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  • Text/Documents:
     
    • GoMiner: a resource for biological interpretation of genomic and proteomic data (2003) (online version)
      Zeeberg et al., NIH, Bethesda, MD
            We have developed GoMiner, a program package that organizes lists of 'interesting' genes (for example, under- and overexpressed genes from a microarray experiment) for biological interpretation in the context of the Gene Ontology. GoMiner provides quantitative and statistical output files and two useful visualizations. The first is a tree-like structure analogous to that in the AmiGO browser and the second is a compact, dynamically interactive 'directed acyclic graph'. Genes displayed in GoMiner are linked to major public bioinformatics resources.
       
    • DNA Microarray Data Analysis, second edition (2006) (Full Text avaliable at website)
      From CSC - the Finnish IT center for science
            This guidebook is written in collaboration between several Finnish researchers from different universities and research institutions. The first edition of the DNA microarray data analysis guidebook was written by M. Minna Laine, Tomi Pasanen, Janna Saarela, Ilana Saarikko, Teemu Toivanen, Martti Tolvanen, Jarno Tuimala, Mauno Vihinen, and Garry Wong. For the second edition, Iiris Hovatta, Katja Kimppa, Antti Lehmussola, Juha Saharinen, and Pekka Tiikkainen joined the writer team. The purpose of this book is to serve as course and teaching material to introduce basic concepts of microarray data analysis. We hope that especially researchers starting their data analysis can benefit from the book.
      Example chapters:
      Part II, Section 10: Data normalization
      Part II, Section 11: Finding differentially expressed genes
       
    • Yeast Two-Hybrid: State of the Art (1999) (PDF, 1MB, 38pgs)
      Wim Van Criekinge and Rudi Beyaert, Flanders Interuniversity Institute for Biotechnology and University of Ghent
            Genome projects are approaching completion and are saturating sequence databases. This paper discusses the role of the two-hybrid system as a generator of hypotheses. Apart from this rather exhaustive, financially and labour intensive procedure, more refined functional studies can be undertaken. Indeed, by making hybrids of two-hybrid systems, customised approaches can be developed in order to attack specific function-related problems. For example, one could set-up a “differential” screen by combining a forward and a reverse approach in a three-hybrid set-up. Another very interesting project is the use of peptide libraries in two-hybrid approaches. This could enable the identification of peptides with very high specificity comparable to “real” antibodies. With the technology available, the only limitation is imagination.
       
    • What is a DNA chip? (2002) (PDF, 1,024KB, 11pgs)
      written for students by Russ Hodge and Christian Schwager, European Molecular Biology Laboratory (EMBL)
            This presentation introduces DNA chips (w/photos of real chips after an experiment), followed by DNA chip analysis software, explaining the meaning of spots seen on the chips. The article then explains DNA chip score charts and correlation graphs through an example in which a healthy and an infected mosquito are compared.
       
    • The Structures of Life (date unkn.) (PDF avaliable at website)
      National Institutes of Health (NIH)
            This document introduces proteins (with various 3D protein models and photos of protein crystals), describes the concept of mutations (or 'errors') followed by the genetic code. The document also covers measurement methods such as X-ray crystallography, and NMR. It discussed also interesting subjects like structure-based drug design, transcription and translation to make proteins. Also, the document includes a glossary and many links throughout the text.
       
    • News Article: "Structure-based Drug Design" (June 4, 2001)
      Chemical & Engineering News
            The article points out and describes the (docking and cystallographic) methods employed and highlights the importance of structure-based design as a shortcut to find better compounds for new drugs. For more information about the company cited, logon to: www.syrrx.com
       
    • Webpage: "How is drug design related to bioinformatics?" (Date unkn.) (in English/German/French)
      Wolfram Altenhofen, University of Bielefeld, Germany
            Well designed webpage with comprehensive graphics (3D molecular models of proteins). Topics covered: A) Proteins as Cellular Targets of Medical Drugs, B) The Molecular Basis of Drug Specificity, C) "Rational" Drug Design, D) Techniques Applied, E) Drug Design Using Known Receptor Structures, F) What if we don't Know the Structure of the Receptor?, and G) Future Perspectives.
       
    • The COG database: an updated version includes eukaryotes (2003) (Online version)
      Tatusov et al., NIH, Bethesda, Maryland.
            We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs) from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups.
       
    • Article: "The Sequence of the Human Genome" (2001) (Online version)
      J. Craig Venter et al. (Science, 16 February 2001)
            A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies--a whole-genome assembly and a regional chromosome assembly--were used, each combining sequence data from Celera and the publicly funded genome effort...
       
    • Article: "The Human Genome" (2001) (Online version)
      Elizabeth Pennisi (Science, 16 February 2001)
            It is an awe-inspiring sight. Open up the folded figure that comes with this issue of Science. There you will see the human genome, chromosome after chromosome, with its major features color-coded and described. Black tick marks show the coding regions along orange, blue, pink, and purple genes, the colors reflecting the function of the corresponding proteins. All told, some 2.9 billion bases of the genome are represented on this beach towel-sized poster...
       
  • Software Downloads:
     
    • EMBOSS
      A free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Please see the documentation for the capabilities of EMBOSS, including this helpful guide to EMBOSS and other bioinformatics tools by Lisa Mullan of the EBI.
       
    • Swiss-PdbViewer
      For viewing proteins and molecules (as PDB files) in 3D. Download includes instruction manual.
       
  • Slide Presentations:
     
    • Biology and computers
      Dr. Jamil Momand, April 5, 2005
      Literature Databases/Primary public domain bioinformatics servers/NCBI ENTREZ/Medline Database/MEDLINE Sample Record/Medical Subject Headings (MeSH)/OMIM-Online Mendelian Inheritance in Man...
       
  • Video Lectures:
     
  • Sample Scripts:
     
  • Sample Data:
     
    • Bacterial Genomes - Search through the genomes (avaliable as TXT files) of 331 (as of 08-07-06) bacterial microorganisms. Made available by the EMBL-EBI.
       
    • Genome Browser FTP server - Bulk downloads of sequences and annotation data made (most data is in compressed form) available via the Genome Browser FTP server.
       
  • General Web Resources:
     
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This page was created on September 23, 2009.