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

[Beg-sysbiol] A Chemical Kinetic Model of Transcriptional Elongation
by Roeland Merks 14 Mar '06

14 Mar '06

-------- Original Message -------- Subject: q-bio daily Subj-class mailing 8 1 Date: Tue, 14 Mar 2006 05:04:33 -0500 From: no-reply(a)arXiv.org (send mail ONLY to q-bio) Reply-To: q-bio(a)arXiv.org To: rabble(a)arXiv.org (q-bio daily title/abstract distribution) ------------------------------------------------------------------------------ ------------------------------------------------------------------------------ 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: Subcellular Processes received from Fri 10 Mar 06 21:00:02 GMT to Mon 13 Mar 06 21:00:02 GMT ------------------------------------------------------------------------------ %-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%-%- ------------------------------------------------------------------------------ \\ Paper: q-bio.BM/0603012 Date: Sun, 12 Mar 2006 02:50:18 GMT (77kb) Title: A Chemical Kinetic Model of Transcriptional Elongation Authors: Yujiro Richard Yamada, Charles S. Peskin Comments: 12 pages, 4 figures Subj-class: Biomolecules; Subcellular Processes \\ A chemical kinetic model of the elongation dynamics of RNA polymerase along a DNA sequence is introduced. Unlike previous models that attempt to explain the motion of RNA polymerase using internal strain and stresses, we propose a chemical kinetic model which governs the discrete movement of the RNA polymerase along a DNA tether, with no consideration given to elastic effects. The model's novel concept is a ``look-ahead'' feature, in which nucleotides bind reversibly to the DNA prior to being incorporated covalently into the nascent RNA chain. Results are presented for specific DNA sequences that have been used in single-molecule experiments of the random walk of RNA polymerase along DNA. \\ ( http://arXiv.org/abs/q-bio/0603012 , 77kb) %%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%%--%% %%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%---%%%--- -- 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] meeting on systems biology ...
by Yves Van de Peer 08 Mar '06

08 Mar '06

Dear All, Since it is very difficult to have a meeting where everybody can be present, and since we do not want to postpone this (first) meeting too much, let's have it on April 10th at 10:30 (sorry Dirk, we will keep you posted and we will have a second meeting later ...). Hope this works out for most of you. See you then. Yves PS. Marnik, Martin will fill you in on this (Martin?) -- 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] next beg-sysbiol meeting confirmed for March 28th, 10:00 am. please mark your agendas!
by Yves Van de Peer 08 Mar '06

08 Mar '06

-- 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] paper Steven on yeast modules (confidential)
by Steven Maere 08 Mar '06

08 Mar '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] review friedman
by Steven Maere 08 Mar '06

08 Mar '06

status of probabilistic graphical models anno 2004, both segal and pe'er are discussed 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] another date for the meeting on systems biology ...
by Yves Van de Peer 08 Mar '06

08 Mar '06

Dear All, This seems to be a difficult mission :-) Since Dirk is not here on April 10 and April 11, but would like to attend the meeting, I'd like to propose April 27th (morning) or April 28th (whole day). Please let me know your preferences. Thanks in advance, 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] meeting on Systems Biology
by Yves Van de Peer 07 Mar '06

07 Mar '06

Dear All, The Bioinformatics and Computational Biology groups are working hard to develop top-down Systems Biology approaches (where regulatory networks are being inferred from large amounts of transcriptome data), and we would like to discuss these with some of the 'experimental' people to see how we can integrate transcriptome data that are generated in the Department with approaches that we develop, for instance to elucidate transcriptional regulation in developing leafs. I would like to propose to have a meeting on this on either April 10th or April 11th. Could you please let me know whether this fits you? Many thanks in advance, Best regards, 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] change of plans ... sorry.
by Yves Van de Peer 07 Mar '06

07 Mar '06

Dear All, I have just found out that I have a meeting at 4pm tomorrow, and I cannot afford to miss that. Therefore, I suggest to have our meeting at 11am. I hope that's ok with all of you. Sorry about that. Thanks, 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] (no subject)
by Yves Van de Peer 07 Mar '06

07 Mar '06

Will you guys be here at Monday 10 and/or Tuesday 11 April? Please confirm. 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] meeting tomorrow ...
by Yves Van de Peer 07 Mar '06

07 Mar '06

Dear All, Could we have our meeting at 3pm instead of 2pm tomorrow? Martin would like to participate. Thanks in advance, 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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