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CACR Publication News: Cellcenter collaboration with developmental biologists yields insight in fruit fly genomics
“High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation” was published in the Genome Research Journal, Advanced Online Access, March 2011. Genome Research focuses on research that provides novel insights into the genome biology of all organisms, including advances in genomic medicine.
From the abstract:
“Cis-regulatory modules (CRMs) function by binding sequence specific transcription factors, but the relationship between in vivo physical binding and the regulatory capacity of factor-bound DNA elements remains uncertain. We investigate this relationship for the well-studied Twist factor in Drosophila melanogaster embryos by analyzing genome-wide factor occupancy and testing the functional significance of Twist occupied regions and motifs within regions … Our results show that high resolution in vivo occupancy data can be used to drive efficient discovery and dissection of global and local cis-regulatory logic.” (more)
CACR staff member Shirley Pepke analyzed the ChIP-seq binding data and found enhanced evolutionary conservation associated with candidate cis regulatory modules.
About Cellcenter: The goal of the Center for Integrative Study of Cell Regulation (Cell Center) is to develop new computational methods for understanding how the many genes and proteins that make up individual cells work together to carry out specialized functions of different cell types, including neurons, plant cells, and bacteria. See www.cellcenter.caltech.edu for further information.
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Below are some recent publications and presentations that have been added to CACR’s publications list. See the full list here. You can also subscribe to get notifications of new publications either via our RSS feed or the CACR Twitter feed.
- Computational Morphodynamics: Integrating Development Over Space and Time.
Nature Reviews Molecular Cell Biology (submitted)
Adrienne H. K. Roeder, Paul T. Tarr, Cory Tobin, Xiaolan Zhang, Vijay Chickarmane, Alexandre Cunha, and Elliot M. Meyerowitz.
- Cloud-based Remote Auscultation Using Mobile Phones – A Demonstration
Presentation and Demonstration at the Diabetes Technology Meeting, Bethesda MD, November 2010
Julian Bunn, Mani Chandy et al
- Discovery of the Extremely Energetic Supernova 2008fz
A.J. Drake, S.G. Djorgovski, J.L. Prieto, A. Mahabal, D. Balam, R. Williams, M.J. Graham, M. Catelan, E. Beshore, S. Larson, 2010
astro-ph, ApJL
- An efficient method for computing steady state solutions with Gillespie’s direct method
J. Chem. Phys. 133, 144108 (2010); doi:10.1063/1.3489354 (7 pages)
S. Mauch and M. Stalzer
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Below is a list of recent publications and presentations added to CACR’s publications list. See the full list here. You can subscribe to get notifications of new publications either via our RSS feed or the CACR Twitter feed.
Enabling Computational Plant Development: From Confocal Images to Finite Element Simulations
In Computational Methods in Image Analysis, 10th US National Congress of Computational Mechanics, Columbus, Ohio, USA, July 16 – 19 2009
Alexandre Cunha
Computation for Chip-seq and RNA-seq studies
Nature Methods, to appear.
Shirley Pepke, Barbara Wold, and Ali Mortazavi
Whole-volume integrated gyrokinetic simulation of plasma turbulence in realistic diverted-tokamak geometry
SciDAC 2009, Journal of Physics: Conference Series. J Phys: Conf Ser 180 (2009) 012057.
C S Chang, S Ku, P Diamond, M Adams, R Barreto, Y Chen, J Cummings, E D’Azevedo, G Dif-Pradalier, S Ethier, L Greengard, T S Hahm, F Hinton, D Keyes, S Klasky, Z Lin, J Lofstead, G Park, S Parker, N Podhorszki, K Schwan, A Shoshani, D Silver, M Wolf, P Worley, H Weitzner, E Yoon and D Zorin
Engineering Computational Science and Engineering
Presentation/Lecture (given at Lousiana State University, Caltech, and the Institute for Defense Analysis, MD)
Mark Stalzer
First results from the Catalina Real-time Transient Survey
2009, ApJ, in press (arXiv:0809.1394)
Drake A.J., Djorgovski S.G., Mahabal A., Beshore E., Larson S., Graham M.J., Williams R., Christensen R., Catelan M., Boattini A., Gibbs A., Hill R., Kowalski R.
