Johannes Gutenberg-Universität Mainz
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Bioinformatics-related links
  • National Center for Biotechnology Information (NCBI): NCBI houses genome sequencing data in GenBank and an index of biomedical research articles in PubMed Central and PubMed, as well as other information relevant to biotechnology. All these databases are available online through the Entrez search engine.
  • Pubmed: PubMed comprises more than 21 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.
  • UCSC Genome Browser: Provides 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; The Genome Browser zooms and scrolls over chromosomes, showing the work of annotators worldwide. The Gene Sorter shows expression, homology and other information on groups of genes that can be related in many ways
  •—A largeconsortium with information pertaining to current issues and technologies, tutorials, resources, mailing lists, as well as a large group of hosted “projects”

Biological databases
  • Nucleotide sequences
    • European Molecular Biology Laboratory (EMBL): EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's primary nucleotide sequence resource. It is supported by 20 European countries and Australia as associate member state.
    • GenBank: GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences located in USA.
    • DNA Data Bank of Japan (DDBJ): DDBJ is a biological database located at the National Institute of Genetics (NIG) in Shizuoka, Japan.
  • Protein sequences
    • UniProt: UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information, many of which are derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the research literature.
    • Protein Information Resource (PIR): PIR has provided databases and proteinsequence analysis tools to the scientific community, including the Protein Sequence Database,which grew out from the Atlas of Protein Sequence and Structure.
  • Protein structures
  • Transcription factors
    • TRANSFAC: TRANSFAC contains data on transcription factors, their experimentelly-proven binding sites, and regulated genes. Its broad compilation of binding sites allows the derivation of positional weight matrices.
  • Specific species
    • DroID: DroID is a comprehensive gene and protein interactions (interactome) database designed specifically for the model organism Drosophila. The database includes protein-protein, TF-gene, miRNA-gene, and genetic interactions.
    • Saccharomyces Genome Database: A searchable and downloadable database for Saccharomyces gene and chromosome data from Stanford University; provides search features and homology and ontology information
    • MGI: Mouse Genome Informatics from the Jackson Laboratory — Well annotated database concerning the mouse genome including knockout and gene information, BLAST, phenotype and locus searches, and information regarding the various strains of mice available for research purposes
    • RatMap: Rat genome database which is focused on rat genes and chromosomal information; provides search and download features
    • WormBase: Large database devoted to C. elegans; includes data mining ad downloadable data options, sequence and gene searches, and other information related to C. elegans

  • Web-based applications
    • BLAST: BLAST finds regions of similarity between biological sequences. Includes nucleotide blast, protein blast, blastx, tblastn and tblastx.
    • EMBOSS: EMBOSS pairwise sequence alignment tools include EMBOSS Needle, Stretcher, Water, Matcher and LALIGN and are used to identify regions of similarity that may indicate functional, structural and/or evolutionary relationships between two biological sequences (protein or nucleic acid).
    • ClustalW2: ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
  • Open access applications
    • Wellcome Trust Sanger Institute: Broad list of software developed by Sanger Institute. Include tools for analysis, annotation, assembly and gene finding.
    • Bioconductor: Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development

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My Previous Employers
  • Johannes Gutenberg-Universität Mainz, Germany 
    Johannes Gutenberg Universität Mainz is is a globally renowned research university of national and international recognition located in Mainz, Rhineland Palatinate, Germany, and named after the inventor of printer Johannes Gutenberg. With approximately 36,500 students (in 2014) in about 150 schools and clinics, it is among the ten largest universities in Germany. Its scientific prowess has been affirmed by its success in the Excellence Initiative by the German federal and state governments to promote top-level research at German universities by receiving approval for Cluster of Excellence as well as approval for a Graduate School of Excellence.
  • National University of Singapore, Singapore 
    NUS is Singapore's oldest university. It is the largest university in Singapore in terms of student enrollment and curriculum offered. The university is widely considered to be one of the most prestigious universities in Asia. In 2011, NUS was ranked 28th in the world and 3rd in Asia by the QS World University Rankings.
  • Nanyang Technological University, Singapore
    NTU is one of the two largest public universities in Singapore with the biggest campus in Singapore and the world's largest engineering college. Ranked 58th globally by QS World Rankings in 2011, with its Engineering faculty ranked 26th, NTU is one of the fastest-growing research universities in the world. As of July 2012, Microsoft Academic Search website ranks NTU's overall engineering as the world's 12th since the last 10 years. Times Higher Education's world university rankings place NTU in the 50th position according to its 2011-2012 Engineering and Technology subject ranking.