Eric Deeds
/in /by Grant Alkin
Email Address:
deeds@ucla.edu
Office Phone Number:
(310) 825-1034
Website
Deeds Lab
Office Address:
Boyer Hall 570 E
Research in my lab is focused on using a combination of computational and experimental techniques to understand the dynamics of complex molecular networks within cells. One major area of interest to us is involves cell signaling and gene regulatory networks. In particular, we make dynamic models of these networks and compare the predictions of these models to data obtained by other groups from single-cell experimental techniques. We have recently begun to focus on single-cell RNA sequencing (scRNA-seq) data, since there is a wealth of experimental data currently emerging based on that technique. One issue with this type of data is its dimensionality; scRNA-seq can measure the expression level of thousands of genes in thousands to millions of single cells. Dimensionality reduction using approaches like PCA or t-SNE is thus a critical component of most scRNA-seq data analysis pipelines. We recently found that dimensionality reduction approaches currently employed in the field end up loosing a significant amount of biologically-relevant information about cell state, and so we are working to develop new dimensionality reduction methods that do not have this problem. Our long-term goal is to improve analyses like cell-type clustering and pseudotime analysis in order to facilitate the comparison between scRNA-seq data and the predictions of computational models of cell signaling and gene regulation.
Another major area of research in my lab involves understanding the assembly of the proteasome, a large molecular machine that is responsible for much of the protein degradation that occurs within cells. We make computational models of this process in my lab, and test predictions from those models using in vitro experimental techniques. This work involves significant experimental biochemistry, biophysics and structural biology.
A selected list of publications:
Vakser, I. A. and Deeds, E. J., “Computational Approaches to Macromolecular Interactions in the Cell”, Curr Opin Struct Biol, 55 : 59-65 (2019).
Shockley, E. M., Rouzer, C. A., Marnett, L. J., Deeds, E. J. and Lopez, C. F., “Signal integration and information transfer in an allosterically regulated network”, npc Syst Biol Appl, 5 (1): 324-333 (2019).
Suderman, R. and Deeds, E. J., “Intrinsic limits on information transfer in cellular signaling networks”, Interface Focus, 8 (6): 20180039- (2018).
Nariya MK, Kim JH, Xiong J, Kleindl PA, Hewarathna A, Fisher AC, Joshi SB, Schneich C, Forrest ML, Middaugh CR, Volkin DB, Deeds EJ, “Comparative Characterization of Crofelemer Samples Using Data Mining and Machine Learning Approaches With Analytical Stability Data Sets”, Journal of pharmaceutical sciences, 106 (11): 3270-3279 (2017).
Rowland MA, Greenbaum JM, Deeds EJ, “Crosstalk and the evolvability of intracellular communication”, Nature communications, 8 : 16009- (2017).
Suderman R, Bachman JA, Smith A, Sorger PK, Deeds EJ, “Fundamental trade-offs between information flow in single cells and cellular populations”, Proceedings of the National Academy of Sciences of the United States of America, 114 (22): 5755-5760 (2017).
Kleindl PA, Xiong J, Hewarathna A, Mozziconacci O, Nariya MK, Fisher AC, Deeds EJ, Joshi SB, Middaugh CR, Schneich C, Volkin DB, Forrest ML, “The Botanical Drug Substance Crofelemer as a Model System for Comparative Characterization of Complex Mixture Drugs”, Journal of pharmaceutical sciences, 106 (11): 3242-3256 (2017).
Hewarathna A, Mozziconacci O, Nariya MK, Kleindl PA, Xiong J, Fisher AC, Joshi SB, Middaugh CR, Forrest ML, Volkin DB, Deeds EJ, Schneich C, “Chemical Stability of the Botanical Drug Substance Crofelemer: A Model System for Comparative Characterization of Complex Mixture Drugs”, Journal of pharmaceutical sciences, 106 (11): 3257-3269 (2017).
Nariya MK, Israeli J, Shi JJ, Deeds EJ, “Mathematical Model for Length Control by the Timing of Substrate Switching in the Type III Secretion System”, PLoS computational biology, 12 (4): e1004851- (2016).
Wani PS, Rowland MA, Ondracek A, Deeds EJ, Roelofs J, “Maturation of the proteasome core particle induces an affinity switch that controls regulatory particle association”, Nature communications, 6 (6384): (2015).
