September 2008 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] papers
by Eric Bonnet 29 Sep '08

29 Sep '08

might be of interest to have a look at those papers: http://www.bio-itworld.com/pb/2008/09/25/gbm-vogelstein.html

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[Beg-sysbiol] For those interested ... Eric (for sure) and Tom and ...
by Yves Van de Peer 25 Sep '08

25 Sep '08

-------- Original Message -------- Subject: RE: Your availability for a meeting (2 hours) on 28 November Date: Thu, 25 Sep 2008 20:51:31 +0200 From: Hilde Govaert <Hilde.Govaert(a)med.kuleuven.be> To: 'Yves Van de Peer' <yves.vandepeer(a)psb.ugent.be> References: <999AE4C8BE3F49DF9617D708277FE883(a)med.ad10.intern.kuleuven.ac.be> <48DBA67C.1010408(a)psb.ugent.be> Geachte professor, Dat is geen enkel probleem. Uw postdocs zijn eveneens welkom. Ik heb er intussen ook even de uurregeling van de treinen bijgenomen. U zou de trein van 8u57 in Gent St Pieters kunnen nemen. Deze komt aan in Leuven om 10u. Normaalgezien bent u dan tegen 10u30 op campus Gasthuisberg, hetzij per bus, hetzij per taxi. Ik stel daarom voor om de vergadering te laten starten rond 10u30. Kan u me bevestigen dat dit in orde is voor u? Dan reserveer ik een vergaderzaal en informeer ik de anderen. Dank en vriendelijke groet, Hilde -----Original Message----- From: Yves Van de Peer [mailto:yves.vandepeer@psb.ugent.be] Sent: donderdag 25 september 2008 16:56 To: Hilde Govaert Cc: 'Stein Aerts'; 'Wim Mandemakers'; 'Sébastien Hébert'; Smaragda Papadopoulou; 'Jos Tournoy'; Yves Van de Peer Subject: Re: Your availability for a meeting (2 hours) on 28 November Hilde Govaert wrote: > > Dear all, > > Gwendoline Degueurce is a candidate for a PhD-position. She will visit > Bart De Strooper in Leuven on Friday, 28 November. > > Bart asked me to arrange a meeting of 2 hours with Gwendoline and all > of you that day, to discuss a bioinformatics project on microRNA for > Gwendoline. > > Could you please inform me about your availability on 28 Nov. 2008 for > a meeting in Leuven at Campus Gasthuisberg? > > Thank you for your response. > Kind regards, > > Hilde > > > > Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm for more > information. > Fine with me (not too early please, I have to come by train). Yves PS. Would it be ok if I bring one or two postdocs? -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/ Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] Re: Hardware requerements
by Eric Bonnet 25 Sep '08

25 Sep '08

I would suggest to: 1/ replace the oldest IBM blade chassis (14 servers) with a brand new one. As we are using double-core cpus now, this would anyway increase the total number of cores available in the cluster. 2/ Buy an extra tornado-like machine (32 Gb RAM), especially useful for the sysbiol group, who is growing quite rapidly now.. Eric Kenny Billiau wrote: > Hi, > > IT has to compile a list of possible hardware requirements for our group. > > If we need more servers with more memory, an internal webserver, > personal development servers, dedicated blast servers, a bigger cluster, > more storage, regular backups, distributed ***** servers.. Tell us :) > > Or if you feel some systems are not up to our requirements and could use > more RAM, a bigger harddrive, more intuitive filesystem mappings, more > support, more or bigger monitors, laptops for everyone, etc .. Tell us ;) > > If you have any suggestions, improvements or demands you can send them > to Thpar and me. > > -Kenny >

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[Beg-sysbiol] at home this morning
by Vanessa Vermeirssen 23 Sep '08

23 Sep '08

Hi, Sien is still ill, so I will be working at home this morning. I will see you at lunch meeting. Vanessa

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[Beg-sysbiol] data integration paper C. elegans
by Vanessa Vermeirssen 19 Sep '08

19 Sep '08

This is the paper I was talking about... Vanessa Nat Genet. <javascript:AL_get(this, 'jour', 'Nat Genet.');> 2008 Feb;40(2):181-8. Epub 2008 Jan 27.Click here to read <http://www.ncbi.nlm.nih.gov/entrez/utils/fref.fcgi?PrId=3094&itool=Abstract…> Links <javascript:PopUpMenu2_Set(Menu18223650);> A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. *Lee I* <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Lee%2…>, *Lehner B* <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Lehne…>, *Crombie C* <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Cromb…>, *Wong W* <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Wong%…>, *Fraser AG* <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Frase…>, *Marcotte EM* <http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=Search&Term=%22Marco…>. Center for Systems and Synthetic Biology, Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, 2500 Speedway, MBB 3.210, Austin, Texas 78712, USA. The fundamental aim of genetics is to understand how an organism's phenotype is determined by its genotype, and implicit in this is predicting how changes in DNA sequence alter phenotypes. A single network covering all the genes of an organism might guide such predictions down to the level of individual cells and tissues. To validate this approach, we computationally generated a network covering most C. elegans genes and tested its predictive capacity. Connectivity within this network predicts essentiality, identifying this relationship as an evolutionarily conserved biological principle. Critically, the network makes tissue-specific predictions-we accurately identify genes for most systematically assayed loss-of-function phenotypes, which span diverse cellular and developmental processes. Using the network, we identify 16 genes whose inactivation suppresses defects in the retinoblastoma tumor suppressor pathway, and we successfully predict that the dystrophin complex modulates EGF signaling. We conclude that an analogous network for human genes might be similarly predictive and thus facilitate identification of disease genes and rational therapeutic targets. -- ================================================================== Vanessa Vermeirssen, PhD Tel:+32 (0)9 331 38 10 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM vamei(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

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[Fwd: [Beg-sysbiol] is this something we can help with?]
by Nathalie Pochet 15 Sep '08

15 Sep '08

more info about the meeting...

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[Beg-sysbiol] [Fwd: Re: Systems Biology for PNS disease?]
by Nathalie Pochet 15 Sep '08

15 Sep '08

Meeting at 2PM in Bio-IT for the ones who want to join. Kind regards, Nathalie

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[Beg-sysbiol] [Fwd: Re: meeting]
by Eric Bonnet 08 Sep '08

08 Sep '08

for people interested, the meeting will take place in the BUD meeting room. Eric

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[Beg-sysbiol] meeting
by Eric Bonnet 08 Sep '08

08 Sep '08

Dear Anja, I'm Eric, a post-doc in Yves Van de peer's lab, mainly working on microRNA's. Yves asked me to set up a meeting with you, so what about next wednesday at 10h in our lab? would that be ok for you? Best regards, Eric

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[Beg-sysbiol] did we suggest a date yet to meet these people? Eric, maybe you can suggest a date? Thanks, Yves
by Yves Van de Peer 07 Sep '08

07 Sep '08

-------- Original Message -------- Subject: RE: Date: Wed, 3 Sep 2008 17:14:46 +0200 From: Anja Lambrechts <Anja.Lambrechts(a)Ugent.be> To: 'Yves Van de Peer' <yves.vandepeer(a)psb.ugent.be> Beste Yves Bedankt voor het snelle antwoord Voor ons past dinsdag namiddag, woensdag voormiddag, donderdag gans de dag of vrijdag voormiddag. Laat ons maar weten wanneer het voor jullie het beste past Anja ******************************* Dr.Anja Lambrechts Dept. Medical Protein Research, VIB Dept. Biochemistry, Fac. Medicine and Health sciences Ghent University A. Baertsoenkaai 3 B-9000 Gent Belgium Tel : +32-9-264.9332 Fax : +32-9-264.9488 anja.lambrechts(a)Ugent.be -----Original Message----- From: Yves Van de Peer [mailto:yves.vandepeer@psb.ugent.be] Sent: woensdag 3 september 2008 16:55 To: Anja Lambrechts Subject: Re: Anja Lambrechts wrote: > Beste Yves > > mijn naam is Anja Lambrechts en ik ben postdoc in het labo van Prof > Vandekerckhove en Prof Christophe Ampe. > Een tijd geleden vertelde Prof Vandekerckhove mij over jouw resultaten > ivm microRNA onderzoek gekoppeld aan de opregulatie van enkele smooth > muscle cell specifieke genen in bepaalde cellen. Wij bestuderen > fibroblasten afgeleid van een beta-actine knock-out embryo. > Wanneer we eiwit en mRNA expressie vergelijken met normale > fibroblasten dan zien we een enorme opregulatie van smooth muscle cell > specifieke genen. We hebben echter geen idee over de mogelijke > regulatorische mechanismen die hierachter steken. Na het lezen van het > artikel van Davis et al. dat in juli verscheen in Nature (TGFb en > microRNA signalisatie), leek het ons interessant toch eens na te gaan > of de regulatie op microRNA niveau gebeurt. > Aangezien wij leken zijn op dit vlak, zouden we het op prijs stellen > indien we eens met jou hierover konden praten. Zou het voor jou ergens > passen in de loop van volgende week of de week erna? > > Met vriendelijke groeten > Anja Beste Anja, Ja, ik moest al lang eens contact opnemen met jullie, maar door mijn drukke agenda is dat er nog niet van gekomen, waarvoor mijn excuses. Ik vertrek seffens naar Dublin, maar vanaf volgende week dinsdag zou ik wat meer tijd hebben. Kan jij volgende week dinsdag, woensdag, donderdag of vrijdag, dan check ik eens bij mijn postdocs die in die zaken veel kundiger zijn dan ikzelf :-) Tot volgende week ergens, Yves -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/ -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.ugent.be http://bioinformatics.psb.ugent.be/

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