- beg-sysbiol@psb.ugent.be - maillist.psb.ugent.be

[Beg-sysbiol] [Fwd: Meta Analysis of Gene Expression Data within and Across Species.]
by Klaas Vandepoele 21 Aug '08

21 Aug '08

Great review from Kathleen her group about comparative transcriptomics. Klaas -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Come on if you think, come on if you think You can take us on, you and whose army?

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[Beg-sysbiol] @home
by Eric Bonnet 20 Aug '08

20 Aug '08

hi there, I'm working at home this morning. see you guys this afternoon. Eric

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[Beg-sysbiol] [Fwd: FW: TG/SCREEN/012]
by Yves Van de Peer 19 Aug '08

19 Aug '08

-------- Original Message -------- Subject: FW: TG/SCREEN/012 Date: Tue, 12 Aug 2008 14:17:31 +0200 From: Rudy Dekeyser <Rudy.Dekeyser(a)vib.be> To: Yves Van de Peer <yves.vandepeer(a)psb.ugent.be> CC: Barbara Leyman <Barbara.Leyman(a)vib.be> Yves, ter info,rudy *From:* Jan Tavernier [mailto:Jan.Tavernier@UGent.be] *Sent:* dinsdag 12 augustus 2008 13:53 *To:* Rudy Dekeyser *Subject:* RE: TG/SCREEN/012 Rudy: De Cell paper is uit en staat op PubMed. De data zijn open-source: dit is wel een “fragmentoom”-map. Ik kan ook zorgen voor toegang tot de S. cerevisiae interactoommap (verschijnt binnenkort in Science). Ik check de beschikbaarheid van de C. elegans an mens-mappen. Bedankt voor de tip: ik kijk het octrooi na. Greetz, Jan ------------------------------------------------------------------------ *From:* Rudy Dekeyser [mailto:Rudy.Dekeyser@vib.be] *Sent:* 12 August 2008 13:17 *To:* Jan Tavernier *Subject:* FW: TG/SCREEN/012 Dag Jan, Twee zaken (ter info) : 1) Gezien yves van de peer en zijn team momenteel hun systeem biologie software ah uitbreiden zijn en ze interesse hebben om meer eiwit-eiwit data te integreren heb ik heb yves daarnet verteld dat jij met marc vidal een groot project hebt op eiwit-eiwit interacties en dat er binnenkort in Cell een publicatie staat. Het zou knn dat yves je contacteert om te checken of hij toegang kan hebben tot de data. 2) In de attached file : een octrooiaanvrage die we lang geleden indienden. Je moet ze vooral NIET lezen, maar ‘ns kijken naar figuur 1. Daar staat een methode om op snelle wijze combinaties van hypotheses te evalueren via een “3D-aanpak”. Ik vroeg me af of die aanpak in een gemodificeerde vorm bruikbaar zou zijn in jouw arrayMAPPIT. Bye for now,rudy -- 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] (no subject)
by Greg Amoutzias 14 Aug '08

14 Aug '08

I accidentally came across this photo :-) --- Greg Amoutzias, Ph.D VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3758 Fax: +32 (0)9 331 3809 email: gramo(a)psb.ugent.be

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[Beg-sysbiol] working @ home tomorrow morning
by Nathalie Pochet 06 Aug '08

06 Aug '08

Hi, Somebody from Belgacom will come tomorrow somewhere between 8h and noon to check my phone connection, so I will be working at home till they have left. Kind regards, Nathalie

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[Beg-sysbiol] Systems Approaches to Identifying Gene Regulatory Networks in Plants
by Tom Michoel 28 Jul '08

28 Jul '08

<http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.cellbio.24.1107…>

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[Beg-sysbiol] Life, logic and information
by Yvan Saeys 24 Jul '08

24 Jul '08

-- ================================================================== Dr. Yvan Saeys, PhD DEPARTMENT OF PLANT SYSTEMS BIOLOGY Fax:32 (0)9 331 38 09 BIOINFORMATICS TEAM Tel:32 (0)9 331 36 95 GHENT UNIVERSITY, Technologiepark 927, B-9052 Gent, Belgium Vlaams Instituut voor Biotechnologie VIB mailto:yvan.saeys@ugent.be http://bioinformatics.psb.ugent.be/ http://www.psb.ugent.be/~yvsae/ ==================================================================

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[Beg-sysbiol] Conservation and topology of protein interaction n...[Proc Natl Acad Sci U S A. 2008] - PubMed Result
by Yves Van de Peer 20 Jul '08

20 Jul '08

http://www.ncbi.nlm.nih.gov/pubmed/18632555?dopt=Abstract -- 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] is this something we can help with?
by Yves Van de Peer 20 Jul '08

20 Jul '08

-------- Original Message -------- Subject: FW: Systems Biology for PNS disease? Date: Fri, 4 Jul 2008 16:07:03 +0200 From: Timmerman Vincent <vincent.timmerman(a)ua.ac.be> To: <yves.vandepeer(a)psb.ugent.be> __________________________________________ *From:* Timmerman Vincent *Sent:* Friday, July 04, 2008 4:03 PM *To:* Yves Van de Peer (_yvdp(a)gengenp.rug.ac.be) _*_Cc_* <mailto:yvdp@gengenp.rug.ac.be%29Cc>*:* Leonardo de Almeida Souza ; sophie janssens *Subject:* Systems Biology for PNS disease? Dear Yves, As I enjoyed your presentation on “Systems Biology” at the VIB DC meeting in June, I would like to come back at our discussion we had. As you know we are studying the molecular genetics and cell biology of the peripheral nervous system (PNS). In particular we study the inherited forms of PNS disease, resulting in peripheral nerve degeneration. Up to date we have 40 genes and more than 800 mutations in these genes causing various types of peripheral neuropathies. For many of these genes, their protein function is “unknown” or it remains a mystery why mutations in these proteins are associated with neurodegeneration. As an example we identified mutations in small heat shock protein genes (HSPB1 and HSPB8) causing motor neuropathies, mutations in amino-acyl-tRNA synthetases (YARS, GARS) causing variants of Charcot-Marie-Tooth (CMT) neuropathies, mutations in small GTP-ases and GEF proteins causing other variants of CMT, etc. Other genes make sense since these are implicated in Schwann-cell biology and myelination, or axonal transport. You can find on this link (_http://www.molgen.ua.ac.be/CMTMutations/_) a database that we developed over the years showing the genes involved and the mutations identified so far in peripheral neuropathies. It would be very interesting and timely to run one of your bio-informatic platforms to compare the wild type protein-protein interaction networks between these 40 known genes, with the mutant protein-protein interactions. This is of interest since we are currently hunting for differential interacting molecular partners (wild type versus mutant) for some of the genes we are currently focusing on in one of our research projects (through TAP purification and mass-spectrometry). The identification of small (or major: although unlikely) differences between wild type and patient/mutation specific protein interaction networks would provide novel insights into which “novel” proteins or genes could explain the neuronal specificity. Would it be possible to meet with you and your colleagues this summer or in September to see what is feasible at the bio-informatics level with the hope to detect some interacting genes that could be relevant for neuropathies. FYI: I will be on holiday in August (1-23). With my best and friendly greetings, Vincent Prof. Dr. Vincent Timmerman, PhD VIB - Department of Molecular Genetics Peripheral Neuropathy Group University of Antwerp - CDE Parking P4, Building V, Room 1.30 Universiteitsplein 1 BE-2610 Antwerpen Belgium Tel: +32-3-265.10.24 Tel: +32-3-265.10.02 (Secretary VIB8: Mrs. Gisèle Smeyers) Fax: +32-3-265.10.12 E-mail: _vincent.timmerman(a)ua.ac.be_ <mailto:vincent.timmerman@ua.ac.be> _http://www.molgen.ua.ac.be/_ _http://www.molgen.ua.ac.be/CMTMutations/_ -- 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] I'm looking for a postdoc (or 2) who can fill this in. Thanks in advance, Yves
by Yves Van de Peer 17 Jul '08

17 Jul '08

-------- Original Message -------- Subject: FW: Studie ivm systems biology en bioinformatics Date: Thu, 17 Jul 2008 11:05:49 +0200 From: monique jansen <moniquejansen(a)telenet.be> Organization: Telenet Internet To: <yvpee(a)psb.ugent.be> Beste Dr. Van de Peer, Ik kreeg Uw naam van Bram De Craene in het VIB. Mijn naam is Monique Jansen en ik werk voor EAC. Wij doen een internationale studie over de impact van genomics technologies op systems biology en bioinformatics. Ik doe daarvoor een aantal interviews in heel Europa, en zou graag met U ook een interview doen. Ik voeg de vragenlijst met de onderwerpen bij deze mail, U kan die invullen ofwel mij contacteren voor een gesprek hierover, Hoogachtend, */Monique Jansen /**//* */Enterprise Analysis Corporation/* */Belgium /* */Office: +32-16-25 72 77/* */Email: /**/mjansen(a)eacorp.com <mailto:mjansen@eacorp.com>/**/ or /**/moniquejansen(a)telenet.be <mailto:moniquejansen@telenet.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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