The genetic code is the set of rules used by living cells to translate information encoded within genetic material into proteins. Translation is accomplished by the ribosome, which links proteinogenic amino acids in an order specified by messenger RNA (mRNA), using transfer RNA (tRNA) molecules to carry amino acids and to read the mRNA three nucleotides at a time. The genetic code is highly similar among all organisms and can be expressed in a simple table with 64 entries.
Carl Richard Woese was an American microbiologist and biophysicist. Woese is famous for defining the Archaea in 1977 through a pioneering phylogenetic taxonomy of 16S ribosomal RNA, a technique that has revolutionized microbiology. He also originated the RNA world hypothesis in 1967, although not by that name. Woese held the Stanley O. Ikenberry Chair and was professor of microbiology at the University of Illinois Urbana–Champaign.
A phylogenetic tree is a branching diagram or a tree showing the evolutionary relationships among various biological species or other entities based upon similarities and differences in their physical or genetic characteristics. All life on Earth is part of a single phylogenetic tree, indicating common ancestry.
Codon usage bias refers to differences in the frequency of occurrence of synonymous codons in coding DNA. A codon is a series of three nucleotides that encodes a specific amino acid residue in a polypeptide chain or for the termination of translation.
Roderic Dugald Morton Page is a New Zealand-born evolutionary biologist at the University of Glasgow, Scotland, and the author of several books. As of 2015 he is professor at the University of Glasgow and was editor of the journal Systematic Biology until the end of 2007. His main interests are in phylogenetics, evolutionary biology and bioinformatics.
In bioinformatics, k-mers are substrings of length contained within a biological sequence. Primarily used within the context of computational genomics and sequence analysis, in which k-mers are composed of nucleotides, k-mers are capitalized upon to assemble DNA sequences, improve heterologous gene expression, identify species in metagenomic samples, and create attenuated vaccines. Usually, the term k-mer refers to all of a sequence's subsequences of length , such that the sequence AGAT would have four monomers, three 2-mers, two 3-mers and one 4-mer (AGAT). More generally, a sequence of length will have k-mers and total possible k-mers, where is number of possible monomers.
In the fields of molecular biology and genetics, a pan-genome is the entire set of genes from all strains within a clade. More generally, it is the union of all the genomes of a clade. The pan-genome can be broken down into a "core pangenome" that contains genes present in all individuals, a "shell pangenome" that contains genes present in two or more strains, and a "cloud pangenome" that contains genes only found in a single strain. Some authors also refer to the cloud genome as "accessory genome" containing 'dispensable' genes present in a subset of the strains and strain-specific genes. Note that the use of the term 'dispensable' has been questioned, at least in plant genomes, as accessory genes play "an important role in genome evolution and in the complex interplay between the genome and the environment". The field of study of the pangenome is called pangenomics.
A codon table can be used to translate a genetic code into a sequence of amino acids. The standard genetic code is traditionally represented as an RNA codon table, because when proteins are made in a cell by ribosomes, it is messenger RNA (mRNA) that directs protein synthesis. The mRNA sequence is determined by the sequence of genomic DNA. In this context, the standard genetic code is referred to as translation table 1. It can also be represented in a DNA codon table. The DNA codons in such tables occur on the sense DNA strand and are arranged in a 5′-to-3′ direction. Different tables with alternate codons are used depending on the source of the genetic code, such as from a cell nucleus, mitochondrion, plastid, or hydrogenosome.
A supertree is a single phylogenetic tree assembled from a combination of smaller phylogenetic trees, which may have been assembled using different datasets or a different selection of taxa. Supertree algorithms can highlight areas where additional data would most usefully resolve any ambiguities. The input trees of a supertree should behave as samples from the larger tree.
David Tudor Jones is a Professor of Bioinformatics, and Head of Bioinformatics Group in the University College London. He is also the director in Bloomsbury Center for Bioinformatics, which is a joint Research Centre between UCL and Birkbeck, University of London and which also provides bioinformatics training and support services to biomedical researchers. In 2013, he is a member of editorial boards for PLoS ONE, BioData Mining, Advanced Bioinformatics, Chemical Biology & Drug Design, and Protein: Structure, Function and Bioinformatics.
Desmond Gerard Higgins is a Professor of Bioinformatics at University College Dublin, widely known for CLUSTAL, a series of computer programs for performing multiple sequence alignment. According to Nature, Higgins' papers describing CLUSTAL are among the top ten most highly cited scientific papers of all time.
Osnat Penn, born in 1981, is an Israeli computational biologist whose work focuses on molecular evolution, cell research, and immunoinformatics. She is the third Israeli scientist in three years to win the UNESCO-L’Oréal fellowship, which she received in 2013 for her work on the genetic origins of autism. Penn is currently a postdoctorate fellow at the University of Washington in Seattle, where she has been working since 2012.
Paul Martin Sharp is Professor of Genetics at the University of Edinburgh, where he holds the Alan Robertson chair of genetics in the Institute of Evolutionary Biology.
Arndt von Haeseler is a German bioinformatician and evolutionary biologist. He is the scientific director of the Max F. Perutz Laboratories at the Vienna Biocenter and a professor of bioinformatics at the University of Vienna and the Medical University of Vienna.
Mary J. O'Connell is an evolutionary genomicist and Associate Professor at the University of Nottingham. She is the Principal Investigator of the Computational & Molecular Evolutionary Biology Group in the School of Life Sciences at the University of Nottingham.
Siv Gun Elisabeth Andersson is a Swedish evolutionary biologist, professor of molecular evolution at Uppsala University. She is member of both the Royal Swedish Academy of Sciences and of Engineering. She is also Head of basic research at the Knut and Alice Wallenberg Foundation and has been co-director of the Swedish national center for large-scale research Science for Life Laboratory between 2017 and 2021. Her research focuses on the evolution of bacteria, mainly on intracellular parasites.
Adam C. Eyre-Walker, is a British evolutionary geneticist, currently Professor of Biology in the School of Life Sciences at the University of Sussex. He is noted for making "significant contributions to our understanding of evolution at the molecular level" and pioneering the use of DNA sequence databases for extracting information about the evolution of genomes.
