Charles Lawrence (mathematician)
Encyclopedia
Charles "Chip" Lawrence is an American bioinformatician
and mathematician, who is the pioneer in developing novel statistical approaches to biological sequence analysis.
After his PhD graduation, Lawrence became the assistant professor in Systems Engineering and Operations Research and Statistics, in Rensselaer Polytechnic Institute
. In the same time period of time (1971–1975), Lawrence worked as the consultant to the Ministry of Maternal and Child Health in Dominican Republic
. From 1975 to 1981, he worked in the New York State Department of Health as the Director of Operations Research and Statistics, in the Division of Epidemiology
.
Now, he is the Professor of Applied Mathematics and Center for computational Molecular Biology, at Brown University. From 2004 to 2006, he was the director of the Center for Computational Biology. Now he is the director of the Statistical Molecular Biology Group (SMBG), at Brown University
.
Lawrence’s key scientific works to date are focusing on algorithmic approaches to biological sequence analysis. In fact, he was one of the first to recognize that the inherent statistical nature of genomic processes and the immense data resulting from genomic sequencing projects could only be fully analyzed by using statistical algorithms.
, majoring in physics.
After the graduation from Rensselaer Polytechnic Institute
, he pursued further education in Cornell University
and moved to another research field: Applied Operation Research and Statistics in Environmental Engineering. He finished his PhD in 1971. His dissertation topic is population dynamics
.
Lawrence did not switch to bioinoformatics until he finished his PhD study.
and Gibbs sampling
strategy. In his seminal paper published in Science
in 1993, the first application of the statistical technique Gibbs sampling
to the problem of multiple sequence alignment
was described and clearly illustrated.
Besides, Lawrence colaborated with others to further develop the Bayesian statistical approaches to RNA secondary structure prediction, which greatly facilitate the predictions on the full ensemble of probable structures that an RNA molecule may adopt.
Lawrence's research continues to be focused on the application of Bayesian algorithms, specifically in the statistical aproaches for the understanding of biological problems, with particular interest in transcription regulation and identification of regulatory motifs in sequences, antisense oligonucleotide and siRNA
design, comparative genomics,the composition of nucleotide sequences and detailed analyses of several protein families.
. Their work are more focued on the applications of the high-D inferences in the biological problems such as the regulatory motif finding, RNAsecondary structure prediction, and genome wide studies of epigenetics; besides, his research interests also expanded into the geoscience areas of change point estimators of paleoclimate records and probabilistic alignment of geological stratigraphic sequences.The application models of stochastic grammars is also studied in Chip Lawrence Lab.
He developed a tutorial on Bayesian statistics and Gibbs sampling, as well as the introduction courses in Bayesian statistics
at Brown University
.
Lawrence has mentored several young investigators before he took the job at Brown University. From 1981 to 2003, his worked as the Chief in Wadsworth Center for Laboratories and Research, New York State Department of Health
, many young bioinformaticians were trained by him, such as Stephen Bryant.
Dr. Bryant now is the senior Investigator in National Center for Biotechnology Information
, National Library of Medicine, and National Institutes of Health
, working in the branch of computational biology. His focus is in the area of structural bioinformatics. Dr. Bryant also leads NCBI
information resource teams in protein structure, protein family classification, and cheminformatics. These teams maintain NCBI’s macromolecular structure database and Cn3D visualization tool, the Conserved Domain Database and CDTree analysis tool, and most recently the PubChem cheminformatics
database and associated analysis tools.
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...
and mathematician, who is the pioneer in developing novel statistical approaches to biological sequence analysis.
After his PhD graduation, Lawrence became the assistant professor in Systems Engineering and Operations Research and Statistics, in Rensselaer Polytechnic Institute
Rensselaer Polytechnic Institute
Stephen Van Rensselaer established the Rensselaer School on November 5, 1824 with a letter to the Rev. Dr. Samuel Blatchford, in which van Rensselaer asked Blatchford to serve as the first president. Within the letter he set down several orders of business. He appointed Amos Eaton as the school's...
. In the same time period of time (1971–1975), Lawrence worked as the consultant to the Ministry of Maternal and Child Health in Dominican Republic
Dominican Republic
The Dominican Republic is a nation on the island of La Hispaniola, part of the Greater Antilles archipelago in the Caribbean region. The western third of the island is occupied by the nation of Haiti, making Hispaniola one of two Caribbean islands that are shared by two countries...
. From 1975 to 1981, he worked in the New York State Department of Health as the Director of Operations Research and Statistics, in the Division of Epidemiology
Epidemiology
Epidemiology is the study of health-event, health-characteristic, or health-determinant patterns in a population. It is the cornerstone method of public health research, and helps inform policy decisions and evidence-based medicine by identifying risk factors for disease and targets for preventive...
.
Now, he is the Professor of Applied Mathematics and Center for computational Molecular Biology, at Brown University. From 2004 to 2006, he was the director of the Center for Computational Biology. Now he is the director of the Statistical Molecular Biology Group (SMBG), at Brown University
Brown University
Brown University is a private, Ivy League university located in Providence, Rhode Island, United States. Founded in 1764 prior to American independence from the British Empire as the College in the English Colony of Rhode Island and Providence Plantations early in the reign of King George III ,...
.
Lawrence’s key scientific works to date are focusing on algorithmic approaches to biological sequence analysis. In fact, he was one of the first to recognize that the inherent statistical nature of genomic processes and the immense data resulting from genomic sequencing projects could only be fully analyzed by using statistical algorithms.
Early life and education
Lawrence got his Bachelor’s degree in 1967, in Rensselaer Polytechnic InstituteRensselaer Polytechnic Institute
Stephen Van Rensselaer established the Rensselaer School on November 5, 1824 with a letter to the Rev. Dr. Samuel Blatchford, in which van Rensselaer asked Blatchford to serve as the first president. Within the letter he set down several orders of business. He appointed Amos Eaton as the school's...
, majoring in physics.
After the graduation from Rensselaer Polytechnic Institute
Rensselaer Polytechnic Institute
Stephen Van Rensselaer established the Rensselaer School on November 5, 1824 with a letter to the Rev. Dr. Samuel Blatchford, in which van Rensselaer asked Blatchford to serve as the first president. Within the letter he set down several orders of business. He appointed Amos Eaton as the school's...
, he pursued further education in Cornell University
Cornell University
Cornell University is an Ivy League university located in Ithaca, New York, United States. It is a private land-grant university, receiving annual funding from the State of New York for certain educational missions...
and moved to another research field: Applied Operation Research and Statistics in Environmental Engineering. He finished his PhD in 1971. His dissertation topic is population dynamics
Population dynamics
Population dynamics is the branch of life sciences that studies short-term and long-term changes in the size and age composition of populations, and the biological and environmental processes influencing those changes...
.
Lawrence did not switch to bioinoformatics until he finished his PhD study.
Research interests and contributions
Since the 1980s, Lawrence started the research in the field of computational biology. focusing on algorithmic approaches, he was a pioneer in developing novel statistical approaches to biological sequence analysis.Gibbs sampling in motif finding
Lawrence has particular contributions in the development of sequence alignment algorithms, which is approaching the modif finding problem by integrating the Bayesian statisticsBayesian statistics
Bayesian statistics is that subset of the entire field of statistics in which the evidence about the true state of the world is expressed in terms of degrees of belief or, more specifically, Bayesian probabilities...
and Gibbs sampling
Gibbs sampling
In statistics and in statistical physics, Gibbs sampling or a Gibbs sampler is an algorithm to generate a sequence of samples from the joint probability distribution of two or more random variables...
strategy. In his seminal paper published in Science
Science (journal)
Science is the academic journal of the American Association for the Advancement of Science and is one of the world's top scientific journals....
in 1993, the first application of the statistical technique Gibbs sampling
Gibbs sampling
In statistics and in statistical physics, Gibbs sampling or a Gibbs sampler is an algorithm to generate a sequence of samples from the joint probability distribution of two or more random variables...
to the problem of multiple sequence alignment
Multiple sequence alignment
A multiple sequence alignment is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor...
was described and clearly illustrated.
Besides, Lawrence colaborated with others to further develop the Bayesian statistical approaches to RNA secondary structure prediction, which greatly facilitate the predictions on the full ensemble of probable structures that an RNA molecule may adopt.
Lawrence's research continues to be focused on the application of Bayesian algorithms, specifically in the statistical aproaches for the understanding of biological problems, with particular interest in transcription regulation and identification of regulatory motifs in sequences, antisense oligonucleotide and siRNA
Sírna
Sírna Sáeglach , son of Dian mac Demal, son of Demal mac Rothechtaid, son of Rothechtaid mac Main, was, according to medieval Irish legend and historical tradition, a High King of Ireland...
design, comparative genomics,the composition of nucleotide sequences and detailed analyses of several protein families.
Softwares and platforms
In the past several years, based on the statistical algorithm development by Lawrence and his collaborators, several programes have also been publically available and widely used, such as the Gibbs Motif Sampler, the Bayes aligner, Sfold, BALSA, Gibbs Gaussian Clustering, and Bayesian Motif Clustering. His work in Bayesian Statistics won the Mitchell Prize for outstanding applied Bayesian statistics paper in 2000.Chip Lawrence Lab
Now, Lawrence is the director of Chip Lawrence Lab at Brown UniversityBrown University
Brown University is a private, Ivy League university located in Providence, Rhode Island, United States. Founded in 1764 prior to American independence from the British Empire as the College in the English Colony of Rhode Island and Providence Plantations early in the reign of King George III ,...
. Their work are more focued on the applications of the high-D inferences in the biological problems such as the regulatory motif finding, RNAsecondary structure prediction, and genome wide studies of epigenetics; besides, his research interests also expanded into the geoscience areas of change point estimators of paleoclimate records and probabilistic alignment of geological stratigraphic sequences.The application models of stochastic grammars is also studied in Chip Lawrence Lab.
Teaching and traineeship
Lawrence has also devoted time to education.He developed a tutorial on Bayesian statistics and Gibbs sampling, as well as the introduction courses in Bayesian statistics
Bayesian statistics
Bayesian statistics is that subset of the entire field of statistics in which the evidence about the true state of the world is expressed in terms of degrees of belief or, more specifically, Bayesian probabilities...
at Brown University
Brown University
Brown University is a private, Ivy League university located in Providence, Rhode Island, United States. Founded in 1764 prior to American independence from the British Empire as the College in the English Colony of Rhode Island and Providence Plantations early in the reign of King George III ,...
.
Lawrence has mentored several young investigators before he took the job at Brown University. From 1981 to 2003, his worked as the Chief in Wadsworth Center for Laboratories and Research, New York State Department of Health
New York State Department of Health
The New York State Department of Health, ', is the governmental body responsible for public health in the state of New York. The cabinet-level department is headed by the Health Commissioner, a position held since January 24, 2011 by Nirav R. Shah, M.D., M.P.H.....
, many young bioinformaticians were trained by him, such as Stephen Bryant.
Dr. Bryant now is the senior Investigator in National Center for Biotechnology Information
National Center for Biotechnology Information
The National Center for Biotechnology Information is part of the United States National Library of Medicine , a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper...
, National Library of Medicine, and National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
, working in the branch of computational biology. His focus is in the area of structural bioinformatics. Dr. Bryant also leads NCBI
NCBI
NCBI may refer to:* National Center for Biotechnology Information, part of the U.S. National Institutes of Health* National Coalition Building Institute, a U.S. non-profit training group...
information resource teams in protein structure, protein family classification, and cheminformatics. These teams maintain NCBI’s macromolecular structure database and Cn3D visualization tool, the Conserved Domain Database and CDTree analysis tool, and most recently the PubChem cheminformatics
Cheminformatics
Cheminformatics is the use of computer and informational techniques, applied to a range of problems in the field of chemistry. These in silico techniques are used in pharmaceutical companies in the process of drug discovery...
database and associated analysis tools.
Career summary
- 1971–1975: Assistant Professor, Systems Engineering and Operations Research and Statistics, Rensselaer Polytechnic Institute.
- 1971–1975: Consultant to the Ministry of Maternal and Child Health, Dominican Republic.
- 1975–1981: Director of Operations Research and Statistics, Division of Epidemiology, New York State Department of Health.
- 1981–2003: Chief of the Biometrics/Bioinformatics Laboratory, Wadsworth Center for Laboratories and Research, New York State Department of Health.
- 1985–1992: Statistical Consultant, Harrison Radiator Division General Motors Corp.
- 1992–1996: Visiting Scientist, National Center for Biotechnology Information, NLM-NIH.
- 2000–2003: Research Professor, Computer Science Department, Rensselaer Polytechnic Institute (one day per week).
- 2004–2006: Director of the Center for Computational Molecular Biology,and Professor of Applied Mathematics, Brown University.
- 2004–present: Professor of Applied Mathematics and Center for Computational Molecular Biology, Brown University.