geuvadis_rnaseq

geuvadis_rnaseq@lists.crg.es

97 discussions

by P.A.C._t_Hoen＠lumc.nl

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

12 years, 3 months

[Geuvadis_rnaseq] Biology of Genomes abstract

by Tuuli Lappalainen

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

12 years, 3 months

[Geuvadis_rnaseq] GEUVADIS- 2 Meeting Announcements

by Gabrielle Anne Bertier

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…>

12 years, 4 months

[Geuvadis_rnaseq] GEUVADIS QC survey

by Mathias Brännvall

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

12 years, 5 months

[Geuvadis_rnaseq] draft RNA-seq qc

by P.A.C._t_Hoen＠lumc.nl

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

12 years, 5 months

[Geuvadis_rnaseq] ASHG poster

by Tuuli Lappalainen

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

12 years, 6 months

[Geuvadis_rnaseq] acknowledgement for funding - GEUVADIS RNAseq project

by Gabrielle Anne Bertier

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

12 years, 6 months

[Geuvadis_rnaseq] Geuvadis RNAseq author list: proposal

by Manolis Dermitzakis

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 >

12 years, 7 months

[Geuvadis_rnaseq] Please forward - Petition to protect EU science budget

by Gabrielle Anne Bertier

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>

12 years, 7 months

[Geuvadis_rnaseq] Geuvadis TC October 19th at 4pm CET

by Tuuli Lappalainen

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

12 years, 7 months

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