[Beg-sysbiol] [Fwd: Re: Chapter]
-------- Original Message -------- Subject: Re: Chapter Date: Tue, 6 Mar 2007 08:34:46 -0500 From: Erich Grotewold <grotewold.1@osu.edu> To: Yves Van de Peer <yves.vandepeer@psb.ugent.be> References: <p06110415be8af01d26ac@[10.250.15.85]> <42767A46.5080900@psb.ugent.be> <p0624083ac1f7745871c1@[128.146.132.31]> <45D22061.7000304@psb.ugent.be> <p06240804c200ece34ab7@[128.146.132.31]> <45DC08DF.5060405@psb.ugent.be> Dear Yves, The silence form your end could mean that the comments are so bad that you are afraid to send them or that you had no time... I will need to submit it in the next week, thus look forward to anything (good or bad) that you may have to say. How is the science going? As you can tell form the references, I have been following some of your pubs pretty closely - I still think that there is plenty of room for doing something together. I plan on spending a year (Oct 2007 - Sept. 2008) at the Mathematical Bioscience Institute here at OSU doing a sabbatical and becoming more familiar with how to apply mathematical tools to model regulatory networks, etc. I am also considering taking a few weeks here and there to visit labs doing research in these areas and become more familiar with areas in which I have little expertise on right now - would you see beneficial the possibility of me spending some time there? Just a thought.... Best regards, Erich
Erich Grotewold wrote:
Dear Yves,
Here goes the chapter - feel free to have those smarter ;-) postdocs read it as well, in particular to pint out significant omissions or mistakes that we may have made. Let me know when you get it so that I can ease my mind from the thought of the e-mail doing with the document whatever it pleases.
Best regards, Erich Dear Erich,
Received your chapter loud and clear! We'll try to give feedback as soon as possible.
Best regrads,
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@psb.ugent.be
-- Erich Grotewold, Professor Dept. of Plant Cellular and Molecular Biology Plant Biotechnology Center The Ohio State University 206 Rightmire Hall, 1060 Carmack Road Columbus, OH 43210 Phone: (614) 292-2483 FAX: (614) 292-5379 E-mail: grotewold.1@osu.edu Our lab website http://www.biosci.ohio-state.edu/~plantbio/osu_pcmb/people/Erich AGRIS - Arabidopsis Gene Regulatory Information Server http://arabidopsis.med.ohio-state.edu/ 2007 Gordon Conference in Plant Metabolic Engineering http://www.grc.org:80/programs.aspx?year=2007&program=plantmet -- 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@psb.ugent.be http://www.psb.ugent.be/bioinformatics/
It seems like a pretty comprehensive review, but I know too little about all the biology to tell if anything is missing or suggest any improvements. Page 7: "There is evidence that TF's are more likely to be retained following a duplication event...". Maybe Steven & Stefanie's paper should be cited there? Page 11: free-scale -> scale-free Tom Yves Van de Peer wrote:
-------- Original Message -------- Subject: Re: Chapter Date: Tue, 6 Mar 2007 08:34:46 -0500 From: Erich Grotewold <grotewold.1@osu.edu> To: Yves Van de Peer <yves.vandepeer@psb.ugent.be> References: <p06110415be8af01d26ac@[10.250.15.85]> <42767A46.5080900@psb.ugent.be> <p0624083ac1f7745871c1@[128.146.132.31]> <45D22061.7000304@psb.ugent.be> <p06240804c200ece34ab7@[128.146.132.31]> <45DC08DF.5060405@psb.ugent.be>
Dear Yves,
The silence form your end could mean that the comments are so bad that you are afraid to send them or that you had no time... I will need to submit it in the next week, thus look forward to anything (good or bad) that you may have to say.
How is the science going? As you can tell form the references, I have been following some of your pubs pretty closely - I still think that there is plenty of room for doing something together. I plan on spending a year (Oct 2007 - Sept. 2008) at the Mathematical Bioscience Institute here at OSU doing a sabbatical and becoming more familiar with how to apply mathematical tools to model regulatory networks, etc. I am also considering taking a few weeks here and there to visit labs doing research in these areas and become more familiar with areas in which I have little expertise on right now - would you see beneficial the possibility of me spending some time there? Just a thought....
Best regards, Erich
Erich Grotewold wrote:
Dear Yves,
Here goes the chapter - feel free to have those smarter ;-) postdocs read it as well, in particular to pint out significant omissions or mistakes that we may have made. Let me know when you get it so that I can ease my mind from the thought of the e-mail doing with the document whatever it pleases.
Best regards, Erich Dear Erich,
Received your chapter loud and clear! We'll try to give feedback as soon as possible.
Best regrads,
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@psb.ugent.be
-- Tom Michoel <http://www.psb.ugent.be/~tomic/>
I've restricted myself to points 3.2 and 5. I agree with Tom that we should be cited on p. 7 ;-) . In point 5 (page 15), I would replace 'regulatory networks' with 'transcriptional regulatory networks' everywhere and add some more references for networks, modules and motifs. A good starting point is Barabasi & Oltvai, Nature Reviews Genetics 5, 101-113 and references therein. p15: superimposed to... -> superimposed on S Tom Michoel wrote:
It seems like a pretty comprehensive review, but I know too little about all the biology to tell if anything is missing or suggest any improvements.
Page 7: "There is evidence that TF's are more likely to be retained following a duplication event...". Maybe Steven & Stefanie's paper should be cited there?
Page 11: free-scale -> scale-free
Tom
Yves Van de Peer wrote:
-------- Original Message -------- Subject: Re: Chapter Date: Tue, 6 Mar 2007 08:34:46 -0500 From: Erich Grotewold <grotewold.1@osu.edu> To: Yves Van de Peer <yves.vandepeer@psb.ugent.be> References: <p06110415be8af01d26ac@[10.250.15.85]> <42767A46.5080900@psb.ugent.be> <p0624083ac1f7745871c1@[128.146.132.31]> <45D22061.7000304@psb.ugent.be> <p06240804c200ece34ab7@[128.146.132.31]> <45DC08DF.5060405@psb.ugent.be>
Dear Yves,
The silence form your end could mean that the comments are so bad that you are afraid to send them or that you had no time... I will need to submit it in the next week, thus look forward to anything (good or bad) that you may have to say.
How is the science going? As you can tell form the references, I have been following some of your pubs pretty closely - I still think that there is plenty of room for doing something together. I plan on spending a year (Oct 2007 - Sept. 2008) at the Mathematical Bioscience Institute here at OSU doing a sabbatical and becoming more familiar with how to apply mathematical tools to model regulatory networks, etc. I am also considering taking a few weeks here and there to visit labs doing research in these areas and become more familiar with areas in which I have little expertise on right now - would you see beneficial the possibility of me spending some time there? Just a thought....
Best regards, Erich
Erich Grotewold wrote:
Dear Yves,
Here goes the chapter - feel free to have those smarter ;-) postdocs read it as well, in particular to pint out significant omissions or mistakes that we may have made. Let me know when you get it so that I can ease my mind from the thought of the e-mail doing with the document whatever it pleases.
Best regards, Erich Dear Erich,
Received your chapter loud and clear! We'll try to give feedback as soon as possible.
Best regrads,
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@psb.ugent.be
-- ================================================================== Steven Maere, PhD Dept. of Plant Systems Biology Bioinformatics & Evolutionary Genomics research group Ghent University / VIB Technologiepark 927 B-9052 Gent BELGIUM tel: +32 9 331 3692 fax: +32 9 331 3809 email: stmae@psb.UGent.be http://www.psb.UGent.be http://bioinformatics.psb.ugent.be/ ==================================================================
participants (3)
-
Steven Maere -
Tom Michoel -
Yves Van de Peer