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Bioinformatics resources
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Information resources Bioinformatics Bibliographies   Databases   Journals   Blogs   Websites   

Bioinformatics Bibliographies
Christy Hightower, Bioinformatics, Bioinformatics Librarian, Univ. of California Santa Cruz Science & Engineering Library, 2002 Not just for bioinformatics. http://www.istl.org/02-winter/internet.html 

Lynda Ellis, What is Bioinformatics? http://www.binf.umn.edu/whatsbinf.html, Graduate Program in Bioinformatics, Univ. of Minnesota, 2003 Selective Bibliography with weblinks

Open Directory Project OPD, Bioinformatics http://dmoz.org/Science/Biology/Bioinformatics/

Selected Bioinformatics Databases The boundaries between print and electronic content, portals, and databases are getting harder and harder to categorize and differentiate. See also  Databases directories  Human genome resources 

Entrez, NCBI, National Center for Biotechnology Information, US http://www3.ncbi.nlm.nih.gov/Entrez/index.html

Genome Bioinformatics Site, University of California, Santa Cruz UCSC, US http://genome.ucsc.edu/ Contains the reference sequence for the human and C. elegans genomes and working drafts for the mouse, rat, Fugu, C. briggsae, and SARS genomes. It also contains the CFTR (cystic fibrosis) region in 13 species.

Global Open Biological Ontologies. http://www.geneontology.org/doc/gobo.html

Third Party sequence Annotation TPA sequence, NCBI, NIH http://www.ncbi.nlm.nih.gov/Genbank/tpa.html  A TPA sequence is derived or assembled from primary sequence data currently found in the DDBJ/ EMBL/ GenBank International Nucleotide Sequence Collaboration Databases. It can be genomic or mRNA sequence, and can be assembled or derived from primary genomic and/or mRNA sequences. These sequences are submitted to DDBJ/ EMBL/ GenBank as part of the process of publishing biological experiments that include the annotation of existing nucleotide sequences in the primary sequence database.

Bioinformatics Journals and periodicals  See also Genomics & proteomics journals  Cheminformatics journals
BMC Bioinformatics, BioMedCentral, 2000-  http://www.biomedcentral.com/1471-2105/ All aspects of computational methods used in the analysis and annotation of sequences and structures, as well as all other areas of computational biology. 

Bioinformatics, Oxford University Press, 1998-  http://www.bioinformatics.oupjournals.org/ New developments in genome bioinformatics and computational biology. Shorter papers: Discovery Notes reports biologically interesting discoveries using computational methods. Application Notes explore the applications used for experiments. Impact factor 4.6 

Briefings in Bioinformatics, http://bib.oxfordjournals.org/  Reviews for the users of databases and analytical tools of contemporary genetics and molecular biology. Practical help and guidance to the non-specialist. Introductory level papers to specific details of protocols and analyses encompassing bacterial, plant, animal and human data. Subject areas covered include: DNA sequencing, expression profiling, alignment methods, gene expression studies, protein profiles and HMMs [Hidden Markov Models], metabolic and signalling pathways, structure and function prediction, mapping and microarrays. 

Bulletin of Mathematical Biology, Elsevier, 1973-  http://www.elsevier.com/locate/issn/0092-8240 Bioresearch at the junction of computational, theoretical and experimental biology. Research Areas Include: Developmental Biology, Ecology, Epidemiology, Immunology, Molecular Biology, Morphology, Neurobiology, Pharmacology, Physiology, Population Biology, Sequence Comparison, Official publication of the Society for Mathematical Biology.

Computational biology and chemistry

Current Protocols in Bioinformatics, Wiley, loose- leaf  http://www.wileycanada.com/WileyCDA/WileyTitle/productCd-0471250937.html  Using and building biological databases, functional domains, homologies, finding genes, modeling structure from sequence, inferring evolutionary relationships, analyzing expression patterns, analyzing molecular interactions, assembling sequences, comparing large sequence sets, protein identification from mass spec, analyzing RNA sequence and structure.

In Silico Biology: International Journal on Computational Molecular Biology, Bioinformation Systems e.V,  and IOS Press (print), 1998-  http://www.bioinfo.de/isb/ Data acquisition, development, and applications of theoretical / mathematical / computational tools onto biological systems rather than on the description of new algorithms. Systematic compilations of biological as well as computational results from various sources, evaluation of original experimental data with biocomputational tools, WWW-online resources for experimental scientists. 

Journal of Computational Biology, Mary Ann Liebert, 1994-  http://www.liebertpub.com/publication.aspx?pub_id=31   Analysis, management, and visualization of cellular information at the molecular level. Includes  genomics, mathematical modeling and simulation, distributed and parallel biological computing, designing biological databases, pattern matching and pattern detection, linking disparate databases and data, new tools for computational biology, relational and object- oriented database technology for bioinformatics, biological expert system design and use, reasoning by analogy, hypothesis formation and testing by machine, and management of biological databases.  Impact factor 3.45 

Journal of Mathematical Biology, Springer, 1974-    http://www.springerlink.com/link.asp?id=100436 Mathematical modelling and reasoning to the understanding of biological systems and the explanation of biological phenomena. Biologically inspired problems of a mathematical nature. Biological insight as a result of mathematical analysis or identify and open up challenging new types of mathematical problems that derive from biological knowledge (in the form of data, or theory, or simulation results). Biofluids, cell biology, physiology, neurobiology and behaviour, development, ecology, population biology, genetics and evolution, epidemiology, immunology, molecular biology, DNA and protein structure and function. It is understood that research in mathematical biology may rely on advanced computational methods and visualization tools, more traditional analytical and stochastic approaches. Official journal of the European Society for Mathematical and Theoretical Biology.

Mathematical Biosciences, Elsevier, 1967-  http://www.elsevier.com/locate/mbs  Formulation, analysis and solution of mathematical models in the biosciences. Serves both mathematicians involved in solving model equations or in reaching conclusions that are testable in the real world, and biologists who are interested in forming mathematical models of biological processes and systems

Mathematical Medicine and Biology, A Journal of the IMA Institute of Mathematics and its Applications ,Oxford University Press, 1999-  http://www3.oup.co.uk/imammb/ Articles with a significant mathematical content addressing topics in medicine and biology. Papers exploiting modern developments in applied mathematics are particularly welcome. The biomedical relevance of mathematical models should be demonstrated clearly and validation by comparison against experiment is strongly encouraged. Contributions relevant to any area of the life sciences welcomed, including: biomechanics, biophysics, cell biology, developmental biology, ecology and the environment, epidemiology, immunology, infectious diseases, neuroscience, pharmacology, physiology, population biology. Was  IMA Journal of Mathematics Applied in Medicine and Biology.

Nucleic Acids Research, Oxford University Press http://nar.oupjournals.org/ First issue of each year is a guide to databases. Physical, chemical, biochemical and biological aspects of nucleic acids and proteins involved in nucleic acid metabolism and/or interactions. RNA, molecular biology, chemistry, genomics, computational biology and structural biology. Impact Factor 7.0 

Bioinformatics Newsletters
BioInform, GenomeWeb http://www.genomeweb.com/informatics 

BIO-IT http://www.bio-itworld.com/  Convergence of information technology and the life sciences for  senior IT/scientific management, pharmaceuticals, biotechnology, drug discovery/ development, genomics and proteomics.

NCBI News, National Center for Biotechnology Information, NIH http://www.ncbi.nlm.nih.gov/news/06-25-2013-welcome-to-ncbi-news/
See also Key news sources

Bioinformatics blogs
Biological Informatics http://biologicalinformatics.blogspot.com/ Marcus P. Zillman,  A Subject Tracer™ Information Blog developed and created by the Virtual Private Library™ for monitoring biological informatics (health informatics, neuroinformatics, biodiversity informatics and biomolecular informatics resources and sites on the Internet. .

nodalpoint.org: a bioinformatics weblog, 2000- http://nodalpoint.org/ A weblog for subjects mostly related to computational chemistry, chemoinformatics, statistical analysis in these areas and some quantum chemistry

snowdeal {biomedical} informatics  http://snowdeal.org/section/informatics/

See also biotech blogs  

Bioinformatics Websites
Encode Encyclopedia of DNA Elements, National Human Genome Research Institute, NIH http://www.genome.gov/10005107  The long-term goal of the ENCODE project is to identify all functional elements in the human genome sequence. For use in a pilot project, defined regions of the human genome - corresponding to 30Mb, roughly 1 percent of the total human genome - have been selected. 

IBM Life Sciences http://www-3.ibm.com/solutions/lifesciences/
IBM Computational Biology http://www.research.ibm.com/compsci/compbio/
IBM Bioinformatics Group – tools and content http://cbcsrv.watson.ibm.com/Tspd.html
IBM Bioinformatics and Pattern Discovery Group http://www.research.ibm.com/bioinformatics/

NIH Roadmap Bioinformatics , NIH, 2003. http://nihroadmap.nih.gov/bioinformatics/index.asp

see also Human Genome websites

Bioinformatics organizations
Association for Computing Machinery, Special Interest Group on Algorithms and Computation Theory http://sigact.acm.org/

Bio-Spice http://www.biospice.org/  Open source framework and software toolset for Systems Biology, is intended to assist biological researchers in the modeling and simulation of spatio-temporal processes in living cells.

EBI: European Bioinformatics Institute, Hinxton, Cambridge, UK. An EMBL outstation.  http://www.ebi.ac.uk/

International Society for Computational Biology http://www.iscb.org/

Open Bioinformatics Foundation OPEN-BIO:  http://open-bio.org/   An umbrella organization for the various bio*.org projects that grew out of the original BioPerl project to provide financial, administrative and technical assistance for our various open source life science projects. which include  BioPerl  BioJava  BioPython  BioRuby  BioPipe BioSQL / OBDA  MOBY  DAS BioPathways†  EMBOSS

Government organizations
Bioinformatics, Canada http://www.bioinformatics.ca/

Bioinformatics at NIH http://www.bisti.nih.gov/
Computational Molecular Biology at NIH http://molbio.info.nih.gov/molbio/
Center for Molecular Modeling, NIH http://cmm.info.nih.gov/modeling/
BIMAS Bioinformatics & Molecular Analysis Section, Center for Information Technology, NIH http://bimas.cit.nih.gov/

DARPA, Bio-Computation, Information Processing Technology Office  http://www.darpa.mil/ipto/programs/biocomp/index.htm  A computational framework that enables the construction of sophisticated models of intracellular processes that can be used to predict and control the behavior of living cells.

NCBI  National Center for Biotechnology Information, NIH  http://www.ncbi.nlm.nih.gov  Established in 1988 as a national  resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease. Part of  NIH.

more Informatics organizations

Informatics Special topics
Taxonomies and ontologies
Robin Cover's XML Cover Pages is described as "a collection of references on matters of Subject Classification, Taxonomies, Ontologies, Indexing, Metadata, Metadata Registries, Controlled Vocabularies, Terminology, Thesauri, Business Semantics" last updated Feb. 12, 2003 http://xml.coverpages.org/classification.html

more on Taxonomies and ontologies 
Ontologies and taxonomies bibliography

Data mining Standards  Markup languages  Visualization/visualisation Social informatics

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