User:Nikolai Slavov: Difference between revisions
No edit summary |
|||
(18 intermediate revisions by the same user not shown) | |||
Line 2: | Line 2: | ||
[[Image:Nslavov.jpg|thumb|right|Nikolai Slavov]] | [[Image:Nslavov.jpg|thumb|right|Nikolai Slavov]] | ||
*Nikolai Slavov | *[http://mit.edu/nslavov/www/ '''''Nikolai Slavov'''''] | ||
*[http://web.mit.edu/biophysics/index.html '''''van Oudenaarden Lab'''''] | |||
*Massachusetts Institute of Technology, 68-359 | *Massachusetts Institute of Technology, 68-359 | ||
*77 Massachusetts Ave Cambridge, MA 02139 | *77 Massachusetts Ave Cambridge, MA 02139 | ||
Line 9: | Line 10: | ||
*[[Special:Emailuser/Nikolai Slavov|Email me through OpenWetWare]] | *[[Special:Emailuser/Nikolai Slavov|Email me through OpenWetWare]] | ||
<!--I work in the [[Your Lab]] at XYZ University. I learned about [[OpenWetWare]] from from a friend, and I've joined because add protocols. --> | <!-- [[Van_Oudenaarden_Lab]] I work in the [[Your Lab]] at XYZ University. I learned about [[OpenWetWare]] from from a friend, and I've joined because add protocols. --> | ||
==Education== | ==Education== | ||
<!--Include info about your educational background--> | <!--Include info about your educational background--> | ||
* 2010, PhD, | * 2010, PhD, [http://www.princeton.edu/genomics/botstein/ '''''Botstein Lab'''''], Princeton University | ||
* 2006, MS, Princeton University | * 2006, MS, Princeton University | ||
* 2004, BS, Massachusetts Institute of Technology | * 2004, BS, Massachusetts Institute of Technology | ||
Line 19: | Line 20: | ||
==Research interests== | ==Research interests== | ||
<!-- Feel free to add brief descriptions to your research interests as well --> | <!-- Feel free to add brief descriptions to your research interests as well --> | ||
I am interested in the dynamics of cell growth, metabolic and regulatory processes during the eukaryotic cell division cycle (CDC), across a wide range of CDC periods. In particular, I study how the growth rate signal - which is function of the availability of nutrients and growth factors - regulates the switch between respiration and fermentation and changes the duration of phases of the cell growth and division cycles. | |||
<!--# Interest 2 --> | <!--# Interest 2 --> | ||
==Publications== | ==Publications== | ||
<!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications. You can add or remove lines as needed --> | <!-- Replace the PubMed ID's ("pmid=#######") below with the PubMed ID's for your publications. You can add or remove lines as needed --> | ||
<biblio> | <biblio> | ||
# | #paper9 Slavov, N., Carey, J., Linse S. (2013) | ||
# | Calmodulin transduces Ca+2 oscillations into differential regulation of its target proteins | ||
ACS Chemical Neuroscience, vol. 4, issue 2 | |||
[http://pubs.acs.org/doi/pdf/10.1021/cn300218d PDF] | |||
//The molecular and network properties of the calmodulin signaling network, combined with its lignad-binding dynamics, can transduce a common signal (calcium levels) through a common signaling hub (calmodulin) and yet send different signals to many downstream proteins. | |||
#Paper8 Slavov N. and Botstein D. (2012) | |||
Decoupling Nutrient Signaling from Growth Rate Causes Aerobic Glycolysis and Deregulation of Cell Size and Gene Expression | |||
Mol. Biol. Cell, vol. 24, no. 2 | |||
[http://www.molbiolcell.org/content/24/2/157.full.pdf PDF] | |||
// The nutrition and the growth rate of a cell are two interacting factors with pervasive physiological effects. Our experiments decouple these factors and demonstrate the role of a growth rate signal, independent of the actual rate of biomass increase, on gene regulation, the cell division cycle, and the switch to a respiro-fermentative metabolism. | |||
#Paper7 Slavov N., van Oudenaarden A.*(2012) How to Regulate a Gene: To Repress or to Activate? Mol. Cell, vol. 46, issue 5, 551-552 | |||
[http://pdn.sciencedirect.com/science?_ob=MiamiImageURL&_cid=272198&_user=501045&_pii=S1097276512004510&_check=y&_origin=article&_zone=toolbar&_coverDate=2012--08&view=c&originContentFamily=serial&wchp=dGLbVlB-zSkzS&md5=e435c638de506531e5d1e1faab59a46f&pid=1-s2.0-S1097276512004510-main.pdf PDF] | |||
#Paper6 Slavov N., Airoldi E., van Oudenaarden A., and Botstein D. (2012) | |||
A Conserved Cell Growth Cycle Can Account for the Environmental Stress Responses of Divergent Eukaryotes | |||
Mol. Biol. Cell, vol. 23, no. 10, 1986-1997 | |||
[http://www.molbiolcell.org/content/23/10/1986.full.pdf PDF] | |||
// We find that transitions between the two phases of the cell growth cycle can account for the environmental stress response, the growth-rate response, and the cross protection between slow growth and various types of stress factors. We suggest that this mechanism is conserved across budding and fission yeast, and normal human cells. | |||
#Paper5 Slavov N., Macinskas J., Caudy A., Botstein D. (2011) | |||
Metabolic Cycling without Cell Division Cycling in Respiring Yeast | |||
PNAS, vol. 108, no. 47, 19090-19095 | |||
[http://www.pnas.org/content/108/47/19090.full.pdf PDF] | |||
#Paper4 Slavov N. and Botstein D. (2011) | |||
Coupling among Growth Rate Response, Metabolic Cycle and Cell Division Cycle in Yeast | |||
Mol. Biol. Cell, vol. 22, 1997-2009 | |||
[http://www.molbiolcell.org/content/22/12/1997.full.pdf PDF] | |||
//We discovered that the relative durations of the phases of the yeast metabolic cycle change with the growth rate. These changes can explain mechanistically the transcriptional growth-rate responses of all yeast genes (25% of the genome) that we find to be the same across all studied nutrient limitations in either ethanol or glucose carbon source. | //We discovered that the relative durations of the phases of the yeast metabolic cycle change with the growth rate. These changes can explain mechanistically the transcriptional growth-rate responses of all yeast genes (25% of the genome) that we find to be the same across all studied nutrient limitations in either ethanol or glucose carbon source. | ||
#Paper3 Slavov N. (2010) | |||
Inference of Sparse Networks with Unobserved Variables. Application to Gene Regulatory Networks, JMLR, vol. 9 | |||
[http://jmlr.csail.mit.edu/proceedings/papers/v9/slavov10a/slavov10a.pdf PDF] | |||
#Paper2 pmid=20335538 | #Paper2 pmid=20335538 | ||
// [http://f1000.com/8103960 '''''F1000 Review'''''] | |||
#Paper1 pmid=19246374 | #Paper1 pmid=19246374 | ||
<!-- #Book1 isbn=0879697164 --> | <!-- #Book1 isbn=0879697164 --> | ||
</biblio> | </biblio> | ||
==Protocols== | |||
*Phosphate-Limited Medium with Ethanol as a Sole Source of Carbon and Energy[http://alum.mit.edu/www/nslavov/PubSlavov/phosphate_limit_ethanol_cs.pdf] | |||
*Glucose-Limited Mineral Medium[http://alum.mit.edu/www/nslavov/PubSlavov/glucose_limit.pdf] | |||
*Ethanol-Limited Mineral Medium[http://www.mit.edu/~nslavov/PubSlavov/ethanol_limit_ethanol_cs.pdf] | |||
<!-- | <!-- |
Revision as of 14:28, 19 February 2013
Contact Info
- Nikolai Slavov
- van Oudenaarden Lab
- Massachusetts Institute of Technology, 68-359
- 77 Massachusetts Ave Cambridge, MA 02139
- http://mit.edu/nslavov/www/
- http://alum.mit.edu/www/nslavov
- Email me through OpenWetWare
Education
- 2010, PhD, Botstein Lab, Princeton University
- 2006, MS, Princeton University
- 2004, BS, Massachusetts Institute of Technology
Research interests
I am interested in the dynamics of cell growth, metabolic and regulatory processes during the eukaryotic cell division cycle (CDC), across a wide range of CDC periods. In particular, I study how the growth rate signal - which is function of the availability of nutrients and growth factors - regulates the switch between respiration and fermentation and changes the duration of phases of the cell growth and division cycles.
Publications
-
Slavov, N., Carey, J., Linse S. (2013)
Calmodulin transduces Ca+2 oscillations into differential regulation of its target proteins
ACS Chemical Neuroscience, vol. 4, issue 2 PDF
The molecular and network properties of the calmodulin signaling network, combined with its lignad-binding dynamics, can transduce a common signal (calcium levels) through a common signaling hub (calmodulin) and yet send different signals to many downstream proteins.
-
Slavov N. and Botstein D. (2012)
Decoupling Nutrient Signaling from Growth Rate Causes Aerobic Glycolysis and Deregulation of Cell Size and Gene Expression
Mol. Biol. Cell, vol. 24, no. 2 PDF
The nutrition and the growth rate of a cell are two interacting factors with pervasive physiological effects. Our experiments decouple these factors and demonstrate the role of a growth rate signal, independent of the actual rate of biomass increase, on gene regulation, the cell division cycle, and the switch to a respiro-fermentative metabolism.
-
Slavov N., van Oudenaarden A.*(2012) How to Regulate a Gene: To Repress or to Activate? Mol. Cell, vol. 46, issue 5, 551-552
-
Slavov N., Airoldi E., van Oudenaarden A., and Botstein D. (2012)
A Conserved Cell Growth Cycle Can Account for the Environmental Stress Responses of Divergent Eukaryotes
Mol. Biol. Cell, vol. 23, no. 10, 1986-1997 PDF
We find that transitions between the two phases of the cell growth cycle can account for the environmental stress response, the growth-rate response, and the cross protection between slow growth and various types of stress factors. We suggest that this mechanism is conserved across budding and fission yeast, and normal human cells.
-
Slavov N., Macinskas J., Caudy A., Botstein D. (2011)
Metabolic Cycling without Cell Division Cycling in Respiring Yeast
PNAS, vol. 108, no. 47, 19090-19095 PDF
-
Slavov N. and Botstein D. (2011)
Coupling among Growth Rate Response, Metabolic Cycle and Cell Division Cycle in Yeast
Mol. Biol. Cell, vol. 22, 1997-2009 PDF
We discovered that the relative durations of the phases of the yeast metabolic cycle change with the growth rate. These changes can explain mechanistically the transcriptional growth-rate responses of all yeast genes (25% of the genome) that we find to be the same across all studied nutrient limitations in either ethanol or glucose carbon source.
-
Slavov N. (2010)
Inference of Sparse Networks with Unobserved Variables. Application to Gene Regulatory Networks, JMLR, vol. 9
- Silverman SJ, Petti AA, Slavov N, Parsons L, Briehof R, Thiberge SY, Zenklusen D, Gandhi SJ, Larson DR, Singer RH, and Botstein D. Metabolic cycling in single yeast cells from unsynchronized steady-state populations limited on glucose or phosphate. Proc Natl Acad Sci U S A. 2010 Apr 13;107(15):6946-51. DOI:10.1073/pnas.1002422107 |
- Slavov N and Dawson KA. Correlation signature of the macroscopic states of the gene regulatory network in cancer. Proc Natl Acad Sci U S A. 2009 Mar 17;106(11):4079-84. DOI:10.1073/pnas.0810803106 |
Protocols
- Phosphate-Limited Medium with Ethanol as a Sole Source of Carbon and Energy[1]
- Glucose-Limited Mineral Medium[2]
- Ethanol-Limited Mineral Medium[3]