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

[Beg-sysbiol] get together
by Eric Bonnet 28 Aug '07

28 Aug '07

Hi there, I'd like to discuss some results that I got for the microRNA network with you guys. What about thursday or friday 11h? Eric

4 3

[Beg-sysbiol] ESF-EMBO Symposia
by Tom Michoel 28 Aug '07

28 Aug '07

http://www.esf.org/activities/esf-conferences/2007-call-for-proposals/esf-e… -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

1 0

[Beg-sysbiol] let's discuss ESF tomorrow?
by Yves Van de Peer 27 Aug '07

27 Aug '07

-------- Original Message -------- Subject: European Conference on Synthetic Biology (ECSB 2007), Spain, November 2007 Date: Mon, 27 Aug 2007 13:52:01 +0200 From: Corinne Wininger - Le Moal <clemoal(a)esf.org> To: clemoal-list <clemoal-list(a)esf.org> FINAL CALL FOR APPLICATIONS * * *ESF-UB Conference in Biomedicine* European Conference on Synthetic Biology (ECSB): Design, Programming and Optimisation of Biological Systems Hotel Eden Roc, Sant Feliu de Guixols (Costa Brava), Spain *24-29 November 2007* Chaired by: Alfonso Valencia (Spanish National Cancer Research Centre, ES), Natalio Krasnogor (University of Nottingham, UK), Sven Panke (ETH, Zürich Institute of Process Engineering, CH) & Victor de Lorenzo (Centro Nacional de Biotecnologia, Madrid, ES) www.esf.org/conferences/07241 <http://www.esf.org/conferences/07241> The field of *synthetic biology* holds a great promise for the design, construction and development of artificial (i.e. man-made) biological (sub)systems, by offering viable new routes to ‘genetically modified’ organisms, smart drugs and hybrid computational-biological devices. The informed manipulation of such biological (sub)systems could have an enormous positive impact on our societies, with its effects being felt across a range of activities such as the provision of healthcare, environmental protection and remediation to the construction of smarter more ubiquitous bio-integrated computing systems, etc. The basic premise of synthetic biology is that methods commonly used to build non-biological systems, such as those employed in the computational sciences and the engineering disciplines that can deal with large and complex systems, could also be use to specify, design, implement, test and deploy novel synthetic biosystems. Synthetic biology lies at the interface of a variety of disciplines ranging from biology through chemistry, physics, computer science, mathematics and engineering. Although undeniably multidisciplinary, this nascent field of research has tended to be locked within the narrow remits of each of its constitutive disciplines. The specific overarching aim of this conference is thus to generate new vigorous interactions between the disciplines that impinge (and contribute to) Synthetic Biology. ECSB 2007 will draw on international expertise from, on the one hand, Biological disciplines (e.g. Genomics, Proteomics, Metabolomics, etc), and on the other hand, Computational and Engineering experts to present a balanced overview of the very latest key technologies and research advances as pertaining to Synthetic Biology in general and the quest for minimal living forms in particular. The conference will bring together some of the most well known international researchers in their respective areas to (1) present introductory tutorials, (2) showcase, through papers and posters presentations, the latest research outputs on this nascent field and (3) to sow the seeds for a more robust and well connected multi-disciplinary research community in synthetic biology. We expect this to be a major international and multi-disciplinary scientific and educational event. Some, but not all, of the *topics* to be presented in the conference include: * DNA Sequencing and Synthesis, * Chemical and Biological Networks, * Computational Techniques (Modelling, Data Mining, Optimisation) for Synthetic Biology, * Minimal Genomes, * Evolution (atural, directed and simulated), * Origins of Life, * Biological Systems, Cell Cycles and Circuits, * Infrastructures for Synthetic Biology, * Minimal Cells, etc. Detailed *scientific programme* (including list of invited speakers) and *application form* accessible on-line from www.esf.org/conferences/07241 <http://www.esf.org/conferences/07241>. Closing Date for Applications: 7 SEPTEMBER 2007 Some *grants* available for young researchers to cover the conference fee and possibly part of the travel costs. Grant requests should be made by ticking appropriate field(s) in the paragraph "Grant application" of the application form <http://www2.esf.org/asp/esfrcaf.asp?confcode=241&meetno=1> (Ctrl + Click to follow the link). For further information, please contact *Ms. Jean Kelly* (jkelly(a)esf.org <mailto:jkelly@esf.org>) from the ESF Conferences Office. Kind regards, Corinne Wininger Communications Officer - ESF Conferences European Science Foundation - Communications Unit 1 quai Lezay-Marnésia, BP 90015 67080 Strasbourg Cedex, France Phone: +33 (0)388 76 21 50 Fax: +33 (0)388 76 71 80 clemoal(a)esf.org <mailto:clemoal@esf.org> www.esf.org/conferences <http://www.esf.org/conferences> -- 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] GR :: Calling cards for DNA-binding proteins
by Klaas Vandepoele 22 Aug '07

22 Aug '07

Calling cards for DNA-binding proteins * Haoyi Wang, Mark Johnston, and Robi David Mitra^1 * / Department of Genetics, Washington University, School of Medicine, Genome Sequencing Center, St. Louis, Missouri 63108, USA / Identifying genomic targets of transcription factors is fundamental^ for understanding transcriptional regulatory networks. Current^ technology enables identification of all targets of a single^ transcription factor, but there is no realistic way to achieve^ the converse: identification of all proteins that bind to a^ promoter of interest. We have developed a method that promises^ to fill this void. It employs the yeast retrotransposon Ty5,^ whose integrase interacts with the Sir4 protein. A DNA-binding^ protein fused to Sir4 directs insertion of Ty5 into the genome^ near where it binds; the Ty5 becomes a "calling card" the DNA-binding^ protein leaves behind in the genome. We constructed customized^ calling cards for seven transcription factors of yeast by including^ in each Ty5 a unique DNA sequence that serves as a "molecular^ bar code." Ty5 transposition was induced in a population of^ yeast cells, each expressing a different transcription factor--Sir4^ fusion and its matched, bar-coded Ty5, and the calling cards^ deposited into selected regions of the genome were identified,^ revealing the transcription factors that visited that region^ of the genome. In each region we analyzed, we found calling^ cards for only the proteins known to bind there: In the /GAL1--10/^ promoter we found only calling cards for Gal4; in the /HIS4/ promoter^ we found only Gcn4 calling cards; in the /PHO5/ promoter we found^ only Pho4 and Pho2 calling cards. We discuss how Ty5 calling^ cards might be implemented for mapping all targets of all transcription^ factors in a single experiment. -- ================================================================== 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/ ==================================================================

1 0

[Beg-sysbiol] [Fwd: Re: smokey2 = tornado]
by Eric Bonnet 20 Aug '07

20 Aug '07

for your info. The 2 machines have 32 Gb RAM and 2 dual-core fast processors (= 4 processors). Eric

1 0

[Beg-sysbiol] paper
by Eric Bonnet 20 Aug '07

20 Aug '07

not so recent (2006), but very nice paper on the possible roles for microRNAs in regulatory networks and evolution. Canalization of development by microRNAs http://www.nature.com/ng/journal/v38/n6s/full/ng1803.html ... nice also to see that the basic concept that underline the paper was published (in Nature) in 1942 !

1 0

[Beg-sysbiol] cell cycle data subsets
by Steven Maere 17 Aug '07

17 Aug '07

Hi, I've divided the cell cycle data in 4 subsets (cc_subset_x in test_data folder) based on complete linkage hierarchical clustering (using Pearson's correlation as similarity measure). There's cell cycle genes in all 4 sets, but subset_3 has most of them (42/87, see .bgo files). Please be aware that when running LeMoNe and successors on these subsets, you make the assumption that not many genes of different subsets ought to end up in the same module. Another preprocessing step that I would like you to consider is to mean-normalize the genewise expression profiles (mean 0, unit stdev) before running LeMoNe, so that genes with similar behavior but different amplitude would end up in the same module. Currently, the expression profiles are not mean-normalized, it's better to provide this option in the program... Cheers, Steven -- ================================================================== 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/ ==================================================================

1 0

[Beg-sysbiol] we should briefly discuss this one of the next days ... a lot concerns you guys and girls! Yves
by Yves Van de Peer 13 Aug '07

13 Aug '07

-------- Original Message -------- Subject: Agenda brainstorm Date: Mon, 13 Aug 2007 15:50:09 +0200 From: Dirk Inze <dirk.inze(a)psb.UGent.be> To: <mc(a)psb.UGent.be> CC: Hilde Diegenant <hidie(a)psb.UGent.be> Dear All, please find a new version of the agenda with incoorperated comments of Gerrit and Wout. I hope to finalize it by wednesday. With kind regards Dirk -- 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

Re: [Beg-sysbiol] systems biology
by Yves Van de Peer 12 Aug '07

12 Aug '07

Yvan Saeys wrote: > Hi Yves, > > As far as Sofie and me concerns, the following two topics are related > to systems biology: > > -text mining approaches to extract knowledge from literature, and thus > enhance/complement/improve other sysbiol approaches > -integration of heterogeneous data sources, both from a data basing > (see thesis Sofie) and a data mining approach (which are the best > techniques for combining data, how can we get more info by combining > things, how can we design new data mining and machine learning > techniques to reason with these different sources of data). > > What do we already have available: the GeneFetch system developed > during the thesis of Sofie, and hopefully a Bioinformatics article in > the following months. The database underlying GeneFetch can already > be used by other people/programs too, but still has to be extended to > other organisms (but this will be quite easy). Later on, we hope to > get some biological validation/feedback, first from the people from > SCK-CEN in Mol when they will start using the tool (probably beginnin > of september, Sofie is giving an initation there at the end of August). Perfect! Tom, steek jij dit in een documentje? Alvast bedankt. 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/

1 0

[Beg-sysbiol] systems biology
by Yves Van de Peer 12 Aug '07

12 Aug '07

Dear All, Soon, August 23 and 24, all PIs have a brainstorm meeting to discuss the future and further strategy of the PSB department. Systems Biology approaches will be high on the agenda, and I was elected :-) to lead the discussion on Systems Biology in the Department. Therefore, I'm trying to compile a list or number of topics that we are already working on and that could be considered systems biology. The idea is to show that we are already doing quite a bit in this field, because it is a general complaint from the experimental labs that nothing (or very little) happens in the department (in a way, many expect some magic analyses to come the computational groups :-). I would like to counter this as much as possible. Therefore, if you all could send me, in a few lines, what topics/subjects your working on and that you consider systems biology projects, please have them compiled (Tom, can you do that?) and send them to me. Many thanks in advance, 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/

1 0