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Topic: Computational biology

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	Computational Biology
		Researchers in the computer science department are engaged in a wide range of computational biology projects, from genetic mapping, to advanced sequence analysis, fold prediction, structure comparison algorithms, protein classification, comparative genomics, and long-time simulation of protein molecules.
		Another key element of the computational biology initiative is the Computational Genomics Institute that combines faculty from all over campus who do active research in computational biology and statistical genomics.
		Computational biology is also a crucial part of the recently announced $160M collaboration between Cornell and the Rockefeller and Sloan-Kettering institutes.
	www.cs.cornell.edu /Research/compbio/index.htm (947 words)

	Computational Biology (via CobWeb/3.1 planetlab2.cs.unc.edu) (Site not responding. Last check: 2007-10-13)
		Cornell faculty work primarily in four subareas of computational biology: biomolecular structure, bioinformatics and data mining, ecology and evolutionary biology, and statistical and computational methods for modeling biological systems.
		Beyond the basic core skills in mathematics, physical sciences and biology, the computational biology program of study requires additional coursework in mathematics, computer programming, a "bridging" course aimed at connecting biology to computation, and an advanced course where the theoretical/computational component of one aspect of biology will be studied.
		Computational biology is a new emerging area that has applications as broad as biology itself.
	www.cis.cornell.edu.cob-web.org:8888 /cb (322 words)

	Sloan-Kettering - Computational Biology
		Computational biologists combine findings in biology with computer algorithms and databases to conduct biological research on powerful computers, using sophisticated software -- so-called "dry" laboratories -- in ways that complement and strengthen traditional laboratory and clinical research.
		Computational biology can help interpret detailed molecular profiles of cancerous and noncancerous cells, molecular response profiles of therapeutic agents, and a person's genetic profile to assist in the development of better diagnostics and prognostics, as well as improved therapies.
		Intelligent use of computational methods using detailed molecular and genomic data is expected to reduce the trial and error of drug development and possibly lead to shorter, more accurate clinical trials.
	www.mskcc.org /mskcc/html/12598.cfm (147 words)

	PhD in Computational Biology & Bioinformatics — Duke University Computational Biology & Bioinformatics
		PhD in Computational Biology and Bioinformatics — Duke University Computational Biology and Bioinformatics
		The new name is representative of the burgeoning field of computational biology – encompassing the study of biology using computational methods, including statistics, mathematics, computer science and informatics – and is seen as critical in the search for biomedical research discoveries.
		Computational Biology and Bioinformatics students are educated and mentored in classes, labs and research projects with faculty from multiple departments and disciplines, spanning the biological and computational disciplines, and medical and non-medical departments.
	bioinformatics.duke.edu (229 words)

	Bioinformatics - Wikipedia, the free encyclopedia (via CobWeb/3.1 planetlab2.cs.unc.edu) (Site not responding. Last check: 2007-10-13)
		Computer simulations model such things as population dynamics, or calculate the cumulative genetic health of a breeding pool (in agriculture) or endangered population (in conservation).
		Systems biology involves the use of computer simulations of cellular subsystems (such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks) to both analyze and visualize the complex connections of these cellular processes.
		Computational technologies are used to accelerate or fully automate the processing, quantification and analysis of large amounts of high-information-content biomedical imagery.
	en.wikipedia.org.cob-web.org:8888 /wiki/Bioinformatics (2777 words)

	UC Berkeley Mathematical and Computational Biology (Site not responding. Last check: 2007-10-13)
		Computational biology is an emerging discipline concerned with analysis of biological data and understanding of biological principles through the use of techniques from mathematics, statistics, and computer science.
		The computational biology group within the mathematics department includes undergraduate and graduate students, postdoctoral researchers, and faculty, many of whom are part of the campus-wide designated emphasis in computational biology.
		There is also a regular research seminar on computational biology, held Wednesdays from 3-4pm in 939 Evans Hall.
	bio.math.berkeley.edu (212 words)

	Computational biology - Wikipedia, the free encyclopedia
		Computational biology is an interdisciplinary field that applies the techniques of computer science and applied mathematics to problems inspired by biology.
		Computational biochemistry and biophysics, which make extensive use of structural modeling and simulation methods such as molecular dynamics and Monte Carlo-inspired Boltzmann sampling methods in an attempt to elucidate the kinetics and thermodynamics of protein functions.
		Journal of Computational Biology, a peer-reviewed journal providing a forum for the communication of technical issues associated with the analysis, management, and visualization of cellular information at the molecular level.
	en.wikipedia.org /wiki/Computational_biology (271 words)

	Genomics:GTL and Computational Biology
		Computation is essential to the GTL program goal of achieving a predictive understanding of microbial cell and community systems.
		Through computational analysis of predictive mathematical models, we will understand how microbial organisms and communities may be manipulated to solve problems, how microbes regulate the expression of genes involved in environmental interactions, and how protein complexes are assembled to carry out important processes.
		This suite of computational biology pages describes the attributes and uses of the community- accessible GTL computational environment, presenting the strategy and roadmaps for establishing essential capabilities that tie together GTL scientists and research facilities.
	genomicsgtl.energy.gov /compbio/index.shtml (1403 words)

	Cornell University Graduate Field of Computational Biology (Site not responding. Last check: 2007-10-13)
		The graduate field of Computational Biology offers Ph.D. degrees in the development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological systems.
		Students majoring in computational biology are expected to obtain a broad, interdisciplinary knowledge of fundamental principles in biology, computational science, and mathematics.
		Instead, students choose from specific subareas of study: They are expected to develop competence in at least one specific subdomain of biology (i.e., genetics, macromolecular biology, cellular biology, organismal biology, behavioral biology or ecology) and in relevant subareas of computational science and mathematics.
	www.cb.cornell.edu (237 words)

	Computational Biology: Challenges and Opportunities
		She states that biology is becoming increasingly multi-disciplinary, "using information from different branches of life sciences; genomics, physiology, biochemistry, biophysics, proteomics, and many more." The model needs to incorporate various classes of biological information as well as similar classes of data from different resources.
		In the "age of biology," computing and biology will unite to solve major global problems such as curing deadly diseases and ending world hunger.
		Computational resources cannot keep up with the data, and questions are piling up faster than answers.
	www.hpcwire.com /hpc/919468.html (828 words)

	NJIT - Graduate Programs: Computational Biology (Site not responding. Last check: 2007-10-13)
		Faculty at NJIT specialize in technological, computational, and mathematical aspects of biology, including the application and development of DNA microarray techniques, modeling of molecules, genetic data mining and warehousing, fluid flow in biological systems, biophysical models of neurons and networks of neurons, and rehabilitation technology, among other areas.
		Cross training in biology, computer science, and mathematics is necessary for all of these subjects.
		An introductory course in biology and at least one course in genetics or molecular biology, equivalent to R120:352 Genetics or R120:356 Molecular Biology or BIOL 603 Molecular Biology for CS.
	catalog.njit.edu /graduate/programs/computationalbiology.php (461 words)

	Technion - Laboratory of Computational Biology (Site not responding. Last check: 2007-10-13)
		Computational Biology is a fast growing field of Computer Science, synthesizing both the information and biological sciences.
		Computational Biology also studies novel algorithmic approaches to efficient assay design, building on new chemical and molecular biology techniques.
		The Laboratory of Computational Biology is part of the Computer Science department at the Technion.
	bioinfo.cs.technion.ac.il (177 words)

	Computational Biology
		One of the major goals of computational biology is to integrate functional genomics data of all types in a global network that reflects the regulatory wiring and modularity of an organism.
		The ultimate goal is to build a computational model on the basis of Arabidopsis gene-expression data that enables prediction of hybrid performance with higher efficiency than the usual genetic markers.
		In the context of the Computational Biology Group, the aim is to model biochemical pathways involved in the cell cycle of Arabidopsis in terms of genes connected in Bayesian networks.
	www.psb.ugent.be /cbd/research.php (1654 words)

	Computational Biology Center at MSKCC
		Computational biology research at Memorial Sloan-Kettering Cancer Center (MSKCC) pursues computational biology research projects and the development of bioinformatics resources in the areas of
		The Bioinformatics Core is responsible for providing various computational and bioinformatics services to MSKCC and the Tri-Institutions of the Upper East Side of Manhattan.
		cBio consists of a vibrant work environment with both research and service components, and provides a number of opportunities to contribute to the fields of computational biology and bioinformatics, as well as to basic and clinical research studies at one of the world's premier cancer research institutes.
	www.cbio.mskcc.org (187 words)

	Penn GCB
		The Graduate Group in Genomics and Computational Biology (GCB) is an interdisciplinary Ph.D. program, administered by the Biomedical Graduate Studies (BGS) office of the University of Pennsylvania.
		While it is not expected that any one student will become an expert in all of these areas, a student who specializes in computational biology, for example, is expected to receive substantial training in areas such as molecular genetics and in particular to obtain laboratory experience in such areas.
		Similarly, a student who specializes in experimental genomics is not expected to become an expert in computer algorithm theory but is expected to understand the theory behind the techniques, tools and algorithms used in practice.
	www.med.upenn.edu /gcb/index.shtml (289 words)

	Computational Molecular Biology
		Computational Molecular Biology (Biochem 218) is a practical, hands-on approach to the field of computational molecular biology.
		The course is recommended for both molecular biologists and computer scientists desiring to understand the major issues concerning representation and analysis of genomes, sequences and proteins.
		Lee Kozar (kozar@stanford.edu) is the Associate Director of the Bioinformatics Resource at Stanford and is in charge of the computing facilities including software and databases that will be used for the homework.
	cmgm.stanford.edu /biochem218 (642 words)

	Computational Molecular Biology: An Introduction
		A complicated exact computation is made -- for instance, given incomplete data such as R (purine), a weighted contribution of 0.5 to A and 0.5 to G is made.
		entropyPlot0.c Program to compute entropy plot of nucleotide and dinucleotide entropies of window contents of a genome (length of window set in a constant) and to shift the window by one position in the genome, etc. Thus one obtains an entropy plot of windows of the genome as a function of position.
		Exercises to a computational biology course at the University of Munich
	www.cs.bc.edu /~clote/ComputationalMolecularBiology (2524 words)

	CS196-1: Algorithmic Foundations of Computational Biology
		The course is an introduction to Computational Biology and Bioinformatics and is open to computer and mathematical sciences students as well as biological and medical students.
		Although "Computational Biology" and "Bioinformatics" are often used interchangeably, we will refer to Bioinformatics as primarily being about applying computational genomics tools, with well-established biological relevance, in large-scale applications in molecular biology and medical laboratories.
		Building upon modeling insights from experimental molecular biology, physics, chemistry, and economics, Computational Biology is harnessing the complexity of biological systems by providing computational models and genomics tools that transform knowledge into understanding.
	www.cs.brown.edu /courses/cs196-1 (468 words)

	CMU SCS - Computational Molecular Biology Research
		Computational molecular biology is an active area of research at Carnegie Mellon, carried out by faculty members who make
		Areas of emphasis include the application of machine learning and data mining techniques to large biological knowledge bases, biological modeling, computational aspects of high-throughput laboratory methodologies for large-scale, systematic studies of protein structure and function, analysis of biological image data and computational genomics.
		Graduate student applicants wishing to participate in the Merck Computational Biology and Chemistry graduate program at Carnegie Mellon must apply to and be accepted into one of the graduate programs of the participating departments: Biological Sciences, Chemistry and Computer Science.
	www-2.cs.cmu.edu /~durand/csd.html (610 words)

	The MathWorks - The MathWorks News & Notes - January 2006 - MATLAB in Computational Biology
		In the relatively new discipline of computational biology, researchers are addressing this challenge by adopting mathematical and statistical software, computer modeling, and other computational and engineering methods.
		Another very large-scale computing problem is an iterative test, commonly referred to as “bootstrapping,” that delves into evolutionary trees to determine the significance of each branch of the tree.
		Computational biologists are currently working to integrate analysis methods, such as microarray and mass spectrometry analysis, to give them multiple views into genomic and proteomic data sets and improve their understanding of diseases and medical conditions.
	www.mathworks.com /company/newsletters/news_notes/jan06/compbio.html (1122 words)

	CSE 549 - Computational Biology (Site not responding. Last check: 2007-10-13)
		Lectures 1/2: Biology for Computer Scientists, Computer Science for Biologists (also in pdf) Audio for Lectures 1 (9/3/02) and 2 (9/5/02).
		Setabal and Meidanis Introduction to Computational Biology, PWS, 1997.
		Computational Biology, CSE 527, University of Washington, Winter 2000.
	www.cs.sunysb.edu /~skiena/549 (1286 words)

	Brown University \| Center for Computational Molecular Biology
		Sea Urchin Genome Is a Biology Boon and a Computational Feat
		The First Annual Computational Biology Poster Session was held in Room 105 of the Center for Genomics and Proteomics on Friday, May 5th, 2006, from 3:00-5:00pm.
		The Center for Computational Molecular Biology (CCMB) at Brown was founded in September 2003 with the aim of establishing a world-class center for research and scholarship in this new discipline.
	www.brown.edu /Research/CCMB (668 words)

	M.S. in Computational Biology
		Carnegie Mellon University has an active research community in computational biology and a strong tradition of interdisciplinary research in the Department of Biological Sciences, which fosters an environment rich in interactions and collaborations.
		The core courses of Computational Biology 03-510, Computational Genomics and Molecular Biology 03-711 and Biological Modeling 03-712 are required and must be completed with at least a grade of B. A minimum of 51 units must be in graduate lecture courses.
		Students interested in gaining experience in computational biology research are encouraged to take Graduate Research (03-700).
	www.cmu.edu /bio/graduate/descriptions/msrequirements.shtml (879 words)

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