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

[Beg-sysbiol] Systems biology at the Institute for Systems Biolo...[Brief Funct Genomic Proteomic. 2008] - PubMed Result
by Yves Van de Peer 29 Jun '08

29 Jun '08

http://www.ncbi.nlm.nih.gov/pubmed/18579616?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] can someone translate for Eric :-)
by Yves Van de Peer 26 Jun '08

26 Jun '08

-------- Original Message -------- Subject: actomyosine Date: Thu, 26 Jun 2008 14:38:22 +0200 From: Joel Vandekerckhove <joel.vandekerckhove(a)ugent.be> To: <Yves.VandePeer(a)UGent.be> CC: 'Joel Vandekerckhove' <joel.vandekerckhove(a)ugent.be>, 'Anja Lambrechts' <Anja.Lambrechts(a)Ugent.be>, 'christophe ampe' <christophe.ampe(a)ugent.be> Beste Yves, Ik wens je hierbij nog eens te feliciteren voor de exciting presentatie tijdens het laatste VIB directiecommittee. Ik heb nog even onze proteomics resultaten van beta-actin KO muis fibroblasten bekeken en vond de volgende zeer sterk opgereguleerde eiwitten: - Alfa smooth muscle actin - Transgelin SM 22 - Calponin – 1 - Myosin regulatory light chain Deze eiwitten gaan alle van nul in normale fibroblasten tot zeer hoge expressie in beta KO fibroblasten. Als ik mij niet vergis waren minstens drie ervan ook in uw preferentiële lijst aanwezig. Het zijn alle ook smooth-muscle specific isovormen van actine en actine-bindende eiwitten. De mensen die het werk hebben uitgevoerd ( Anja Lambrechts en Christoph Ampe) beschikken nog over een groot pak bijkomende proteomics en microarray data van de beide cellijnen en deze data hadden ze graag aan uw mensen even “getoond”. Is het nog mogelijk om een slot vrij te maken bij jullie om even samen te zitten? Met de beste groeten, Joël. Prof. Dr. Joël Vandekerckhove Department of Biochemistry, Ghent University (UGent) Department of Medical Protein Research, Flanders Institute for Biotechnology (VIB) Albert Baertsoenkaai 3 B-9000 Gent - Belgium Tel: +32 (0)9 264 93 17 (secr.) - 93 03 (direct) Fax: +32(0)9 264 94 90 -- 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] International Conference on Systems Biology, Göteborg, 2008
by Yves Van de Peer 25 Jun '08

25 Jun '08

http://www.icsb-2008.org/ -- 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] luxembourg sponsors US systems biology science
by Steven Maere 23 Jun '08

23 Jun '08

They don't have systems biologists, but they do have the money... Maybe we could convince the grand-duke to sponsor us too ? http://www.caltechcancer.org/node/260 S -- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3810 fax: +32 9 331 3809 email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================

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[Beg-sysbiol] Inferring ancestral protein interaction networks. [Methods Mol Biol. 2008] - PubMed Result
by Yves Van de Peer 22 Jun '08

22 Jun '08

http://www.ncbi.nlm.nih.gov/pubmed/18566775?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] TiG :: Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal?
by Klaas Vandepoele 19 Jun '08

19 Jun '08

Sorry for double posting. Comparison of transcription regulatory interactions inferred from high-throughput methods: what do they reveal? <http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TCY-4SMX82D-2&_u…> /*In Press, Corrected Proof*/, /Available online 31 May 2008 Trends in Genetics/ S. Balaji, Lakshminarayan M. Iyer, M. Madan Babu, L. Aravind -- 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/ --------------------------------------------------------- Not shy of a spark, a knife twists at the thought that I should fall short of the mark

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[Beg-sysbiol] [Fwd: DREAM3 Biological Prediction Challenges]
by Tom Michoel 18 Jun '08

18 Jun '08

-------- Original Message -------- Subject: DREAM3 Biological Prediction Challenges Date: Wed, 18 Jun 2008 00:34:57 -0400 From: Gustavo Stolovitzky <gustavo(a)us.ibm.com> To: Gustavo Stolovitzky <gustavo(a)us.ibm.com> PLEASE LET ME KNOW IF YOU PREFER NOT TO RECEIVE ANNOUNCEMENTS FROM THE DREAM PROJECT SINCERE APOLOGIES IF YOU RECEIVE THIS ANNOUNCEMENT MORE THAN ONCE *Call for Network Inference and Biological Predictions* *DREAM 3 * *The 3rd DIALOGUE ON REVERSE ENGINEERING * *ASSESSMENT AND METHODS* Dear Colleague, We would like to cordially invite you to submit network inferences and answers to our new biological prediction challenges. To access the data sets, and descriptions of the challenges, please go to http://wiki.c2b2.columbia.edu/dream/index.php/The_DREAM3_Challenges. The best performers in these challenges will be invited to present in the joint RECOMB Systems Biology/Regulatory Genomics/DREAM3 conference. See _http://compbio.mit.edu/recombsat/_ for details on this conference. To learn more about the DREAM3 conference, please go to http://wiki.c2b2.columbia.edu/dream/index.php/The_3rd_DREAM_Conference To learn more about the DREAM project, please go to http://wiki.c2b2.columbia.edu/dream/index.php/The_DREAM_Project *Network Inference and Predictions Submission Timeline* Mid June, 2008 Call for participation in the challenges. Challenges posted. Sep 15, 2008 Predictions Submission deadline. Oct 15, 2008 Notifications to predictors of their scores and ranks. Oct 29-Nov 2, 2008 RECOMB Systems Biology/Regulatory Genomics/DREAM3 conference. (The DREAM3 conference track is on October 31.) Prediction Submissions must be received in electronic form by 11:59pm (EST) of Sep 15, 2008. Sincerely, DREAM3 Conference and Challenge Organizers: Gustavo Stolovitzky (chair), IBM Research Andrea Califano, Columbia University DREAM3 is part of a project we call the DREAM (Dialogue for Reverse Engineering Assessments and Methods) project. Its main objective is to catalyze the interaction between experiment and theory in the area of cellular network inference. The fundamental question for DREAM is simple: How can researchers assess how well they are describing the networks of interacting molecules that underlie biological systems, and how well can they predict the results of a biological experiment? The answer is not so simple. Researchers have used a variety of algorithms to deduce the structure of very different biological and artificial networks, and evaluated their success using various metrics. What is still needed, and what DREAM aims to achieve, is a fair comparison of the strengths and weaknesses of the methods and a clear sense of the reliability of the network models they produce. -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] Is this helpful, new, ...?
by Yves Van de Peer 17 Jun '08

17 Jun '08

-------- Original Message -------- Subject: MaskerAID Date: Sun, 15 Jun 2008 19:55:38 +0000 From: jmh.neefs(a)pandora.be <jmh.neefs(a)telenet.be> To: yves.vandepeer(a)psb.ugent.be Professor, Zoals afgesproken de informatie over MaskerAid. MaskerAid: a 30-fold* speed enhancement to RepeatMasker http://blast.wustl.edu/maskeraid/ RepeatMasker gebruikt Smith-Waterman algoritme om gebieden van maximale locale similariteit te vinden. Zeer goed, maar erg traag bij genomen en databases van repeats. Daarom werkt RepeatMasker beduidend sneller als je de genoom sequenties in stukken van ~10 000 residus knipt. MaskerAid gebruikt BLAST om juist hetzelfde te doen: minstens 99 gelijk, maar veel sneller klaar: minuten in plaats van uren. En knippen van genoom sequenties is niet nodig. Het kan nog simpeler: ik heb vroeger zelf een PERL script geschreven (zorro.pl) om met BLAST genoom sequenties te maskeren: alle hits tegen repeat databases worden in de query vervangen door 'x' zodat BLAST die in het vervolg niet meer gebruikt. Je kan de hoofdletters ook vervangen door kleine letters en met de aangepaste BLAST opties hetzelfde effect krijgen. Succes met Maskeraid, Jean-Marc -- 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] [Fwd: Condens]
by Yves Van de Peer 10 Jun '08

10 Jun '08

-------- Original Message -------- Subject: Condens Date: Mon, 9 Jun 2008 18:14:19 +0200 From: Vincent Temmerman <vincent.Temmerman(a)vib.be> To: <yvpee(a)psb.ugent.be> CC: 'David De Weirdt' <dawei(a)psb.ugent.be> Beste Yves, Wegens koelingsproblemen in het overvolle server lokaal op het 1^ste verdiep is er vandaag extra koud water door de koelbalken gejaagd om zo de temperatuur te kunnen laten zakken. Helaas heeft het voor condens gezorgd op de koelbalken die beginnen druppen is, mijn excuus hiervoor. Wij zijn op zoek naar een oplossing om het lokaal beter te kunnen koelen, daar een andere lokatie momenteel geen optie is. Indien wij terug genoodzaakt worden om dit te herhalen zal ik David hiervan op de hoogte brengen zodat hij de nodige mensen kan verwittigen om niet onder de koelbalken te werken. Met vriendelijke groeten, Vincent *------------------------------------------------------* *Vincent Temmerman* /Verantwoordelijke gebouwen en technieken/ / / Rijvisschestraat 120, 9052 Zwijnaarde (Gent) Belgium BTW: BE 0456 343 923 Tel: 09/331 36 99 - 09/244 66 11 Fax: 09/388 41 29 GSM: 0477 545 170 E-mail: vincent.temmerman(a)vib.be <mailto:vincent.temmerman@vib.be> www.vib.be <http://www.vib.be/> ----------------------------------------- Handtekening_DagvdBio -- 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] working @ home this morning
by Tom Michoel 06 Jun '08

06 Jun '08

waiting for a package in the mail. see you later, tom -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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