Published in Mol Syst Biol on January 20, 2009
Functional motifs in biochemical reaction networks. Annu Rev Phys Chem (2010) 2.04
Global coordination of transcriptional control and mRNA decay during cellular differentiation. Mol Syst Biol (2010) 1.34
Feedforward regulation ensures stability and rapid reversibility of a cellular state. Mol Cell (2013) 1.09
A comprehensive molecular interaction map of the budding yeast cell cycle. Mol Syst Biol (2010) 1.06
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
Boolean network model predicts knockout mutant phenotypes of fission yeast. PLoS One (2013) 0.89
Modelling the response of FOXO transcription factors to multiple post-translational modifications made by ageing-related signalling pathways. PLoS One (2010) 0.89
System-level feedbacks control cell cycle progression. FEBS Lett (2009) 0.88
Transcriptional regulation is a major controller of cell cycle transition dynamics. PLoS One (2012) 0.81
Modeling Dose-response at Low Dose: A Systems Biology Approach for Ionization Radiation. Dose Response (2010) 0.81
Computational modeling of signaling pathways mediating cell cycle checkpoint control and apoptotic responses to ionizing radiation-induced DNA damage. Dose Response (2011) 0.81
The coupling of pathways and processes through shared components. BMC Syst Biol (2011) 0.80
Integrating phosphorylation network with transcriptional network reveals novel functional relationships. PLoS One (2012) 0.79
Quantitative analysis of cellular metabolic dissipative, self-organized structures. Int J Mol Sci (2010) 0.78
A dynamical model of oocyte maturation unveils precisely orchestrated meiotic decisions. PLoS Comput Biol (2012) 0.77
Differential gene expression regulated by oscillatory transcription factors. PLoS One (2012) 0.76
A Clb/Cdk1-mediated regulation of Fkh2 synchronizes CLB expression in the budding yeast cell cycle. NPJ Syst Biol Appl (2017) 0.76
Model-Based Analysis of Cell Cycle Responses to Dynamically Changing Environments. PLoS Comput Biol (2016) 0.75
Communicating oscillatory networks: frequency domain analysis. BMC Syst Biol (2011) 0.75
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell (1998) 62.20
Transcriptional regulatory networks in Saccharomyces cerevisiae. Science (2002) 43.52
Structure and function of the feed-forward loop network motif. Proc Natl Acad Sci U S A (2003) 12.50
The B-type cyclin kinase inhibitor p40SIC1 controls the G1 to S transition in S. cerevisiae. Cell (1994) 11.08
Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol (2003) 8.91
PEST sequences and regulation by proteolysis. Trends Biochem Sci (1996) 8.90
The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes. Nucleic Acids Res (2004) 8.79
Targets of the cyclin-dependent kinase Cdk1. Nature (2003) 8.05
Polo-like kinases and the orchestration of cell division. Nat Rev Mol Cell Biol (2004) 7.22
CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Res (2005) 5.25
The coherent feedforward loop serves as a sign-sensitive delay element in transcription networks. J Mol Biol (2003) 5.20
Dynamic complex formation during the yeast cell cycle. Science (2005) 5.11
Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry. Proc Natl Acad Sci U S A (2007) 5.09
Phosphorylation of Sld2 and Sld3 by cyclin-dependent kinases promotes DNA replication in budding yeast. Nature (2006) 4.94
Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell (2004) 4.77
The YEASTRACT database: a tool for the analysis of transcription regulatory associations in Saccharomyces cerevisiae. Nucleic Acids Res (2006) 4.53
Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature (2000) 4.52
CDK-dependent phosphorylation of Sld2 and Sld3 initiates DNA replication in budding yeast. Nature (2006) 4.51
Cyclin specificity in the phosphorylation of cyclin-dependent kinase substrates. Nature (2005) 4.08
Fission yeast condensin complex: essential roles of non-SMC subunits for condensation and Cdc2 phosphorylation of Cut3/SMC4. Genes Dev (1999) 3.37
Positive feedback of G1 cyclins ensures coherent cell cycle entry. Nature (2008) 3.32
Co-evolution of transcriptional and post-translational cell-cycle regulation. Nature (2006) 3.28
A single fission yeast mitotic cyclin B p34cdc2 kinase promotes both S-phase and mitosis in the absence of G1 cyclins. EMBO J (1996) 2.58
Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior. Proc Natl Acad Sci U S A (2002) 2.53
The transcription factor Swi5 regulates expression of the cyclin kinase inhibitor p40SIC1. Mol Cell Biol (1996) 2.49
S-Cdk-dependent phosphorylation of Sld2 essential for chromosomal DNA replication in budding yeast. Nature (2002) 2.46
Men and sin: what's the difference? Nat Rev Mol Cell Biol (2001) 2.46
Preventing re-replication of DNA in a single cell cycle: evidence for a replication licensing factor. J Cell Biol (1993) 2.44
Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions. J Theor Biol (2001) 2.42
The incoherent feed-forward loop can generate non-monotonic input functions for genes. Mol Syst Biol (2008) 2.13
Positive feedback sharpens the anaphase switch. Nature (2008) 2.07
Regulation of the mitotic exit protein kinases Cdc15 and Dbf2. Mol Biol Cell (2001) 1.72
Irreversible cell-cycle transitions are due to systems-level feedback. Nat Cell Biol (2007) 1.68
Temporal organization of the cell cycle. Curr Biol (2008) 1.63
The role of CDK in the initiation step of DNA replication in eukaryotes. Cell Div (2007) 1.18
Phosphorylation of the Sic1 inhibitor of B-type cyclins in Saccharomyces cerevisiae is not essential but contributes to cell cycle robustness. Genetics (2007) 1.04
Modeling the septation initiation network (SIN) in fission yeast cells. Curr Genet (2007) 1.01
Adaptive dynamics with a single two-state protein. J R Soc Interface (2008) 0.93
Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77
The genetic landscape of a cell. Science (2010) 16.52
Drug target identification using side-effect similarity. Science (2008) 9.24
Protein disorder prediction: implications for structural proteomics. Structure (2003) 7.93
A new non-linear normalization method for reducing variability in DNA microarray experiments. Genome Biol (2002) 7.12
Systematic discovery of in vivo phosphorylation networks. Cell (2007) 6.94
Dosage sensitivity and the evolution of gene families in yeast. Nature (2003) 6.77
A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol (2010) 6.75
The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet (2004) 5.79
Dynamic complex formation during the yeast cell cycle. Science (2005) 5.11
Cohesin relocation from sites of chromosomal loading to places of convergent transcription. Nature (2004) 5.00
STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res (2007) 4.88
Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell (2004) 4.77
Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proc Natl Acad Sci U S A (2002) 4.58
Design principles of biochemical oscillators. Nat Rev Mol Cell Biol (2008) 4.55
Feature-based prediction of non-classical and leaderless protein secretion. Protein Eng Des Sel (2004) 4.54
Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature (2004) 4.06
SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res (2007) 3.82
Linear motif atlas for phosphorylation-dependent signaling. Sci Signal (2008) 3.77
Eco1-dependent cohesin acetylation during establishment of sister chromatid cohesion. Science (2008) 3.72
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Extraction of regulatory gene/protein networks from Medline. Bioinformatics (2005) 3.43
STITCH 2: an interaction network database for small molecules and proteins. Nucleic Acids Res (2009) 3.06
Identification of cis-acting sites for condensin loading onto budding yeast chromosomes. Genes Dev (2008) 2.87
Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics (2004) 2.83
NetworKIN: a resource for exploring cellular phosphorylation networks. Nucleic Acids Res (2007) 2.69
A non-proteolytic function of separase links the onset of anaphase to mitotic exit. Nat Cell Biol (2003) 2.57
Steady states and oscillations in the p53/Mdm2 network. Cell Cycle (2005) 2.45
Cdc14 phosphatase induces rDNA condensation and resolves cohesin-independent cohesion during budding yeast anaphase. Cell (2004) 2.40
A model for ATP hydrolysis-dependent binding of cohesin to DNA. Curr Biol (2003) 2.40
Plasticity of genetic interactions in metabolic networks of yeast. Proc Natl Acad Sci U S A (2007) 2.40
Establishment of sister chromatid cohesion at the S. cerevisiae replication fork. Mol Cell (2006) 2.39
Downregulation of PP2A(Cdc55) phosphatase by separase initiates mitotic exit in budding yeast. Cell (2006) 2.29
A nondegenerate code of deleterious variants in Mendelian loci contributes to complex disease risk. Cell (2013) 2.28
Pre-Clovis mastodon hunting 13,800 years ago at the Manis site, Washington. Science (2011) 2.11
Stabilization of microtubule dynamics at anaphase onset promotes chromosome segregation. Nature (2005) 2.09
STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Res (2011) 2.05
A mechanism for chromosome segregation sensing by the NoCut checkpoint. Nat Cell Biol (2009) 2.04
Functional motifs in biochemical reaction networks. Annu Rev Phys Chem (2010) 2.04
Hos1 deacetylates Smc3 to close the cohesin acetylation cycle. Mol Cell (2010) 1.92
Text mining for biology--the way forward: opinions from leading scientists. Genome Biol (2008) 1.91
A model for restriction point control of the mammalian cell cycle. J Theor Biol (2004) 1.86
Analysis of a generic model of eukaryotic cell-cycle regulation. Biophys J (2006) 1.86
Sli15(INCENP) dephosphorylation prevents mitotic checkpoint reengagement due to loss of tension at anaphase onset. Curr Biol (2010) 1.82
Cdk-counteracting phosphatases unlock mitotic exit. Curr Opin Cell Biol (2008) 1.80
BioStar: an online question & answer resource for the bioinformatics community. PLoS Comput Biol (2011) 1.80
Mutations in mouse Aspm (abnormal spindle-like microcephaly associated) cause not only microcephaly but also major defects in the germline. Proc Natl Acad Sci U S A (2010) 1.76
Irreversible cell-cycle transitions are due to systems-level feedback. Nat Cell Biol (2007) 1.68
Drug-induced regulation of target expression. PLoS Comput Biol (2010) 1.65
An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet (2011) 1.62
Bacterial evolution of antibiotic hypersensitivity. Mol Syst Biol (2013) 1.58
Modeling networks of coupled enzymatic reactions using the total quasi-steady state approximation. PLoS Comput Biol (2007) 1.58
Integration of horizontally transferred genes into regulatory interaction networks takes many million years. Mol Biol Evol (2007) 1.56
Large-scale prediction of drug-target relationships. FEBS Lett (2008) 1.56
Mathematical modeling as a tool for investigating cell cycle control networks. Methods (2007) 1.55
Impact of the Advisa MRI pacing system on the diagnostic quality of cardiac MR images and contraction patterns of cardiac muscle during scans: Advisa MRI randomized clinical multicenter study results. Heart Rhythm (2013) 1.54
Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Res (2007) 1.50
Evolution of cis-regulatory elements in duplicated genes of yeast. Trends Genet (2003) 1.49
Identification and analysis of evolutionarily cohesive functional modules in protein networks. Genome Res (2006) 1.48
Division of the nucleolus and its release of CDC14 during anaphase of meiosis I depends on separase, SPO12, and SLK19. Dev Cell (2003) 1.48
Endoplasmic reticulum stress, the unfolded protein response, autophagy, and the integrated regulation of breast cancer cell fate. Cancer Res (2012) 1.47
Exploring the roles of noise in the eukaryotic cell cycle. Proc Natl Acad Sci U S A (2009) 1.46
Stochastic exit from mitosis in budding yeast: model predictions and experimental observations. Cell Cycle (2011) 1.46
Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Mol Syst Biol (2011) 1.45
A systematic screen for protein-lipid interactions in Saccharomyces cerevisiae. Mol Syst Biol (2010) 1.43
The SPECIES and ORGANISMS Resources for Fast and Accurate Identification of Taxonomic Names in Text. PLoS One (2013) 1.41
Irreversibility of mitotic exit is the consequence of systems-level feedback. Nature (2009) 1.41
In vivo analysis of cohesin architecture using FRET in the budding yeast Saccharomyces cerevisiae. EMBO J (2007) 1.40
Meiotic homologue alignment and its quality surveillance are controlled by mouse HORMAD1. Nat Cell Biol (2011) 1.40
The dual mechanism of separase regulation by securin. Curr Biol (2002) 1.39
Natural selection promotes the conservation of linkage of co-expressed genes. Trends Genet (2002) 1.39
Bifurcation analysis of a model of the budding yeast cell cycle. Chaos (2004) 1.38
Exploring mechanisms of the DNA-damage response: p53 pulses and their possible relevance to apoptosis. Cell Cycle (2007) 1.37
A model of yeast cell-cycle regulation based on multisite phosphorylation. Mol Syst Biol (2010) 1.33
Mathematical model of the morphogenesis checkpoint in budding yeast. J Cell Biol (2003) 1.33
Conserved features of cohesin binding along fission yeast chromosomes. Genome Biol (2009) 1.31
A quantitative model for ordered Cdk substrate dephosphorylation during mitotic exit. Cell (2011) 1.31
Switches and latches: a biochemical tug-of-war between the kinases and phosphatases that control mitosis. Philos Trans R Soc Lond B Biol Sci (2011) 1.30
Systematic identification of proteins that elicit drug side effects. Mol Syst Biol (2013) 1.28
Preferential cleavage of chromatin-bound cohesin after targeted phosphorylation by Polo-like kinase. EMBO J (2004) 1.28
Bistability by multiple phosphorylation of regulatory proteins. Prog Biophys Mol Biol (2009) 1.28
Condensin, chromatin crossbarring and chromosome condensation. Curr Biol (2012) 1.26
Phosphorylation network dynamics in the control of cell cycle transitions. J Cell Sci (2012) 1.26
Cell-cycle regulation of cohesin stability along fission yeast chromosomes. EMBO J (2007) 1.25
The JigCell model builder: a spreadsheet interface for creating biochemical reaction network models. IEEE/ACM Trans Comput Biol Bioinform (2006) 1.25
Meiotic DNA double-strand breaks and chromosome asynapsis in mice are monitored by distinct HORMAD2-independent and -dependent mechanisms. Genes Dev (2012) 1.24
Budding yeast Wapl controls sister chromatid cohesion maintenance and chromosome condensation. Curr Biol (2012) 1.24
Systems-biology approaches for predicting genomic evolution. Nat Rev Genet (2011) 1.23
Condensin-dependent rDNA decatenation introduces a temporal pattern to chromosome segregation. Curr Biol (2008) 1.23
Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Res (2009) 1.20
Another turn for p53. Mol Syst Biol (2006) 1.19
Genes adopt non-optimal codon usage to generate cell cycle-dependent oscillations in protein levels. Mol Syst Biol (2012) 1.19
A mathematical model for the reciprocal differentiation of T helper 17 cells and induced regulatory T cells. PLoS Comput Biol (2011) 1.18
Separase cooperates with Zds1 and Zds2 to activate Cdc14 phosphatase in early anaphase. J Cell Biol (2008) 1.17
the JigCell model builder and run manager. Bioinformatics (2004) 1.17