141. Bioinformatics Software On The Web Emotif ranks the motifs that it finds by both their specificity and the number of supplied sequences that it covers.(Stanford bioinformatics Group); http://www.cs.jhu.edu/~salzberg/appendixa.html

Appendix A. Software and Databases for Computational Biology on the Internet This page is a supplement to the book Computational Methods in Molecular Biology , edited by Steven Salzberg, David Searls, and Simon Kasif. The publisher is Elsevier Sciences. Please contact Steven Salzberg (salzberg@cs.jhu.edu) if you wish to have your software referenced on this site, or if you wish to change the description of your software already listed here. The on-line version of this page, in which all the systems below are hot links, can be found at http://www.tigr.org/~salzberg/compbio-book.html. Databases Motif Search Secondary Structure Prediction Other software and information sources Gene finders and other sequence analysis programs Glimmer is a system that uses Interpolated Markov Models (IMMs) to identify coding regions in microbial DNA. IMMs are a generalization of Markov models that allow great flexibility in the choice of the "context"; i.e., how many previous bases to use in predicting the next base. Glimmer has been tested on the complete genomes of H. influenzae, E. coli, H. pylori, M. genitalium, and other genomes, and results to date have proven it to be highly accurate. Glimmer was the principal gene finder for the genomes of B.

142. Keygene.com // Home Company doing contract research in bioinformatics and genomic databasing using AFLP. In Wageningen, The Netherlands. http://www.keygene.nl/

you are here: HOME Contact Info Welcome to Keygene Keygene N.V. P.O. Box 216 6700 AE Wageningen The Netherlands T +31 (0)317 466 866 F +31 (0)317 424 939 E info@keygene.com Keygene is a service provider in the life-sciences value to you. You will find information about: The services that Keygene provides in the genetic analysis of plants, animals and micro-organisms; The technologies that Keygene applies in providing these services; The technologies that Keygene can provide to support your own research activities.

143. Bioinformatics Research Center: Home Welcome. to the NC State University bioinformatics Research Center and Programs in bioinformatics and Statistical Genetics. Graduate Program in bioinformatics. http://statgen.ncsu.edu/brcwebsite/home.php

Degree Programs People Summer ... Resources Home Research Program in Bioinformatics Program in Statistical Genetics Recent Publications ... >Upcoming Symposia Welcome to the NC State University Bioinformatics Research Center and Programs in Bioinformatics and Statistical Genetics The Bioinformatics Research Center (BRC) at North Carolina State University is one of the world's premier centers for education and research in bioinformatics, the field that integrates information science and statistics with the study of genomics. Established by the Board of Governors of the University of North Carolina System in 2000, the BRC is located on NC State University's Centennial Campus in Raleigh. The BRC has two important missions: Research: Our research focuses on the development of new computational and statistical tools for the analysis and interpretation of genomic data. Our research addresses both theoretical and practical issues in human, plant, and animal genetics. Education: The BRC is dedicated to providing outstanding educational and training opportunities for graduate students and genomic scientists. We offer graduate programs in bioinformatics and statistical genetics.

144. Argonne Biotechnology Research - Home Conducts clinical studies in the areas of bioinformatics, genomics, protein engineering, biochips, proteomics, biobased chemicals, structural biology, and environmental technologies. Lists research areas and patents. http://www.ipd.anl.gov/biotech/

Privacy and Security Notice Home What's New Site Index Privacy and Security Notice Home What's New Site Index ... Argonne National Laboratory

145. A Bioinformatics Weblog - Nodalpoint.org 0 A bioinformatics weblog. relevant to bioinformatics. For example see all the recent publications in the journal of bioinformatics. http://www.nodalpoint.org/

A bioinformatics weblog home archives user blogs documentation ... Log In Username: Password: Remember me REGISTER Browse archives S M T W T F S Bioinformatics Books @ Amazon R for Bioinformatics Science @ Amazon Eugene Thacker - Biomedia (Electronic Mediations, V. 11) Snowdeal: Bioinformatics Science Daily Junk DNA Yields New Kind Of Gene: Regulates Neighboring Gene Simply By Being Switched On Houston Chronicle Despite reports to contrary, high-tech jobs are out there News.Com IBM looms large in life sciences quest Forbes The Drug Research War ... more DNAjobs.com DNAjobs.com Jobs of the Week: May 22, 2004 DNAjobs.com Jobs of the Week: May 15, 2004 DNAjobs.com Jobs of the Week: May 8, 2004 DNAjobs.com Jobs of the Week: May 1, 2004. ... more Yuching's research diary Modularization microarray data handling labor intensive work vs. automated pipeline data management ... more Cosmas Ligand-Protein Interactions Conference To Show Your Appreciation... It's All Go Here Cheminformatics Training Course ... more Powered By Syndicate Chihuahuas Aren't Dogs Genetics Mad Science submitted by Neil on Wednesday, May 26, 2004 - 20:42

146. Institute Of Bio-IT (Computational & Systems Biology Research Center) Research on bioinformatics topics include Genomics, Drug discovery, intelligent agent applications, sequencing, pattern matching, complex algorithms, distributed Databases, pharmaceogenomics, http://www.Bio-IT.org

In the Name of God CO MP UT AT IO NAL SYS TE MS B IO LO GY RE SE AR CH CENT ER Silico Biotech Privacy Statement

147. Center For Bioinformatics & Computational Biology Welcome to CBCB, the Duke Center for bioinformatics and Computational Biology. The Center was established in 2000 as the focus for http://www.cbcb.duke.edu/

W elcome to CBCB, the Duke Center for Bioinformatics and Computational Biology. The Center was established in 2000 as the focus for the development and coordination of programs integrating the computational and biological sciences. Mathematical, statistical and computional concepts and methods, already pervasive in biological and medical research, are becoming increasingly central to major research programs as biomedical experiments and observations expand the scale and scope of biological data resources, and present challenges of modeling and understanding to computational bioscientists. A s part of Duke's response to these challenges, CBCB is a university-wide, cross-disciplinary center that links together faculty, students and research groups across departments, schools and scientific areas. CBCB faculty and participants are drawn from many departments: basic biology, biomedicine and clinical sciences; the mathematical, statistical and computational sciences; and also engineering and environmental areas. The broad and diverse faculty participation represents one of the core goals of CBCB the promotion of broad-ranging research interactions between biological and computational scientists. CBCB has a broad focus, within which genomics is currently key. CBCB is a participating Center in the IGSP: Duke's

148. Science Functional Genomics Resources Provides a range of links to information on genomics, postgenomics, and bioinformatics. http://www.sciencemag.org/feature/plus/sfg/resources/index.shtml

features centers organisms sequence ... maps In the past several years, the World Wide Web has exploded with information on genomics, post-genomics, and bioinformatics. In this section of Science Functional Genomics, we offer a guide to some of the more interesting, useful, or just plain offbeat Web resources out there for the genomics specialist, the scientist in a related (or unrelated) field, and the curious layperson. We've attempted to organize these resources under some useful headings; in the future weeks and months we'll be posting additional resources in categories such as gene therapy. Stop back frequently to get a reading on the Web's latest offerings. (And don't forget to check out our pages on educational resources and the biotech business Featured scientific sites Research centers Model organisms ... Featured scientific sites A brief introduction to some of the Web's most useful and interesting sites for genomic and postgenomic science, selected and reviewed by contributing editor Kevin Ahern. The featured sites change periodically, so come back often. Research centers A substantial, alphabetical index of links to the top centers worldwide in genomics, postgenomics, and bioinformatics.

149. This Page Has Been Moved! the page, A list of bioinformatics courses , has been moved to a new location (August 19, 2003) http//www.nslijgenetics.org/bioinfotraining/ http://linkage.rockefeller.edu/wli/bioinfocourse/

the page, A list of bioinformatics courses , has been moved to a new location (August 19, 2003): http://www.nslij-genetics.org/bioinfotraining/ if you have trouble accessing it due to network problem, return to the old page at: here

150. Home Page Of The UW-Madison Machine Learning Research Group Research on information retrieval and extraction, bioinformatics, connectionist models, hybrid systems. http://www.cs.wisc.edu/~shavlik/uwml.html

This page contains relevant information about, and for, the members of the Machine Learning Research Group (MLRG) at the University of Wisconsin - Madison. Table of Contents Group Members MLRG's Archive of Recent Papers MLRG's Archive of Datasets and Domain Theories CS 760 - Machine Learning (graduate course) Relevant Local Links Some Useful External Links Group Members (as of Summer 2002) Frank Dimaio ... Jude Shavlik Also see the web pages of Mark Craven Olvi Mangasarian David Page , and Grace Wahba MLRG's Archive of Recent Papers Visit the page describing our recent publications . (An ASCII file containing a list of our recent abstracts is also available.) MLRG's Archive of Datasets and Domain Theories You can access our ftp directory that contains several ML testbeds . (You can also access via ftp the Wisconsin Breast Cancer Database , which is from Prof. Olvi Mangasarian's group). Relevant Local Links CS 760 - Machine Learning (graduate course) UW-Madison Machine-Learning/Math-Programming Group Computational Biology in the UW-Madison CS Dept UW-Madison Computational Neuroscience UW-Madison AI Group ... Agents that Learn from Other Agents , held at the 1995 International Machine Learning Conference.

151. ACE BioSciences ACE is based on a broad biotechnology platform integrating infectious disease biology with analytical protein chemistry and bioinformatics with a core competence in protein interaction technology. http://www.acebiosciences.com

Welcome to ACE BioSciences A/S ACE BioSciences A/S focus on infectious diseases and is based on a broad biotechnology platform integrating infectious disease biology with analytical protein chemistry and bioinformatics. The core competence of the company is our protein interaction technology, which enables a continuous supply of validated targets and promising lead molecules to our portfolio of pipeline projects. Key projects are within the food borne bacteria Campylobacter jejuni and the fungal pathogen Aspergillus fumigatus Mission statement ACE BioSciences is pursuing discovery, pre-clinical and early clinical development of new drug targets and drug leads for better treatment of infectious diseases caused by pathogenic microorganisms. It is the aim of ACE BioSciences to be the world leader in providing innovative novel drug leads in the anti-infectives field.

152. The University Of Michigan Bioinformatics bioinformatics Program 5622 Medical Science II Box 0621 Ann Arbor, MI 481090621. Phone 734-615-5510 Fax 734-615-6553 E-mail bioinformatics @ umich . edu. http://www.bioinformatics.med.umich.edu/

General About Us Facilities Opportunities Contacts ... Pilot Grant Academic Graduate Program Admissions Courses Current Students ... Publications People Affiliated Faculty Staff Students Research Research Labs Affiliated Departments Links Tutorials Events Bioinformatics Seminars External Seminars Conferences Journal Club Computing Services BiCC UM Restricted Page Current Students Special Seminars ... For Employers Bioinformatics Program 5622 Medical Science II Box 0621 Ann Arbor, MI 48109-0621 Phone: 734-615-5510 Fax: 734-615-6553 E-mail: bioinformatics @ umich . edu Announcements - Last Updated 03/19/2004 Bioinformatics 511 No Longer Offered The Bioinformatics Program is no longer offering the "Bioinformatics, Proteomics and Functional Genomics Seminar Series" as a course (BIOINF/BIOLCHEM 511). Bioinformatics students are still strongly encouraged to attend the seminar series. New Course Offering in Bioinformatics Bioinformatics 800, Special Topics: Proteome Informatics is going to be offered for the very first time next semester (WT 2004)! For more information, please go to:

153. JaMBW: Java Molecular Biology Directory Java based Molecular Biologist's Workbench by Luca I.G.Toldo. http://www.bioinformatics.org/JaMBW/

154. Biotechnology Center At University Of Nebraska-Lincoln Does research on genomics, proteomics, flow spectrometry, mass spectrometry, plant transformation, bioinformatics, and microscopy. Lists services offered, seminar schedule, faculty and bioinformatics club meeting times. http://www.biotech.unl.edu/index.html

155. Bioweircom.org -- Site For Bioinformatics Developers tools and info for bioinformatics newbies and gurus alike! http://bioweircom.org

Sun Jun 6 07:36:01 PDT 2004 Best viewed with Mozilla IE 5.x/6.x Sign up for a free account? Local Tools Hot Topic: Oracle on Linux Bio/CS Projects flash slides Cell Culture ... User Profile Manager Online Resources fPathwayBuilder OpenBlast BioPerl BioXML ... More Links... User Profile Management Username: Password: Don't have an account yet? Please sign up first. Biotechnology and computer science have advanced in an unimaginable speed in recent years. Now it's the time for us to combine these two great technologies together and do something really beneficial to our mankind. On one hand, with the Human Genome Project beginning to bear fruits, the biological data is piling up (imagine how fast the genome size grows). On the other hand, the speed of CPU and computer as a whole increases beyond our expectation. Nowadays, a PC equipped with the latest generations of CPU and enough memory can do what used to be done only by workstations, high-end servers, or even mainframes. So now comes the time for people having background in both these fields to play important roles in a new field called Bioinformatics, which has become so hot that many traditional hardware and software giants such as IBM, Sun, Oracle, Compaq, have put a lot of effort in making their products "bioinformatics compliant". Most of these companies have donated hardware/software to the bioinformatics community and tried very hard not to lose the battle in this emerging market. The main goal of this site is to design and develop bioinformatics software which will expedite the processing of biological data. Since the motto for this site is "Open source is the source for success", our development of software will follow the

156. Bioinformatics 2003 http://bioinf.uta.fi/bio2003/

157. CFG: Molecular Biology, Genomics, Proteomics, Mass Spectrometry, Microarray, Aff Promote interdisciplinary research in genomics, bioinformatics, proteomics, microarray, and confocal imaging. Includes facilities, staff details, employment, and graduate programs. http://www.albany.edu/genomics/index.html

Molecular Biology Bioinformatics Biochemistry Mouse Transgenesis ... Cancer Genomics Center The Center for Functional Genomics University at Albany State University of New York The Center for Functional Genomics (CFG) maintains a comprehensive state-of-the-art research facility to support a wide range of services that are offered on a fee-per service basis to commercial and academic organizations. We are able to coordinate efforts among our different Facilities so that we can accommodate researchers in projects from start to finish. For example, the CFG is able to isolate genes, design and make DNA constructs through our Molecular Biology Facility, then coordinate with the Mouse Transgenic Facility to make Transgenic or Knock-out mice and then the mice generated can be analyzed at the DNA, RNA or Protein levels through our Molecular Biology, Microarray, Laser Capture Microdissection or Proteomics Facilities. The genomics services include a comprehensive range of custom services including gene cloning, gene discovery/characterization, gene expression and protein expression and characterization. We also offer standard oligonucleotide synthesis and DNA sequencing services using Applied Biosystems instrumentation and reagents. Our proteomics core facility is well equipped for detailed studies on protein separation and characterization as well as related services including high-resolution 2D gel electrophoresis. We provide de-novo sequencing analysis of protein and peptides by mass spectrometry using a high sensitivity Q-tof mass spectrometer from Micromass/Waters.

158. BiBiServ - Bielefeld University Bioinformatics Server - The BiBiServ Tool section currently offers bioinformatics tools for a large variety of tasks Genome Comparison; Alignments; Primer http://bibiserv.techfak.uni-bielefeld.de/

The BiBiServ Tool section currently offers bioinformatics tools for a large variety of tasks: Genome Comparison Alignments Primer Design RNA Studio Evolutionary Relationships Others As some analyses can take a long time - sometimes over several hours - BiBiServ provides two different result delivery mechanisms. Results of short analyses (less than 5 minutes compute time) are shown immediately in the browser. For longer analyses (maximum of one day compute time) the result is stored on a temporary web-site and the corresponding URL is sent to the user via E-mail. BiBiServ runs in a UNIX environment. The data stored locally can be accessed only by the BiBiServ administrators. The result of a calculation is stored temporarily for three days and deleted afterwards. We do not offer encrypted submissions.

159. CBCL Homepage Research on theory of learning, neuroscience, bioinformatics functional genomics, information extraction in text multimedia, object detection/recognition, manmachines interfaces, virtual financial markets. http://www.ai.mit.edu/projects/cbcl/

MIT was founded with the belief that learning is at the very core of the problem of intelligence, both biological and artificial, and is the gateway to understanding how the human brain works and to making intelligent machines. CBCL studies the problem of learning within a multidisciplinary approach. Its main goal is to nurture serious research on the mathematics, the engineeering and the neuroscience of learning. Established in 1992 (two years earlier than CLM) with support from the National Science Foundation , CBCL is in the at MIT (click here for map information) and in the McGovern Institute for Brain Research , and is associated with the Artificial Intelligence Laboratory , which recently merged with the Lab for Computer Science and was renamed (CSAIL). Restricted to CBCL Members (including CBCL Frequent Web Helpers Program) CBCL research is currently sponsored by Government grants from: Office of Naval Research (DARPA) Contract No. N00014-00-1-0907, Office of Naval Research (DARPA) Contract No. N00014-02-1-0915, National Science Foundation (ITR/IM) Contract No. IIS-0085836, National Science Foundation (ITR/SYS) Contract No. IIS-0112991, National Science Foundation (ITR) Contract No. IIS-0209289, National Science Foundation-NIH (CRCNS) Contract No. EIA-0218693, National Science Foundation-NIH (CRCNS) Contract No. EIA-0218506, and National Institutes of Health (Conte) Contract No. 1 P20 MH66239-01A1.

160. EPitope Informatics - Epitope Prediction And Protein Analysis ePitope Informatics is an Internetbased applied bioinformatics company specialising in epitope prediction and protein analysis. Epitope prediction and protein analysis services for proteomics, diagnostics, therapeutics, life science research and commercial antibody production. http://www.epitope-informatics.com/

Google PubMed BioMed This Site We are ePitope Informatics - an Internet-based applied bioinformatics company specialising in protein annotation. A particular focus is epitope prediction for the identification and targeting of protein B cell epitopes. Benefits of using ePitope Informatics Our specialist expertise and experience , spanning more than a decade. We utilise consensus epitope prediction for best accuracy. We offer a flexible, tailor-made service that can incorporate: analysis of solved 3-D structure regions of interest of your target protein protein database searching optimised for epitope analysis sequence motif analysis and protease cut-site mapping Significant savings of your time. A quick and easy-to-use Internet-based service. Respect of your privacy and confidentiality of your information For a list of further benefits of choosing ePitope Informatics to assist you. We offer Proteomics services Protein annotation including epitope prediction.

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