February 2010 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] Towards genome-scale signalling-network reconstructions
by Tom Michoel 24 Feb '10

24 Feb '10

nice review: <http://www.nature.com/nrg/journal/vaop/ncurrent/abs/nrg2750.html> -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

1 0

[Beg-sysbiol] new paper
by jehol＠psb.vib-ugent.be 20 Feb '10

20 Feb '10

Hi, ... free-access link of my DASS-GUI paper ... Abstract: http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq071?ijkey=… PDF: http://bioinformatics.oxfordjournals.org/cgi/reprint/btq071?ijkey=9OSMHJpAB… Greetings, Jens

1 0

[Beg-sysbiol] book probabilistic graphical models
by Steven Maere 18 Feb '10

18 Feb '10

For anyone interested in probabilistic graphical modeling theory, we now have the new book of Daphne Koller and Nir Friedman on that subject (in my office) Steven ================================================================== Steven Maere, PhD Group leader, Evolutionary Systems Biology group Dept. of Plant Systems Biology VIB / Ghent University Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3805 fax: +32 9 331 3809 email: stmae(a)psb.vib-ugent.be http://www.psb.ugent.be/esb/ ==================================================================

1 0

[Beg-sysbiol] Regulatory Impact Factors: Unraveling the transcri... [Bioinformatics. 2010] - PubMed result
by Yves Van de Peer 14 Feb '10

14 Feb '10

http://www.ncbi.nlm.nih.gov/pubmed/20144946?dopt=Abstract -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Associate Department Director, VIB Department of Plant Systems Biology Group Leader Bioinformatics and Systems Biology 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.vib-ugent.be http://bioinformatics.psb.ugent.be/

1 0

[Beg-sysbiol] Nature Protocols: Expander: from expression microarrays to networks and functions
by Tom Michoel 08 Feb '10

08 Feb '10

http://www.natureprotocols.com/2010/01/28/expander_from_expression_micro.php

2 1

[Beg-sysbiol] @leuven
by Eric Bonnet 08 Feb '10

08 Feb '10

I'll be at a VIB training session tomorrow in Leuven, so cu guys on wednesday.. e.

1 0

[Beg-sysbiol] Transcriptional profiling of growth perturbations of the human malaria parasite Plasmodium falciparum
by Klaas Vandepoele 08 Feb '10

08 Feb '10

Transcriptional profiling of growth perturbations of the human malaria parasite /Plasmodium falciparum/ Guangan Hu^1 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…>, ^3 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…> , Ana Cabrera^2 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…>, ^3 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…> , Maya Kono^2 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…> , Sachel Mok^1 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…> , Balbir K Chaal^1 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…> , Silvia Haase^2 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…> , Klemens Engelberg^2 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…> , Sabna Cheemadan^1 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…> , Tobias Spielmann^2 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…> , Peter R Preiser^1 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…> , Tim-W Gilberger^2 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…> & Zbynek Bozdech^1 <https://vibportal.vib.be/f5-w-687474703a2f2f7777772e6e61747572652e636f6d$$/…> ------------------------------------------------------------------------ Abstract Functions have yet to be defined for the majority of genes of /Plasmodium falciparum/, the agent responsible for the most serious form of human malaria. Here we report changes in /P. falciparum/ gene expression induced by 20 compounds that inhibit growth of the schizont stage of the intraerythrocytic development cycle. In contrast with previous studies, which reported only minimal changes in response to chemically induced perturbations of /P. falciparum/ growth, we find that ~59% of its coding genes display over three-fold changes in expression in response to at least one of the chemicals we tested. We use this compendium for guilt-by-association prediction of protein function using an interaction network constructed from gene co-expression, sequence homology, domain-domain and yeast two-hybrid data. The subcellular localizations of 31 of 42 proteins linked with merozoite invasion is consistent with their role in this process, a key target for malaria control. Our network may facilitate identification of novel antimalarial drugs and vaccines. -- Klaas Vandepoele, PhD

1 0

[Beg-sysbiol] Fwd: [SYSTeMS dialogues] Lecture on Genetic regulatory networks
by Tom Michoel 06 Feb '10

06 Feb '10

Begin forwarded message: > From: Jonathan Rogge <Jonathan.Rogge(a)UGent.be> > Date: Fri 5 Feb 2010 09:59:33 GMT+01:00 > To: yvpee(a)psb.ugent.be, Dirk.Inze(a)UGent.be, tomic(a)psb.ugent.be, krwab(a)psb.ugent.be > , martin.kuiper(a)psb.ugent.be, researchers(a)systems.ugent.be > Subject: [SYSTeMS dialogues] Lecture on Genetic regulatory networks > > Dear colleagues, > > I would like to invite you to the following SYSTeMS Dialogue. The > talk will take place in the SYSTeMS classroom (Technologiepark > Zwijnaarde 914, 2nd floor) on Wednesday, February 24th, at 2pm. > It will be given by Dirk De Vos, researcher at the Centrum Wiskunde > en informatica in Amsterdam. Title and abstract of the presentation > are included below. Feel free to inform fellow researchers which > might be interested in this talk. > > Kind regards, > Jonathan Rogge > > --- > ABSTRACT > Title: Modeling and Identification of Genetic Regulatory > Networks Programming Erythropoiesis > > The development of mature blood cells of distinct lineages from > multipotent stem cells (hematopoiesis) involves a progressive > restriction of differentiation potential and the establishment of > lineage-specific gene expression profiles. The establishment of > these profiles relies on lineage-specific transcription factors to > modulate the expression of their target genes [1]. This work is > embedded in a wider ErasmusMC/CWI collaboration that develops the > informatics and mathematics to underpin studies on gene expression > regulation by mapping and analysing the regulatory pathways and > networks of transcription factors that control cellular functions > (so called "Gene Regulatory Networks" or "GRN’s"). This project is > concerned with the mathematical part and concentrates on a GRN > central to erythropoiesis. Among the many housekeeping and tissue- > specific genes involved in the dfferentiation and the commitment of > haematopoietic stem cells to erythrocytes (erythropoiesis), we focus > on a small pool of genes (Gata-1, Gata-2, Pu.1, EKLF, FOG-1, α/ > β -globin) known to be critically involved in an intricate but > well-less investigated regulatory circuit. > > Based on the regulatory interactions in the GRN we have developed a > model in the form of a system to account for the dynamics of gene > expression and regulation involved in this process. Time series of > the levels of all relevant mRNA’s are available from micro-array > analysis of G1E cells, a murine cell line which recapitulates > erythropoiesis. Because of the lack of information about a > significant number of model parameters, our focus is on system > identification. > > This will eventually allow for a thorough analysis of the role of > various characterized as well as hypothetical regulatory mechanisms. > In depth characterization of the necessary expression patterns and > gene regulatory interactions responsible for the the set of > commitments all along the erythroid lineage is essential to gain > fundamental insight into the behaviour of these complex networks and > to design further experiments. Ultimately, this may lead to ways to > rescue erythroid differentiation in several anemic diseases. > > [1] G Swiers, R Patient and M Loose. Genetic regulatory networks > programming hematopoietic stem cells and erythroid lineage > specification. Dev. Biol, 294, 2006. -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

1 0

[Beg-sysbiol] Plant SB
by Klaas Vandepoele 05 Feb '10

05 Feb '10

For those not (yet) reading Plant Physiology. Klaas ----------------------------------------------------------------- UPDATES - FOCUS ISSUE ----------------------------------------------------------------- Gene Expression Analysis, Proteomics, and Network Discovery Sacha Baginsky, Lars Hennig, Philip Zimmermann, and Wilhelm Gruissem Plant Physiol. 2010;152 402-410 http://www.plantphysiol.org/cgi/content/full/152/2/402?etoc Systems Biology Update: Cell Type-Specific Transcriptional Regulatory Networks Li Pu and Siobhan Brady Plant Physiol. 2010;152 411-419 http://www.plantphysiol.org/cgi/content/full/152/2/411?etoc Systems Biology of Organ Initiation at the Shoot Apex Jan Traas and Francoise Moneger Plant Physiol. 2010;152 420-427 http://www.plantphysiol.org/cgi/content/full/152/2/420?etoc Metabolic Networks: How to Identify Key Components in the Regulation of Metabolism and Growth Mark Stitt, Ronan Sulpice, and Joost Keurentjes Plant Physiol. 2010;152 428-444 http://www.plantphysiol.org/cgi/content/full/152/2/428?etoc A Systems View of Responses to Nutritional Cues in Arabidopsis: Toward a Paradigm Shift for Predictive Network Modeling Sandrine Ruffel, Gabriel Krouk, and Gloria M. Coruzzi Plant Physiol. 2010;152 445-452 http://www.plantphysiol.org/cgi/content/full/152/2/445?etoc Signaling between Chloroplasts and the Nucleus: Can a Systems Biology Approach Bring Clarity to a Complex and Highly Regulated Pathway? Hou-Sung Jung and Joanne Chory Plant Physiol. 2010;152 453-459 http://www.plantphysiol.org/cgi/content/full/152/2/453?etoc Bioinformatic and Systems Biology Tools to Generate Testable Models of Signaling Pathways and Their Targets Andrea Pitzschke and Heribert Hirt Plant Physiol. 2010;152 460-469 http://www.plantphysiol.org/cgi/content/full/152/2/460?etoc Hope for Humpty Dumpty: Systems Biology of Cellular Signaling Sarah M. Assmann Plant Physiol. 2010;152 470-479 http://www.plantphysiol.org/cgi/content/full/152/2/470?etoc Systems Biology Uncovers the Foundation of Natural Genetic Diversity Daniel J. Kliebenstein Plant Physiol. 2010;152 480-486 http://www.plantphysiol.org/cgi/content/full/152/2/480?etoc ----------------------------------------------------------------- BREAKTHROUGH TECHNOLOGIES - FOCUS ISSUE ----------------------------------------------------------------- AGRONOMICS1: A New Resource for Arabidopsis Transcriptome Profiling Hubert Rehrauer, Catharine Aquino, Wilhelm Gruissem, Stefan R. Henz, Pierre Hilson, Sascha Laubinger, Naira Naouar, Andrea Patrignani, Stephane Rombauts, Huan Shu, Yves Van de Peer, Marnik Vuylsteke, Detlef Weigel, Georg Zeller, and Lars Hennig Plant Physiol. 2010;152 487-499 Open Access http://www.plantphysiol.org/cgi/content/abstract/152/2/487?etoc ----------------------------------------------------------------- BIOINFORMATICS - FOCUS ISSUE ----------------------------------------------------------------- VirtualPlant: A Software Platform to Support Systems Biology Research Manpreet S. Katari, Steve D. Nowicki, Felipe F. Aceituno, Damion Nero, Jonathan Kelfer, Lee Parnell Thompson, Juan M. Cabello, Rebecca S. Davidson, Arthur P. Goldberg, Dennis E. Shasha, Gloria M. Coruzzi, and Rodrigo A. Gutierrez Plant Physiol. 2010;152 500-515 Open Access http://www.plantphysiol.org/cgi/content/abstract/152/2/500?etoc -- 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.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/ --------------------------------------------------------- Come on out and change the world (around us)

1 0