Bioinformatics is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The subsequent process of analyzing and interpreting data is referred to as computational biology.
In biology, phylogenetics is the study of the evolutionary history and relationships among or within groups of organisms. These relationships are determined by phylogenetic inference methods that focus on observed heritable traits, such as DNA sequences, protein amino acid sequences, or morphology. The result of such an analysis is a phylogenetic tree—a diagram containing a hypothesis of relationships that reflects the evolutionary history of a group of organisms.
A quantum computer is a computer that takes advantage of quantum mechanical phenomena.
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has foundations in applied mathematics, chemistry, and genetics. It differs from biological computing, a subfield of computer science and engineering which uses bioengineering to build computers.
In mathematics and computer science, the Krohn–Rhodes theory is an approach to the study of finite semigroups and automata that seeks to decompose them in terms of elementary components. These components correspond to finite aperiodic semigroups and finite simple groups that are combined in a feedback-free manner.
A phylogenetic network is any graph used to visualize evolutionary relationships between nucleotide sequences, genes, chromosomes, genomes, or species. They are employed when reticulation events such as hybridization, horizontal gene transfer, recombination, or gene duplication and loss are believed to be involved. They differ from phylogenetic trees by the explicit modeling of richly linked networks, by means of the addition of hybrid nodes instead of only tree nodes. Phylogenetic trees are a subset of phylogenetic networks. Phylogenetic networks can be inferred and visualised with software such as SplitsTree, the R-package, phangorn, and, more recently, Dendroscope. A standard format for representing phylogenetic networks is a variant of Newick format which is extended to support networks as well as trees.
Noah Aubrey Rosenberg is a geneticist working in evolutionary biology, mathematical phylogenetics, and population genetics, and is the Stanford Professor of Population Genetics and Society. His research focuses on mathematical modeling and statistical methods for genetics and evolution and he is the editor-in-chief of Theoretical Population Biology.
A Boolean network consists of a discrete set of boolean variables each of which has a Boolean function assigned to it which takes inputs from a subset of those variables and output that determines the state of the variable it is assigned to. This set of functions in effect determines a topology (connectivity) on the set of variables, which then become nodes in a network. Usually, the dynamics of the system is taken as a discrete time series where the state of the entire network at time t+1 is determined by evaluating each variable's function on the state of the network at time t. This may be done synchronously or asynchronously.
Josef "Sepp" Hochreiter is a German computer scientist. Since 2018 he has led the Institute for Machine Learning at the Johannes Kepler University of Linz after having led the Institute of Bioinformatics from 2006 to 2018. In 2017 he became the head of the Linz Institute of Technology (LIT) AI Lab. Hochreiter is also a founding director of the Institute of Advanced Research in Artificial Intelligence (IARAI). Previously, he was at the Technical University of Berlin, at the University of Colorado at Boulder, and at the Technical University of Munich. He is a chair of the Critical Assessment of Massive Data Analysis (CAMDA) conference.
Tandy Warnow is an American computer scientist and Grainger Distinguished Chair in Engineering at the University of Illinois at Urbana–Champaign. She is known for her work on the reconstruction of evolutionary trees, both in biology and in historical linguistics, and also for multiple sequence alignment methods.
Jason H. Moore is a translational bioinformatics scientist, biomedical informatician, and human geneticist, the Edward Rose Professor of Informatics and Director of the Institute for Biomedical Informatics at the Perelman School of Medicine at the University of Pennsylvania, where he is also Senior Associate Dean for Informatics and Director of the Division of Informatics in the Department of Biostatistics, Epidemiology, and Informatics.
Mathieu Daniel Blanchette is a computational biologist and Director of the School of Computer Science at McGill University. His research focuses on developing new algorithms for the detection of functional regions in DNA sequences.
Daniel Mier Gusfield is an American computer scientist, Distinguished Professor of Computer Science at the University of California, Davis. Gusfield is known for his research in combinatorial optimization and computational biology.
Machine learning in bioinformatics is the application of machine learning algorithms to bioinformatics, including genomics, proteomics, microarrays, systems biology, evolution, and text mining.
Christos A. Ouzounis is a computational biologist, a director of research at the CERTH, and Professor of Bioinformatics at Aristotle University in Thessaloniki.
Genome Informatics is a scientific study of information processing in genomes.
Barbara Elizabeth Engelhardt is an American computer scientist and specialist in bioinformatics. Working as a Professor at Stanford University, her work has focused on latent variable models, exploratory data analysis for genomic data, and QTLs. In 2021, she was awarded the Overton Prize by the International Society for Computational Biology.
Katharina Theresia Huber is a German applied mathematician and mathematical biologist whose research concerns phylogenetic trees, evolutionary analysis, their mathematical foundations, and their mathematical visualization. She is an associate professor in the School of Computing Sciences at the University of East Anglia in England, and the school's director of postgraduate research.
In phylogenetics, reconciliation is an approach to connect the history of two or more coevolving biological entities. The general idea of reconciliation is that a phylogenetic tree representing the evolution of an entity can be drawn within another phylogenetic tree representing an encompassing entity to reveal their interdependence and the evolutionary events that have marked their shared history. The development of reconciliation approaches started in the 1980s, mainly to depict the coevolution of a gene and a genome, and of a host and a symbiont, which can be mutualist, commensalist or parasitic. It has also been used for example to detect horizontal gene transfer, or understand the dynamics of genome evolution.
