21. Learning Methods For Data Exploration: Research Group Analysis of functional genomics data, Construction of datadependent metrics for focusing data analysis on relevant or important aspects of the data. http://www.cis.hut.fi/projects/mi/

HELSINKI UNIVERSITY OF TECHNOLOGY LABORATORY OF COMPUTER AND INFORMATION SCIENCE NEURAL NETWORKS RESEARCH CENTRE CIS Home NNRC Home Group ... Home LEARNING METHODS FOR DATA EXPLORATION The group studies statistical models that are useful especially for exploratory data analysis, but also more generally in data mining, information visualization, and probabilistic modeling. The methods have close connections to machine learning, neural computation, and computational statistics. Data exploration is the first, data-driven phase of data analysis. Previously unknown dependencies are sought for in the data. The hypotheses discovered in the first phase are then verified in later stages of analysis. Our current focus is on a new approach to data analysis that we call learning metrics . The developed methods are used particularly in bioinformatics applications, but have also been used for information retrieval, analysis of bankruptcy risk, etc. BIOINFORMATICS Analysis of functional genomics data. LEARNING METRICS Construction of data-dependent metrics for focusing data analysis on relevant or important aspects of the data. PROACTIVE INFORMATION RETRIEVAL Models of co-occurrence data and implicit user feedback in information retrieval.

22. BioMed Central | BMC Bioinformatics BioMed Central. PubMed Central. PubMed. Jump to article. vol. article no. BMC bioinformatics. Welcome to BMC bioinformatics published by BioMed Central. http://www.biomedcentral.com/bmcbioinformatics/

home journals A-Z journals by subject advanced search ... my BioMed Central Quick Search BMC Bioinformatics BioMed Central PubMed Central PubMed Jump to article BMC Bioinformatics Home About this journal Archive Advanced search Most viewed ... Instructions for authors Editorial board Adam Arkin Peer Bork Chris Burge Tim Ting Chen George Church Richard Durbin Sean Eddy Daniel Gautheret Tao Jiang Minoru Kanehisa Anders Krogh Ping Qiu Steven Salzberg Toshihisa Takagi Masaru Tomita Martin Vingron Michael Waterman Michael Zhang Welcome to BMC Bioinformatics published by BioMed Central BMC Bioinformatics publishes original research articles in all aspects of computational methods used in the analysis and annotation of sequences and structures, as well as all other areas of computational biology. BMC Bioinformatics (ISSN 1471-2105) is indexed/tracked/covered by PubMed, MEDLINE, BIOSIS and ISI. Research highlights Snappy gene prediction BMC Bioinformatics Using a gene-finding program trained on one species to predict genes in another species can produce highly inaccurate results, but the new SNAP gene finder is designed to adapt easily to a variety of genomes. Predicting protein partners BMC Bioinformatics A probabilistic decision tree approach to the prediction of co-complexed protein pairs in yeast has been developed, validated and shown to have some advantages over other methods.

23. ExPASy - Biochemical Pathways Digitized version of wall charts courtesy Boehringer Mannheim et al, divided into Metabolic Pathways and Cellular and Molecular Processes, maintained by the Swiss Institute of bioinformatics, Geneva, Switzerland. http://www.expasy.ch/cgi-bin/search-biochem-index

ExPASy Home page Site Map Search ExPASy Contact us ENZYME Search Swiss-Prot/TrEMBL Swiss-Prot/TrEMBL (full text) PROSITE SWISS-2DPAGE ENZYME NEWT Taxonomy HAMAP families ExPASy web site for Biochemical Pathways This page gives access to the digitized version of the Roche Applied Science "Biochemical Pathways" wall chart. Please note that the German publishing company Spektrum Akademischer Verlag GmbH, Slevogtstrasse 3-5, 69126 Heidelberg owns the rights for commercial applications of the Biochemical Pathways. If you wish to use any of the information obtained from this site commercially please contact Ms. Ina Schibel at Spektrum Verlag for approval. For enquiries on how to obtain a paper copy of the wall chart, please contact Roche Applied Science directly, and do not email the ExPASy staff. Keyword Search Please enter one or more keyword(s) or partial word(s). For example, you may type Oxoacyl . You will then be given a list of all matching entries of the "Biochemical Pathways" wall chart. If you enter more than one keyword, only the entries matching all keywords will be listed. This list contains links to the ENZYME Database and, for each entry, links to all maps of "Biochemical Pathways" in which this entry appears.

24. The Bioinformatics Resource 11). CCP11 was established to foster bioinformatics in the UK research community. Its ECCB) . read more. bioinformatics and Disease SIG. CCP http://www.hgmp.mrc.ac.uk/CCP11/index.jsp

25. Welcome To Bioinformatics Institute Of India Postgraduate diploma program in biomedical informatics. http://www.bioinformaticscentre.org/biomedicalinformatics/index.html

26. UCSC Genome Browser Home About the UCSC Genome bioinformatics Site. This site contains the reference sequence for the human and C. elegans genomes and working http://genome.ucsc.edu/

Genome Browser Family Browser Blat Table Browser ... Contact Us About the UCSC Genome Bioinformatics Site This site contains the reference sequence for the human and C. elegans genomes and working drafts for the chimpanzee, mouse, rat, chicken, Fugu Drosophila C. briggsae , yeast, and SARS genomes. It also shows the CFTR (cystic fibrosis) region in 13 species. We encourage you to explore these sequences with our tools. The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. The Family Browser shows expression, homology and other information on groups of genes that can be related in many ways. The Proteome Browser displays protein property data and links to a wealth of related information. The Table Browser provides convenient access to the underlying database. Blat quickly maps your sequence to the genome. News 19 May 2004 - Change in UCSC FTP site URL We have changed the URL for the UCSC Genome Browser ftp site to ftp://hgdownload.cse.ucsc.edu/

27. Integrative BioInformatics - Home Page Leveraging technology to bridge cell biology and genomics by providing computational biology and database technology software and consulting services for modeling complex biological problems faced by scientists in public and private research institutes, biotechnology companies, and universities. http://www.integrativebioinformatics.com

Leveraging Technology to bridge Cell Biology and Genomics Bioinformatics : Research, development or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze or visualize such data. Computational Biology : 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. (NIH Biomedical Information Science and Technology Initiative) Science is made up of facts just as a house is built up of stones, but a collection of facts is no more a science than a heap of stones is a house. H. Poincare Our Mission Integrative BioInformatics is a biotech consulting firm with expertise in computational biology and database technology. We specialize in bringing our software solutions to bear on complex biological and data analysis problems faced by scientists in public and private research institutes, biotechnology companies, and universities.

28. Bioinformatic Centre Take a look at our MSc Students. Press Release The S* bioinformatics Education Symposium. Do watch out this space for any upcoming events. http://www.bic.nus.edu.sg/

BIC website gets a facelift Take a look at our MSc Students Press Release - The S* Bioinformatics Education Symposium Do watch out this space for any upcoming events. Click to find out our past events help FAQs feedback sitemap

29. Paolo Frasconi's Home Page Universit  di Firenze. Machine learning for sequential and structured data, bioinformatics, text and natural language, pattern recognition. http://www.dsi.unifi.it/~paolo

Paolo Frasconi Associate Professor of Computer Science Machine Learning and Neural Networks Group (AI Lab) Department of Systems and Computer Science my first name dot u n i f i dot ... Bookmarks Research interests Machine learning for sequential and structured data, bioinformatics, text and natural language, pattern recognition New book P. Baldi, P. Frasconi and P. Smyth. Modeling the Internet and the Web : Probabilistic Methods and Algorithms Wiley , 2003. Sample pdf chapter: Text Analysis Recent papers Open Access Initiative A. Vullo and P. Frasconi. Disulfide Connectivity Prediction Using Recursive Neural Networks and Multiple Alignments . Bioinformatics (to appear, 2004). A. Passerini, M. Pontil and P. Frasconi. New Results on Error Correcting Codes of Kernel Machines IEEE Trans. on Neural Networks (accepted for publication). A. Ceroni, Frasconi P., A. Passerini, A. Vullo. Pre dicting the Disulfide Bonding State of Cysteines with Combinations of Kernel Machines Journal of VLSI SIgnal Processing A. Vullo and P. Frasconi Prediction of Protein Coarse Contact Maps

30. The RCSB Protein Data Bank San Diego; and the Center for Advanced Research in Biotechnology/UMBI/NIST three members of the Research Collaboratory for Structural bioinformatics (RCSB). http://www.rcsb.org/pdb/

DEPOSIT data DOWNLOAD files browse LINKS BETA TEST new features ... BETA XML files Current Holdings 25667 Structures Last Update: 25-May-2004 PDB Statistics ... Serpins The Protein Data Bank (PDB) is operated by Rutgers, The State University of New Jersey; the San Diego Supercomputer Center at the University of California, San Diego; and the Center for Advanced Research in Biotechnology/UMBI/NIST three members of the Research Collaboratory for Structural Bioinformatics (RCSB) The RCSB PDB is supported by funds from the National Science Foundation (NSF) , the National Institute of General Medical Sciences (NIGMS) , the Office of Science, Department of Energy (DOE) , the National Library of Medicine (NLM) , the National Cancer Institute (NCI) , the National Center for Research Resources (NCRR) , the National Institute of Biomedical Imaging and Bioengineering (NIBIB) , and the National Institute of Neurological Disorders and Stroke (NINDS) Welcome to the PDB, the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. RCSB Home wwPDB Home Contact Us Help Did you find what you wanted?

31. VanBUG - Vancouver Bioinformatics User Group - Association of researchers, professionals and students in the Lower Mainland, British Columbia, Canada area, who have an interest in the field of bioinformatics. Meeting and contact information. http://vanbug.org/

About Meetings Directions Mailing Lists ... Contact VanBUG: Vancouver Bioinformatics User Group VanBUG (Vancouver Bioinformatics Users Group) is an association of researchers, other professionals and students in the B.C. Lower Mainland who have an interest in the field of bioinformatics. Through monthly presentations we present our work, ask questions, share ideas, tips and tricks. Meetings will be commonly held in the Chan Auditorium at the BC Research Institute for Children's and Women's Health and are free and open to all. sponsored by: next meeting: VanBUG's next season will resume September 9, 2004 and continue on the second Thursday of every month. XHTML CSS credits contact

32. WIS Bioinformatics And Biological Computing New Bulletin Board. BBCU Activities. Made in Weizmann Portal. Google, Positions available in bioinformatics and Computational Biology. Hosting http://bioportal.weizmann.ac.il/

Weizmann Institute of Science Department of Biological Services and Crown Human Genome Center Positions available in Bioinformatics and Computational Biology Hosting Israeli C enter o ... nfrastructure COBI I sraeli N ational ... ode INN of the European Molecular Biology network Israel National Laboratory for Genome Infrastructure e-mail: bioinfo@weizmann.ac.il Last modified document.write(document.lastModified);

33. Poxvirus Bioinformatics Resource Center The Poxvirus bioinformatics Resource Center has been established to provide resources to the scientific community for basic research and to facilitate the development of novel antiviral therapies and vaccines against human orthopoxvirus infections as well as approaches for environmental detection of virions and the rapid diagnosis of disease. http://www.poxvirus.org

Welcome to the Poxvirus Bioinformatics Resource Center. This Center has been established to provide resources to the scientific community for basic research and to facilitate the development of novel antiviral therapies and vaccines against human orthopoxvirus infections as well as approaches for environmental detection of virions and the rapid diagnosis of disease. The Center provides a relational database that supports data storage of poxvirus genomic sequences, and annotation and analysis of poxvirus genes; web-based data mining and sequence analysis tools; software for analysis of complete genomes; a poxvirus literature resource; a repository of poxvirus species and strains (at ATCC); and a discussion forum. The Poxvirus Bioinformatics Resource Center was created by a consortium of laboratories. An Advisory Committee has been established to help guide the development of this Center. Funding for this project is being provided by the National Institute for Allergy and Infectious Diseases , and the Defense Advanced Research Projects Agency . Suggestions for improvement of the Center are welcomed (see Feedback). Click for information on changes to the PBR virus designations.

34. NWFSC Molecular Biology Protocols Protocol collection, with interactive forum for over ten topics, covering DNA, PCR, RNA and proteins techniques and links to online journals and bioinformatics resources, from the Northwest Fisheries Science Center Microbial Pathogenesis Lab, Seattle, WA. http://micro.nwfsc.noaa.gov/protocols/

US Dept Commerce/NOAA/NMFS/NWFSC Wednesday May 26, 2004 Protocols Forums Bioinformatics Journals Other Resources ... Science Center NMFS/NOAA last modified October 29, 2003 Molecular Biology Protocols Welcome to the NWFSC Fish Health/Microbiology Molecular Biology Protocols (served since 1995). Ask and answer questions in the newly redesigned Molecular Biology Forums (registration with valid email address required). [ Current Seattle Weather DNA Purification Techniques DNA purification (plasmids, cosmids and p1) using Diatomaceous Earth (Bruce Roe Lab) Introduction Maxi-preps and all media, solutions Midi-preps Mini-preps DNA purification, plasmid mini-preps, diatomaceous earth contributed by Kyung-Soo Kim and Charles K. Pallaghy 2/10/97 DNA purification , bacterial-genomic, triton extraction method DNA purification , bacterial-genomic via Qiagen columns DNA purification , bacterial genomic, specifically Gram positive bacteria DNA isolation from low melting-temperature agarose Low copy plasmid purification using Qiagen Midi columns Plasmid "Miniprep" Isolation: tried and true!

35. International Conference On Legume Genomics And Genetics: Translation To Crop Im To inform the international scientific community of the current status of legume genomics, genetics, and bioinformatics initiatives in crops and model species. June 26, 2002 in Minneapolis-St. Paul, MN, USA. http://www.agro.agri.umn.edu/iclgg/

Home Program Abstracts Participant List Registration ... Twin Cities Metro Area The first International Conference on Legume Genomics and Genetics will be held in Minneapolis-St. Paul, Minnesota, June 2-6, 2002. This conference aims to apprise the international scientific community of the current status of legume genomics, genetics, and bioinformatics initiatives in legume crops and model species. Seeking to articulate in theory and practice how genomic, genetic, and bioinformatic information can be translated into legume crop improvement in both the developed and developing worlds, the conference will identify comparative approaches that can be utilized to enhance our fundamental understanding of all legumes, facilitate collaboration among groups and individuals, and lay a foundation and framework for subsequent legume genomics and genetics meetings. To this end, we cordially invite scholars and researchers to join in the first ICLGG. If you have questions regarding registration, please email Heather Dorr at

36. NCBI Education useful. More NCBI also provides focused bioinformatics minicourses for researchers, teachers, and college students. NCBI mini http://www.ncbi.nlm.nih.gov/Education/

PubMed Entrez BLAST OMIM ... Structure Search Entrez NCBI Web Site PubMed Protein Nucleotide Structure Genome Books CancerChromosomes Domains 3D Domains Gene GEO GEO Datasets HomoloGene Journals LocusLink MeSH OMIM PMC PopSet SNP Taxonomy UniGene UniSTS for NCBI Site Map Guide to NCBI resources NCBI Courses Field Guide MiniCourses Medical Library Association Course Exhibits Tutorials Structure Entrez PubMed About NCBI ... A Science Primer BLAST / PSI-BLAST Information and tutorials BLAST statistics Genes and disease ... Glossary of genetic terms Bioinformatics Milestones Similarity searching Glossary of terms References Courses Keeping up with enhancements and the increasing diversity of NCBI molecular biology resources can be challenging. To help scientists meet this challenge, the NCBI service desk provides a free training course, A Field Guide to GenBank and NCBI Resources . All researchers, educators and students will find the Field Guide to be a useful introduction and survey of the available NCBI tools and databases, even experienced NCBI users will learn something new and useful. More ...

37. Southampton - SBDS - Top Level Menu DNA and Protein sequencing resources. http://molbiol.soton.ac.uk/

Southampton BioInformatics Data Server To find out more about the databases available through SRS you should consult the DataBanks database. DNA/RNA protein Molecular Biology Protein modelling and crystallography Biology Bionet newsgroups Chemistry Commercial links Documentation FAQs Journals and publishing Medicine Miscellaneous subjects Software archives Universities, research councils and charities Weather forecasts and satelite images School of Biological Sciences Biochemistry and Molecular Biology School of Medicine Biosciences Imaging Group Human Genetics ILDIS UoS on-line directories (email, telephone, etc) BIDS NISS Any query about, or suggestions regarding the contents of, these pages should be directed to Ian Giles Last update: 24th November 2000

38. ADB Welcome A resource for apoptosis researchers from The Burnham Inst. http://www.apoptosis-db.org/

A POPTOSIS- DB .ORG ... The Burnham Institute Version 3 Proteins from 2002-10-01 A bioinformatics resource for apoptosis researchers About Domains Proteins Structures BLAST The Apoptosis-db.org resources are still under construction, but many resources are available, as described on the Project Page Domains involved in apoptosis. List of proteins with homology for a domain.(Example of Bcl-2) List of protein families having those domains. ... Statistics on Domains and Proteins included in the database. Hosted at: Funded by: NSF DBI Labs: Philip E. Bourne Adam Godzik John C. Reed Contact: Kutbuddin S. Doctor Comments/Suggestions/Corrections Last Modified $Date: 2002/12/29 21:43:06 $ External Apoptosis Sites. Apoptosis site with an Apoptopedia containing over entries related to the field Roche, Apoptosis Resource Guide Includes a pathway diagram and links to many other sites. Cell Death Society (New York) Discussion Groups, meetings, job mart, etc.

39. Bioinformatics Factsheet Just the Facts A Basic Introduction to the Science Underlying NCBI Resources. bioinformatics. The derived. What Is bioinformatics? http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html

National Center for Biotechnology Information About NCBI NCBI at a Glance A Science Primer Databases and Tools ... Site Map Science Primer: Genome Mapping Molecular Modeling SNPs ESTs ... Phylogenetics Just the Facts: A Basic Introduction to the Science Underlying NCBI Resources BIOINFORMATICS The completion of a "working draft" of the human genomean important milestone in the Human Genome Projectwas announced in June 2000 at a press conference at the White House and was published in the February 15, 2001 issue of the journal Nature Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in the biological information generated by the scientific community. This deluge of genomic information has, in turn, led to an absolute requirement for computerized databases to store, organize, and index the data and for specialized tools to view and analyze the data. What Is a Biological Database?

40. WABI 2001 - 1st Workshop On Algorithms In BioInformatics First Workshop on Algorithms in bioinformatics covering research in all aspects of algorithmic work in bioinformatics. The emphasis is on discrete algorithms that address important problems in molecular biology, that are founded on sound models, that are computationally efficient, and that have been implemented and tested in simulations and on real datasets. Jointly organized and colocated with ESA 2001 and WAE 2001 in the context of ALGO 2001. BRICS, University of Aarhus, Denmark; 2831 August 2001. http://www.brics.dk/wabi2001/

WABI 2001 1st Workshop on Algorithms in BioInformatics BRICS, University of Aarhus, Denmark, August 28-31, 2001 ALGO 2002 September 16-21 Rome ``La Sapienza'' ALGO 2001 Online Registration (closed) Registration fees Accommodation Travel and tourist Information Program ... [ Site map ] Announcements Online proceedings (LNCS 2149) Accepted papers ascii Accepted posters ... ascii Electronic submission (closed) Call for papers expired pdf postscript ascii Call for posters expired ascii For further information see the web site of ALGO 2001 Scope The Workshop on Algorithms in Bioinformatics covers research in all aspects of algorithmic work in bioinformatics. The emphasis is on discrete algorithms that address important problems in molecular biology, that are founded on sound models, that are computationally efficient, and that have been implemented and tested in simulations and on real datasets. The goal is to present recent research results, including significant work-in-progress, and to identify and explore directions of future research. WABI 2001 is sponsored by BRICS and EATCS (the European Association for Theoretical Computer Science) and jointly organized and colocated with ESA 2001 and WAE 2001 in the context of ALGO 2001 Topics Original research papers (including significant work-in-progress) or state-of-the-art surveys are solicited in all aspects of algorithms in bioinformatics, including, but not limited to:

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