| P50 | author | Erik van Nimwegen | Q16914877 |
| | Nacho Molina | Q42216174 |
| P2860 | cites work | PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny | Q21145693 |
| | Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen | Q22122393 |
| | The genomic rate of adaptive evolution | Q22162494 |
| | The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications | Q24498207 |
| | Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes | Q24534193 |
| | DBD: a transcription factor prediction database | Q24538686 |
| | Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison | Q24548803 |
| | MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model | Q24557460 |
| | The Pfam protein families database | Q24599089 |
| | A novel method for accurate operon predictions in all sequenced prokaryotes | Q24791071 |
| | A simple model based on mutation and selection explains trends in codon and amino-acid usage and GC composition within and across genomes | Q24797873 |
| | PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences | Q24799381 |
| | RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions | Q25257226 |
| | TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing | Q27860512 |
| | Evolutionary trees from DNA sequences: A maximum likelihood approach | Q27860898 |
| | Dating of the human-ape splitting by a molecular clock of mitochondrial DNA | Q27860908 |
| | T-Coffee: A novel method for fast and accurate multiple sequence alignment | Q27860999 |
| | PAML: a program package for phylogenetic analysis by maximum likelihood | Q27861096 |
| | A Hidden Markov Model approach to variation among sites in rate of evolution | Q28274647 |
| | Phylogenetic analysis. Models and estimation procedures | Q28764664 |
| | Molecular signatures of natural selection | Q29614731 |
| | The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites | Q29618224 |
| | Evolutionary comparisons suggest many novel cAMP response protein binding sites in Escherichia coli | Q30535293 |
| | Congruent evolution of different classes of non-coding DNA in prokaryotic genomes | Q31113360 |
| | Codon bias at the 3'-side of the initiation codon is correlated with translation initiation efficiency in Escherichia coli | Q32062779 |
| | Regulation of transcription in a reduced bacterial genome: nutrient-provisioning genes of the obligate symbiont Buchnera aphidicola | Q33855505 |
| | Codon usage between genomes is constrained by genome-wide mutational processes | Q33976278 |
| | Evolutionary population genetics of promoters: predicting binding sites and functional phylogenies. | Q34115908 |
| | Scaling laws in the functional content of genomes | Q34228161 |
| | Comparative genomic structure of prokaryotes | Q34371888 |
| | The evolution of DNA regulatory regions for proteo-gamma bacteria by interspecies comparisons | Q35003675 |
| | Neutral mutations and neutral substitutions in bacterial genomes | Q35209355 |
| | Transcription-induced mutations: increase in C to T mutations in the nontranscribed strand during transcription in Escherichia coli | Q35937258 |
| | Transcriptional regulation by the numbers: models. | Q36083228 |
| | Translation in Bacillus subtilis: roles and trends of initiation and termination, insights from a genome analysis | Q38321725 |
| | A space-time process model for the evolution of DNA sequences. | Q38394477 |
| | Reduced synonymous substitution rate at the start of enterobacterial genes | Q40415708 |
| | Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila. | Q40497920 |
| | Analyzing and enhancing mRNA translational efficiency in an Escherichia coli in vitro expression system | Q42626227 |
| | Codon and base biases after the initiation codon of the open reading frames in the Escherichia coli genome and their influence on the translation efficiency | Q43627626 |
| | Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics | Q47812666 |
| | Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies | Q47873575 |
| | A probabilistic method to detect regulatory modules. | Q50792656 |
| | Detecting putative orthologs. | Q51982540 |
| | A maximum likelihood approach to the detection of selection from a phylogeny. | Q52449811 |
| | Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. | Q52603460 |
| | Base composition bias might result from competition for metabolic resources. | Q52940121 |
| | The regional rule for bacterial base composition. | Q54483443 |
| | Genome size and operon content | Q73139060 |
| P433 | issue | 1 | |
| P304 | page(s) | 148-160 | |
| P577 | publication date | 2007-11-21 | |
| P1433 | published in | Genome Research | Q5533485 |
| P1476 | title | Universal patterns of purifying selection at noncoding positions in bacteria | |
| P478 | volume | 18 | |