June 2009 - beg-sysbiol@psb.ugent.be

[Beg-sysbiol] Identification of yeast transcriptional regulation...[PLoS Comput Biol. 2009] - PubMed Result
by Yves Van de Peer 28 Jun '09

28 Jun '09

http://www.ncbi.nlm.nih.gov/pubmed/19543377?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.vib-ugent.be http://bioinformatics.psb.ugent.be/

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[Beg-sysbiol] A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide -- Wren 25 (13): 1694 -- Bioinformatics
by Klaas Vandepoele 25 Jun '09

25 Jun '09

A study that uses a co-expression framework (evaluating different similarity measures) to predict gene functions and tries to evaluate these predictions using literature-derived data (I am not sure if you can call it text mining). http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/13/1694 Klaas -- 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/ --------------------------------------------------------- it's hard to keep the animo from driftin' away nowadays

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[Beg-sysbiol] Fwd: RECOMB Regulatory Genomics, Systems Biology, and DREAM4 2009 announcement
by Tom Michoel 17 Jun '09

17 Jun '09

Begin forwarded message: > From: Manolis Kellis <manoli(a)MIT.EDU> > Date: Wed 17 Jun 2009 20:50:03 GMT+02:00 > To: Tom Michoel <tom.michoel(a)psb.ugent.be> > Subject: RECOMB Regulatory Genomics, Systems Biology, and DREAM4 > 2009 announcement > Reply-To: recombsat(a)MIT.EDU > > Dear Tom, > > Thank you again for your participation in RECOMB RegulatoryGenomics/ > SystemsBiology/DREAM3 last year. We hope you enjoyed the meeting, > the online videos and materials, the conference program, and the > high quality of presentations. > > The 2009 joint meeting will be back at MIT, and we really hope you > can make it! This year we are partnering with PLoS Computational > Biology and PLoS ONE to publish all accepted papers, and we hope to > see again a strong response. > > Manuscript submissions are now open, and we attach below the call > for papers, abstracts, and challenge predictions. Please do forward > the email to your group and colleages that may find it of interest, > and we hope to see you at MIT this December for what promises to be > a great meeting! > > With best regards, > Manolis Kellis, Ziv Bar-Joseph, Andrea Califano, and Gustavo > Stolovitzky > > ----- > > Call for Papers, Abstracts, and Challenge Predictions > > JOINT CONFERENCE ON REGULATORY GENOMICS AND SYSTEMS BIOLOGY > > 6th RECOMB Satellite Meeting on Regulatory Genomics > 5th RECOMB Satellite Meeting on Systems Biology > 4rd Dialogue on Reverse Engineering Assessment and Methods (DREAM4) > > In partnership with: PLoS Computational Biology and PLoS ONE > > Wed Dec 2, 2009 (5pm) - Sun Dec 6, 2009 (1pm) > The Broad Institute of MIT and Harvard > http://compbio.mit.edu/recombsat/ > > Following the success of last year we have once again combined three > key conferences in regulatory and systems biology in what promises > to be a very exciting meeting. The goal of the joint meeting is to > bring computational and experimental scientists together towards a > systems-level understanding of gene regulation, cell signaling and > other cellular processes. The meeting will consist of invited > keynote presentations, oral presentations of accepted papers and > abstracts, DREAM4 presentations of reverse engineering challenge > responses, and four poster sessions. > > The 2008 meeting drew more than 500 participants, including 103 > international participants from 24 countries. We received 250+ > abstract submissions, 400+ challenge predictions, and 50+ paper > submissions, resulting in 93 oral presentations, 160 poster > presentations, and 24 papers published in our partner journals, and > we expect a similar response this year. > > We are once again collaborating with two leading journals, PLoS > Computational Biology and PLoS ONE, and all accepted manuscripts > will appear in one of the two journals, based on the recommendation > of the program committee and the journal editors. We are working > closely with PLoS to make sure all accepted papers can appear online > by the date of the meeting, and referenced in PubMed accordingly. > All accepted papers will be guaranteed an oral presentation at the > meeting, with links to the recorded video presentations accompanying > each paper in PLoS. In addition, all accepted papers published in > both PLoS journals will become part of a PLoS Collection, with > additional content and features. > > In addition to paper submissions, we will consider abstract > submissions for oral or poster presentations. All abstracts will be > treated as personal communication, and authors will reserve the > right to submit their work elsewhere for publication. > > Topics for papers and abstracts include: > * RG: Modeling and recognition of regulatory motifs and modules. > * RG: Chromatin state establishment, maintenance, and role in > development. > * RG: Post-transcriptional regulation and small regulatory RNAs. > * RG & SB: Regulatory networks, metabolic networks, proteomic > networks. > * RG & SB & DREAM: Pathway inference and reverse engineering of > cellular networks. > * SB: Cellular signatures of biological responses and disease states. > * SB: Phosphorylation, metabolic fluxes, systematic phenotyping. > * SB: Mathematical modeling and simulation of biological systems. > * DREAM: experimental/algorithmic designs of reverse engineering > protocols. > * DREAM: assessment and comparison of reverse engineering methods. > > Keynote speakers: Naama Barkai, Mark Biggin, Walter Fontana, Nevan > Krogan, Ihor Lemischka, Ed Marcotte, Franziska Michor, Garry Nolan, > Nikolaus Rajewsky, Bob Waterston, Kevin White, Michael Yafee, Rick > Young. > > Key Dates: > Paper submission deadline: Fri July 24, 2009 > Notification of journal assignments by: Tue, Sept 15 2009 > Abstract submission deadline: Thu Oct 1st, 2009 > Registration deadline: Thu Oct 1st, 2009 > DREAM challenge response date: Thu Oct 15, 2009 > > Submission website is now open: > http://www.easychair.org/conferences/?conf=recombsbrgdream2009 > > DREAM4 challenges are available for download: > http://wiki.c2b2.columbia.edu/dream/index.php/The_DREAM_Project > > Conference registration website (opens on July 1st 2009): > http://regonline.com/recombsat09 > > Detailed submission instructions and additional information is at: > http://compbio.mit.edu/recombsat/ > > We look forward to welcoming you in Boston and Cambridge this > December! > > The Conference Chairs: > Manolis Kellis, Ziv Bar-Joseph, Andrea Califano, Gustavo Stolovitzky. > > Program Committees: > * Regulatory Genomics: Orly Alter, Nitin S Baliga, Panayiotis > (Takis) Benos, Mathieu Blanchette, Michael Brent, Albert Erives, > Eleazar Eskin, Ernest Fraenkel, Nir Friedman, Mikhail Gelfand, > Sridhar Hannenhalli, Tim Hughes, Uri Keich, Christina Leslie, Hao > Li, Adam Margolin, Uwe Ohler, Aviv Regev, Mireille Regnier, Eran > Segal, Ron Shamir, Saurabh Sinha, Mona Singh, Christopher Workman > > * Systems Biology/DREAM: M. Madan Babu, Gary Bader, Joel Bader, Jim > Collins, Diego di Bernardo, Joaquin Dopazo, Peicheng Du, Eleazar > Eskin, Pablo Iglesias, Igor Jurisica, Pascal Kahlem, Yuval > Kluger,Seungchan Kim, Reinhard Laubenbacher, Andre Levchenko, Avi > Ma'ayan, Andrew McCulloch, Kathleen Marchal, Adam Margolin, Satoru > Miyano, Ilya Nemenman, Theodore Perkins, Raul Rabadan, Timothy > Ravasi, Frederick Roth, Michael Samoilov, Roded Sharan, Ilya > Shmulevich, Mona Singh, Pavel Sumazin, Jesper Tegner, Yuhai Tu, John > Wagner, Ioannis Xenarios. -- Tom Michoel <http://www.psb.ugent.be/~tomic/>

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[Beg-sysbiol] [Fwd: DREAM4 Predictive Network Modeling]
by Tom Michoel 16 Jun '09

16 Jun '09

-------- Original Message -------- Subject: DREAM4 Predictive Network Modeling Date: Tue, 16 Jun 2009 01:11:16 -0400 From: Gustavo Stolovitzky <gustavo(a)us.ibm.com> To: DREAM N-Z <DREAM_N-Z%IBMUS(a)us.ibm.com> References: <OF08B4380A.7CD282CD-ON85257326.001A79DE-8525746C.000A6CB0(a)us.ibm.com> <ED9E9926-15CA-4B62-BB92-D251CAD0E4BE(a)mskcc.org> <OF69A5C81A.982F0911-ON8525746C.00186AD1-8525746C.00191257(a)us.ibm.com> <338178E6-627F-41DF-91A0-8301F3E0B987(a)mskcc.org> 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* * DREAM4: The 4^th DIALOGUE ON REVERSE ENGINEERING ASSESSMENT AND METHODS* Dear Colleague, We would like to cordially invite your submissions 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/Challenges_ . The best performers in these challenges will be invited to present in the joint RECOMB Systems Biology/Regulatory Genomics/DREAM4 conference. See _http://compbio.mit.edu/recombsat/_ for details on this conference. To learn more about the DREAM4 conference, please go to _http://wiki.c2b2.columbia.edu/dream/index.php/DREAM4conf_ To learn more about the DREAM project, please go to _http://wiki.c2b2.columbia.edu/dream/index.php/The_DREAM_Project_ * Predictive Network Modeling Submission Timeline* * Mid June, 2009* Call for participation in the challenges. Challenges posted. * Oct 15, 2009* Predictions Submission Deadline. * Nov 15, 2009* Notifications to Predictors of their Scores and Ranks.* Dec 2-Dec 6, 2009* RECOMB Systems Biology/Regulatory Genomics/DREAM4 conference. (The DREAM4 conference track is on Friday December 4th.) Prediction Submissions must be received in electronic form by 11:59pm (EST) of October 15, 2009. Sincerely, DREAM4 Conference and Challenge Organizers: Gustavo Stolovitzky (chair), IBM Research Robert J Prill, IBM Research Andrea Califano, Columbia University DREAM4 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] pics
by Eric Bonnet 15 Jun '09

15 Jun '09

hi there, A couple of pictures from keystone, see you on tuesday.. Eric

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[Beg-sysbiol] paper
by Eric Bonnet 10 Jun '09

10 Jun '09

maybe another interesting source of data for Arabidopsis? plant histone methylation http://genomebiology.com/2009/10/6/R62 Eric

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[Beg-sysbiol] sysbiol slides
by Eric Bonnet 02 Jun '09

02 Jun '09

the final version of the sysbiol slides is under biocomp/doc/presentations/brainstorm_2009/brainstorm_sysbiol_final.ppt Eric

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