Schisto Genome Data Analysis - an offer of assistance/collaboration.

Dave Johnston daj at nhm.ac.uk
Fri Nov 1 05:15:57 EST 1996

Dear All,

3 pieces of news:

(1) I have been contacted by Saira Mian of the Lawrence Berkely 
National Laboratoty in the USA (saira at cse.ucsc.edu) with the offer of 
assistance in analysis of schisto genome data and of acting as a 
contact point for people with data analysis problems, queries etc.

she writes:

"My research interests include genome informatics, the structure, 
function and evolution of macromolecules and processes that subvert 
the linear reading of genomic sequences..... see 
http://www.cse.ucsc.edu/research, in particular the descriptions of 
hidden Markov models for modelling proteins and stochastic context 
free grammars of RNA. I would be interested in becoming involved in 
analysis of Schistosoma DNA...... Apart from the intrinsic scientific 
interest, it's one way of contributing to efforts aimed at 
understanding an organism that has such devasting consequences for 
health in less-well developed countries.........Looking at the figures 
for EST hits, it seems as if there is plenty of work to do........ I 
would be happy to act a general resource/point of contact for anyone 
in the Schisto Network if they have questions or need help with 
analysis of their data from a theoretical and/or computational 
perspective. My interests lie both in developing new methods and 
applying them to problems of specific "biological"
interest. I have a number of fruitful collaborations with researchers 
who are primarily experimentalists so I'm familiar with working with 
individuals having little or no background in this area. If there are 
others who end up expressing interest in analysing the data from the 
Schisto project, I would have no objections to collaborating with 
them. As you say, there is no lack of data to go round...... If any 
projects (developed from the EST data) feel their chances of being
funded would be improved were there a computational component to the 
proposal and would thus benefit from including me, let me know. 

I look forward to hearing from you soon.


Saira is keen to receive ideas as to the sorts of analyses you wish to 
see done on your data, your priorities etc. so please feel free to 
contact her with your suggestions. This is a very generous offer and 
one which, I am sure, will bring significant benefits to the 
initiative so please take advantage of it and talk with her.


(2) I am shortly to begin updating the schisto EST records in DBEST to 
reflect the agreed new clone/EST nomenclature. Your original clone and 
sequence IDs will be preserved as comment lines in the records. 
Submitters are therfore likely to receive mail from NCBI, informing 
them of the proposed changes and asking for their approval for the 
changes (since I didn't submit them, it is their policy to check with 
the original submitters). We are withholding release of version 1 of 
SchistoDB until the records have been updated. I will keep you 
informed of progress.


(3) Hopefully, people will hear from WHO in the next week or so 
whether their applications have been successful or not (but its no 
good writing to Mette or I because we don't know anything).

With best wishes to everyone,


David A Johnston
Researcher, Biomedical Parasitology, Dept. of Zoology,
The Natural History Museum, Cromwell Road, London SW7 5BD.

tel: 0171 9389297 (from outside UK: 44 171 9389297)
fax: 0171 9388754 (from outside UK: 44 171 9388754)
eMail daj at nhm.ac.uk

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