From csbi-events at mit.edu  Fri Oct  5 05:37:17 2007
From: csbi-events at mit.edu (CSBi events)
Date: Fri, 05 Oct 2007 05:37:17 -0400
Subject: [CSBi-events] CSbi FLYER, October 12, 2007 Seminar
Message-ID: <6.2.3.4.2.20071005053536.034772b0@po11.mit.edu>

FYI

SAVE THE DATE, The First CSBi Seminar of the Year

From csbi-events at mit.edu  Sun Oct  7 06:25:58 2007
From: csbi-events at mit.edu (CSBi events)
Date: Sun, 07 Oct 2007 06:25:58 -0400
Subject: [CSBi-events] Friday, October 12, 2007;
 3:00- 4:00 PM, Rm. 4-370 Reminder ! Fall 2007 Seminar Series on
 Computational and Systems Biology!
Message-ID: <6.2.3.4.2.20071007062521.035378a0@po11.mit.edu>


>
>
>Reminder !  Fall 2007 Seminar Series on Computational and Systems Biology!
>
>Friday, October 12, 2007; 3:00- 4:00 PM, Rm. 4-370
>Dr. Gurol Suel
>UT Southwestern Medical Center
>
>Title:
>Noisy out of necessity: Probabilistic behavior during cellular 
>differentiation.
>
>Light refreshments to be served at 2:45 p.m.
>
>Host:  Dr. Alexander van Oudenaarden
>Department of Physics
>
>Abstract
>
>Diverse organisms ranging from bacteria to mammalian stem cells 
>undergo pluripotent
>differentiation where a single cell can commit to one out of several 
>cell fates.
>How do underlying genetic circuits allow cells to "choose" a 
>specific cell fate and
>execute the appropriate differentiation program? To address this 
>question we investigate
>a simple bacterial differentiation system utilizing mathematical 
>modeling and quantitative
>single cell measurements. In particular we are interested in 
>elucidating the significance
>of circuit dynamics and stochastic behavior during cellular differentiation.
>
>Suel et al. Science 315, 1716-1719 (2007)
>Suel et al. Nature 440, 545-550 (2006)
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From csbi-events at mit.edu  Wed Oct 10 07:57:13 2007
From: csbi-events at mit.edu (CSBi events)
Date: Wed, 10 Oct 2007 07:57:13 -0400
Subject: [CSBi-events] Reminder, CSbi seminar October 12, 2007,
	(Dr. Gurol Suel)
Message-ID: <470CBE19.3000408@mit.edu>

*Reminder !  Fall 2007 Seminar Series on Computational and Systems Biology!
*
*Friday, October 12, 2007; 3:00- 4:00 PM, Rm. 4-370
Dr. Gurol Suel
UT Southwestern Medical Center *

Title:
*Noisy out of necessity: Probabilistic behavior during cellular 
differentiation. *

Light refreshments to be served at 2:45 p.m.

Host:  Dr. Alexander van Oudenaarden
Department of Physics

Abstract

Diverse organisms ranging from bacteria to mammalian stem cells undergo 
pluripotent
differentiation where a single cell can commit to one out of several 
cell fates.
How do underlying genetic circuits allow cells to "choose" a specific 
cell fate and
execute the appropriate differentiation program? To address this 
question we investigate
a simple bacterial differentiation system utilizing mathematical 
modeling and quantitative
single cell measurements. In particular we are interested in elucidating 
the significance
of circuit dynamics and stochastic behavior during cellular 
differentiation.

Suel et al. Science 315, 1716-1719 (2007)
Suel et al. Nature 440, 545-550 (2006)


From csbi-events at mit.edu  Thu Oct 11 09:22:35 2007
From: csbi-events at mit.edu (CSBi events)
Date: Thu, 11 Oct 2007 09:22:35 -0400
Subject: [CSBi-events] [Fwd: Fwd: RECOMB Regulatory Genomics 2007 starting
	at 5pm today!]
Message-ID: <470E239B.90604@mit.edu>


From: "Manolis Kellis" <manoli at MIT.EDU>
To: "CSBi events" <csbi-events at MIT.EDU>
Date: Thu, 11 Oct 2007 07:42:36 -0400
Subject: *RECOMB Regulatory Genomics 2007 starting at 5pm today!*

Hi all,

Just a final reminder that the 4th Annual RECOMB satellite
on Regulatory Genomics is starting at 5pm today at the Broad
Institute Auditorium and Lobby, and runs till Saturday at 2:30pm.

We have 200 participants coming from around the world,
83 presentations, including keynotes by Drs. Eisen, Church,
Birney, O'Shea, Friedman, Levine, Bartel, Ideker and Collins,
27 talks by some of the leading labs on Genome Regulation
from around the world, and 50+ posters that will remain at the
Broad Lobby throughout the event.

You can still register online at http://compbio.mit.edu/recombsat
and attend the talks, poster sessions, and evening receptions.
Lastly, we are still looking for a couple of additional volunteers
to help out with registration and logistics.

I hope to see many of you at the meeting over the next three days,
and I do encourage you to register as we'll be pretty strict about
name tags given the large number of registered attendees.
Scientific program is online at:  http://compbio.mit.edu/recombsat

Hope to see you soon!

Manolis
--
Manolis Kellis - manoli at mit.edu - http://mit.edu/manoli
Assistant Professor, MIT EECS, CSAIL, Broad Institute



From csbi-events at mit.edu  Wed Oct 17 08:15:26 2007
From: csbi-events at mit.edu (CSBi events)
Date: Wed, 17 Oct 2007 08:15:26 -0400
Subject: [CSBi-events] Publishing Forum at Harvard]
Message-ID: <4715FCDE.5020805@mit.edu>


>>> *From: *"Zeba Wunderlich" <wunderl at fas.harvard.edu 
>>> <mailto:wunderl at fas.harvard.edu> >
>>> *Date: *October 16, 2007 3:01:42 PM EDT
>>> *To: *lkn at mit.edu <mailto:lkn at mit.edu>
>>> *Subject: Publishing Forum at Harvard
>>> *
>>> Dear Ms. Earle,
>>>
>>> I'm writing on behalf of the organizing committee for an upcoming 
>>> conference on scientific publishing in biology, to be held on Nov. 9 
>>> at Harvard Medical School. It is open to all, and we think it may be 
>>> of interest to faculty members, post docs, graduate students and 
>>> other researchers in the Biology Department at MIT. Is there any way 
>>> you might help with publicity (a blurb is included below)? In the 
>>> newsletter or elsewhere?
>>>
>>> Thanks very much!
>>>
>>> Zeba Wunderlich
>>> Conference Co-Chair
>>> PhD Candidate, Harvard Biophysics Program
>>> Mirny Lab, http://www.mit.edu/~leonid <http://www.mit.edu/%7Eleonid>
>>>
>>>
>>>
>>>
>>>
>>> /What's the impact of the "impact factor"?
>>> Do you believe that more journals should adopt open-access policies?
>>> Are you satisfied with the current scientific publishing process?
>>> Will the internet revolutionize publishing?
>>> /If you have thoughts or questions about the future or scientific 
>>> publishing (and who doesn't?), please join us at:
>>>
>>> *"Publishing in the New Millennium: A Forum on Publishing in the 
>>> Biosciences"*
>>> *Friday, November 9, 1:00 - 6:00 pm*
>>> *TMEC Walter Amphitheater, Harvard Medical School
>>> *260 Longwood Ave, Boston, MA 02115
>>> www.harvardpublishingforum.com <http://www.harvardpublishingforum.com/>
>>> This is a student-organized conference that will convene experts 
>>> from across the world to discuss the state of publishing in the 
>>> biological sciences.
>>>
>>> /KEYNOTE ADDRESS: /
>>> *Harold Varmus, M.D.*
>>> Nobel-Laureate and Co-founder of PLoS, former Director of the NIH, 
>>> and CEO of Memorial-Sloan Kettering Cancer Center
>>> Dr. Varmus will draw on his experience as Director of the NIH and as 
>>> a co-founder of the Public Library of Science to reflect on the 
>>> current and future state of scientific publishing.
>>>
>>> /PANELS: /
>>> *The State of Publishing *will critically assess the impact that 
>>> scientific publishing has on scientific research.
>>> _Panelists include:_
>>> ? Robert Kiley, Head of e-Strategy, Wellcome Library, Wellcome Trust
>>> ? Isaac Kohane, Director, Countway Library, Harvard University
>>> ? Emilie Marcus, Editor-in-Chief, Cell Press and Editor, Cell
>>> ? Stuart Shieber, Professor, Harvard University
>>>
>>> *Publishing 2.0* will examine the future of publishing in an 
>>> increasingly digital world.
>>> _Panelists include:
>>> _? Moshe Pritsker, Editor-in-Chief and Founder, Journal of 
>>> Visualized Experiments
>>> ? Hilary Spencer, Product Manager, Nature Precedings
>>> ? John Wilbanks, Executive Director, Science Commons
>>> ? Bora Zivkovic, Community Manager, PLoS ONE
>>>
>>> We also want to know what you think! Please take a moment to 
>>> complete a brief online poll at www.harvardpublishingforum.com 
>>> <http://www.harvardpublishingforum.com/> and register (optional, but 
>>> strongly encouraged) for this half-day event.
>>>
>>> A reception, sponsored in part by the Nature Publishing Group/Nature 
>>> Network, will follow the forum.
>>>
>>> /This student-organized forum is generously sponsored by the Harvard 
>>> Biophysics Program and the Harvard Integrated Life Sciences (HILS) 
>>> Program. Questions? Contact Kishore Kuchibhotla 
>>> [kuchibh at fas.harvard.edu <mailto:kuchibh at fas.harvard.edu>] or Zeba 
>>> Wunderlich [ wunderl at fas.harvard.edu <mailto:wunderl at fas.harvard.edu>]./
>>>
>>> All are invited so please forward widely!
>>>
>>>
>>>
>>
>> Linda K. Earle,
>> Resource Development Coordinator
>> Department of Biology
>> Massachusetts Institute of Technology
>> 77 Massachusetts Avenue, Bldg. 68-132
>> Cambridge, MA 02139
>> (617)324-2297
>> (617 253-8699
>>


From csbi-events at mit.edu  Tue Oct 23 10:11:08 2007
From: csbi-events at mit.edu (CSBi events)
Date: Tue, 23 Oct 2007 10:11:08 -0400
Subject: [CSBi-events] SAVE THE DATE:  CSBi November 2,
 2007 seminar (Attached PDF of CSBi flyer)
Message-ID: <471E00FC.6060001@mit.edu>

SAVE THE DATE!!!!!

Reminder !  Fall 2007 Seminar Series on Computational and Systems Biology!

Friday, November 2, 2007; 3:00- 4:00 PM, Rm. 4-370
Dr. Aviv Regev
Department of Biology/The Broad Institute/MIT

Title:  Natural history and evolutionary principles of gene duplication 
in fungi

Abstract:
Gene duplication and loss is a powerful source of functional innovation. 
However, the general principles that govern this process are still 
largely unknown. With the growing number of sequenced genomes, it is now 
possible to examine these events in a comprehensive and unbiased manner. 
Here, we develop a procedure that resolves the evolutionary history of 
all genes in a large group of species. We apply our procedure to 
seventeen fungal genomes to create a genome-wide catalogue of gene trees 
that determine precise orthology and paralogy relations across these 
species. We show that gene duplication and loss is highly constrained by 
the functional properties and interacting partners of genes. In 
particular, stress-related genes exhibit many duplications and losses, 
whereas growth-related genes show selection against such changes. 
Whole-genome duplication circumvents this constraint and relaxes the 
dichotomy, resulting in an expanded functional scope of gene 
duplication. By characterizing the functional fate of duplicate genes we 
show that duplicated genes rarely diverge with respect to biochemical 
function, but typically diverge with respect to regulatory control. 
Surprisingly, paralogous modules of genes rarely arise, even after 
whole-genome duplication. Rather, gene duplication may drive the 
modularization of functional networks through specialization, thereby 
disentangling cellular systems.

Light refreshments to be served at 2:45 p.m.

Host:  Dr. Alexander van Oudenaarden
Department of Physics
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From csbi-events at mit.edu  Wed Oct 24 10:04:49 2007
From: csbi-events at mit.edu (CSBi events)
Date: Wed, 24 Oct 2007 10:04:49 -0400
Subject: [CSBi-events] CANCELLED:  CSBi seminar on November 2, 2007
Message-ID: <471F5101.1030903@mit.edu>

TO ALL:

The following seminar on November 2, 2007 has been canceled and is 
rescheduled.   I will
be sending out the new date of this rescheduled seminar as soon as I 
confirm the date and location.  Thank you.

Karen Griffin
CSBi assistant



-------- Original Message --------
Subject: 	SAVE THE DATE: CSBi November 2, 2007 seminar (Attached PDF of 
CSBi flyer)
Date: 	Tue, 23 Oct 2007 10:11:08 -0400
From: 	Karen Griffin <dori123 at mit.edu>
To: 	CSBi-events at mit.edu



SAVE THE DATE!!!!!

Reminder !  Fall 2007 Seminar Series on Computational and Systems Biology!

Friday, November 2, 2007; 3:00- 4:00 PM, Rm. 4-370
Dr. Aviv Regev
Department of Biology/The Broad Institute/MIT

Title:  Natural history and evolutionary principles of gene duplication 
in fungi

Abstract:
Gene duplication and loss is a powerful source of functional innovation. 
However, the general principles that govern this process are still 
largely unknown. With the growing number of sequenced genomes, it is now 
possible to examine these events in a comprehensive and unbiased manner. 
Here, we develop a procedure that resolves the evolutionary history of 
all genes in a large group of species. We apply our procedure to 
seventeen fungal genomes to create a genome-wide catalogue of gene trees 
that determine precise orthology and paralogy relations across these 
species. We show that gene duplication and loss is highly constrained by 
the functional properties and interacting partners of genes. In 
particular, stress-related genes exhibit many duplications and losses, 
whereas growth-related genes show selection against such changes. 
Whole-genome duplication circumvents this constraint and relaxes the 
dichotomy, resulting in an expanded functional scope of gene 
duplication. By characterizing the functional fate of duplicate genes we 
show that duplicated genes rarely diverge with respect to biochemical 
function, but typically diverge with respect to regulatory control. 
Surprisingly, paralogous modules of genes rarely arise, even after 
whole-genome duplication. Rather, gene duplication may drive the 
modularization of functional networks through specialization, thereby 
disentangling cellular systems.

Light refreshments to be served at 2:45 p.m.

Host:  Dr. Alexander van Oudenaarden
Department of Physics




From csbi-events at mit.edu  Wed Oct 24 11:26:53 2007
From: csbi-events at mit.edu (CSBi events)
Date: Wed, 24 Oct 2007 11:26:53 -0400
Subject: [CSBi-events] CSBi Seminar Series: Rescheduled seminar to be
	November 9, 2007
Message-ID: <471F643D.10004@mit.edu>

SAVE THE DATE!!!!!

Reminder !  Fall 2007 Seminar Series on Computational and Systems Biology!

Friday, November 9,2007; 3:00- 4:00 PM, Rm. 4-370
Dr. Aviv Regev
Department of Biology/The Broad Institute/MIT

Title:  Natural History and Evolutionary Principles of Gene Duplication 
in Fungi

Abstract:
Gene duplication and loss is a powerful source of functional innovation. 
However, the general principles that govern this process are still 
largely unknown. With the growing number of sequenced genomes, it is now 
possible to examine these events in a comprehensive and unbiased manner. 
Here, we develop a procedure that resolves the evolutionary history of 
all genes in a large group of species. We apply our procedure to 
seventeen fungal genomes to create a genome-wide catalogue of gene trees 
that determine precise orthology and paralogy relations across these 
species. We show that gene duplication and loss is highly constrained by 
the functional properties and interacting partners of genes. In 
particular, stress-related genes exhibit many duplications and losses, 
whereas growth-related genes show selection against such changes. 
Whole-genome duplication circumvents this constraint and relaxes the 
dichotomy, resulting in an expanded functional scope of gene 
duplication. By characterizing the functional fate of duplicate genes we 
show that duplicated genes rarely diverge with respect to biochemical 
function, but typically diverge with respect to regulatory control. 
Surprisingly, paralogous modules of genes rarely arise, even after 
whole-genome duplication. Rather, gene duplication may drive the 
modularization of functional networks through specialization, thereby 
disentangling cellular systems.

Light refreshments to be served at 2:45 p.m.

Host:  Dr. Alexander van Oudenaarden
Department of Physics