Published in J R Soc Interface on April 12, 2012
Multi-level modeling of light-induced stomatal opening offers new insights into its regulation by drought. PLoS Comput Biol (2014) 1.63
SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Syst Biol (2013) 1.20
Logic-based models in systems biology: a predictive and parameter-free network analysis method. Integr Biol (Camb) (2012) 0.90
Mathematical modeling of an oscillating gene circuit to unravel the circadian clock network of Arabidopsis thaliana. Front Plant Sci (2013) 0.87
Gene regulatory networks in plants: learning causality from time and perturbation. Genome Biol (2013) 0.84
Circadian systems biology: When time matters. Comput Struct Biotechnol J (2015) 0.81
Function does not follow form in gene regulatory circuits. Sci Rep (2015) 0.81
Mathematical model of a telomerase transcriptional regulatory network developed by cell-based screening: analysis of inhibitor effects and telomerase expression mechanisms. PLoS Comput Biol (2014) 0.78
Defining the robust behaviour of the plant clock gene circuit with absolute RNA timeseries and open infrastructure. Open Biol (2015) 0.76
Phenotypic robustness and the assortativity signature of human transcription factor networks. PLoS Comput Biol (2014) 0.76
Latent phenotypes pervade gene regulatory circuits. BMC Syst Biol (2014) 0.76
A Compact Model for the Complex Plant Circadian Clock. Front Plant Sci (2016) 0.76
A Boolean gene regulatory model of heterosis and speciation. BMC Evol Biol (2015) 0.75
Neutral space analysis for a Boolean network model of the fission yeast cell cycle network. Biol Res (2014) 0.75
An Integrated Qualitative and Quantitative Biochemical Model Learning Framework Using Evolutionary Strategy and Simulated Annealing. Cognit Comput (2015) 0.75
Optimization by simulated annealing. Science (1983) 71.02
Network motifs: simple building blocks of complex networks. Science (2002) 35.80
Metabolic stability and epigenesis in randomly constructed genetic nets. J Theor Biol (1969) 13.14
Time zones: a comparative genetics of circadian clocks. Nat Rev Genet (2001) 8.98
Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science (2005) 6.92
Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics (2002) 6.90
Circadian rhythms from multiple oscillators: lessons from diverse organisms. Nat Rev Genet (2005) 6.87
Reciprocal regulation between TOC1 and LHY/CCA1 within the Arabidopsis circadian clock. Science (2001) 6.63
On schemes of combinatorial transcription logic. Proc Natl Acad Sci U S A (2003) 6.02
Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics (1998) 5.42
Extension of a genetic network model by iterative experimentation and mathematical analysis. Mol Syst Biol (2005) 3.88
Resonating circadian clocks enhance fitness in cyanobacteria. Proc Natl Acad Sci U S A (1998) 3.84
Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci U S A (2002) 3.78
Toward a detailed computational model for the mammalian circadian clock. Proc Natl Acad Sci U S A (2003) 3.69
Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Mol Syst Biol (2006) 3.68
Robustness of circadian rhythms with respect to molecular noise. Proc Natl Acad Sci U S A (2002) 3.13
A model for circadian oscillations in the Drosophila period protein (PER). Proc Biol Sci (1995) 3.09
A detailed predictive model of the mammalian circadian clock. Proc Natl Acad Sci U S A (2003) 3.07
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol (2009) 2.98
Clocks not winding down: unravelling circadian networks. Nat Rev Mol Cell Biol (2010) 2.95
The molecular basis of temperature compensation in the Arabidopsis circadian clock. Plant Cell (2006) 2.84
A model for circadian rhythms in Drosophila incorporating the formation of a complex between the PER and TIM proteins. J Biol Rhythms (1998) 2.76
A circadian clock in macrophages controls inflammatory immune responses. Proc Natl Acad Sci U S A (2009) 2.71
Limit cycle models for circadian rhythms based on transcriptional regulation in Drosophila and Neurospora. J Biol Rhythms (1999) 2.71
Dynamic properties of network motifs contribute to biological network organization. PLoS Biol (2005) 2.58
A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9. Mol Syst Biol (2006) 2.48
Modeling circadian oscillations with interlocking positive and negative feedback loops. J Neurosci (2001) 2.44
The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Mol Syst Biol (2012) 2.34
Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana. J Theor Biol (2005) 2.34
Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor. Proc Natl Acad Sci U S A (2012) 2.19
Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm. J Theor Biol (2001) 2.12
Synchronous versus asynchronous modeling of gene regulatory networks. Bioinformatics (2008) 1.85
Weather and seasons together demand complex biological clocks. Curr Biol (2009) 1.80
Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model. Mol Syst Biol (2010) 1.73
Temperature Compensation of Circadian Period Length in Clock Mutants of Neurospora crassa. Plant Physiol (1981) 1.64
ON/OFF and beyond--a boolean model of apoptosis. PLoS Comput Biol (2009) 1.53
Quantitative analysis of regulatory flexibility under changing environmental conditions. Mol Syst Biol (2010) 1.48
A model of the cell-autonomous mammalian circadian clock. Proc Natl Acad Sci U S A (2009) 1.46
Modeling feedback loops of the Mammalian circadian oscillator. Biophys J (2004) 1.45
The circadian clock Period 2 gene regulates gamma interferon production of NK cells in host response to lipopolysaccharide-induced endotoxic shock. Infect Immun (2006) 1.43
The relationship between FRQ-protein stability and temperature compensation in the Neurospora circadian clock. Proc Natl Acad Sci U S A (2005) 1.42
Simulation of Drosophila circadian oscillations, mutations, and light responses by a model with VRI, PDP-1, and CLK. Biophys J (2004) 1.38
Circadian rhythms and cancer. Cell Cycle (2010) 1.31
Circadian regulation of cell cycle: Molecular connections between aging and the circadian clock. Ann Med (2010) 1.25
Shift of monocyte function toward cellular immunity during sleep. Arch Intern Med (2006) 1.22
Genetic flexibility of regulatory networks. Proc Natl Acad Sci U S A (2010) 1.20
Noisy attractors and ergodic sets in models of gene regulatory networks. J Theor Biol (2007) 1.13
Isoform switching facilitates period control in the Neurospora crassa circadian clock. Mol Syst Biol (2008) 1.11
The plant clock shows its metal: circadian regulation of cytosolic free Ca(2+). Trends Plant Sci (2005) 1.11
Scalable steady state analysis of Boolean biological regulatory networks. PLoS One (2009) 1.11
Modeling temperature compensation in chemical and biological oscillators. Chronobiol Int (1997) 1.10
Entrainment dissociates transcription and translation of a circadian clock gene in neurospora. Curr Biol (2004) 1.09
Logic models of pathway biology. Drug Discov Today (2008) 1.04
A logical analysis of T cell activation and anergy. Proc Natl Acad Sci U S A (1999) 1.03
Basin entropy in Boolean network ensembles. Phys Rev Lett (2007) 1.02
How temperature affects the circadian clock of Neurospora crassa. Chronobiol Int (2006) 0.96
Simulating dark expressions and interactions of frq and wc-1 in the Neurospora circadian clock. Biophys J (2007) 0.94
A model for the Neurospora circadian clock. Biophys J (2005) 0.93
Robustness from flexibility in the fungal circadian clock. BMC Syst Biol (2010) 0.91
Circadian clock and vascular disease. Hypertens Res (2010) 0.91
A two variable delay model for the circadian rhythm of Neurospora crassa. J Theor Biol (2004) 0.89
Towards a logical analysis of the immune response. J Theor Biol (1985) 0.89
The effects of feedback loops on disease comorbidity in human signaling networks. Bioinformatics (2011) 0.87
Circadian rhythm dysregulation in bipolar disorder. Curr Opin Investig Drugs (2010) 0.83
Use of logic theory in understanding regulatory pathway signaling in response to infection. Future Microbiol (2010) 0.79
Noisy signaling through promoter logic gates. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.78
Inferring Boolean networks with perturbation from sparse gene expression data: a general model applied to the interferon regulatory network. Mol Biosyst (2008) 0.76
Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat Biotechnol (2008) 12.96
The Systems Biology Graphical Notation. Nat Biotechnol (2009) 8.53
Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science (2005) 6.92
Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods (2009) 4.76
Synaptic NMDA receptor activity boosts intrinsic antioxidant defenses. Nat Neurosci (2008) 4.04
Extension of a genetic network model by iterative experimentation and mathematical analysis. Mol Syst Biol (2005) 3.88
Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana. Mol Syst Biol (2006) 3.68
The ELF4 gene controls circadian rhythms and flowering time in Arabidopsis thaliana. Nature (2002) 3.40
High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay. RNA (2008) 3.13
FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock. Plant Cell (2006) 2.98
Peroxiredoxins are conserved markers of circadian rhythms. Nature (2012) 2.95
Circadian rhythms persist without transcription in a eukaryote. Nature (2011) 2.87
Screening for mammalian neural genes via fluorescence-activated cell sorter purification of neural precursors from Sox1-gfp knock-in mice. Proc Natl Acad Sci U S A (2003) 2.86
Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science (2005) 2.86
The molecular basis of temperature compensation in the Arabidopsis circadian clock. Plant Cell (2006) 2.84
Volition and conflict in human medial frontal cortex. Curr Biol (2005) 2.38
The clock gene circuit in Arabidopsis includes a repressilator with additional feedback loops. Mol Syst Biol (2012) 2.34
The TIME FOR COFFEE gene maintains the amplitude and timing of Arabidopsis circadian clocks. Plant Cell (2003) 2.14
The transcription factor STAT-1 couples macrophage synthesis of 25-hydroxycholesterol to the interferon antiviral response. Immunity (2012) 1.96
FKF1 conveys timing information for CONSTANS stabilization in photoperiodic flowering. Science (2012) 1.85
Weather and seasons together demand complex biological clocks. Curr Biol (2009) 1.80
Transcriptome profile of murine gammaherpesvirus-68 lytic infection. J Gen Virol (2003) 1.75
SPRINT: a new parallel framework for R. BMC Bioinformatics (2008) 1.75
Data assimilation constrains new connections and components in a complex, eukaryotic circadian clock model. Mol Syst Biol (2010) 1.73
Proteasome function is required for biological timing throughout the twenty-four hour cycle. Curr Biol (2011) 1.70
Temporal repression of core circadian genes is mediated through EARLY FLOWERING 3 in Arabidopsis. Curr Biol (2011) 1.69
Natural allelic variation in the temperature-compensation mechanisms of the Arabidopsis thaliana circadian clock. Genetics (2005) 1.67
Genome-wide expression profiling of in vivo-derived bloodstream parasite stages and dynamic analysis of mRNA alterations during synchronous differentiation in Trypanosoma brucei. BMC Genomics (2009) 1.67
ELF4 is required for oscillatory properties of the circadian clock. Plant Physiol (2007) 1.65
Arabidopsis thaliana circadian clock is regulated by the small GTPase LIP1. Curr Biol (2007) 1.62
Action control in visual neglect. Neuropsychologia (2005) 1.59
Host defense against viral infection involves interferon mediated down-regulation of sterol biosynthesis. PLoS Biol (2011) 1.56
Prediction of photoperiodic regulators from quantitative gene circuit models. Cell (2009) 1.52
A logic-based diagram of signalling pathways central to macrophage activation. BMC Syst Biol (2008) 1.49
Quantitative analysis of regulatory flexibility under changing environmental conditions. Mol Syst Biol (2010) 1.48
Discrete clusters of virus-encoded micrornas are associated with complementary strands of the genome and the 7.2-kilobase stable intron in murine cytomegalovirus. J Virol (2007) 1.39
TIME FOR COFFEE encodes a nuclear regulator in the Arabidopsis thaliana circadian clock. Plant Cell (2007) 1.38
The circadian clock that controls gene expression in Arabidopsis is tissue specific. Plant Physiol (2002) 1.37
Distinct regulation of CAB and PHYB gene expression by similar circadian clocks. Plant J (2002) 1.36
Circadian rhythms of ethylene emission in Arabidopsis. Plant Physiol (2004) 1.36
Meeting Report from the Second "Minimum Information for Biological and Biomedical Investigations" (MIBBI) workshop. Stand Genomic Sci (2010) 1.35
High-throughput sequence analysis of variants of human cytomegalovirus strains Towne and AD169. J Gen Virol (2009) 1.34
PEDRo: a database for storing, searching and disseminating experimental proteomics data. BMC Genomics (2004) 1.34
Transcriptomal analysis of varicella-zoster virus infection using long oligonucleotide-based microarrays. J Gen Virol (2005) 1.31
The Arabidopsis SRR1 gene mediates phyB signaling and is required for normal circadian clock function. Genes Dev (2003) 1.28
Forward genetic analysis of the circadian clock separates the multiple functions of ZEITLUPE. Plant Physiol (2006) 1.27
Reconstruction of transcriptional dynamics from gene reporter data using differential equations. Bioinformatics (2008) 1.27
Self-control during response conflict by human supplementary eye field. Nat Neurosci (2003) 1.21
Neutrality of the canonical NF-kappaB-dependent pathway for human and murine cytomegalovirus transcription and replication in vitro. J Virol (2004) 1.21
The circadian clock. A plant's best friend in a spinning world. Plant Physiol (2003) 1.21
Combined agonist-antagonist genome-wide functional screening identifies broadly active antiviral microRNAs. Proc Natl Acad Sci U S A (2010) 1.20
Response regulator homologues have complementary, light-dependent functions in the Arabidopsis circadian clock. Planta (2003) 1.19
A reduced-function allele reveals that EARLY FLOWERING3 repressive action on the circadian clock is modulated by phytochrome signals in Arabidopsis. Plant Cell (2011) 1.12
Isoform switching facilitates period control in the Neurospora crassa circadian clock. Mol Syst Biol (2008) 1.11
Viral mediated redirection of NEMO/IKKγ to autophagosomes curtails the inflammatory cascade. PLoS Pathog (2012) 1.11
Spatial working memory capacity in unilateral neglect. Brain (2005) 1.11
Modelling the widespread effects of TOC1 signalling on the plant circadian clock and its outputs. BMC Syst Biol (2013) 1.11
Locus-specific gene expression pattern suggests a unique propagation strategy for a giant algal virus. J Virol (2006) 1.09
Multiple light inputs to a simple clock circuit allow complex biological rhythms. Plant J (2011) 1.09
Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis. Genome Biol (2011) 1.08
Multi-factorial analysis of class prediction error: estimating optimal number of biomarkers for various classification rules. J Bioinform Comput Biol (2010) 1.08
Shotgun proteomic analysis of the unicellular alga Ostreococcus tauri. J Proteomics (2011) 1.07
Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures. Mol Syst Biol (2013) 1.07
General and specific alterations in programming of global viral gene expression during infection by VP16 activation-deficient mutants of herpes simplex virus type 1. J Virol (2002) 1.06
Logic models of pathway biology. Drug Discov Today (2008) 1.04
Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler. Bioinformatics (2008) 1.03
Practical approaches to long oligonucleotide-based DNA microarray: lessons from herpesviruses. Prog Nucleic Acid Res Mol Biol (2002) 1.03
Mechanistic investigation of the oxygen-atom-transfer reactivity of dioxo-molybdenum(VI) complexes. Chemistry (2006) 1.02
STAT2 deficiency and susceptibility to viral illness in humans. Proc Natl Acad Sci U S A (2013) 1.01
The contributions of interlocking loops and extensive nonlinearity to the properties of circadian clock models. PLoS One (2010) 1.00
Spontaneous spatiotemporal waves of gene expression from biological clocks in the leaf. Proc Natl Acad Sci U S A (2012) 1.00
Light inputs shape the Arabidopsis circadian system. Plant J (2011) 1.00
The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways. BMC Syst Biol (2010) 0.99
Construction of a large scale integrated map of macrophage pathogen recognition and effector systems. BMC Syst Biol (2010) 0.98
Circadian genetics in the model higher plant, Arabidopsis thaliana. Methods Enzymol (2005) 0.98
A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication. PLoS Pathog (2013) 0.98
Regulation of the transcription and replication cycle of human cytomegalovirus is insensitive to genetic elimination of the cognate NF-kappaB binding sites in the enhancer. J Virol (2006) 0.96
Non-transcriptional oscillators in circadian timekeeping. Trends Biochem Sci (2012) 0.96
Fluorescence lifetime imaging of quantum dot labeled DNA microarrays. Int J Mol Sci (2009) 0.95
Stochastic properties of the plant circadian clock. J R Soc Interface (2011) 0.94
Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus. BMC Syst Biol (2011) 0.93
Temporal profiling of the coding and noncoding murine cytomegalovirus transcriptomes. J Virol (2011) 0.93
FLOWERING LOCUS C-dependent and -independent regulation of the circadian clock by the autonomous and vernalization pathways. BMC Plant Biol (2006) 0.92
Gamma flicker triggers attentional selection without awareness. Proc Natl Acad Sci U S A (2009) 0.92
Phenotypes of major immediate-early gene mutants of mouse cytomegalovirus. Med Microbiol Immunol (2008) 0.92
Combined genome-wide expression profiling and targeted RNA interference in primary mouse macrophages reveals perturbation of transcriptional networks associated with interferon signalling. BMC Genomics (2009) 0.92
Robustness from flexibility in the fungal circadian clock. BMC Syst Biol (2010) 0.91
Functional characterization of phytochrome interacting factor 3 for the Arabidopsis thaliana circadian clockwork. Plant Cell Physiol (2005) 0.91
Ubiquitin ligase switch in plant photomorphogenesis: A hypothesis. J Theor Biol (2010) 0.90
Transcriptional responses of murine macrophages to the adenylate cyclase toxin of Bordetella pertussis. Microb Pathog (2007) 0.89
Quantitative assessment of human whole blood RNA as a potential biomarker for infectious disease. Analyst (2007) 0.89
Online period estimation and determination of rhythmicity in circadian data, using the BioDare data infrastructure. Methods Mol Biol (2014) 0.88
Dielectrophoretic manipulation of ribosomal RNA. Biomicrofluidics (2011) 0.88
A multiplexed protein microarray for the simultaneous serodiagnosis of human immunodeficiency virus/hepatitis C virus infection and typing of whole blood. Anal Biochem (2008) 0.88