Heba Sailem's List: Bioinformatics

• RNA Genomics - Anton Enright

   

   PhD projects can be within any area of the group's interests, covering  small RNA genomics and analysis from algorithm development to data  analysis, data mining and potentially wet-dry collaborations with labs  within EMBL or the Cambridge area. Candidates from a variety of  scientific backgrounds (including computational ) are invited to apply  and previous data analysis experience or programming is desirable.

• Molecular Evolution and Phylogenetics - Nick Goldman

    <!--<p>The <a href="/goldman/">Goldman Group</a> expects to take  one PhD student in the 2009 selection round of the EMBL  International PhD Programme. The student is expected to commence studies in October 2009, although this can be varied by mutual agreement.</p>--> 

   PhD projects can be in any area of the group's interests, which concentrate on methods of data analysis  that use evolutionary information in sequence data and phylogenies to  infer the history of living organisms, to describe and understand  processes of evolution, and to use this information to make predictions  about the function of genomic sequence. We have also worked on, for example, applied evolutionary studies and algorithms in sequence analysis and conservation biology.

   

   PhD candidates will typically have degree-level backgrounds in one or more of mathematics, statistics, computer science, molecular biology or similar areas. Lack of experience in some of these areas is not considered a problem, so long as candidates demonstrate aptitude and enthusiasm to learn.

• Primary or archived databases contain information and annotation of   DNA and protein sequences, DNA and protein structures and DNA and protein expression   profiles.
• Secondary or derived databases are so called because they contain the   results of analysis on the primary resources including information on sequence   patterns or motifs, variants and mutations and evolutionary relationships.   Information from the literature is contained in bibliographic databases, such as Medline.
• EMBL database for nucleotide sequence data, UniProtKB/Swiss-Prot protein database and PDBe a 3D protein structure database.
  
• SRS (Sequence Retrieval System)   is a powerful, querying tool provided by the EBI that links information from more than 150 heterogeneous   resources.

2 more annotations...

• Viruses are very small in size, characteristically they are about 0.05 - 0.1 micron. Compare this with a eukaryotic human red blood cell which has a size of 5 microns and a prokaryotic cell is about 1micron in size.

• Prokaryotes are sometimes also known as microbes.

• The bibliographical databases are with the   exception of MEDLINE/PUBMED only available through commercial database vendors.   
  

• MEDLINE contains bibliographic citations and author abstracts from more than 4,000 biomedical journals published in the United States and 70 other countries. The file contains over 12 million citations dating back to the mid-1960's. Coverage is worldwide, but most records are from English-language sources or have English abstracts.

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    The nucleotide sequence databases are data   repositories, accepting nucleic acid sequence data from the scientific community and making   it freely available. The databases strive for completeness, with the aim of   recording every publicly known nucleic acid sequence. These data are heterogenous,   they vary with respect to the source of the material (e.g. genomic versus cDNA),   the intended quality  (e.g. finished versus single pass sequences), the extent of sequence annotation and   the intended completeness of the sequence relative to its biological target   (e.g. complete versus partial coverage of a gene or a genome).   The nucleotide databases are distributed free of charge over the internet.
• DDBJ, GenBank and EMBL-Bank exchange new and updated data on a daily basis to achieve optimal synchronisation. The result is that they contain exactly the same   information, except for sequences that have been added in the last 24 hours. 
  

• Although the nucleotide sequence data are checked for integrity and obvious errors by the data  library staff, the quality of the data is the responsibility of the submitter. As a consequence,  there are many errors in the database: many sequence entries are either mislabelled, contaminated,  incompletely or erroneously annotated, or contain sequencing errors. In addition, the database is  very redundant, in the sense that the same sequence from the same organism may be included many  times, simply reflecting the redundancy of the original scientific reports.

• • Could be a research area
• ArrayExpress is storing all this information, the details of which is called Minimum Information About a Microarray Experiment (MIAME) defined by the Microarray Gene Expression Database (MGED) consortium. MGED is a grass roots movement that was founded at a meeting at the EBI in 1999, is supported by most of the important players in the microarray community, and has evolved far beyond the EBI.