Matthew Stephens | |
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| Academic career | |
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| Thesis | Bayesian Methods for Mixtures of Normal Distributions |
| Doctoral advisor | Brian D. Ripley |
| Academic advisor | Peter Donnelly |
| Notable students | John Novembre |
Matthew Stephens FRS (born 1970) is a Bayesian statistician and professor in the departments of human genetics and statistics at the University of Chicago. He is known for the Li and Stephens model as an efficient coalescent.
Stephens has a PhD from Magdalen College, Oxford University where his advisor was Brian D. Ripley. [1] He then went on to work with Peter Donnelly as a postdoctoral researcher.
Stephens conducted postdoctoral research with Peter Donnelly at the University of Oxford. It was there that he developed the Structure computer program, along with Jonathan Pritchard, which is used for determining population structure and estimating individual admixture. [2] He then went on to develop the influential Li and Stephens model as an efficient model for linkage disequilibrium. [3]
Stephens was awarded the Guy Medal (bronze) in 2006. [4] He was elected a Fellow of the Royal Society in 2023. [5]
Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure.
In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at different loci in a given population. Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is higher or lower than expected if the loci were independent and associated randomly.
A DNA segment is identical by state (IBS) in two or more individuals if they have identical nucleotide sequences in this segment. An IBS segment is identical by descent (IBD) in two or more individuals if they have inherited it from a common ancestor without recombination, that is, the segment has the same ancestral origin in these individuals. DNA segments that are IBD are IBS per definition, but segments that are not IBD can still be IBS due to the same mutations in different individuals or recombinations that do not alter the segment.
Alfred Henry Sturtevant was an American geneticist. Sturtevant constructed the first genetic map of a chromosome in 1911. Throughout his career he worked on the organism Drosophila melanogaster with Thomas Hunt Morgan. By watching the development of flies in which the earliest cell division produced two different genomes, he measured the embryonic distance between organs in a unit which is called the sturt in his honor. On February 13, 1968, Sturtevant received the 1967 National Medal of Science from President Lyndon B. Johnson.
Tomoko Ohta is a Japanese scientist and Professor Emeritus of the National Institute of Genetics. Ohta works on population genetics/molecular evolution and is known for developing the nearly neutral theory of evolution.
Genetic hitchhiking, also called genetic draft or the hitchhiking effect, is when an allele changes frequency not because it itself is under natural selection, but because it is near another gene that is undergoing a selective sweep and that is on the same DNA chain. When one gene goes through a selective sweep, any other nearby polymorphisms that are in linkage disequilibrium will tend to change their allele frequencies too. Selective sweeps happen when newly appeared mutations are advantageous and increase in frequency. Neutral or even slightly deleterious alleles that happen to be close by on the chromosome 'hitchhike' along with the sweep. In contrast, effects on a neutral locus due to linkage disequilibrium with newly appeared deleterious mutations are called background selection. Both genetic hitchhiking and background selection are stochastic (random) evolutionary forces, like genetic drift.
WormBook is an open access, comprehensive collection of original, peer-reviewed chapters covering topics related to the biology of the nematode worm Caenorhabditis elegans . WormBook also includes WormMethods, an up-to-date collection of methods and protocols for C. elegans researchers.
Barbara J. Meyer is a biologist and genetist, noted for her pioneering research on lambda phage, a virus that infects bacteria; discovery of the master control gene involved in sex determination; and studies of gene regulation, particularly dosage compensation. Meyer's work has revealed mechanisms of sex determination and dosage compensation—that balance X-chromosome gene expression between the sexes in Caenorhabditis elegans that continue to serve as the foundation of diverse areas of study on chromosome structure and function today.
Population structure is the presence of a systematic difference in allele frequencies between subpopulations. In a randomly mating population, allele frequencies are expected to be roughly similar between groups. However, mating tends to be non-random to some degree, causing structure to arise. For example, a barrier like a river can separate two groups of the same species and make it difficult for potential mates to cross; if a mutation occurs, over many generations it can spread and become common in one subpopulation while being completely absent in the other.
In genetics, association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of historic linkage disequilibrium to link phenotypes to genotypes, uncovering genetic associations.
Ziheng Yang FRS is a Chinese biologist. He holds the R.A. Fisher Chair of Statistical Genetics at University College London, and is the Director of R.A. Fisher Centre for Computational Biology at UCL. He was elected a Fellow of the Royal Society in 2006.
Jonathan Karl Pritchard is an English-born professor of genetics at Stanford University, best known for his development of the STRUCTURE algorithm for studying population structure and his work on human genetic variation and evolution. His research interests lie in the study of human evolution, in particular in understanding the association between genetic variation among human individuals and human traits.
Jonathan Alan Hodgkin is a British biochemist, Professor of Genetics at the University of Oxford and an emeritus fellow of Keble College, Oxford.
Norbert Perrimon is a French geneticist and developmental biologist. He is the James Stillman Professor of Developmental Biology in the Department of Genetics at Harvard Medical School, an Investigator at the Howard Hughes Medical Institute, and an Associate of the Broad Institute. He is known for developing a number of techniques for used in genetic research with Drosophila melanogaster, as well as specific substantive contributions to signal transduction, developmental biology and physiology.
Joanne Chory is an American plant biologist and geneticist. Chory is a professor and director of the Plant Molecular and Cellular Biology Laboratory, at the Salk Institute for Biological Studies and an investigator of the Howard Hughes Medical Institute.
Daniel L. Hartl is the Higgins Professor of Biology in the Department of Organismic and Evolutionary Biology at Harvard University. He is also a principal investigator at the Hartl Laboratory at Harvard University. His research interests are focused on evolutionary genomics, molecular evolution, and population genetics.
Polygenic adaptation describes a process in which a population adapts through small changes in allele frequencies at hundreds or thousands of loci.
Daniel Gianola is a geneticist based at the University of Wisconsin-Madison (US), reputed for his contributions in quantitative genetics to the fields of animal and plant breeding. In the early 1980s, Gianola extended best linear unbiased prediction to the non-linear domain for analysis of categorical traits, using the classical threshold model of Sewall Wright. Subsequently, he pioneered the use of Bayesian methodologies and Monte Carlo Markov chain methods in quantitative genetics. He also revived early work by Sewall Wright on structural equation models and cast their application in the context of modern quantitative genetics and statistical methodology. His group in Wisconsin was the first in the world applying non-parametric methods, such as reproducing Kernel Hilbert spaces regression and Bayesian neural networks, to genome-enabled selection in animal breeding, agriculture and whole-genome prediction of complex traits or diseases. Gianola published extensively on thresholds models, Bayesian theory, prediction of complex traits using mixed model methodology, hierarchical Bayesian regression procedures and machine learning techniques. Gianola has been also involved in whole-genome prediction of skin and bladder cancer in humans. He has taught extensively in more than twenty countries including recurrent visiting professorships at the Universidad Politecnica de Valencia (Spain), the Norwegian University of Life Sciences (Norway), Aarhus University (Denmark), Georg-August University (Germany) and the Technical University of Munich (Germany). He has been an Honorary Researcher at the Pasteur Institut de Montevideo since 2016. In an Editorial contained in a volume published in Gianola's honor in the Journal of Animal Breeding and Genetics (2017), it was stated that "He is probably the one lecturer in animal breeding and genetics, who has the biggest impact on the largest number of followers in the numerous classes and courses he has taught with never-ending energy all across the world."
R. Scott Hawley is an American geneticist and investigator at the Stowers Institute for Medical Research in Kansas City, Missouri, a member of the US National Academy of sciences and fellow of the American Association for the Advancement of Science. He has been President of the Genetics Society of America, and leads a research team focused on the molecular mechanisms that regulate chromosome behavior during meiosis.
Amanda M. Hulse-Kemp is a computational biologist with the United States Department of Agriculture – Agricultural Research Service. She works in the Genomics and Bioinformatics Research Unit and is stationed on the North Carolina State University campus in Raleigh, North Carolina.
