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

[Beg-sysbiol] Fwd: [statseq] [Call for contributed talks] Gene network inference meeting, Paris, 28-29 March
by Klaas Vandepoele 25 Jan '13

25 Jan '13

fyi -------- Original Message -------- From: Thomas Schiex <Thomas.Schiex(a)toulouse.inra.fr> Sent: Fri Jan 25 15:01:52 CET 2013 To: statseq(a)listes.inra.fr Subject: [statseq] [Call for contributed talks] Gene network inference meeting, Paris, 28-29 March Dear colleagues, We would like to invite you to submit a proposal for a contributed talk to be presented in the forthcoming 'Gene Network Inference' meeting organized by the STATSEQ COST action (www.statseq.eu) in Paris, March 28-29. The meeting is presented in more details on: http://carlit.toulouse.inra.fr/wikiz/index.php/Gene_Network_Inference_Meeti… If you want to propose a talk, just send a one page PDF abstract (using a Times font in 11pt) to GNISG13-bia-org(a)toulouse.inra.fr before: the 15th of February if you want an early feedback on acceptation or before the 20th of March if you are ready to come to the meeting on short notice. Note that room being quite limited, priority will be given to early submissions. Best regards B. Mangin & T. Schiex INRA, Toulouse, France -- Klaas Vandepoele Sent from my Android phone.

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[Beg-sysbiol] cake
by Vanessa Vermeirssen 23 Jan '13

23 Jan '13

Hi all, because of my birthday last week, I will serve some self-baked (artisanal almost, because our mixer broke down ;-) ) apple cake this afternoon around 3 pm in the lounge room. Come and taste it! Vanessa -- ===================================================================== Vanessa Vermeirssen, PhD Tel:+32 (0)9 331 35 36 Fax:+32 (0)9 331 38 09 Bioinformatics and Systems Biology VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM room V311 vamei(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/ ======================================================================

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[Beg-sysbiol] MotifLab: a tools and data integration workbench
by Bram Slabbinck 23 Jan '13

23 Jan '13

FYI MotifLab: a tools and data integration workbench for motif discovery and regulatory sequence analysis Background Traditional methods for computational motif discovery often suffer from poor performance. In particular, methods that search for sequence matches to known binding motifs tend to predict many non-functional binding sites because they fail to take into consideration the biological state of the cell. In recent years, genome-wide studies have generated a lot of data that has the potential to improve our ability to identify functional motifs and binding sites, such as information about chromatin accessibility and epigenetic states in different cell types. However, it is not always trivial to make use of this data in combination with existing motif discovery tools, especially for researchers who are not skilled in bioinformatics programming. Results Here we present MotifLab, a general workbench for analysing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules. MotifLab supports comprehensive motif discovery and analysis by allowing users to integrate several popular motif discovery tools as well as different kinds of additional information, including phylogenetic conservation, epigenetic marks, DNase hypersensitive sites, ChIP-Seq data, positional binding preferences of transcription factors, transcription factor interactions and gene expression. MotifLab offers several data-processing operations that can be used to create, manipulate and analyse data objects, and complete analysis workflows can be constructed and automatically executed within MotifLab, including graphical presentation of the results. Conclusions We have developed MotifLab as a flexible workbench for motif analysis in a genomic context. The flexibility and effectiveness of this workbench has been demonstrated on selected test cases, in particular two previously published benchmark data sets for single motifs and modules, and a realistic example of genes responding to treatment with forskolin. MotifLab is freely available at http://www.motiflab.org. http://www.biomedcentral.com/1471-2105/14/9/abstract -- ========================================================== Bram Slabbinck, PhD Bioinformatics & Systems Biology Division VIB Department of Plant Systems Biology, UGent Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 537 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://bioinformatics.psb.ugent.be ========================================================== Services and consulting in bioinformatics http://www.arctix.be ========================================================== Please consider the environment before printing this email

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[Beg-sysbiol] Network rewiring is an important mechanism of gene essentiality change
by Klaas Vandepoele 12 Dec '12

12 Dec '12

http://www.nature.com/srep/2012/121129/srep00900/full/srep00900.html -- Prof. Dr. Klaas Vandepoele 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/cig/ Twitter: http://twitter.com/plaza_genomics ---------------------------------------------------------

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[Beg-sysbiol] BRM
by Bram Slabbinck 23 Nov '12

23 Nov '12

FYI. Anybody heard or used this already? http://www.biomedcentral.com/content/pdf/1471-2105-13-311.pdf http://www.sysbio.org/dataresources/brm.stm -- ========================================================== Bram Slabbinck, PhD Bioinformatics & Systems Biology Division VIB Department of Plant Systems Biology, UGent Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 537 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://bioinformatics.psb.ugent.be ========================================================== Services and consulting in bioinformatics http://www.arctix.be ========================================================== Please consider the environment before printing this email

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[Beg-sysbiol] Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
by Klaas Vandepoele 10 Jul '12

10 Jul '12

http://genome.cshlp.org/content/22/7/1334.abstract?etoc Predictive regulatory models in/Drosophila melanogaster/by integrative inference of transcriptional networks 1. Daniel Marbach <http://genome.cshlp.org/search?author1=Daniel+Marbach&sortspec=date&submit=…>1 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-1>,2 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-2>,7 <http://genome.cshlp.org/content/22/7/1334.abstract#fn-1>, 2. Sushmita Roy <http://genome.cshlp.org/search?author1=Sushmita+Roy&sortspec=date&submit=Su…>1 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-1>,2 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-2>,3 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-3>,7 <http://genome.cshlp.org/content/22/7/1334.abstract#fn-1>, 3. Ferhat Ay <http://genome.cshlp.org/search?author1=Ferhat+Ay&sortspec=date&submit=Submit>1 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-1>,2 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-2>,4 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-4>,5 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-5>, 4. Patrick E. Meyer <http://genome.cshlp.org/search?author1=Patrick+E.+Meyer&sortspec=date&submi…>1 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-1>,2 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-2>,6 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-6>, 5. Rogerio Candeias <http://genome.cshlp.org/search?author1=Rogerio+Candeias&sortspec=date&submi…>1 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-1>,2 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-2>, 6. Tamer Kahveci <http://genome.cshlp.org/search?author1=Tamer+Kahveci&sortspec=date&submit=S…>5 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-5>, 7. Christopher A. Bristow <http://genome.cshlp.org/search?author1=Christopher+A.+Bristow&sortspec=date…>1 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-1>,2 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-2>and 8. Manolis Kellis <http://genome.cshlp.org/search?author1=Manolis+Kellis&sortspec=date&submit=…>1 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-1>,2 <http://genome.cshlp.org/content/22/7/1334.abstract#aff-2>,8 <http://genome.cshlp.org/content/22/7/1334.abstract#fn-2> + <http://genome.cshlp.org/content/22/7/1334.abstract#>Author Affiliations 1. ^1 Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, USA; 2. ^2 Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02140, USA; 3. ^3 Biostatistics and Medical Informatics, University of Wisconsin, Madison, Wisconsin 53706, USA; 4. ^4 Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA; 5. ^5 Computer and Information Science and Engineering, University of Florida, Gainesville, Florida 32611, USA; 6. ^6 Machine Learning Group, Faculté des Sciences, FNRS, Université Libre de Bruxelles, Brussels 1050, Belgium 1. ? <http://genome.cshlp.org/content/22/7/1334.abstract#xref-fn-1-1>7These authors contributed equally to this work. Abstract Gaining insights on gene regulation from large-scale functional data sets is a grand challenge in systems biology. In this article, we develop and apply methods for transcriptional regulatory network inference from diverse functional genomics data sets and demonstrate their value for gene function and gene expression prediction. We formulate the network inference problem in a machine-learning framework and use both supervised and unsupervised methods to predict regulatory edges *by integrating transcription factor (TF) binding, evolutionarily conserved sequence motifs, gene expression, and chromatin modification data sets as input features*. Applying these methods to/Drosophila melanogaster,/we predict ?300,000 regulatory edges in a network of ?600 TFs and 12,000 target genes. We validate our predictions using known regulatory interactions, gene functional annotations, tissue-specific expression, protein--protein interactions, and three-dimensional maps of chromosome conformation. We use the inferred network *to identify putative functions for hundreds of previously uncharacterized genes*, including many in nervous system development, which are independently confirmed based on their tissue-specific expression patterns. Last, we use the regulatory network to predict target gene expression levels as a function of TF expression, and find significantly higher predictive power for integrative networks than for motif or ChIP-based networks. Our work reveals the complementarity between physical evidence of regulatory interactions (TF binding, motif conservation) and functional evidence (coordinated expression or chromatin patterns) and demonstrates the power of data integration for network inference and studies of gene regulation at the systems level. -- Prof. Dr. Klaas Vandepoele 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/cig/ ---------------------------------------------------------

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[Beg-sysbiol] Gene network inference and visualization tools for biologists: application to new human transcriptome datasets
by Klaas Vandepoele 28 Mar '12

28 Mar '12

http://nar.oxfordjournals.org/content/40/6/2377.abstract -- Prof. Dr. Klaas Vandepoele 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/cig/ ---------------------------------------------------------

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[Beg-sysbiol] Toward Systems Biology in Brown Algae ... [OMICS 2011]
by Bram Slabbinck 06 Dec '11

06 Dec '11

Seems somewhat similar to Bram's IWT project :) http://www.liebertonline.com/doi/pdf/10.1089/omi.2011.0089 -- ========================================================== Bram Slabbinck, PhD Bioinformatics& Systems Biology Division VIB Department of Plant Systems Biology, UGent Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 822 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://bioinformatics.psb.ugent.be ========================================================== Services and consulting in bioinformatics http://www.arctix.be ========================================================== Please consider the environment before printing this email

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[Beg-sysbiol] Inferring gene regulatory networks from gene expression data ... [Bioinformatics, 2011]
by Bram Slabbinck 16 Nov '11

16 Nov '11

interesting extension of the technique of using mutual information for inferring GRN http://bioinformatics.oxfordjournals.org/content/early/2011/11/14/bioinform… regards Bram -- ========================================================== Bram Slabbinck, PhD Bioinformatics& Systems Biology Division VIB Department of Plant Systems Biology, UGent Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 822 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://bioinformatics.psb.ugent.be ========================================================== Services and consulting in bioinformatics http://www.arctix.be ========================================================== Please consider the environment before printing this email

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[Beg-sysbiol] Unraveling networks of co-regulated genes ... [NAR 2011]
by Bram Slabbinck 05 Sep '11

05 Sep '11

Interesting and extensive paper on co-regulation networks based on promotor motifs. Brohée, S. et al (2011). Unraveling networks of co-regulated genes on the sole basis of genome sequences<http://nar.oxfordjournals.org/search?author1=Sylvain+Broh%C3%A9e&sortspec=d…>, NAR. Link: http://nar.oxfordjournals.org/content/39/15/6340.short -- ========================================================== Bram Slabbinck, PhD Bioinformatics& Systems Biology Division VIB Department of Plant Systems Biology, UGent Technologiepark 927, 9052 Gent, BELGIUM Tel:+32 (0)9 33 13 822 Fax:+32 (0)9 33 13 809 Email: Bram.Slabbinck(a)psb.ugent.be WWW: http://bioinformatics.psb.ugent.be ========================================================== Services and consulting in bioinformatics http://www.arctix.be ========================================================== Please consider the environment before printing this email

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