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 process of analyzing and interpreting data can some times referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term computational biology refers to building and using models of biological systems.
Systems biology is the computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach to biological research.
A biochemical cascade, also known as a signaling cascade or signaling pathway, is a series of chemical reactions that occur within a biological cell when initiated by a stimulus. This stimulus, known as a first messenger, acts on a receptor that is transduced to the cell interior through second messengers which amplify the signal and transfer it to effector molecules, causing the cell to respond to the initial stimulus. Most biochemical cascades are series of events, in which one event triggers the next, in a linear fashion. At each step of the signaling cascade, various controlling factors are involved to regulate cellular actions, in order to respond effectively to cues about their changing internal and external environments.
The Systems Biology Ontology (SBO) is a set of controlled, relational vocabularies of terms commonly used in systems biology, and in particular in computational modeling.
Systems immunology is a research field under systems biology that uses mathematical approaches and computational methods to examine the interactions within cellular and molecular networks of the immune system. The immune system has been thoroughly analyzed as regards to its components and function by using a "reductionist" approach, but its overall function can't be easily predicted by studying the characteristics of its isolated components because they strongly rely on the interactions among these numerous constituents. It focuses on in silico experiments rather than in vivo.
Paulien Hogeweg is a Dutch theoretical biologist and complex systems researcher studying biological systems as dynamic information processing systems at many interconnected levels. In 1970, together with Ben Hesper, she defined the term bioinformatics as "the study of informatic processes in biotic systems".
Michael Spencer Waterman is a Professor of Biology, Mathematics and Computer Science at the University of Southern California (USC), where he holds an Endowed Associates Chair in Biological Sciences, Mathematics and Computer Science. He previously held positions at Los Alamos National Laboratory and Idaho State University.
Biochemical systems theory is a mathematical modelling framework for biochemical systems, based on ordinary differential equations (ODE), in which biochemical processes are represented using power-law expansions in the variables of the system.
Dame Janet Maureen Thornton, is a senior scientist and director emeritus at the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL). She is one of the world's leading researchers in structural bioinformatics, using computational methods to understand protein structure and function. She served as director of the EBI from October 2001 to June 2015, and played a key role in ELIXIR.
Søren Brunak is a Danish biological and physical scientist working in bioinformatics, systems biology, and medical informatics. He is a professor of Disease Systems Biology at the University of Copenhagen and professor of bioinformatics at the Technical University of Denmark. As Research Director at the Novo Nordisk Foundation Center for Protein Research at the University of Copenhagen Medical School, he leads a research effort where molecular-level systems biology data are combined with phenotypic data from the healthcare sector, such as electronic patient records, registry information, and biobank questionnaires. A major aim is to understand the network biology basis for time-ordered comorbidities and discriminate between treatment-related disease correlations and other comorbidities in disease trajectories. Søren Brunak also holds a position as a Medical Informatics Officer at Rigshospitalet, the Capital Region of Denmark.
Junhyong Kim is the Edmund J. and Louise W. Kahn Term Endowed Professor of Biology at the University of Pennsylvania and the author of over eighty published scientific papers.
Stefan Schuster is a German biophysicist. He is professor for bioinformatics at the University of Jena.
Michael Joseph Ezra Sternberg is a professor at Imperial College London, where he is director of the Centre for Integrative Systems Biology and Bioinformatics and Head of the Structural bioinformatics Group.
Multi-state modeling of biomolecules refers to a series of techniques used to represent and compute the behaviour of biological molecules or complexes that can adopt a large number of possible functional states.
Sarah Amalia Teichmann is a German scientist, the former head of cellular genetics at the Wellcome Sanger Institute and a visiting research group leader at the European Bioinformatics Institute (EMBL-EBI). She serves as director of research in the Cavendish Laboratory, Professor at the University of Cambridge and Cambridge Stem Cell Institute, and is a senior research fellow at Churchill College, Cambridge.
Greg N. Stephanopoulos is an American chemical engineer and the Willard Henry Dow Professor in the department of chemical engineering at the Massachusetts Institute of Technology. He has worked at MIT, Caltech, and the University of Minnesota in the areas of biotechnology, bioinformatics, and metabolic engineering especially in the areas of bioprocessing for biochemical and biofuel production. Stephanopoulos is the author of over 400 scientific publications with more than 35,000 citations as of April 2018. In addition, Greg has supervised more than 70 graduate students and 50 post-docs whose research has led to more than 50 patents. He was elected a fellow of the American Association for the Advancement of Science (2005), a member of the National Academy of Engineering (2003), and received the ENI Prize on Renewable Energy 2011.
An array of protein tandem repeats is defined as several adjacent copies having the same or similar sequence motifs. These periodic sequences are generated by internal duplications in both coding and non-coding genomic sequences. Repetitive units of protein tandem repeats are considerably diverse, ranging from the repetition of a single amino acid to domains of 100 or more residues.
Eberhard O. Voit is a Clinical Professor at the University of Texas at Dallas. Until 2024, he was a Professor and David D. Flanagan Chair in Biological Systems at the Georgia Institute of Technology, where is now Professor Emeritus, and a Georgia Research Alliance Eminent Scholar. He leads the Laboratory for Biological Systems Analysis.
libRoadRunner is a C/C++ software library that supports simulation of SBML based models.. It uses LLVM to generate extremely high-performance code and is the fastest SBML-based simulator currently available. Its main purpose is for use as a reusable library that can be hosted by other applications, particularly on large compute clusters for doing parameter optimization where performance is critical. It also has a set of Python bindings that allow it to be easily used from Python as well as a set of bindings for Julia.
