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Postdoc position on fungal transposable element annotation at INRA-URGI, Paris France

2009-04-26T06:24:22Z

Bioinformatics post-doc position on fungal transposable element annotation and analysis

REF: URGI-blugen2009-05

An INRA post doctoral position is available for 2 years (1 year renewable) at URGI (Genomic-Info Research Unit, Versailles 15 km West of Paris, France).

Context :

The candidate will work on the annotation of the fungal barley pathogen Blumeria graminis genome in the URGI fungal bioinformatics team in close relationship with the "Blumeria" genome bioinformatics team located at the Imperial College (London, UK).

URGI (http://urgi.versailles.inra.fr) hosts a bioinformatics platform for plants and pathogens/pests genomic and genetic data integration. Domains covered are structural and functional genome annotation, genetic and physical mapping, transcriptomics, proteomics and genetic resources. The URGI research activities cover data integration and functional and evolutionary genomic studies. A strong emphasis is made on repeats: their annotation, their impact on the genome, and their evolution.

Job description:

The applicant will actively contribute to the annotation of Blumeria graminis genomic sequence (http://www.blugen.org) focusing on transposable elements. As these elements represent a very large part of the genome (80%), he/she will study their organization and distribution as well as their impact on the genome and its evolution. The applicant will participate to the comparative analysis of these repeats to those of other fungi, including related species annotated at URGI such as Botrytis cinerea (INRA-URGI/Bioger), and Sclerotinia sclerotiorum (Broad Institute-NSF/USDA). The annotation will be performed with REPET, a transposable element detection and annotation pipeline developed at URGI (http://urgi.versailles.inra.fr/research/transposable_elements.php). The development and improvement of bioinformatics tools will be necessary.

Profile:

To be considered applicants must have a non-French nationality and have a PhD degree in bioinformatics or genomics, a strong experience in computational genomics, and good programming skills. Basic knowledge on transposable elements will be much appreciated.

Applications:

Applications should provide a motivation letter, a curriculum vitae, a list of publications, letters of support from two reference scientists or their names and addresses to obtain further information.

Position opened as soon as possible

Requests for information or applications (REF-URGI-blugen2009-05) to: joelle.amselem@...

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Applied Computational Genomics Course

2009-04-04T18:38:23Z

Genome Canada
APPLIED COMPUTATIONAL GENOMICS COURSE (ACGC)
Led by Dr. Brian Fristensky

WESTERN CANADA- JULY 14 TO JULY 20, 2009 -
Calgary, Alberta, Canada

EASTERN CANADA- AUGUST 25 TO AUGUST 31, 2009 -
Montreal, Quebec, Canada

www.gcbioinformatics.ca/training

Since 2003, the ACGC courses have helped laboratory biologists become power users of the latest software tools. Through mastery of fundamental bioinformatics skills, this week-long course enables working biologists to take charge of their data and their projects. The ACGC course utilizes a wide array of popular software, within the context of a portable and comprehensive bioinformatics system.

1. BIRCH (Biological Research Computer Heirarchy) (http://home.cc.umanitoba.ca/~psgendb):

o Provides a complete bioinformatics suite for analysis of sequences, molecular markers, phylogenetic trees, mircoarrays, and data mining and management.

o Automates use of a wide range of programs (for example, BLAST, FASTA, clustalw, Phylip and many others) through a highly accessible graphic interface.

o Fosters a unique environment for experimentation with data.

2. The Bluejay genome browser (http://bluejay.ucalgary.ca/)

o Creates a means for visualization of the wealth of information hidden within the complexity of the genomes.

o Permits comparisons of the organization of two or more chromosomes.

o Allows for visualization of hot spots of gene expression.

o Facilitates the annotation of new genomes.

3. Genome Canada Bioinformatics Help Desk (http://gchelpdesk.ualberta.ca/)

o Beginner-level introduction to Perl scripting .

o Gives consultation on bioinformatics problems on a fee-for-service basis.

o Offers a repository of software.

o Provides web tools, including BASys (Bacterial Annotation System), PlasMapper, BacMap CGView and others.

4. BioMoby (http://www.biomoby.org/)

o Automatically discovers web services worldwide that work with almost any kind of biological data.

o Facilitates the learning of Perl Scripts for leveraging web services for maximizing research outcomes.

o Creates high-throughput data pipelines through implementation of the Taverna workbench.

Proficiency with bioinformatics tools raises the bar with success in pure and applied research activity, thesis supervisory roles, publication potential, career placement opportunities, and the viability of funding avenues.

After the course, attendees of the ACGC will have FREE internet access to all the Bioinformatics Platform tools and databases used in this course. All software is also freely downloadable.

Faculty

Faculty for the ACGC include some of the best recognized bioinformaticians from across Canada, including Drs. Christoph Sensen, Brian Fristensky, David Wishart, and Mark Wilkinson. Dr. Christoph Sensen was recently featured in international media for his breakthrough research on degenerative disorders linked to chronic wasting disease (CWD) in elk and Mad Cow Disease. Dr. Mark Wilkinson has recently been profiled in publications from a diverse range of international research organizations such as the Heart and Stroke Foundation of Canada, Microsoft Research, and the National E-Science Centre of the UK for his groundbreaking work into data and knowledge representation in the biological sciences, and in cardiovascular research in particular. Dr. David Wishart has been actively involved in teaching and developing bioinformatics training programs across Canada and the United States for more than 10 years. He has published more than 150 papers on bioinformatics and various "omics!
" technologies. Dr. Fristensky has been a contributor to the fields of bioinformatics and plant molecular biology since the early 1980's. Publications span a range of interests, including resistance to biotic and abiotic stress in crops, software for DNA and protein sequence analysis, management of biological databases, and improving software usability in bioinformatics.

Registration and further information

Early Bird enrolment in the week-long course extends now to June 1, 2009 for the Calgary course and to July 1, 2009 for the Montreal course, at a reduced fee of $1,250 Cdn. for Canadian participants and $1,500 Cdn. for international participants.

To register, and for further information, please visit our website at www.gcbioinformatics.ca/training

Enquiries can be made to Susanne Cardwell in Canada at 403-210-6661, email smcardwe@...

Also, it would be greatly appreciated by BIP if you would consider sending out this message to your mailing lists and/or posting the information on your websites (a sponsorship agreement can be arranged for interested parties).

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Re: Genes Structure

2008-10-04T13:58:15Z

In article <mailman.240.1223081681.29717.genstruc@...>,
Erik Corona <ecoronap@...> wrote:
>What is the specific purpose of this newsgroup? Why is it empty?

Find this and other Bionet newsgroup archives at http://www.bio.net/

THe first question can be answered at the newsgroup archive,
http://www.bio.net/bionet/mm/genstruc/

See in particular [Genstruc Charter] that has the 1997
description of discussion topics.

Why is it empty? As a guess, people moved on to other topics
and/or other venues for this subject. Feel free to revive it
if it seems a useful newsgroup.

- Don Gilbert

--
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd@...--http://marmot.bio.indiana.edu/

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Genes Structure

2008-10-03T12:04:52Z

What is the specific purpose of this newsgroup? Why is it empty?

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Webinar Event: Whole Genome Association Study of Schizophrenia

2007-05-04T11:54:31Z

WHOLE GENOME ASSOCIATION OF SCHIZOPHRENIA

A Golden Helix Webinar

Presenter: Todd Lencz, Ph.D., Feinstein Institute for Medical Research
Date: Wednesday, May 9th
Time: 1:00pm ET
Abstract: Dr. Lencz will discuss the various data management and
analysis steps conducted in his recently published WGA study of
schizophrenia.

Register Now!: <https://www.gotomeeting.com/register/625338501>

----------------

Schizophrenia is a complex disease marked by high heritability
(70-80%), yet few disease genes have been clearly identified and
linkage studies have failed to converge.

Whole genome association (WGA) is a promising, hypothesis-free
approach to discovering novel genetic susceptibility loci for diseases
such as schizophrenia. However, WGA entails numerous methodological
challenges, including:

- Management and manipulation of very large datasets

- Multiple quality control procedures

- Statistical analysis correcting for multiple comparisons.

Join Todd Lencz, Ph.D., Senior Psychologist at The Feinstein Institute
for Medical Research (FIMR), to learn how he and his team used Golden
Helix' HelixTree software to overcome these difficult challenges on
their quest to discover a novel gene that appears to increase the risk
of developing schizophrenia.

In a sample of 178 patients with schizophrenia and 144 controls, Dr.
Lencz and his team of psychiatric researchers from FIMR utilized
HelixTree software to analyze WGA data derived from Affymetrix 500K
microarrays. They identified a novel susceptibility locus in the
pseudoautosomal region of the X/Y chromosomes. The results were
published last month in the high-impact journal, Molecular
Psychiatry.

In this webinar Dr. Lencz will walk through the data management and
analytic steps conducted in HelixTree that helped make this discovery
possible.

Don't miss this opportunity to learn how you can apply these same
technologies to accelerate your research!

Register Now! <https://www.gotomeeting.com/register/625338501>

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Open Lecture on Cellular Differentiation: Enabling Stem Cell Research. Wed 18th Oct 2006, Hinxton, Cambridge, UK

2006-09-27T05:32:02Z

OPEN LECTURE SERIES Revolutionizing Life Sciences: Tools, Innovations & Insights
USA West Coast | USA East Coast | United Kingdom | Singapore | Japan

In celebration of the 25th anniversary of Applied Biosystems, The Applera Charitable Foundation is proud to sponsor an inspiring series of lectures entitled "Revolutionizing Life Sciences: Tools, Innovations & Insights."

In this series, leading scientists and researchers will gather to discuss the past, present and future of important developments in the life sciences and the role technology has played in spurring these breakthroughs.

Please join us at Hinxton, Cambridge, UK for our next event:

Cellular Differentiation: Enabling Stem Cell Research

DATE: Wednesday, October 18, 2006

TIME: 13:00 - 17:00

LOCATION: The Francis Crick Auditorium, Wellcome Trust Conference Centre, Hinxton, Cambridge, UK
( http://www.wtconference.org.uk )

MODERATORS:

Michael Ashburner, Ph.D., Sc.D., F.R.S.
University of Cambridge

Elizabeth Robertson, Ph.D., F.R.S.
Wellcome Trust Centre for Human Genetics

SPEAKERS:

Austin Smith, Ph.D., F.R.S.
Chairperson, Institute for Stem Cell Biology
University of Cambridge
"The Ground State of Pluripotency"

Roger Pedersen, Ph.D.
Professor of Regenerative Medicine
Department of Surgery and Cambridge Institute for Medical Research
University of Cambridge
"Mechanisms of Pluripotency and Epigenesis in Human Embryonic Stem Cells"

Azim Surani, Ph.D., F.R.S.
Mary Marshall and Arthur Walton Professor of Physiology and Reproduction
University of Cambridge
"Germ Line and Pluripotent Stem Cells"

*******************************************************************************
Reception to follow. This event is FREE and open to the public,
but seating is limited.

Please register in advance at http://info.appliedbiosystems.com/sls
and arrive early to secure your seat.

The first 200 people to arrive will receive a special gift!
*******************************************************************************

Dr Deborah Carley
Science Programme Manager / Head of Conference Centre
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1RQ

tel: +44 (0)1223 495006
fax: +44 (0)1223 495141

email: d.carley@...

Check out the Wellcome Trust Conference Programme at www.wellcome.ac.uk/conferences and the Wellcome Trust Conference Centre at www.wtconference.org.uk

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GUS/GFP tagged promoters or GUS/GFP fusion proteins

2006-09-16T20:16:18Z

I am a Genetics students and I've got the following doubt:

I read some papers that described experiments where plants were
transformed with both a GUS and a GFP tagged promoter (same promoter in
both cases) or with a GUS and a GFP fusion protein (same protein in
both cases). Why is it that two different reporter constructs were
used for transformation? Perhaps because there is always the
possibility that GFP will not fluoresce (due to tagging/fusion), or
that the glucuronidase gene will not be (properly) transcribed, due to
the same reasons?

Cheers

Gwen

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New Yeast Resource ...

2006-04-17T08:35:24Z

All,

I'm setting up my own lab in a few months (S.cerevisiae as a model system for chromatin studies) but have already collected together many of the protocols we use in the Buratowski lab - some of you may find them useful ...

See Protocols section at http://mckeogh.googlepages.com/

Best,

Michael ..

________________________________________________________

Dr Michael-Christopher Keogh,

Bldg C1, Rm 207,

Dept of Biological Chemistry and Molecular Pharmacology,

Harvard Medical School,

240 Longwood Ave,

Boston, MA 02115,

USA.

Tel. 617 432 0366

Fax. 617 738 0516

Email. Michael_Keogh@...

Web. http://mckeogh.googlepages.com

________________________________________________________

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[Employment] Post-doc wanted

2006-04-10T13:37:36Z

Our client is looking for someone who has completed or will be completing
their post doc within the next 2 months with a background in ChIP assay
technology to work for an oncology company that wants to study interactions
of proteins with nucleic acids. This person should have experience with
transcription, rRNA and be interested in studying mechanisms and setting up
screens.

Interested people should contact me at the below address, phone or email.

Amy B. Lurier

President

TechFind, Inc.

P.O. Box 626

Natick, MA 01760

<mailto:amy@...> amy@...

(508) 647-0111

The future, according to some scientists, will be exactly like the past,
only far more expensive.

John Sladek <http://www.quotationspage.com/quotes/John_Sladek/>

<http://www.quotationspage.com/quotes/Joe_Weinstein/>

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