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

[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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[Beg-sysbiol] Bio-IT World
by Yves Van de Peer 16 Jul '08

16 Jul '08

http://www.bio-itworld.com/issues/2008/july-august/russell-transcript.html -- 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] looking for a webcam
by Frederick Depuydt 15 Jul '08

15 Jul '08

Hi, the webcam from the meeting room seems to be missing, does anybody know where it went or whether there's a replacement ? regards, Frederick

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[Beg-sysbiol] Allee, precies toch ne goeie talk gegeven :-)
by Yves Van de Peer 14 Jul '08

14 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] Shall we try submit something with another VIB department?
by Yves Van de Peer 14 Jul '08

14 Jul '08

-------- Original Message -------- Subject: VIB International Ph.D. Program 2009 Date: Mon, 14 Jul 2008 17:29:59 +0200 From: Mark Veugelers <Mark.Veugelers(a)vib.be> To: Mark Veugelers <Mark.Veugelers(a)vib.be> Dear VIB-colleague, In 2009, VIB will again support 4 talented, international students to obtain a Ph.D. as part of VIB’s International Ph.D. Program. We are again launching a call to all VIB group leaders to submit interdisciplinary projects, involving a promoter and a co-promoter from two different VIB departments, for the VIB International Ph.D. Program Projects can be submitted, starting tomorrow, through a web form, available on the VIB website (http://www.vib.be/VIB/EN/Ph.D.+program/Projects+for+Group+Leaders/) The project proposals will be made accessible to prospective candidates on the VIB website in parallel with the worldwide advertisement of the program in November 2008 (time-schedule – see below). *_Background (See also www.vib.be/phd <http://www.vib.be/phd>) _* The framework for the 2009 call will be similar to the previous calls, whereby each group leader can be involved in two project proposals: once as a promoter and once as a co-promoter. Project proposals for VIB’s International Ph.D. Program must be interdepartmental and interdisciplinary, addressing a biological question that needs the expertise of different research groups to be solved. *Project proposals should aim for a 50/50 distribution between two VIB-labs *and include 1) a well defined scientific problem or biological question, 2) clearly stated, ambitious, but not unrealistic goals that can be reasonably achieved by 1 student within 4 years, and 3) a brief but clear description of how the proposal incorporates knowledge and expertise from 2 VIB Departments. The work distribution between the two labs should be explicitly stated. Please also indicate whether there has already been collaborative research performed relevant to the project. Since the project proposals are also aimed towards students, complex terminology and long texts should be avoided (project proposals cannot be longer than 1500 characters, not counting spaces). Applications for the VIB International Ph.D. Program are limited to non-Belgians currently living abroad. Applications from candidates who have been working in Belgium in the year leading up to the application deadline will not be considered. Candidates should hold a university degree or satisfy equivalent requirements to start a doctoral program at a Flemish university. VIB will provide financial support to the selected Ph.D. candidates for 2 periods of 2 years towards a Ph.D. degree after 4 years. Students apply by filling out an application form, downloadable from the VIB website. In their application, prospective candidates will indicate and argument their top three choices from the available projects without ranking them. The Group Leader Committee will be responsible for evaluating the applications and selecting the best candidates. The top 15 candidates will be invited for an interview. Out of this applicant pool, the top 4 will be selected for the VIB International Ph.D. Program. Accepted candidates will have a promoter and a co-promoter from a different VIB department. The Ph.D. degree would be from the university of the promoter. The non-selected students form a reserve waiting list which can be tapped into. VIB will support the interview travel costs and salaries of the selected Ph.D. students (2 periods of 2 years). Progress of accepted candidates will be evaluated after two years. Continuation of financial support will depend on the results obtained. Bench fees for the Ph.D. students must be supplied by the host departments or groups. 15 July 2008 Call for interdepartmental projects (3 months). 27 October 2008 Deadline for project submission. 1 November 2008 International advertisement of the program and projects. Call for applications (3.5 months). 15 February 2009 Deadline for applications. 13 March 2009 Selection step 1: evaluation of written applications and selection of candidates for interviews. 11-14 May ^ 2009 Selection step 2: interviews of candidates from step 1 and selection of 4 top candidates. June-Sept 2009 Candidates choose promoters and start work in their department or group. For more information, contact the GLC-representative from your department or, alternatively, Mark Veugelers (Mark.Veugelers(a)vib.be <mailto:Mark.Veugelers@vib.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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[Beg-sysbiol] Systems Approaches to Identifying Gene Regulatory ...[Annu Rev Cell Dev Biol. 2008] - PubMed Result
by Yves Van de Peer 13 Jul '08

13 Jul '08

http://www.ncbi.nlm.nih.gov/pubmed/18616425?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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