Mark Bender Gerstein
Encyclopedia
Professor Mark B. Gerstein is an American
scientist working in bioinformatics
. , he is co-director of the Yale
Computational Biology
and Bioinformatics program, and
Albert L. Williams Professor
of Biomedical Informatics
, Professor of Molecular Biophysics
& Biochemistry
and Professor of Computer Science
at Yale University
.
in Physics
in 1989,
Gerstein studied under Ruth Lynden-Bell in the chemistry department of Cambridge University and Cyrus Chothia
of the British Medical Research Council
,
earning a doctorate
in 1993 from the University of Cambridge
. He then went on to
postdoctoral research
in bioinformatics at Stanford University
from
1993-1996 under Michael Levitt
.
Distinguished Young Scholars award, Gerstein has received awards from the US Navy, IBM
, Pharmaceutical Research and Manufacturers of America
, and the Donaghue Foundation. He is a Fellow of the AAAS
. Other awards include a Herchel-Smith
Scholarship supporting his doctoral work at Emmanuel College
and a Damon Runyon Cancer Research Foundation
Postdoctoral Fellowship. He is a contributor to a number of scientific consortia including ENCODE
, modENCODE and the 1000 Genomes Project.
. This involves applying a range of computational approaches to problems in molecular biology
, including data mining and machine learning, molecular simulation, and database design. His research group has a number of foci including annotating the human genome, personal genomics
, building tools in support of genome technologies (such as next-generation sequencing), analyzing molecular networks, and simulating macromolecular motions. Notable databases and tools that the group has developed include the Database of Macromolecular Motions, which categorizes macromolecular conformational change
; tYNA, which helps analyze molecular networks; PubNet, which analyzes publication networks; PeakSeq, which identifies regions in the genome bound by particular transcription factors; and PEMer, which categorizes block variants in the genome. Gerstein has also written extensively on scientific communication and ways in which computational issues in molecular biology interface with broader aspects of computation in society.
United States
The United States of America is a federal constitutional republic comprising fifty states and a federal district...
scientist working in bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
. , he is co-director of the Yale
Yale University
Yale University is a private, Ivy League university located in New Haven, Connecticut, United States. Founded in 1701 in the Colony of Connecticut, the university is the third-oldest institution of higher education in the United States...
Computational Biology
Computational biology
Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems...
and Bioinformatics program, and
Albert L. Williams Professor
Professor
A professor is a scholarly teacher; the precise meaning of the term varies by country. Literally, professor derives from Latin as a "person who professes" being usually an expert in arts or sciences; a teacher of high rank...
of Biomedical Informatics
Informatics (academic field)
Informatics is the science of information, the practice of information processing, and the engineering of information systems. Informatics studies the structure, algorithms, behavior, and interactions of natural and artificial systems that store, process, access and communicate information...
, Professor of Molecular Biophysics
Molecular biophysics
Molecular biophysics is a rapidly evolving interdisciplinary area of research that combines concepts in physics, chemistry, engineering, mathematics and biology...
& Biochemistry
Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...
and Professor of Computer Science
Computer science
Computer science or computing science is the study of the theoretical foundations of information and computation and of practical techniques for their implementation and application in computer systems...
at Yale University
Yale University
Yale University is a private, Ivy League university located in New Haven, Connecticut, United States. Founded in 1701 in the Colony of Connecticut, the university is the third-oldest institution of higher education in the United States...
.
Education
After graduating from Harvard College summa cum laude with an A.B.Bachelor of Arts
A Bachelor of Arts , from the Latin artium baccalaureus, is a bachelor's degree awarded for an undergraduate course or program in either the liberal arts, the sciences, or both...
in Physics
Physics
Physics is a natural science that involves the study of matter and its motion through spacetime, along with related concepts such as energy and force. More broadly, it is the general analysis of nature, conducted in order to understand how the universe behaves.Physics is one of the oldest academic...
in 1989,
Gerstein studied under Ruth Lynden-Bell in the chemistry department of Cambridge University and Cyrus Chothia
Cyrus Chothia
Cyrus Chothia FRS is an emeritus scientist at the Medical Research Council Laboratory of Molecular Biology and emeritus fellow of Wolfson College, Cambridge....
of the British Medical Research Council
Medical Research Council (UK)
The Medical Research Council is a publicly-funded agency responsible for co-ordinating and funding medical research in the United Kingdom. It is one of seven Research Councils in the UK and is answerable to, although politically independent from, the Department for Business, Innovation and Skills...
,
earning a doctorate
Doctorate
A doctorate is an academic degree or professional degree that in most countries refers to a class of degrees which qualify the holder to teach in a specific field, A doctorate is an academic degree or professional degree that in most countries refers to a class of degrees which qualify the holder...
in 1993 from the University of Cambridge
University of Cambridge
The University of Cambridge is a public research university located in Cambridge, United Kingdom. It is the second-oldest university in both the United Kingdom and the English-speaking world , and the seventh-oldest globally...
. He then went on to
postdoctoral research
Postdoctoral researcher
Postdoctoral research is scholarly research conducted by a person who has recently completed doctoral studies, normally within the previous five years. It is intended to further deepen expertise in a specialist subject, including acquiring novel skills and methods...
in bioinformatics at Stanford University
Stanford University
The Leland Stanford Junior University, commonly referred to as Stanford University or Stanford, is a private research university on an campus located near Palo Alto, California. It is situated in the northwestern Santa Clara Valley on the San Francisco Peninsula, approximately northwest of San...
from
1993-1996 under Michael Levitt
Michael Levitt
Professor Michael Levitt FRS is a British biophysicist. He has been Professor of Structural biology, Stanford University, California, since 1987 working in computational biology and bioinformatics....
.
Publications and editorial positions
Gerstein has a number of scientific publications and non-scientific publications in more popular forums. He serves on a number of editorial and advisory boards, including those of PLOS Computational Biology, Genome Research, GenomeBiology, and Molecular Systems Biology.Awards and memberships
In addition to a W. M. Keck FoundationW. M. Keck Foundation
The W. M. Keck Foundation is an American charitable foundation supporting scientific, engineering, and medical research in the United States. It was founded in 1954 by William Myron Keck, founder and president of Superior Oil Company . The Foundation's trust fund currently has assets in excess of 1...
Distinguished Young Scholars award, Gerstein has received awards from the US Navy, IBM
IBM
International Business Machines Corporation or IBM is an American multinational technology and consulting corporation headquartered in Armonk, New York, United States. IBM manufactures and sells computer hardware and software, and it offers infrastructure, hosting and consulting services in areas...
, Pharmaceutical Research and Manufacturers of America
Pharmaceutical Research and Manufacturers of America
Pharmaceutical Research and Manufacturers of America , founded in 1958, is a trade group representing the pharmaceutical research and biopharmaceutical companies in the United States. PhRMA's stated mission is advocacy for public policies that encourage the discovery of new medicines for patients...
, and the Donaghue Foundation. He is a Fellow of the AAAS
Fellow of the AAAS
Fellow of the AAAS is an honor accorded by the American Association for the Advancement of Science to distinguished persons who are members of the Association. Fellows are elected annually by the AAAS Council for "efforts on behalf of the advancement of science or its applications [which] are...
. Other awards include a Herchel-Smith
Herchel Smith
Herchel Smith was an Anglo-American organic chemist. His discoveries include the key inventions underlying oral and injectable contraceptives. In later life, he was a major benefactor to university science....
Scholarship supporting his doctoral work at Emmanuel College
Emmanuel College
Emmanuel College may refer to one of several academic institutions:in Australia* Emmanuel College, University of Queensland, part of the University of Queensland in Brisbane, Australia...
and a Damon Runyon Cancer Research Foundation
Damon Runyon Cancer Research Foundation
The Damon Runyon Cancer Research Foundation is a not-for-profit cancer research organization focused "discovering the talent to discover the cure." The Foundation states that its goals are to: "identify the best and brightest early career scientists in cancer research, accelerate the translation...
Postdoctoral Fellowship. He is a contributor to a number of scientific consortia including ENCODE
ENCODE
ENCODE is a public research consortium launched by the US National Human Genome Research Institute in September 2003. The goal is to find all functional elements in the human genome, one of the most critical projects by NHGRI after it completed the successful Human Genome Project...
, modENCODE and the 1000 Genomes Project.
Research
Gerstein does research in the field of bioinformaticsBioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
. This involves applying a range of computational approaches to problems in molecular biology
Molecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
, including data mining and machine learning, molecular simulation, and database design. His research group has a number of foci including annotating the human genome, personal genomics
Personal genomics
Personal genomics is the branch of genomics concerned with the sequencing and analysis of the genome of an individual. The genotyping stage employs different techniques, including single-nucleotide polymorphism analysis chips , or partial or full genome sequencing...
, building tools in support of genome technologies (such as next-generation sequencing), analyzing molecular networks, and simulating macromolecular motions. Notable databases and tools that the group has developed include the Database of Macromolecular Motions, which categorizes macromolecular conformational change
Conformational change
A macromolecule is usually flexible and dynamic. It can change its shape in response to changes in its environment or other factors; each possible shape is called a conformation, and a transition between them is called a conformational change...
; tYNA, which helps analyze molecular networks; PubNet, which analyzes publication networks; PeakSeq, which identifies regions in the genome bound by particular transcription factors; and PEMer, which categorizes block variants in the genome. Gerstein has also written extensively on scientific communication and ways in which computational issues in molecular biology interface with broader aspects of computation in society.