Published in Bioinformatics on July 10, 2004
Analysis of a generic model of eukaryotic cell-cycle regulation. Biophys J (2006) 1.86
Evolutionary tinkering with conserved components of a transcriptional regulatory network. PLoS Biol (2010) 1.67
A multilevel data integration resource for breast cancer study. BMC Syst Biol (2010) 1.32
Temporal self-organization of the cyclin/Cdk network driving the mammalian cell cycle. Proc Natl Acad Sci U S A (2009) 1.28
Modeling of the role of a Bax-activation switch in the mitochondrial apoptosis decision. Biophys J (2007) 1.14
Parameter estimation in systems biology models using spline approximation. BMC Syst Biol (2011) 1.14
Cell size at S phase initiation: an emergent property of the G1/S network. PLoS Comput Biol (2007) 1.03
A skeleton model for the network of cyclin-dependent kinases driving the mammalian cell cycle. Interface Focus (2010) 0.99
Inverse bifurcation analysis: application to simple gene systems. Algorithms Mol Biol (2006) 0.97
An age-and-cyclin-structured cell population model for healthy and tumoral tissues. J Math Biol (2007) 0.96
A two-dimensional model of the colonic crypt accounting for the role of the basement membrane and pericryptal fibroblast sheath. PLoS Comput Biol (2012) 0.94
Network Inference and Biological Dynamics. Ann Appl Stat (2012) 0.94
Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation. BMC Bioinformatics (2009) 0.91
Modeling the role of p53 pulses in DNA damage- induced cell death decision. BMC Bioinformatics (2009) 0.88
An integrative model links multiple inputs and signaling pathways to the onset of DNA synthesis in hepatocytes. FEBS J (2012) 0.86
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. BMC Syst Biol (2007) 0.84
From quiescence to proliferation: Cdk oscillations drive the mammalian cell cycle. Front Physiol (2012) 0.83
Strategic cell-cycle regulatory features that provide mammalian cells with tunable G1 length and reversible G1 arrest. PLoS One (2012) 0.83
Molecular signaling network motifs provide a mechanistic basis for cellular threshold responses. Environ Health Perspect (2014) 0.82
Robustness analysis of stochastic biochemical systems. PLoS One (2014) 0.81
The balance between cell cycle arrest and cell proliferation: control by the extracellular matrix and by contact inhibition. Interface Focus (2014) 0.80
A continuous optimization approach for inferring parameters in mathematical models of regulatory networks. BMC Bioinformatics (2014) 0.78
Minimal models for cell-cycle control based on competitive inhibition and multisite phosphorylations of Cdk substrates. Biophys J (2013) 0.78
A data-driven, mathematical model of mammalian cell cycle regulation. PLoS One (2014) 0.78
Differentiation resistance through altered retinoblastoma protein function in acute lymphoblastic leukemia: in silico modeling of the deregulations in the G1/S restriction point pathway. BMC Syst Biol (2016) 0.77
T160‐phosphorylated CDK2 defines threshold for HGF dependent proliferation in primary hepatocytes. Mol Syst Biol (2015) 0.77
Systems level modeling of the cell cycle using budding yeast. Cancer Inform (2007) 0.76
A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations. BMC Syst Biol (2012) 0.75
T160-phosphorylated CDK2 defines threshold for HGF-dependent proliferation in primary hepatocytes. Mol Syst Biol (2015) 0.75
Stochastic modeling suggests that noise reduces differentiation efficiency by inducing a heterogeneous drug response in glioma differentiation therapy. BMC Syst Biol (2016) 0.75
Biological profiling of gene groups utilizing Gene Ontology. Genome Inform (2005) 4.10
Differential effects of PER2 phosphorylation: molecular basis for the human familial advanced sleep phase syndrome (FASPS). Genes Dev (2006) 3.78
TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res (2006) 2.55
Spontaneous synchronization of coupled circadian oscillators. Biophys J (2005) 2.55
UniHI: an entry gate to the human protein interactome. Nucleic Acids Res (2006) 2.45
Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability. PLoS Comput Biol (2006) 2.30
Molecular insights into human daily behavior. Proc Natl Acad Sci U S A (2008) 2.03
TiProD: the Tissue-specific Promoter Database. Nucleic Acids Res (2006) 1.89
Coupling governs entrainment range of circadian clocks. Mol Syst Biol (2010) 1.85
Effects of sequestration on signal transduction cascades. FEBS J (2006) 1.84
Identification of cyanobacterial non-coding RNAs by comparative genome analysis. Genome Biol (2005) 1.82
Comparison of human protein-protein interaction maps. Bioinformatics (2007) 1.79
Synchronization-induced rhythmicity of circadian oscillators in the suprachiasmatic nucleus. PLoS Comput Biol (2007) 1.71
Regulation of clock-controlled genes in mammals. PLoS One (2009) 1.65
Beta-TrCP1-mediated degradation of PERIOD2 is essential for circadian dynamics. J Biol Rhythms (2007) 1.64
Toward more transparent and reproducible omics studies through a common metadata checklist and data publications. OMICS (2014) 1.49
How robust are switches in intracellular signaling cascades? J Theor Biol (2003) 1.47
Functioning and robustness of a bacterial circadian clock. Mol Syst Biol (2007) 1.46
Modeling feedback loops of the Mammalian circadian oscillator. Biophys J (2004) 1.45
Comparison of biomechanical modeling of register transitions and voice instabilities with excised larynx experiments. J Acoust Soc Am (2007) 1.43
Ablation of key oncogenic pathways by RITA-reactivated p53 is required for efficient apoptosis. Cancer Cell (2009) 1.43
Recurrent design patterns in the feedback regulation of the mammalian signalling network. Mol Syst Biol (2008) 1.41
Modelling transcriptional feedback loops: the role of Gro/TLE1 in Hes1 oscillations. Philos Trans A Math Phys Eng Sci (2006) 1.36
Activation of TLX3 and NKX2-5 in t(5;14)(q35;q32) T-cell acute lymphoblastic leukemia by remote 3'-BCL11B enhancers and coregulation by PU.1 and HMGA1. Cancer Res (2007) 1.34
Aberrant intestinal expression and allelic variants of mucin genes associated with inflammatory bowel disease. J Mol Med (Berl) (2006) 1.32
Inferring combinatorial regulation of transcription in silico. Nucleic Acids Res (2005) 1.26
Small RNAs establish delays and temporal thresholds in gene expression. Biophys J (2008) 1.24
Are we overestimating the number of cell-cycling genes? The impact of background models on time-series analysis. Bioinformatics (2008) 1.20
Tuning the mammalian circadian clock: robust synergy of two loops. PLoS Comput Biol (2011) 1.18
Experimental and computational analysis of transcriptional start sites in the cyanobacterium Prochlorococcus MED4. Nucleic Acids Res (2003) 1.18
Nonlinear analysis of irregular animal vocalizations. J Acoust Soc Am (2002) 1.17
Inhibition of glycolytic enzymes mediated by pharmacologically activated p53: targeting Warburg effect to fight cancer. J Biol Chem (2011) 1.16
Quantification of circadian rhythms in single cells. PLoS Comput Biol (2009) 1.14
Competing docking interactions can bring about bistability in the MAPK cascade. Biophys J (2007) 1.13
Measuring similarities between transcription factor binding sites. BMC Bioinformatics (2005) 1.13
Identification of Y-box binding protein 1 as a core regulator of MEK/ERK pathway-dependent gene signatures in colorectal cancer cells. PLoS Genet (2010) 1.12
Global parameter search reveals design principles of the mammalian circadian clock. BMC Syst Biol (2008) 1.08
Quantitative analysis of ultrasensitive responses. FEBS J (2005) 1.08
Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database. Genome Inform (2004) 1.06
Identification of distinct antibody epitopes and mimotopes from a peptide array of 5520 randomly generated sequences. J Immunol Methods (2002) 1.05
Periodicities of 10-11bp as indicators of the supercoiled state of genomic DNA. J Mol Biol (2004) 1.05
Identification of dominant signaling pathways from proteomics expression data. J Proteomics (2008) 1.05
How to achieve fast entrainment? The timescale to synchronization. PLoS One (2009) 1.04
Entrainment in a model of the mammalian circadian oscillator. J Biol Rhythms (2005) 1.03
HuSiDa--the human siRNA database: an open-access database for published functional siRNA sequences and technical details of efficient transfer into recipient cells. Nucleic Acids Res (2005) 1.02
TRANSPATH--a high quality database focused on signal transduction. Comp Funct Genomics (2004) 1.01
Creating PWMs of transcription factors using 3D structure-based computation of protein-DNA free binding energies. BMC Bioinformatics (2010) 1.00
Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information. BMC Bioinformatics (2014) 0.98
Nonlinear phenomena in contemporary vocal music. J Voice (2004) 0.98
DNA motifs and sequence periodicities. In Silico Biol (2006) 0.98
Systematic functional assessment of human protein-protein interaction maps. Genome Inform (2006) 0.97
Biomechanical modeling of register transitions and the role of vocal tract resonators. J Acoust Soc Am (2010) 0.96
Ultrasensitization: switch-like regulation of cellular signaling by transcriptional induction. PLoS Comput Biol (2005) 0.95
Repeats and correlations in human DNA sequences. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.94
Bifurcations and chaos in register transitions of excised larynx experiments. Chaos (2008) 0.93
The interplay of cis-regulatory elements rules circadian rhythms in mouse liver. PLoS One (2012) 0.93
Why do cells cycle with a 24 hour period? Genome Inform (2006) 0.92
Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Res (2009) 0.92
Biomechanics and control of vocalization in a non-songbird. J R Soc Interface (2008) 0.91
Mechanism for 12 hr rhythm generation by the circadian clock. Cell Rep (2013) 0.91
Human chronotypes from a theoretical perspective. PLoS One (2013) 0.90
Promoter analysis of Mammalian clock controlled genes. Genome Inform (2007) 0.90
Visualization of system dynamics using phasegrams. J R Soc Interface (2013) 0.90
High reproducibility of large-gel two-dimensional electrophoresis. Electrophoresis (2004) 0.89
Reverse engineering a hierarchical regulatory network downstream of oncogenic KRAS. Mol Syst Biol (2012) 0.88
Tumor growth rate determines the timing of optimal chronomodulated treatment schedules. PLoS Comput Biol (2010) 0.88
Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. BMC Genomics (2007) 0.87
Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer. PLoS One (2011) 0.86
Circadian desynchronization. Interface Focus (2010) 0.84
Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of different functional categories. Mol Genet Genomics (2007) 0.83
Prediction of regulatory transcription factors in T helper cell differentiation and maintenance. Genome Inform (2010) 0.83
3D-Image analysis platform monitoring relocation of pluripotency genes during reprogramming. Nucleic Acids Res (2011) 0.83
Global analysis of host tissue gene expression in the invasive front of colorectal liver metastases. Int J Cancer (2006) 0.83
Prediction of cis-regulatory elements of coregulated genes. Genome Inform (2004) 0.83
Dissecting the action of an evolutionary conserved non-coding region on renin promoter activity. Nucleic Acids Res (2007) 0.83
HOMGL-comparing genelists across species and with different accession numbers. Bioinformatics (2004) 0.82
Regulation of mammalian cell cycle progression in the regenerating liver. J Theor Biol (2011) 0.80
Stable IL-2 decision making by endogenous c-Fos amounts in peripheral memory T-helper cells. J Biol Chem (2012) 0.80
Kinetic mechanisms for overexpression insensitivity and oncogene cooperation. FEBS Lett (2008) 0.80
IL-2 Expression in Activated Human Memory FOXP3(+) Cells Critically Depends on the Cellular Levels of FOXP3 as Well as of Four Transcription Factors of T Cell Activation. Front Immunol (2012) 0.80
A model of the mammalian circadian oscillator including the REV-ERBalpha module. Genome Inform (2004) 0.79
Building a knowledge base for systems pathology. Brief Bioinform (2008) 0.79
Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates. BMC Bioinformatics (2010) 0.79
Death of neuronal clusters contributes to variance of age at onset in Huntington's disease. Neurogenetics (2006) 0.79
Graph-theoretical comparison reveals structural divergence of human protein interaction networks. Genome Inform (2007) 0.78
CYCLONET--an integrated database on cell cycle regulation and carcinogenesis. Nucleic Acids Res (2007) 0.78
A mesoscale model of G1/S phase transition in liver regeneration. J Theor Biol (2008) 0.78
A minimal circadian clock model. Genome Inform (2007) 0.78
A discriminative approach for unsupervised clustering of DNA sequence motifs. PLoS Comput Biol (2013) 0.78
From transcriptional regulation to aggressive behavior. Behav Genet (2003) 0.77
Regulatory elements of marine cyanobacteria. Genome Inform (2007) 0.77
Aggregation in Huntington's disease: insights through modelling. Genome Inform (2005) 0.77
Mild mitochondrial uncoupling does not affect mitochondrial biogenesis but downregulates pyruvate carboxylase in adipocytes: role for triglyceride content reduction. Am J Physiol Endocrinol Metab (2012) 0.76
Modeling IL-2 gene expression in human regulatory T cells. Genome Inform (2008) 0.76
Detecting synchronizations in an asymmetric vocal fold model from time series data. Chaos (2005) 0.76
Identification of key mechanisms controlling gene expression in Leishmania infected macrophages using genome-wide promoter analysis. Infect Genet Evol (2010) 0.75
Alternans and 2:1 rhythms in an ionic model of heart cells. Biosystems (2002) 0.75
Ablation of Key Oncogenic Pathways by RITA-Reactivated p53 Is Required for Efficient Apoptosis. Cancer Cell (2017) 0.75
Sequence-related human proteins cluster by degree of evolutionary conservation. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.75