Published in BMC Syst Biol on September 03, 2010
Robust non-linear differential equation models of gene expression evolution across Drosophila development. BMC Res Notes (2012) 0.83
Integrative systems and synthetic biology of cell-matrix adhesion sites. Cell Adh Migr (2016) 0.75
Modeling the Drosophila gene cluster regulation network for muscle development. PLoS One (2014) 0.75
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell (1998) 62.20
Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol Biol Cell (2002) 17.32
Using Bayesian networks to analyze expression data. J Comput Biol (2000) 15.98
Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol (2003) 8.91
A fast, robust and tunable synthetic gene oscillator. Nature (2008) 6.85
Harmonics of circadian gene transcription in mammals. PLoS Genet (2009) 4.97
Identifying periodically expressed transcripts in microarray time series data. Bioinformatics (2004) 4.62
Design principles of biochemical oscillators. Nat Rev Mol Cell Biol (2008) 4.55
A tunable synthetic mammalian oscillator. Nature (2009) 4.33
Analyzing time series gene expression data. Bioinformatics (2004) 3.45
Computational approaches to cellular rhythms. Nature (2002) 3.40
Recent developments in parameter estimation and structure identification of biochemical and genomic systems. Math Biosci (2009) 2.58
Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms. Bioinformatics (2005) 2.22
Robust detection of periodic time series measured from biological systems. BMC Bioinformatics (2005) 2.14
Rapid and sustained nuclear-cytoplasmic ERK oscillations induced by epidermal growth factor. Mol Syst Biol (2009) 2.10
A reduced model clarifies the role of feedback loops and time delays in the Drosophila circadian oscillator. Biophys J (2002) 1.39
Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods. Nucleic Acids Res (2002) 1.22
Delay model of the circadian pacemaker. J Theor Biol (2000) 1.20
Small-scale copy number variation and large-scale changes in gene expression. Proc Natl Acad Sci U S A (2008) 1.20
Identification of significant periodic genes in microarray gene expression data. BMC Bioinformatics (2005) 1.05
Gene copy number and cell cycle arrest. Phys Biol (2005) 0.80
Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0. Bioinformatics (2009) 2.03
PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality. BMC Bioinformatics (2011) 1.76
BeAtMuSiC: Prediction of changes in protein-protein binding affinity on mutations. Nucleic Acids Res (2013) 1.21
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins (2013) 1.20
Enhancing the stability and solubility of TEV protease using in silico design. Protein Sci (2007) 1.17
Specificity and phenetic relationships of iron- and manganese-containing superoxide dismutases on the basis of structure and sequence comparisons. J Biol Chem (2003) 1.09
Evidence that interaction between conserved residues in transmembrane helices 2, 3, and 7 are crucial for human VPAC1 receptor activation. Mol Pharmacol (2010) 0.99
The first peptides: the evolutionary transition between prebiotic amino acids and early proteins. J Theor Biol (2009) 0.98
A conserved cysteine residue is involved in disulfide bond formation between plant plasma membrane aquaporin monomers. Biochem J (2012) 0.96
Sequence-structure signals of 3D domain swapping in proteins. J Mol Biol (2003) 0.96
Probing the energetic and structural role of amino acid/nucleobase cation-pi interactions in protein-ligand complexes. J Biol Chem (2002) 0.94
Flanking domain stability modulates the aggregation kinetics of a polyglutamine disease protein. Protein Sci (2011) 0.93
Structure-based mutant stability predictions on proteins of unknown structure. J Biotechnol (2012) 0.90
Stair motifs at protein-DNA interfaces: nonadditivity of H-bond, stacking, and cation-pi interactions. J Am Chem Soc (2004) 0.89
Development of novel statistical potentials describing cation-pi interactions in proteins and comparison with semiempirical and quantum chemistry approaches. J Chem Inf Model (2006) 0.88
Thermostability of salt bridges versus hydrophobic interactions in proteins probed by statistical potentials. J Chem Inf Model (2007) 0.88
In vitro and in silico design of alpha1-antitrypsin mutants with different conformational stabilities. J Mol Biol (2003) 0.86
Free-energy calculations of protein-ligand cation-pi and amino-pi interactions: from vacuum to proteinlike environments. J Am Chem Soc (2003) 0.86
SODa: an Mn/Fe superoxide dismutase prediction and design server. BMC Bioinformatics (2008) 0.86
Thermo- and mesostabilizing protein interactions identified by temperature-dependent statistical potentials. Biophys J (2010) 0.85
Revisiting the correlation between proteins' thermoresistance and organisms' thermophilicity. Protein Eng Des Sel (2008) 0.84
Cation-π, amino-π, π-π, and H-bond interactions stabilize antigen-antibody interfaces. Proteins (2014) 0.84
Database-derived potentials dependent on protein size for in silico folding and design. Biophys J (2004) 0.84
Modeling the temporal evolution of the Drosophila gene expression from DNA microarray time series. Phys Biol (2009) 0.84
Mn/Fe superoxide dismutase interaction fingerprints and prediction of oligomerization and metal cofactor from sequence. Proteins (2008) 0.84
Robust non-linear differential equation models of gene expression evolution across Drosophila development. BMC Res Notes (2012) 0.83
Dynamic modeling of gene expression in prokaryotes: application to glucose-lactose diauxie in Escherichia coli. Syst Synth Biol (2011) 0.80
Design principles of a genetic alarm clock. PLoS One (2012) 0.79
Prelude and Fugue, predicting local protein structure, early folding regions and structural weaknesses. Bioinformatics (2006) 0.75