NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents

Codon Pair Bias Is a Direct Consequence of Dinucleotide Bias

(2016) Dusan Kunec et al.   Cell Reports

Inferring Contacting Residues within and between Proteins: What Do the Probabilities Mean?

(2016) Erik van Nimwegen   PLoS Computational Biology

GC-Content Evolution in Bacterial Genomes: The Biased Gene Conversion Hypothesis Expands

(2015) Florent Lassalle et al.   PLoS Genetics

Motif depletion in bacteriophages infecting hosts with CRISPR systems

(2014) Anne Kupczok et al.   BMC GENOMICS

RNA virus attenuation by codon pair deoptimisation is an artefact of increases in CpG/UpA dinucleotide frequencies

(2014) Fiona Tulloch et al.   eLife

Amino Acid Usage Is Asymmetrically Biased in AT- and GC-Rich Microbial Genomes

(2013) Jon Bohlin et al.   PLoS One

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Overlapping codes within protein-coding sequences

(2010) S. Itzkovitz et al.   GENOME RESEARCH

GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes

(2010) Amrita Pati et al.   NATURE METHODS

Translation efficiency is determined by both codon bias and folding energy

(2010) Tamir Tuller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evidence of Selection upon Genomic GC-Content in Bacteria

(2010) Falk Hildebrand et al.   PLoS Genetics

Virus Attenuation by Genome-Scale Changes in Codon Pair Bias

(2008) J. R. Coleman et al.   SCIENCE