April 2006 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] module painting
by Tom Michoel 30 Apr '06

30 Apr '06

It was a dirty job but someone had to do it ... I wrote some java-code to automatically generate regulation program figures. It needs some tidying up before putting it in the repository, if you're curious see Module.java in my src/ directory. I guess you all owe me a beer now :-) Tom PS: the attached figure is a true hierarchical clustering tree, but with a dummy regulator variable on each node.

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[Beg-sysbiol] FYI
by Steven Maere 26 Apr '06

26 Apr '06

-- ================================================================== Steven Maere Dept. of Plant Systems Biology, Biocomputing research group Ghent University / VIB tel: +32 9 33 13 692 Technologie Park 927 fax: +32 9 33 13 809 B-9052 Gent BELGIUM email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://www.psb.ugent.be/cbd/ ==================================================================

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[Beg-sysbiol] Alignment of biological networks [Fwd: q-bio daily Subj-class mailing 2 26]
by Roeland Merks 21 Apr '06

21 Apr '06

Is this paper interesting for you? Cheers, Roeland ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ send mail only to q-bio(a)arXiv.org, do not reply to no-reply@... send any complaints regarding submissions directly to submitter. use a single `get' to request multiple papers, `list macros' for available macro packages, and `help' for a list of available commands and other info. ------------------------------------------------------------------------------ point your www client at http://arXiv.org/ To unsubscribe, e-mail To: q-bio(a)arXiv.org, Subject: cancel ------------------------------------------------------------------------------ Submissions to: Molecular Networks received from Wed 19 Apr 06 20:00:03 GMT to Thu 20 Apr 06 20:00:03 GMT ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ \\ Paper: q-bio.MN/0604026 Date: Thu, 20 Apr 2006 12:18:25 GMT (78kb) Title: Alignment of biological networks Authors: Johannes Berg and Michael L\"assig Comments: 10 pages, 7 figures, 1 colour figure. Supporting text is available from the authors Subj-class: Molecular Networks; Genomics \\ Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction networks by {\em alignment}, which maps bona fide functional relationships between genes in different organisms. Network alignment is based on a scoring function measuring mutual similarities between networks in their interaction patterns as well as sequence similarities between their nodes. High-scoring alignments as well as optimal alignment parameters are inferred by a systematic Bayesian analysis. We apply this method to analyze the evolution of co-expression networks between human and mouse. We find evidence for significant conservation of gene expression clusters and give network-based predictions of gene function. We discuss examples where cross-species functional relationships between genes do not concur with sequence similarity. \\ ( http://arXiv.org/abs/q-bio/0604026 , 78kb) %-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%- %%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%% %%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%--- -- Roeland Merks Department of Plant Systems Biology VIB / Ghent University Technologiepark 927 B-9052 Ghent, Belgium http://www.psb.ugent.be Tel. +32-(0)9-33 13825 email: post(a)roelandmerks.nl http://www.roelandmerks.nl weblog: http://biolog.volkskrantblog.nl

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[Beg-sysbiol] Bayesian Hierarchical Clustering
by Tom Michoel 20 Apr '06

20 Apr '06

This paper presents precisely the regression tree building I had in mind, and fits perfectly in the Segal-framework. Thanks to Eric for name dropping "hierarchical clustering" when I tried to explain it, and to google for turning this one up so quickly :-) Tom -- Abstract: We present a novel algorithm for agglomer- ative hierarchical clustering based on evalu- ating marginal likelihoods of a probabilistic model. This algorithm has several advan- tages over traditional distance-based agglom- erative clustering algorithms.[...]

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[Beg-sysbiol] segal meeting
by Steven Maere 19 Apr '06

19 Apr '06

Dear comrades, What about a short 15 min meeting somewhere at the end of the week to discuss progress and deadlines ? Friday 15.00 ? S -- ================================================================== Steven Maere Dept. of Plant Systems Biology, Biocomputing research group Ghent University / VIB tel: +32 9 33 13 692 Technologie Park 927 fax: +32 9 33 13 809 B-9052 Gent BELGIUM email: stmae(a)psb.UGent.be http://www.psb.UGent.be http://www.psb.ugent.be/cbd/ ==================================================================

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[Beg-sysbiol] Entrez PubMed
by Yves Van de Peer 16 Apr '06

16 Apr '06

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&dopt=Abstract&db…

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[Beg-sysbiol] please write down in your agendas!
by Yves Van de Peer 13 Apr '06

13 Apr '06

Dear All, Let's have our second 'systems biology' meeting on May 15th (this was the preferred date for most people), 10am. See you all then. Ann will book the Apex or Leaf room. Cheers, Yves -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Department of Plant 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.ugent.be http://www.psb.ugent.be/bioinformatics/

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[Beg-sysbiol] Journal of Computational Biology - 13(2):165
by Tom Michoel 13 Apr '06

13 Apr '06

Is it really only Israeli's doing this kind of thing? Anyway, interesting paper: <http://www.liebertonline.com/doi/abs/10.1089/cmb.2006.13.165> A Probabilistic Methodology for Integrating Knowledge and Experiments on Biological Networks Mar 2006, Vol. 13, No. 2: 165-181 Irit Gat-Viks School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel. Amos Tanay School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel. Daniela Raijman School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel. Ron Shamir School of Computer Science, Tel-Aviv University, Tel-Aviv 69978, Israel. Biological systems are traditionally studied by focusing on a specific subsystem, building an intuitive model for it, and refining the model using results from carefully designed experiments. Modern experimental techniques provide massive data on the global behavior of biological systems, and systematically using these large datasets for refining existing knowledge is a major challenge. Here we introduce an extended computational framework that combines formalization of existing qualitative models, probabilistic modeling, and integration of high-throughput experimental data. Using our methods, it is possible to interpret genomewide measurements in the context of prior knowledge on the system, to assign statistical meaning to the accuracy of such knowledge, and to learn refined models with improved fit to the experiments. Our model is represented as a probabilistic factor graph, and the framework accommodates partial measurements of diverse biological elements. We study the performance of several probabilistic inference algorithms and show that hidden model variables can be reliably inferred even in the presence of feedback loops and complex logic. We show how to refine prior knowledge on combinatorial regulatory relations using hypothesis testing and derive p-values for learned model features. We test our methodology and algorithms on a simulated model and on two real yeast models. In particular, we use our method to explore uncharacterized relations among regulators in the yeast response to hyper-osmotic shock and in the yeast lysine biosynthesis system. Our integrative approach to the analysis of biological regulation is demonstrated to synergistically combine qualitative and quantitative evidence into concrete biological predictions.

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[Beg-sysbiol] [Fwd: status implementatie van segal paper]
by Tom Michoel 11 Apr '06

11 Apr '06

Email from Tim who is also working on Segal-like stuff, could be very helpful for our current problem of overlapping modules. I put his code as well as the two papers mentioned in a directory "timvdb" in the java directory of the segal project. Tom -------- Original Message -------- Subject: status implementatie van segal paper Date: Wed, 05 Apr 2006 16:42:08 +0200 From: Tim Van den Bulcke <Tim.VandenBulcke(a)esat.kuleuven.be> To: tom.michoel(a)psb.ugent.be Hey Tom, lang geleden dat ik nog van mij laten horen heb, maar ik wou je even een update geven van de implementatie van de Battle paper over overlappende modules (paper in attach). De situatie is als volgt: de grote lijnen van het algoritme zijn geimplementeerd, maar er zit nog (minstens) 1 grote bug in een deel van het EM algoritme, namelijk in de assignatie van activiteiten-niveau's. Verder heb ik een aantal vereenvoudigingen in het model die gaandeweg kunnen uitgebreid worden, zoals de veronderstelling dat de leaf nodes Gaussiaans verdeeld zijn in plaats van linear Gaussians en een andere prior die ik voorlopig uniform veronderstel. Mijn algemene indruk was dat heel wat zaken nogal summier in de paper vermeld zijn en het niet altijd even duidelijk is hoe het concreet werkt. Verder zou mijn thesisstudent tegen juni de andere paper (Segal, zie attach) geimplementeerd moeten hebben. Die paper is eigenlijk de voorloper van de Battle-paper, met een eenvoudiger model zonder regulatorisch programma. Ik ben nu even met andere dingen bezig rond het gebruik van synthetische data voor inferentie algoritmes (we gebruiken onze Syntren-generator daarvoor), dus voorlopig staat Segal even op 'hold'. Als het je interesseert: de source code staat op: http://homes.esat.kuleuven.be/~vdbulcke/tmp/cellproc.zip, paswoord is dp@#tree. De belangrijkse klasse is EMAlgorithm.java in package esat.bioi.prm.model.copr en het ding maakt voorlopig ook gebruik van matlab voor het bounded least squares algoritme. Mocht je tijd en interesse hebben: ik zou met jou wel eens over enkele afleidingen willen gaan die ik gedaan heb in de verschillende stappen. Het is mogelijk dat ik ergens een fout heb gemaakt, maar ik zie het voorlopig niet. Ik hoop dat jullie nu weer iets meer op de hoogte zijn van mijn activiteiten rond PRMs! Hebben jullie nog nieuws rond de module-netwerk implementatie? Groeten, Tim. -- _______________________________________________________ ir. Tim Van den Bulcke research assistant ESAT-SCD K.U. Leuven Kasteelpark Arenberg 10 B-3001 Leuven-Heverlee Belgium room: 03.11/14 tel: +32 16 32.86.43 fax: +32 16 32.19.70 email: tim.vandenbulcke(a)esat.kuleuven.be homepage: http://homes.esat.kuleuven.be/~vdbulcke/ personal homepage: http://timvandenbulcke.objectis.net _______________________________________________________ -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] follow up meeting ...
by Yves Van de Peer 10 Apr '06

10 Apr '06

Dear All, I suggest to have our next ' systems biology' meeting at one of the following dates (please let me know which suits you): Monday, May 8th Tuesday, May 9th (only morning) Monday, May 15th (before 3pm) Monday, May 22nd Other days are virtually impossible for me in May, but of course you can also have a meeting without me, if the dates listed above prove to be too difficult for most. Cheers, Yves -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Department of Plant 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.ugent.be http://www.psb.ugent.be/bioinformatics/

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