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

[Beg-sysbiol] Re: invitation for our annual departmental meeting ...
by Yves Van de Peer 13 Jul '08

13 Jul '08

Dear Ron, That is great news! We will be in touch shortly to work out the practical details. Thanks again for accepting our invitation and we'll make sure you have a great time in Ghent! Best regards, Yves > Hi Yves, > I will be happy to come. > Best, > Ron. -- 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/

1 0

[Beg-sysbiol] The Systems Biology Research Tool: evolvable open-...[BMC Syst Biol. 2008] - PubMed Result
by Yves Van de Peer 13 Jul '08

13 Jul '08

http://www.ncbi.nlm.nih.gov/pubmed/18588708?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/

1 0

[Beg-sysbiol] paper
by Eric Bonnet 09 Jul '08

09 Jul '08

might be interesting: a network reconstruction method that do not start from scratch but uses prior knowledge Seeded Bayesian Networks: constructing genetic networks from microarray data http://www.biomedcentral.com/1752-0509/2/57/abstract

1 0

[Beg-sysbiol] More about Erdos
by Greg Amoutzias 08 Jul '08

08 Jul '08

http://amphetamines.com/paul-erdos.html --- 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

2 1

[Beg-sysbiol] Are you guys in the lab then? Thanks, Yves
by Yves Van de Peer 04 Jul '08

04 Jul '08

-------- Original Message -------- Subject: P&G Date: Wed, 2 Jul 2008 17:03:43 +0200 From: Barbara Leyman <Barbara.Leyman(a)vib.be> To: Yves Van de Peer <yvpee(a)psb.ugent.be> CC: Rosalinde Van Lipzig <rolip(a)psb.UGent.be> Beste Yves, 12 augustus 9u is prima voor Rudy en mij (ik hoop dat Rosalinde dan ook kan). Maar we zouden liever tot bij u komen, dan kunnen we misschien ook een demonstratie krijgen op jouw computers. OK? Wat P&G betreft vind ik nu toch dat dit lang wachten is. Heb jij een idee of we toch al iets kunnen antwoorden, naar hen? Ik ben er niet tot dinsdag, dan weer wel voor 2 weken. Groetjes Barbara ----------------------------------------- Barbara Leyman, Ph D Licensing Manager *VIB *Rijvisschestraat 120 9052 GENT BELGIUM Tel. +32 9 244 66 11 Fax +32 9 244 66 10 E-mail: barbara.leyman(a)vib.be <mailto:barbara.leyman@vib.be> Website: www.vib.be <http://www.vib.be/> ----------------------------------------- /CONFIDENTIALITY NOTICE:// //This e-mail message and all its attachments are intended solely for the use of the addressee(s) and may contain information that is confidential and privileged. Any unauthorized review, use, disclosure, alteration or distribution is strictly prohibited. If you are not the intended recipient, please delete this message and all attachments and advise the sender by return e-mail. //Thank you./ -- 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/

2 1

[Beg-sysbiol] Is this something we could help with? Please send your opinions/suggestions to me. Thanks in advance, Yves
by Yves Van de Peer 03 Jul '08

03 Jul '08

-------- Original Message -------- Subject: P&G request bioinformatics Date: Tue, 1 Jul 2008 17:37:11 +0200 From: Barbara Leyman <Barbara.Leyman(a)vib.be> To: Yves Van de Peer <yvpee(a)psb.ugent.be> Beste Yves, Alles ok? Ik kwam vorige week terug van BioUS in San Diego alwaar we heel veel bedrijven hebben ontmoet. Een ervan is P&G en die hebben volgende vraag (zie hieronder) Ik heb gezegd dat ik even hulp bij jou zou zoeken om hierop een duidelijk antwoord te geven. Kan je mij helpen aub Bedankt Vriendelijke groeten Barbara *From:* Meller, Steve [mailto:meller.st@pg.com] *Sent:* maandag 30 juni 2008 19:37 *To:* Barbara Leyman *Cc:* Lurieluke, Elena … Separately, one of our Biotech organizations noted that VIB had expertise in the development of informatics tools. We have some specifics that I’d like to understand if there could be a match: We have Affymetrix gene expression experiments on both human and mouse samples. There are two types of microarray experiments available for analysis; (1) time courses and (2) two-sample comparison studies with activation and inactivation of the desired biology. There are also metadata available for some studies such as subject age and target tissue histology. We wish to explore new approaches that can be applied to an in-house set of gene expression studies. A number of widely used conventional approaches have been applied to this problem but they have failed to identify key drug targets meeting success criteria based on subsequent validation testing. So, we looking for novel algorithms that may contain new data formulations and/or well established machine learning or data mining techniques. The ideal solutions should work on both time course data and data taken from the two-sample classes and take advantage of available metadata to reveal unseen correlations between gene expression patterns and metadata. Likewise the methods should work across both human and mouse microarray experiments. We are not interested in standard applications of conventional bioinformatic methods for clustering or for the identification of over represented pathways and processes such as Gene Set Enrichment Analysis, or methods available in GeneSpring, Partek, Omniviz or Bioconductor. In other words, we are well aware of the mainstream solutions and are not interested in approaches based on them unless dramatic improvement in performance is expected. Please let me know if you thought there might be such approaches at VIB that might be able to: 1. Describe novel approaches for analysis of Affymetrix gene expression datasets and if possible provide examples of successful use of those approaches to identify therapeutic targets. 2. Work effectively with gene expression datasets from both Human and Mouse samples. 3. Be useful for the analysis of gene expression and across multiple studies and with time-course data. 4. Be reasonable and practical to implement and test the solution Please let me know. Cheers Steve Meller, PhD Procter and Gamble 11810 East Miami River Road Cincinnati, OH, 45253 (w) +1 (513) 627-0822 (cell) +1 (513) 205-1967 ------------------------------------------------------------------------ *From:* Barbara Leyman [mailto:Barbara.Leyman@vib.be] *Sent:* Thursday, June 26, 2008 10:53 AM *To:* Meller, Steve *Cc:* Lurieluke, Elena *Subject:* Nanobodies for cosmetics and cleaning products Dear Stephen, It was a great pleasure to have met you at Bio in San Diego last week. I hope you had a successful meeting, at least we had. I include Elena in this e-mail so she can also see the follow up, as I have been communicating with her about this opportunity before Bio. Please find in the attachment a corporate flyer of VIB and in addition a presentation on the possible applications of nanobodies in cosmetics and cleaning products. Especially slide 7 (examples) shall be of interest to you. VIB is open to collaborate in different ways, ranging from purely licensing deals to R&D collaborations, we have a facility that can generate nanobodies for discovery purposes. Should you wish to discuss this further or if you have any questions, please do not hesitate to contact me. With kind regards Barbara ----------------------------------------- Barbara Leyman, Ph D Licensing Manager *VIB *Rijvisschestraat 120 9052 GENT BELGIUM Tel. +32 9 244 66 11 Fax +32 9 244 66 10 E-mail: barbara.leyman(a)vib.be <mailto:barbara.leyman@vib.be> Website: www.vib.be <http://www.vib.be/> ----------------------------------------- /CONFIDENTIALITY NOTICE:// This e-mail message and all its attachments are intended solely for the use of the addressee(s) and may contain information that is confidential and privileged. Any unauthorized review, use, disclosure, alteration or distribution is strictly prohibited. If you are not the intended recipient, please delete this message and all attachments and advise the sender by return e-mail. //Thank you./ -- 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/

1 0

[Beg-sysbiol] Erdos number
by Nathalie Pochet 03 Jul '08

03 Jul '08

http://www.oakland.edu/enp/

2 1