Dear all
I intend to submit this abstract (or a very similar version) to:
-the annual meeting of the Netherlands Bioinformatics Center
-ISMB (likely HitSeq SIG)
Please let me know if you have any comments
Best
Peter
Dr. Peter A.C. 't Hoen
Department of Human Genetics
Leiden University Medical Center
Room S4-36
Postal zone S4-P
PO Box 9600
2300 RC Leiden
The Netherlands
phone: +31-71-5269421
fax: +31-71-5268285
e-mail: p.a.c.hoen(a)lumc.nl
Dear all,
Enclosed please find the abstract of the Geuvadis RNAseq main paper that
I'm planning to submit to the Biology of Genomes meeting in Cold Spring
Harbor. The deadline is on Friday, so if you have any comments, please
send them immediately.
Biology of Genomes only allows 18 authors and 12 affiliations, which is
why I've had to cut many names from the abstract author list - apologies
to those who didn't make it, you will be acknowledged in the poster/talk.
best regards,
Tuuli
--
Tuuli Lappalainen, PhD
Department of Genetics, Stanford University School of Medicine , and
Department of Genetic Medicine and Development, University of Geneva
Email: tuuli.e.lappalainen(a)gmail.com / tlappala(a)stanford.edu
Tel: +1 415 351 9713
Bustamante lab
Department of Genetics
300 Pasteur Dr. Lane L301
Stanford, CA 94305-5120
USA
Dear all,
First of all let me with you a very happy new year ! Let's hope 2013 will be an extremely successful closing year for GEUVADIS !
1) Brocher foundation meeting: Note that places are still available for the Brocher foundation meeting<http://www.brocher.ch/en/events/data-protection-in-an-era-of-consumer-targe…> organized by Jane Miller and Anne Cambon Thomsen in the context of the project: "Data protection in an era of consumer-targeted genome sequencing". Geneva, 4th - 5th February 2013.
Please don't hesitate to register and remember that these travel costs can be covered by your GEUVADIS budget-
http://www.brocher.ch/en/events/data-protection-in-an-era-of-consumer-targe…
2) The Next NGS Challenge Conference: Please find below the announcement for this conference, which would be a good place to get exposure for GEUVADIS. "Data Processing and Integration". Valencia, 14th - 16th May 2013.
We encourage you to submit abstracts for poster or oral presentation. Ivo Gut is a Keynote speaker at this even. Let me know if you are planning to attend !
Kind regards,
Gabrielle
Gabrielle Bertier
Scientific Project Manager
International and Scientific Affairs
CRG, Center for Genomic Regulation
Carrer Dr. Aiguader, 88
08003 Barcelona, España
Tel: +34933160374
Mobile: +34639960656
email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es>
web: www.geuvadis.eu; www.fliact.eu
________________________________
From: ISCB Conferences [mailto:iscb.12all.com@s230.acemserv.com] On Behalf Of ISCB Conferences
Sent: 16 January 2013 15:04
To: Hoen, P.A.C. 't (HG)
Subject: The Next NGS Challenge Conference 2013
[cid:image001.jpg@01CDF573.261B9B40]<http://iscb.12all.com/lt.php?c=224&m=240&nl=4&s=b33e1f1b2f91ed9f38536f3c364…>
The Next NGS Challenge Conference, a joint event of the EU COST Action SeqAhead, the EMBnet, the International Society of Computational Biology (ISCB) and the 7FP Project STATegra, is dedicated to the presentation of innovative computational approaches to the analysis of high-throughput sequencing data.
The conference will be held in Valencia, Spain, on May 14-16, 2013.
The Conference will consist of keynote lectures, oral presentations and lively poster sessions. The organizers invite submissions that describe novel applications of NGS, as well as bioinformatic algorithms for data processing and analysis. Submissions dealing with efficient solutions to the management and storage of these large datasets are also welcomed
The Conference will be preceded by an EMBnet Workshop on data analysis.
We are proud to announce the participation of the following keynote speakers:
* Ivo Gut, National Centre for Genome Analysis (CNAG), Barcelona, Spain
* Janet Kelso, Max Planck Institute for Evolutionary Anthropology, Leipig, Germany.
* Leif Andersson, Uppsala University, Sweden.
You can find further information at the Conference site: http://www.thenextngschallenge.org/<http://iscb.12all.com/lt.php?c=224&m=240&nl=4&s=b33e1f1b2f91ed9f38536f3c364…>.
Abstract submission deadline is the 15th of February.
Deadline for registration is the 15th of April.
We look forward to seeing you in Spain!
Ana Conesa, CIPF (Spain)
Chair, The Next NGS Conference 2013
Your Subscription:
Change your subscription<http://iscb.12all.com/lt.php?c=224&m=240&nl=4&s=b33e1f1b2f91ed9f38536f3c364…>
Unsubscribe<http://iscb.12all.com/proc.php?nl=4&c=224&m=240&s=b33e1f1b2f91ed9f38536f3c3…>
<http://iscb.12all.com/lt.php?c=224&m=240&nl=4&s=b33e1f1b2f91ed9f38536f3c364…>
Dear colleagues,
Here at last is the QC-survey for geuvadis. I kindly ask each partner to
answer it and send back to me by *11 August* at the latest.
As the survey covers both laboratory details and bioinformatics I
suggest that each principal investigator at each site delegates the task
to the appropriate person(s).
For question 11 and 22: You don't have to describe every data analysis
pipeline you have, that would be to much to ask. Please choose one or
two you use the most and/or one that you have particular expertise in.
Please don't hesitate to ask me if there is something that is unclear.
Thank you and best summer greetings to all of you.
Mathias
--
_____________________________________________
Mathias Brännvall, PhD
Project coordinator
Dept. of Medical Sciences, sect. Molecular Medicine,
Uppsala University
Akademiska sjukhuset, ing. 70, 3 tr
phone: +46-(0)18-6114934
mobile: +46-(0)70-1679446
e-mail: Mathias.Brannvall(a)medsci.uu.se
Dear all
I attach the current draft of the RNA-seq QC paper, which was submitted as supplementary material for the main paper.
We intend to submit the QC paper to Nat Biotechnology within the coming weeks.
Please send your comments and edits (with track changes) to the current draft ulitmately December 21st
Have a very good X-mas!
Best wishes
Peter
Dr. Peter A.C. 't Hoen
Center for Human and Clinical Genetics
Leiden University Medical Center
Postal zone S4-P
PO Box 9600
2300 RC Leiden
The Netherlands
phone: +31-71-5269421
fax: +31-71-5268285
e-mail: p.a.c.hoen(a)lumc.nl
Hello all,
Here's the almost-final draft of Geuvadis RNAseq poster for ASHG. I'll
get it printed on Monday, so if you have any last minute comments or
suggestions, please send them to me as soon as possible.
best,
Tuuli
--
Tuuli Lappalainen, PhD
Department of Genetic Medicine and Development
University of Geneva Medical School
CMU / Rue Michel-Servet 1
1211 Geneva 4
Switzerland
Tel. +41-(0)22-3795550
tuuli.lappalainen(a)unige.ch
Dear all,
As decided during our Annual Meeting last week, we will include links to our data within EBI databases on the GEUVADIS web page.
In this webpage we will include the full author list of the RNAseq paper and an embargo statement.
At the request of Manolis and Tuuli, could you please send me the list of any additional funding source or agency that you want to acknowledge for this work apart from GEUVADIS ? Please do so ASAP, and before tomorrow Tuesday 10:00 CET, time when the page will go live.
Thank you for your collaboration, and sorry for the last minute request,
Kind regards,
Gabrielle
Gabrielle Bertier
Scientific Project Manager
International and Scientific Affairs
CRG, Center for Genomic Regulation
Carrer Dr. Aiguader, 88
08003 Barcelona, España
Tel: +34933160374
Mobile: +34639960656
email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es>
web: www.geuvadis.eu; www.fliact.eu
Dear all,
Please find attached a proposal for the author list of the main RNAseq
paper.
Please let me know your comments/additions/objections
Many thanks,
Manolis
------------------------------------------
Emmanouil (Manolis) Dermitzakis, PhD
Louis-Jeantet Professor
Department of Genetic Medicine and Development
University of Geneva Medical School
1 Rue Michel-Servet (CMU office 9088)
Geneva 1211
Switzerland
Email: emmanouil.dermitzakis(a)unige.ch
Tel: +41 (0) 22 379 5483
Fax: +41 (0) 22 379 5706
website: http://funpopgen.unige.ch/
Admin assistant: Ancilla Stefani,
Tel: +41 22 379 5551
e-mail: Ancilla.Stefani(a)unige.ch
------------------------------------------
Tuuli Lappalainen wrote:
> Hello,
>
> Here are the minutes of the call. The next call will be in one week,
> November 1st.
>
> - deadline to send text and figures is *this Friday, *so Tuuli is
> expecting a lot of emails. Thanks to those of you who have already
> sent material.
> - Tuuli presented the draft of the ASHG poster; discussion of recent
> analyses. The miRNA analysis is challenging - there are some signals
> that are interesting but few very strong and expected genome-wide trends.
> - Jean presented slides of sQTL analysis; plenty of interesting
> signals and ideas how to take this forward. His sQTLs are running for
> the Europeans combined, and they will be then compared to
> gene-RPKM-eQTLs that Tuuli calculated.
>
> best,
> Tuuli
>
> Tuuli Lappalainen, PhD
> Department of Genetic Medicine and Development
> University of Geneva Medical School
> CMU / Rue Michel-Servet 1
> 1211 Geneva 4
> Switzerland
> Tel. +41-(0)22-3795550
> tuuli.lappalainen(a)unige.ch
> On /25/1012 12:54 PM, Tuuli Lappalainen wrote:
>> Hello,
>>
>> We'll have a Geuvadis analysis group call today Oct 25th at 2pm CET.
>> Apologies for the late reminder.
>>
>> On the agenda:
>> - ASHG poster
>> - analysis updates
>> - sQTL presentation from Jean
>>
>> best,
>> Tuuli
>>
>> Call details:
>> Germany +49 692 573 804 41 <tel:%2B49%20692%20573%20804%2041>
>> Netherlands +31 108 920 271 <tel:%2B31%20108%20920%20271>
>> Spain +34 931 816 661 <tel:%2B34%20931%20816%20661>
>> Sweden +46 840 309 949 <tel:%2B46%20840%20309%20949>
>> Switzerland +41 58 262 07 22 <tel:%2B41%2058%20262%2007%2022>
>> United Kingdom +44 203 370 57 19
>> <tel:%2B44%20203%20370%2057%2019>
>> United States +1 646 381 08 89 <tel:%2B1%20646%20381%2008%2089>
>> /Access code: 611683 /
>>
>>
>>
>> --
>> Tuuli Lappalainen, PhD
>> Department of Genetic Medicine and Development
>> University of Geneva Medical School
>> CMU / Rue Michel-Servet 1
>> 1211 Geneva 4
>> Switzerland
>> Tel. +41-(0)22-3795550
>> tuuli.lappalainen(a)unige.ch
>>
>>
>> _______________________________________________
>> Geuvadis_rna_analysis mailing list
>> Geuvadis_rna_analysis(a)lists.crg.es
>> http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
>>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Geuvadis_rna_analysis mailing list
> Geuvadis_rna_analysis(a)lists.crg.es
> http://davinci.crg.es/mailman/listinfo/geuvadis_rna_analysis
>
Dear GEUVADIS partners,
I would like to draw your attention to the petition from Anna Leptin. We highly encourage everybody to sign up and to forward it to colleagues at your institute and outside.
http://www.no-cuts-on-research.eu
Thanks
Best
Gabrielle
Gabrielle Bertier
Scientific Project Manager
International and Scientific Affairs
CRG, Center for Genomic Regulation
Carrer Dr. Aiguader, 88
08003 Barcelona, España
Tel: +34933160374
Mobile: +34639960656
email: gabrielle.bertier(a)crg.es<mailto:gabrielle.bertier@crg.es>
web: www.geuvadis.eu; www.fliact.eu
-----Original Message-----
From: Maria Leptin [mailto:maria.leptin@embo.org]
Sent: martes, 23 de octubre de 2012 02:13 p.m.
Subject: Please forward - Petition to protect EU science budget
Dear colleagues,
The discussions at the next summit of the European Union heads of state or government, which is scheduled for 22 and 23 November, will be decisive in determining the EU research budget for the next seven years. Several Member States are demanding severe cuts on the total EU budget and research will have to compete with other policy priorities.
This is a time when we, the scientific community, should act together and make our case to protect research funding, including that of the European Research Council (ERC), from cuts. Decisions will be prepared in discussions among politicians at the national level. All of us must look for opportunities to affect these decisions and send a strong signal to the heads of state or government.
An open letter signed by European Nobel laureates has been published in top European newspapers this week. The impact of this letter will be increased if it is followed by a mobilization of the national scientific communities. To keep the momentum going, an online petition has been launched:
http://www.no-cuts-on-research.eu
I would like to ask you to sign it and to encourage all your colleagues to do likewise. Note that in the past, less than 30 000 scientists signed the largest petition for a European scientific cause compared to the hundreds of thousands of signatures on petitions from other groups of society. We must do better than that.
This action is coordinated by the Initiative for Science in Europe (ise(a)i-se.org<mailto:ise@i-se.org>; www.initiative-science-europe.org<http://www.initiative-science-europe.org>), of which EMBO is a member. Please contact Wolfgang Eppenschwandtner, Executive Coordinator of the ISE if you have any questions or suggestions.
Best regards,
Maria Leptin
Director
EMBO - excellence in life sciences
Meyerhofstr. 1
69117 Heidelberg, Germany
tel +49-6221-8891-102
fax +49-6221-8891-202
maria.leptin(a)embo.org<mailto:maria.leptin@embo.org>
Dear all,
We will have a Geuvadis RNAseq workpackage call on Friday October 19th
at 4pm CET.
Agenda:
- Update on the analysis
- Outlines of the papers:
- main paper
- QC companion
- splicing companion
- loss-of-function companion
- Publication and authorship
- AOB
Call details:
Germany +49 692 573 804 41 <tel:%2B49%20692%20573%20804%2041>
Netherlands +31 108 920 271 <tel:%2B31%20108%20920%20271>
Spain +34 931 816 661 <tel:%2B34%20931%20816%20661>
Sweden +46 840 309 949 <tel:%2B46%20840%20309%20949>
Switzerland +41 58 262 07 22 <tel:%2B41%2058%20262%2007%2022>
United Kingdom +44 203 370 57 19 <tel:%2B44%20203%20370%2057%2019>
United States +1 646 381 08 89 <tel:%2B1%20646%20381%2008%2089>
/Access code: 611683
/People calling from CRG: Recently there have been some problems in
calling to the Spanish number above. The problem seems to be in your
end, and Gabrielle is checking what can be done. If it doesn't work,
please call e.g. to the German number.
best regards,
Tuuli
--
Tuuli Lappalainen, PhD
Department of Genetic Medicine and Development
University of Geneva Medical School
CMU / Rue Michel-Servet 1
1211 Geneva 4
Switzerland
Tel. +41-(0)22-3795550
tuuli.lappalainen(a)unige.ch