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Local sequence alignments statistics: deviations from Gumbel statistics in the rare-event tail. Algorithms Mol Biol (2007) 0.95

Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penalty. BMC Bioinformatics (2009) 0.85

A simple derivation of the distribution of pairwise local protein sequence alignment scores. Evol Bioinform Online (2008) 0.83

Geometric aspects of biological sequence comparison. J Comput Biol (2009) 0.75

Protein database searches using compositionally adjusted substitution matrices. FEBS J (2005) 8.14

Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol (2006) 2.90

Heat conduction process on community networks as a recommendation model. Phys Rev Lett (2007) 2.72

Adaptive evolution of transcription factor binding sites. BMC Evol Biol (2004) 2.03

Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications. BMC Evol Biol (2004) 2.01

Information flow in interaction networks. J Comput Biol (2007) 1.75

Cross-species analysis of biological networks by Bayesian alignment. Proc Natl Acad Sci U S A (2006) 1.69

Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies. Proc Natl Acad Sci U S A (2005) 1.68

PSI-BLAST pseudocounts and the minimum description length principle. Nucleic Acids Res (2008) 1.68

Local graph alignment and motif search in biological networks. Proc Natl Acad Sci U S A (2004) 1.56

The construction and use of log-odds substitution scores for multiple sequence alignment. PLoS Comput Biol (2010) 1.54

From fitness landscapes to seascapes: non-equilibrium dynamics of selection and adaptation. Trends Genet (2009) 1.50

Energy-dependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites. Proc Natl Acad Sci U S A (2008) 1.49

Adaptations to fluctuating selection in Drosophila. Proc Natl Acad Sci U S A (2007) 1.45

Calibrating E-values for MS2 database search methods. Biol Direct (2007) 1.44

Clonal interference in the evolution of influenza. Genetics (2012) 1.37

Biodiversity in model ecosystems, I: coexistence conditions for competing species. J Theor Biol (2005) 1.34

Enhancing peptide identification confidence by combining search methods. J Proteome Res (2008) 1.34

Emergent neutrality in adaptive asexual evolution. Genetics (2011) 1.32

Fitness flux and ubiquity of adaptive evolution. Proc Natl Acad Sci U S A (2010) 1.29

RAId_DbS: peptide identification using database searches with realistic statistics. Biol Direct (2007) 1.27

Robust accurate identification of peptides (RAId): deciphering MS2 data using a structured library search with de novo based statistics. Bioinformatics (2005) 1.21

Electrostatics of charged dielectric spheres with application to biological systems. Phys Rev E Stat Nonlin Soft Matter Phys (2006) 1.15

Robust and accurate data enrichment statistics via distribution function of sum of weights. Bioinformatics (2010) 1.08

Correlated random networks. Phys Rev Lett (2002) 1.04

Biodiversity in model ecosystems, II: species assembly and food web structure. J Theor Biol (2005) 1.03

On the inference of dirichlet mixture priors for protein sequence comparison. J Comput Biol (2011) 1.00

Molecular evolution under fitness fluctuations. Phys Rev Lett (2008) 1.00

Solvable sequence evolution models and genomic correlations. Phys Rev Lett (2005) 0.99

Nonlinear fitness landscape of a molecular pathway. PLoS Genet (2011) 0.98

Statistical Characterization of a 1D Random Potential Problem - with applications in score statistics of MS-based peptide sequencing. Physica A (2008) 0.98

Compositional adjustment of Dirichlet mixture priors. J Comput Biol (2010) 0.96

RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration. BMC Genomics (2008) 0.95

Simple electrostatic model applicable to biomolecular recognition. Phys Rev E Stat Nonlin Soft Matter Phys (2010) 0.95

ITM Probe: analyzing information flow in protein networks. Bioinformatics (2009) 0.94

Policy and data-intensive scientific discovery in the beginning of the 21st century. OMICS (2011) 0.91

The effectiveness of position- and composition-specific gap costs for protein similarity searches. Bioinformatics (2008) 0.90

ppiTrim: constructing non-redundant and up-to-date interactomes. Database (Oxford) (2011) 0.90

RAId_aPS: MS/MS analysis with multiple scoring functions and spectrum-specific statistics. PLoS One (2010) 0.89

Information flow in interaction networks II: channels, path lengths, and potentials. J Comput Biol (2012) 0.88

Scale-free networks versus evolutionary drift. Comput Biol Chem (2004) 0.86

Detection of co-eluted peptides using database search methods. Biol Direct (2008) 0.86

Formation of regulatory modules by local sequence duplication. PLoS Comput Biol (2011) 0.85

Combining independent, weighted P-values: achieving computational stability by a systematic expansion with controllable accuracy. PLoS One (2011) 0.85

Reentrant synclinic phase in an electric-field-temperature-phase diagram for enantiomeric mixtures of an antiferroelectric liquid crystal. Phys Rev E Stat Nonlin Soft Matter Phys (2003) 0.84

Dimensional crossover in the purple bronze Li0.9Mo6O17. Phys Rev Lett (2007) 0.84

Universality and predictability in molecular quantitative genetics. Curr Opin Genet Dev (2013) 0.82

GraphAlignment: Bayesian pairwise alignment of biological networks. BMC Syst Biol (2012) 0.81

From protein interactions to functional annotation: graph alignment in Herpes. BMC Syst Biol (2008) 0.80

Improving peptide identification sensitivity in shotgun proteomics by stratification of search space. J Proteome Res (2013) 0.80

Assigning statistical significance to proteotypic peptides via database searches. J Proteomics (2010) 0.80

Score statistics of global sequence alignment from the energy distribution of a modified directed polymer and directed percolation problem. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 0.79

Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. Rapid Commun Mass Spectrom (2012) 0.79

CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores. Bioinformatics (2012) 0.79

Cysteine-cysteine contact preference leads to target-focusing in protein folding. Biophys J (2007) 0.79

CytoITMprobe: a network information flow plugin for Cytoscape. BMC Res Notes (2012) 0.77

Significance analysis and statistical mechanics: an application to clustering. Phys Rev Lett (2010) 0.76

Rigorous treatment of electrostatics for spatially varying dielectrics based on energy minimization. Phys Rev E Stat Nonlin Soft Matter Phys (2009) 0.76

Fitness landscape for nucleosome positioning. Proc Natl Acad Sci U S A (2013) 0.76

Using dissociation energies to predict observability of b- and y-peaks in mass spectra of short peptides. II. Results for hexapeptides with non-polar side chains. Rapid Commun Mass Spectrom (2013) 0.75

Geometric aspects of biological sequence comparison. J Comput Biol (2009) 0.75

Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy. J Am Soc Mass Spectrom (2013) 0.75

Of statistics and genomes. Trends Genet (2004) 0.75

Delocalization transitions of semiflexible manifolds. Phys Rev E Stat Nonlin Soft Matter Phys (2002) 0.75

Method for analyzing second-order phase transitions: application to the ferromagnetic transition of a polaronic system. Phys Rev Lett (2005) 0.75

Challenges of information retrieval and evaluation in data-centric biology. OMICS (2011) 0.75