- Genomic Regulatory Networks and the Regulatory Genome
- Computational Models of SNPs and Disease Associations
- CELLARIUM: An Integrated Framework for Genome Browsers and Bioinformatics Workflows
- Medical Bioinformatics and Beyond
- Algorithmic Theory of Protein Folding and Misfolding
- Statistical Mechanics and Computational Complexity
This work was funded by the National Science Foundation
Project Resources
- Overview
- Collaborators
- Publications
- Related Software
- Presentations
- Posters
Development of Western science is based on two great achievements:
the invention of the formal logical system (in Euclidean geometry)
by the Greek philosophers, and the discovery of the possibility to
find out causal relationships by systematic experiment (during
Renaissance).
Albert Einstein (1953)
Albert Einstein (1953)
Overview
The Genome and the Transcriptome
........overview of project..........This work focuses on inferring logic functions of genomic cis-regulatory code and the principles of information processing of genomic regulation .......sea urchin developmental gene regulatory networks................. building a high-resolution transcriptome map of the embryo...................... inferring logic functions of genomic cis-regulatory code and the principles of information processing of genomic regulation...........
The Logicome
Text...text....
The Regulatory Genome
Text...text....
The Systeome
Text...text....
Current project members: Ryan Tarpine
Project
alumni: Rohan Maddamsetti, Sanjay Trehan, and David Moskowitz
Collaborators
- Norman Chandler Professor of Cell Biology Eric Davidson, California Institute of Technology
- Joel Smith, Ph.D., Marine Biological Laboratory, Woods Hole
- Russel Turner, Ph.D.
- Professor Gary Wessel, Brown University
Publications
| 2012 | |
| [8] | Hagit Shatkay, Ramya Narayanaswamy, Santosh Nagaral, Na Harrington, Dorothea Blostein, Ryan Tarpine, Kyle Schutter, Rohith Mv, Gowri Somanath, Sorin Istrail, Chandra Kambahmettu, "OCR-based Image Features for Biomedical Image and Article Classification: Identifying Documents Relevant to Cis-Regulatory Elements", In ACM BCB, 2012. [bib] [pdf] |
| 2010 | |
| [7] | Jongmin Nam, Ping Dong, Ryan Tarpine, Sorin Istrail, Eric H. Davidson, "Functional cis-regulatory genomics for systems biology", In Proceedings of the National Academy of Sciences, vol. 107, no. 8, pp. 3930-3935, 2010. [bib] [pdf] [doi] |
| [6] | Sorin Istrail, Ryan Tarpine, Kyle Schutter, Derek Aguiar, "Practical Computational Methods for Regulatory Genomics: A cisGRN-Lexicon and cisGRN-Browser for Gene Regulatory Networks", Chapter in Computational Biology of Transcription Factor Binding, Humana Press, vol. 674, pp. 369-399, 2010. [bib] [pdf] [doi] |
| 2009 | |
| [5] | Ryan Tarpine, Sorin Istrail, "On the Concept of Cis-Regulatory Information: From Sequence Motifs to Logic Functions", Chapter in Algorithmic Bioprocesses, Springer-Verlag, pp. 731-742, 2009. [bib] [pdf] |
| 2007 | |
| [4] | Sorin Istrail, Smadar Ben-Tabou De-Leon, Eric H. Davidson, "The regulatory genome and the computer", In Developmental Biology, vol. 310, no. 2, pp. 187-195, 2007. [bib] [pdf] [doi] |
| 2006 | |
| [3] | Manoj P. Samanta, Waraporn Tongprasit, Sorin Istrail, R. Andrew Cameron, Qiang Tu, Eric H. Davidson, Viktor Stolc, "The Transcriptome of the Sea Urchin Embryo", In Science, vol. 314, no. 5801, pp. 960-962, 2006. [bib] [pdf] [doi] |
| [2] | Sea Urchin Genome Sequencing Consortium, Erica Sodergren, George M. Weinstock, Eric H Davidson, R. Andrew Cameron, Richard A. Gibbs, Robert C. Angerer, Lynne M. Angerer, Maria Ina Arnone, David R. Burgess, Robert D. Burke, James A. Coffman, Michael Dean, Maurice R. Elphick, Charles A. Ettensohn, Kathy R. Foltz, Amro Hamdoun, Richard O. Hynes, William H. Klein, William Marzluff, David R. McClay, Robert L. Morris, Arcady Mushegian, Jonathan P. Rast, L. Courtney Smith, Michael C. Thorndyke, Victor D. Vacquier, Gary M. Wessel, Greg Wray, Lan Zhang, Christine G. Elsik, Olga Ermolaeva, Wratko Hlavina, Gretchen Hofmann, Paul Kitts, Melissa J. Landrum, Aaron J. Mackey, Donna Maglott, Georgia Panopoulou, Albert J. Poustka, Kim Pruitt, Victor Sapojnikov, Xingzhi Song, Alexandre Souvorov, Victor Solovyev, Zheng Wei, Charles A. Whittaker, Kim Worley, K. James Durbin, Yufeng Shen, Olivier Fedrigo, David Garfield, Ralph Haygood, Alexander Primus, Rahul Satija, Tonya Severson, Manuel L. Gonzalez-Garay, Andrew R. Jackson, Aleksandar Milosavljevic, Mark Tong, Christopher E. Killian, Brian T. Livingston, Fred H. Wilt, Nikki Adams, Robert Bell??, Seth Carbonneau, Rocky Cheung, Patrick Cormier, Bertrand Cosson, Jenifer Croce, Antonio Fernandez-Guerra, Anne-Marie Genevi??re, Manisha Goel, Hemant Kelkar, Julia Morales, Odile Mulner-Lorillon, Anthony J. Robertson, Jared V. Goldstone, Bryan Cole, David Epel, Bert Gold, Mark E. Hahn, Meredith Howard-Ashby, Mark Scally, John J. Stegeman, Erin L. Allgood, Jonah Cool, Kyle M. Judkins, Shawn S. McCafferty, Ashlan M. Musante, Robert A. Obar, Amanda P. Rawson, Blair J. Rossetti, Ian R. Gibbons, Matthew P. Hoffman, Andrew Leone, Sorin Istrail, Stefan C. Materna, Manoj P. Samanta, Viktor et al. Stolc, "The Genome of the Sea Urchin Strongylocentrotus purpuratus", In Science, vol. 314, no. 5801, pp. 941-952, 2006. [bib] [pdf] [doi] |
| 2005 | |
| [1] | Sorin Istrail, Eric Davidson, "Logic functions of the genomic cis-regulatory code", In Proceedings of the National Academy of Sciences, vol. 102, no. 14, pp. 4954-4959, 2005. [bib] [pdf] |
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