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

[Beg-sysbiol] anyone wants to help me with this one ?
by Yves Van de Peer 22 Apr '10

22 Apr '10

-------- Original Message -------- Subject: Subject: Invitation to review for Molecular Systems Biology - MSB-10-2067 Date: Tue, 20 Apr 2010 12:26:35 -0400 From: msb(a)embo.org To: yvpee(a)psb.ugent.be ***PLEASE DO NOT REPLY TO THIS EMAIL*** *** USE THE LINKS BELOW INSTEAD *** Dear Prof Van de Peer, Would you (or a senior member of your lab) be prepared to review the manuscript below for us within 21 days of receipt? WOULD YOU NEED MORE TIME? Manuscript Reference: MSB-10-2067 Authors: Todd Treangen and Eduardo Rocha Title: Prevalence of xenology over paralogy shapes the evolution of prokaryotic systems Type of Article: Article Abstract: Gene duplication is regarded as the main source of adaptive functional novelty in eukaryotes. Adaptive gene duplication has also been proposed to outweigh the contribution of horizontal gene transfer in gene family expansion in prokaryotes. Using many closely related genomes and after explicitly controlling for transposable and phage elements in a population genomics framework, we show that the vast majority of gene family expansions in prokaryotes are due to transfer, especially among larger genomes. Transferred genes persist longer in genomes, suggesting a higher/longer adaptive role. Duplicated genes are more expressed and evolve slower at synonymous and non-synonymous positions suggesting selection for gene dosage and frequent gene conversion. Importantly, pairs of duplicated genes share most protein-protein interactions and genetic regulators, but transferred genes share very few. Thus, transfer outweighs duplication in the expansion of gene families and due to the high divergence of xenologs produces very different adaptive paths for prokaryotic biological systems. Since prokaryotes invented the majority of life's biochemical diversity, models of network evolution should explicitly account for the role of horizontal gene transfer. Please click on the appropriate link: to ACCEPT, <http://mts-msb.nature.com/cgi-bin/main.plex?el=A6BL2BGK3A4Dct4D2A98G1FQKjv3…> to DECLINE, <http://mts-msb.nature.com/cgi-bin/main.plex?el=A4BL1BGK1A5Dct3E1A98G1FQKjv3…> If you are unable to review this manuscript at this time, I would be grateful if you could forward suggestions of other potential reviewers. You can do this by using the "Send Manuscript Correspondence" option when declining or by email to msb(a)embo.org. Should you have any problems entering the site, please e-mail msb(a)nature.com. Thank you for your consideration and support of Molecular Systems Biology. Yours sincerely, Andrew L. Hufton, PhD Section Editor Molecular Systems Biology Please note that your contact details are being held on our editorial database which is used only for this journal's management of the peer review process. If you would prefer us not to contact you in the future please let us know by emailing msb(a)nature.com. MSB - This email has been sent through the NPG Manuscript Tracking System NY-610A-NPG&MTS -- 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/

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[Beg-sysbiol] [Fwd: [Fwd: Molecular Systems Biology - New articles published 20 April 2010]]
by Yves Van de Peer 22 Apr '10

22 Apr '10

-------- Original Message -------- Subject: [Fwd: Molecular Systems Biology - New articles published 20 April 2010] Date: Thu, 22 Apr 2010 11:09:29 +0200 From: Kathleen Marchal <kathleen.marchal(a)biw.kuleuven.be> To: Yves Van De Peer <Yves.vandepeer(a)psb.ugent.be> check the embo meeting -------- Original Message -------- Subject: Molecular Systems Biology - New articles published 20 April 2010 Date: Tue, 20 Apr 2010 18:39:18 +0200 From: Molecular Systems Biology <Molecular_Systems_Biology(a)ealert.nature.com> Reply-To: Molecular_Systems_Biology(a)ealert.nature.com <Molecular_Systems_Biology(a)ealert.nature.com> To: Kathleen Marchal <Kathleen.Marchal(a)biw.kuleuven.be> <http://links.ealert.nature.com/ctt?kn=50&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> 20 April 2010 The EMBO Meeting 2010 - advancing the life sciences 4-7 September 2010, Barcelona Featuring: • Plenary lecture sessions devoted to modern evolutionary biology, molecular developmental biology and the rapidly developing field of systems biology • 21 workshops juxtapose classical fields of research with those exploring new frontiers in molecular biology • /Next generation sequencing: technologies & biological insights/ workshop organized by /Molecular Systems Biology/ chief editor Thomas Lemberger • Daily meet the speaker lunches and poster sessions • Popular career development activities For further information, to submit abstracts and to register visit: www.the-embo-meeting.org <http://links.ealert.nature.com/ctt?kn=6&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&j…> *Featured article* Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity <http://links.ealert.nature.com/ctt?kn=2&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&j…> By quantifying metabolite, transcript and enzyme abundances upon local and global perturbations in /Saccharomyces cerevisiae/, we provide evidence that enzyme capacity and metabolite concentrations control metabolic reactions /in vivo/, thereby facilitating flux homeostasis. The observed inverse relationship between substrate metabolite and enzyme concentrations provides a straightforward interpretation for metabolomics data in functional genomics. *Latest articles* *Tradeoff between enzyme and metabolite efficiency maintains metabolic homeostasis upon perturbations in enzyme capacity* Sarah-Maria Fendt, Joerg Martin Buescher, Florian Rudroff, Paola Picotti, Nicola Zamboni & Uwe Sauer 13 April 2010 Synopsis <http://links.ealert.nature.com/ctt?kn=44&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Full Text <http://links.ealert.nature.com/ctt?kn=2&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&j…> | Supplementary info <http://links.ealert.nature.com/ctt?kn=45&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> *Pre-dispositions and epigenetic inheritance in the /Escherichia coli/ lactose operon bistable switch* Lydia Robert, Gregory Paul, Yong Chen, François Taddei, Damien Baigl& Ariel B Lindner 13 April 2010 Synopsis <http://links.ealert.nature.com/ctt?kn=42&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Full Text <http://links.ealert.nature.com/ctt?kn=43&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Supplementary info <http://links.ealert.nature.com/ctt?kn=48&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> *Short-term memory in gene induction reveals the regulatory principle behind stochastic IL-4 expression* Luca Mariani, Edda G Schulz, Maria H Lexberg, Caroline Helmstetter, Andreas Radbruch, Max Löhning & Thomas Höfer 13 April 2010 Synopsis <http://links.ealert.nature.com/ctt?kn=49&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Full Text <http://links.ealert.nature.com/ctt?kn=46&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Supplementary info <http://links.ealert.nature.com/ctt?kn=47&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> *Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch* Chunbo Lou, Xili Liu, Ming Ni, Yiqi Huang, Qiushi Huang, Longwen Huang, Lingli Jiang, Dan Lu, Mingcong Wang, Chang Liu, Daizhuo Chen, Chongyi Chen, Xiaoyue Chen, Le Yang, Haisu Ma, Jianguo Chen & Qi Ouyang 09 March 2010 Synopsis <http://links.ealert.nature.com/ctt?kn=30&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Full Text <http://links.ealert.nature.com/ctt?kn=10&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Supplementary info <http://links.ealert.nature.com/ctt?kn=11&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> *Bacterial adaptation through distributed sensing of metabolic fluxes* Oliver Kotte, Judith B Zaugg & Matthias Heinemann 09 March 2010 Synopsis <http://links.ealert.nature.com/ctt?kn=8&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&j…> | Full Text <http://links.ealert.nature.com/ctt?kn=9&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&j…> | Supplementary info <http://links.ealert.nature.com/ctt?kn=5&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&j…> *Dynamics within the CD95 death-inducing signaling complex decide life and death of cells* Leo Neumann, Carina Pforr, Joel Beaudouin, Alexander Pappa, Nicolai Fricker, Peter H Krammer, Inna N Lavrik & Roland Eils 09 March 2010 Synopsis <http://links.ealert.nature.com/ctt?kn=7&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&j…> | Full Text <http://links.ealert.nature.com/ctt?kn=3&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&j…> | Supplementary info <http://links.ealert.nature.com/ctt?kn=4&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&j…> *GINS motion reveals replication fork progression is remarkably uniform throughout the yeast genome* Matthew D Sekedat, David Fenyö, Richard S Rogers, Alan J Tackett, John D Aitchison & Brian T Chait 09 March 2010 Synopsis <http://links.ealert.nature.com/ctt?kn=15&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Full Text <http://links.ealert.nature.com/ctt?kn=14&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Supplementary info <http://links.ealert.nature.com/ctt?kn=25&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> *Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development* Daria Onichtchouk, Florian Geier, Bozena Polok, Daniel M Messerschmidt, Rebecca Mössner, Björn Wendik, Sungmin Song, Verdon Taylor, Jens Timmer & Wolfgang Driever 09 March 2010 Synopsis <http://links.ealert.nature.com/ctt?kn=20&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Full Text <http://links.ealert.nature.com/ctt?kn=21&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Supplementary info <http://links.ealert.nature.com/ctt?kn=22&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> *Reports* *Target mRNA abundance dilutes microRNA and siRNA activity* Aaron Arvey, Erik Larsson, Chris Sander, Christina S Leslie & Debora S Marks 20 April 2010 Full Text <http://links.ealert.nature.com/ctt?kn=24&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Supplementary info <http://links.ealert.nature.com/ctt?kn=16&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> *Transcript counting in single cells reveals dynamics of rDNA transcription* Rui Zhen Tan & Alexander van Oudenaarden 13 April 2010 Full Text <http://links.ealert.nature.com/ctt?kn=17&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Supplementary info <http://links.ealert.nature.com/ctt?kn=18&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> *A functional metagenomic approach for expanding the synthetic biology toolbox for biomass conversion* Morten OA Sommer, George M Church & Gautam Dantas 13 April 2010 Full Text <http://links.ealert.nature.com/ctt?kn=19&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Supplementary info <http://links.ealert.nature.com/ctt?kn=27&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> *Precision and scaling in morphogen gradient read-out* Aitana Morton de Lachapelle & Sven Bergmann 09 March 2010 Full Text <http://links.ealert.nature.com/ctt?kn=38&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> | Supplementary info <http://links.ealert.nature.com/ctt?kn=39&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> *Editorials* Reconstruction annotation jamborees: a community approach to systems biology <http://links.ealert.nature.com/ctt?kn=33&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> Ines Thiele & Bernhard Ø Palsson 13 April 2010 *Reviews* Strategies for cellular decision-making <http://links.ealert.nature.com/ctt?kn=26&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> Theodore J Perkins & Peter S Swain 17 November 2009 Applications of genome-scale metabolic reconstructions <http://links.ealert.nature.com/ctt?kn=28&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> Matthew A Oberhardt, Bernhard Ø Palsson & Jason A Papin 3 November 2009 *Perspectives* Shifts in growth strategies reflect tradeoffs in cellular economics <http://links.ealert.nature.com/ctt?kn=12&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> Douwe Molenaar, Rogier van Berlo, Dick de Ridder & Bas Teusink 3 November 2009 *Erratum* Inferring condition-specific transcription factor function from DNA binding and gene expression data <http://links.ealert.nature.com/ctt?kn=37&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> Rachel Patton McCord, Michael F Berger, Anthony A Philippakis & Martha L Bulyk 13 April 2010 ADVERTISEMENT <http://links.ealert.nature.com/ctt?kn=41&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> You have been sent this Table 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You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your nature.com account at: www.nature.com/nams/svc/myaccount <http://links.ealert.nature.com/ctt?kn=13&m=34803880&r=MTc2MzUzMTkxNAS2&b=0&…> (You will need to log in to be recognised as a nature.com registrant). For further technical assistance, please contact our registration department <mailto:registration@nature.com%20> For print subscription enquiries, please contact our subscription department <mailto:subscriptions@nature.com%20> For other enquiries, please contact our customer feedback department <mailto:feedback@nature.com%20> Nature Publishing Group | 75 Varick Street, 9th Floor | New York | NY 10013-1917 | USA Nature Publishing Group's worldwide offices: London - Paris - Munich - New Delhi - Tokyo - Melbourne - San Diego - San Francisco - Washington - New York - Boston Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at Brunel Road, Houndmills, Basingstoke, Hampshire RG21 6XS. ©2010 Nature Publishing Group nature publishing group -- Kathleen Marchal CMPG/Bioinformatics Dep Microbial and Molecular Systems, K.U.Leuven Kasteelpark Arenberg 20 3001 Leuven +32 16329685 http://homes.esat.kuleuven.be/~kmarchal/ http://www.bioframe.net/ -- 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/

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[Beg-sysbiol] paper
by Eric Bonnet 20 Apr '10

20 Apr '10

fyi, the plos one paper is online: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0010162 e.

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[Beg-sysbiol] home sweet home
by Steven Maere 20 Apr '10

20 Apr '10

I made it home, at last :-) But I also caught an upper respiratory tract infection along the way, I'll come in tomorrow when the antibiotics have kicked in (could be afternoon). Christine, I suppose the SAB prep meeting of tomorrow morning is cancelled ? 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/ ==================================================================

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[Beg-sysbiol] Reconstruction annotation jamborees: a community a... [Mol Syst Biol. 2010] - PubMed result
by Yves Van de Peer 18 Apr '10

18 Apr '10

http://www.ncbi.nlm.nih.gov/pubmed/20393581?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/

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[Beg-sysbiol] stuck in Sardinia
by stmae＠psb.vib-ugent.be 17 Apr '10

17 Apr '10

Hi guys, I'm currently stuck in Cagliari, Sardinia because of the Iceland volcanic eruption. All northbound flights out of here are cancelled, and the only way off the island is by boat. We hope to find some spots on a ferry to Marseille tomorrow from the north and then find a tgv, bus, rental car or lift home, none of which is very likely. In the best-case scenario, I'm back home on Monday evening, but it might take longer... I'll keep you posted. Arrivederci, Steven For urgent matters, call 0032 494908579

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[Beg-sysbiol] modular domain recombination
by Jens Hollunder 16 Apr '10

16 Apr '10

http://www.sciencemag.org/cgi/content/full/328/5976/368 -- ================================================================== Dr. Jens Hollunder Tel:+32 (0)9 331 38 10 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM Jens.Hollunder(a)psb.vib-ugent.be ==================================================================

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[Beg-sysbiol] Revealing strengths and weaknesses of methods for ... [Proc Natl Acad Sci U S A. 2010] - PubMed result
by Yves Van de Peer 29 Mar '10

29 Mar '10

http://www.ncbi.nlm.nih.gov/pubmed/20308593?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/

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[Beg-sysbiol] (no subject)
by Eric Bonnet 26 Mar '10

26 Mar '10

hi there, I have a flexware (SBO project) meeting this morning, will be in the lab this afternoon. cu later, e.

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[Beg-sysbiol] FW: Next SAM Meeting and Bioinf challenge
by Klaas Vandepoele 25 Mar '10

25 Mar '10

Dear, who from sysbiol can join us in the week of April 19th to help? Preferably someone who has access to the Lemone/Enigma plant modules. thanks, Stefanie Dirk Klaas *Bioinformatics challenge: Background info:* We all face the situation, that we have a gene sequence in our hand and don´t know the function. Usually we have limited time (max a few hours) to find data and to decide on whether the gene is of interest for us or not. We also have a limited understanding how good or bad we are in comparison to others, since a pure *quantitative* comparison of softwares and hardwares would only lead to limited results. In order to compare our capabilities in a more* qualitative* way we agreed to do a joint test case by cross comparing our capabilities to find functions for a give gene (sequence). * The principle is a follows:* Each of the 4 entities (Dirk, Lothar, Xing Wang, Jürgen) will provide one gene sequence (out of yield area, where the respective entity is a specialist) to all other entities with request to come up with suggestions about the function(s) - time to deliver : one day (24hours). The entities are challenged to find out everything they can about that particular gene and a potential gene product. The respective gene providing entity will compare the findings -- what findings were similar, different, new, and why and will report to the others. The results corresponding to the provided gene belong to the entity that provided the gene sequence. * Detailed workflow:* Each entity provides - a s_equence file_ (nucleotides/protein)*/ in a wild type form, with start and stop codon/* / *- the organism of origin */ - the _contact emai_l to Jürgen Logemann prior to the start time. At 9:00 hrs german time Jürgen Logemann will distribute the 4 sequence files to all contact emails with a cc to the SAM members. Each entity will work on the 3 sequences with */approx. 2 FTEs./* 24 hrs later, at 9:00 hrs german time the feedback of each entity has to be in the e-mail of Jürgen Logemann. The feedback should be in a digestable form, so that a person, being not an expert understands the message (sequence, function, structure etc.) Jürgen Logemann will distribute the feedback to all entities, the respective gene providing entity will check and compare/rank the content related to its gene At the next SAM meeting all entities discuss the results by phone. * Open points:* - Metalife might join as a 5th entity (Jürgen L to check) - We will need a short contract being signed before starting day, describing who owns what (Jürgen L and all) *options: everybody owns his own results - everybody owns all results on his sequences* - What happens to the ownership of results, if one entity provides a gene sequence, where the other entity is also working on ? (all) - The final day for the challenge and for the results discussion needs to be agreed - week of April 19th ? (all) *- What about negative controls? What about also adding three random nucleotide sequences ( containing ORF´s obviously) (all)* *- Do we need to define what description / annotation level we want to reach (all)* *Juergen Logemann* Vice President Technology Management Phone: +49 621 60-27204, Mobile: +49 172 7470513, Fax: +49 621 60-28685, E-Mail: juergen.logemann(a)basf.com Postal Address: BASF Plant Science Company GmbH, BPS_TECM - LI439, 67117 Limburgerhof, Germany *BASF - The Chemical Company* BASF Plant Science Company GmbH Legal Headquarter 67056 Ludwigshafen, Germany Registration Office: Amtsgericht Ludwigshafen Eintragungsnummer HRB 4516Lu Executive Management: Peter Eckes, Jürgen Schweden, Marc Ehrhardt -- 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)

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