evolution and diversification of lamprey antigen receptors: evidence for involvement of an AID-APOBEC family cytosine deaminase. Nat Immunol (2007) 3.14

Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. J Mol Biol (2006) 3.10

Malaria parasite clag3 genes determine channel-mediated nutrient uptake by infected red blood cells. Cell (2011) 3.06

Evolutionary history, structural features and biochemical diversity of the NlpC/P60 superfamily of enzymes. Genome Biol (2003) 3.02

Novel families of putative protein kinases in bacteria and archaea: evolution of the "eukaryotic" protein kinase superfamily. Genome Res (1998) 2.91

START: a lipid-binding domain in StAR, HD-ZIP and signalling proteins. Trends Biochem Sci (1999) 2.89

Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange. Trends Genet (1999) 2.87

New connections in the prokaryotic toxin-antitoxin network: relationship with the eukaryotic nonsense-mediated RNA decay system. Genome Biol (2003) 2.77

The U box is a modified RING finger - a common domain in ubiquitination. Curr Biol (2000) 2.73

SUPFAM: a database of sequence superfamilies of protein domains. BMC Bioinformatics (2004) 2.72

Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. J Mol Biol (2001) 2.68

Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily. Proteins (2001) 2.65

Prediction of the archaeal exosome and its connections with the proteasome and the translation and transcription machineries by a comparative-genomic approach. Genome Res (2001) 2.65

Comparative genomics, evolution and origins of the nuclear envelope and nuclear pore complex. Cell Cycle (2004) 2.65

Comparative genomics of the FtsK-HerA superfamily of pumping ATPases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. Nucleic Acids Res (2004) 2.62

The NACHT family - a new group of predicted NTPases implicated in apoptosis and MHC transcription activation. Trends Biochem Sci (2000) 2.58

Congenital heart block: development of late-onset cardiomyopathy, a previously underappreciated sequela. J Am Coll Cardiol (2001) 2.57

Genome-wide analyses of transcription factor GATA3-mediated gene regulation in distinct T cell types. Immunity (2011) 2.53

Diversification and spectral tuning in marine proteorhodopsins. EMBO J (2003) 2.53

Evolution and classification of P-loop kinases and related proteins. J Mol Biol (2003) 2.52

Origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. Nucleic Acids Res (2005) 2.49

Classification of intrinsically disordered regions and proteins. Chem Rev (2014) 2.48

Mechanistic insight into site-restricted monoubiquitination of FANCD2 by Ube2t, FANCL, and FANCI. Mol Cell (2008) 2.45

Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J Mol Biol (2006) 2.44

Did DNA replication evolve twice independently? Nucleic Acids Res (1999) 2.44

Identification of the prokaryotic ligand-gated ion channels and their implications for the mechanisms and origins of animal Cys-loop ion channels. Genome Biol (2004) 2.39

The bacterial replicative helicase DnaB evolved from a RecA duplication. Genome Res (2000) 2.39

Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J Mol Biol (2006) 2.36

esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function. Nat Cell Biol (2011) 2.29

Chromatin poises miRNA- and protein-coding genes for expression. Genome Res (2009) 2.28

Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Appl Environ Microbiol (2002) 2.24

Human and mouse homologs of Escherichia coli DinB (DNA polymerase IV), members of the UmuC/DinB superfamily. Proc Natl Acad Sci U S A (1999) 2.15

Comparative genomics of transcription factors and chromatin proteins in parasitic protists and other eukaryotes. Int J Parasitol (2007) 2.15

An antisense RNA controls synthesis of an SOS-induced toxin evolved from an antitoxin. Mol Microbiol (2007) 2.11

STAND, a class of P-loop NTPases including animal and plant regulators of programmed cell death: multiple, complex domain architectures, unusual phyletic patterns, and evolution by horizontal gene transfer. J Mol Biol (2004) 2.10

Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily. Nucleic Acids Res (2002) 2.08

Discovery of Novel DENN Proteins: Implications for the Evolution of Eukaryotic Intracellular Membrane Structures and Human Disease. Front Genet (2012) 2.08

The STAS domain - a link between anion transporters and antisigma-factor antagonists. Curr Biol (2000) 2.07

Polymorphic toxin systems: Comprehensive characterization of trafficking modes, processing, mechanisms of action, immunity and ecology using comparative genomics. Biol Direct (2012) 2.05

Origin and evolution of eukaryotic apoptosis: the bacterial connection. Cell Death Differ (2002) 2.04

Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks. Mol Cell (2012) 2.02

Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation. Mol Cell (2012) 2.02

A novel superfamily of predicted cysteine proteases from eukaryotes, viruses and Chlamydia pneumoniae. Trends Biochem Sci (2000) 2.01

Classification and evolutionary history of the single-strand annealing proteins, RecT, Redbeta, ERF and RAD52. BMC Genomics (2002) 1.99

SPOUT: a class of methyltransferases that includes spoU and trmD RNA methylase superfamilies, and novel superfamilies of predicted prokaryotic RNA methylases. J Mol Microbiol Biotechnol (2002) 1.95

Evolving nature of the AP2 alpha-appendage hub during clathrin-coated vesicle endocytosis. EMBO J (2004) 1.87

A specialized version of the HD hydrolase domain implicated in signal transduction. J Mol Microbiol Biotechnol (1999) 1.86

The C. elegans Polycomb gene SOP-2 encodes an RNA binding protein. Mol Cell (2004) 1.85

Themis is a member of a new metazoan gene family and is required for the completion of thymocyte positive selection. Nat Immunol (2009) 1.84