JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for ALLSTAT Archives


ALLSTAT Archives

ALLSTAT Archives


allstat@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

ALLSTAT Home

ALLSTAT Home

ALLSTAT  September 2014

ALLSTAT September 2014

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Postdoctoral position in Statistics/Bioinformatics/Computer science at AgroParisTech / LBBE (Lyon)

From:

Stéphane Robin <[log in to unmask]>

Reply-To:

Stéphane Robin <[log in to unmask]>

Date:

Tue, 30 Sep 2014 17:13:56 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (39 lines)

Postdoctoral position in Statistics/Bioinformatics/Computer science at AgroParisTech / LBBE (Lyon)

Subject: Alternative splicing: On the unicity of the solution to the variant identification problem

New sequencing technologies can now be applied to the study of mRNA, through the RNA-seq protocol. These techniques yield large amounts of short reads, which then need to be reassembled to identify and quantify the full-length mRNAs initially present in the sample. While this problem is simple when there is only one mRNA per gene, it becomes challenging when a gene gives rises to several alternative splicing variants, with different exon content. Recent studies estimate that up to 90% of multi-exon genes in human are alternatively spliced. Hence, what was thought to be once an exception seems in fact to be the rule. Idenfifying and quantifying all the variants of a gene is therefore a major challenge in the field, for which various methods have been proposed, including penalized regression approaches [Li et al., 2011, Bernard et al., 2014].

Unambiguously assigning an expression level to each variant is however not always possible, essentially because sequencing reads are short, and genes may have many (unannotated) variants Lacroix et al. [2008]. In practice, several sets of variants may give solutions which are equally good in terms of penalized or constrained likelihood. Yet, most methods output only one best solution, without mentionning that there could be other equally good ones. This is not satisfactory and could lead to spurious biological conclusions. The purpose of this post-doc is to carefully analyze the conditions under which a solution is unique and, most importantly, when it is not the case to characterize the set of solutions and propose possibly unique sub-solutions.

Context
The postdoctoral fellow will work either in the UMR 518 AgroParisTech-INRA de Mathématiques et Informatique Appliquees (MIA) in Paris or in the UMR CNRS 5558 de Biométrie et de Biologie Évolutive (LBBE) in Lyon. Both groups are specialized in statistics and bioinformatics.
This postdoctoral position is offered in the framework of ABS4NGS ANR project https://sites. google.com/site/abs4ngs/. The postdoctoral fellow will thus discuss and collaborate with the different partners of this project Institut Curie and which started at the end of 2012.

Background
The applicant should have a strong background in applied statistics, bioinformatics and/or computer science; typically a PhD in one of these fields. A strong experience in programming is also highly desirable.

Localization.
• UMR 518 AgroParisTech-INRA MIA: 16 Rue Claude Bernard, Paris 5ème, www.agroparistech.fr/mia/
• UMR CNRS 5558 LBBE: Campus de La Doua - Université Claude Bernard - Lyon 1, 16 rue Raphael Dubois (Bâtiment Grégoire Mendel), Villeurbanne, lbbe.univ-lyon1.fr/

Salary.
Depending of the past experience of the applicant: 1968 euros per month (2398 euros before taxes) or 2142 euros per month (2611 euros before taxes).Duration. 

The position is for 18 months.

Contact.
• MIA 518: Stéphane Robin: [log in to unmask]
• LBBE: Laurent Jacob: [log in to unmask], Vincent Lacroix: [log in to unmask]

References
• Elsa Bernard, Laurent Jacob, Julien Mairal, and Jean-Philippe Vert. Efficient RNA isoform identification and quantification from rna-seq data with network flows. Bioinformatics, 30(17):2447–2455, 2014. doi: 10.1093/bioinformatics/btu317. URL http://dx.doi.org/10.1093/bioinformatics/btu317.
• Vincent Lacroix, Michael Sammeth, Roderic Guigó, and Anne Bergeron. Exact transcriptome reconstruction from short sequence reads. In Keith A. Crandall and Jens Lagergren, editors, Algorithms in Bioinformatics, 8th International Workshop, WABI 2008, Karlsruhe, Germany, September 15-19, 2008. Proceedings, volume 5251 of Lecture Notes in Computer Science, pages 50–63. Springer, 2008. ISBN 978-3-540-87360-0. doi: 10.1007/978-3-540-87361-7_5. URL http://dx.doi.org/10.1007/978-3-540-87361-7_5.
• Jingyi Jessica Li, Ci-Ren Jiang, James B Brown, Haiyan Huang, and Peter J Bickel. Sparse linear modeling of next-generation mrna sequencing (rna-seq) data for isoform discovery and abundance estimation. Proc Natl Acad Sci U S A, 108(50):19867–19872, Dec 2011. doi: 10.1073/pnas.1113972108. URL http://dx.doi.org/10.1073/pnas.1113972108.

You may leave the list at any time by sending the command

SIGNOFF allstat

to [log in to unmask], leaving the subject line blank.

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001
2000
1999
1998


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager