Tools and Methods
|- M. Chevalier and H. El-Samad, Towards a minimal stochastic model for a large class of diffusion-reactions on biological membranes , J. Chemical Physics, Vol. 137, 084103, 2012.|
|- M. Chevalier and H. El-Samad, A Data-Integrated Method for Analyzing Stochastic Biochemical Networks , J. Chemical Physics, Vol. 135, No. 21, 214110, 2011.|
|- Melykuti B, Papachristodoulou A, August E and El-Samad H, Discriminating between rival biochemical network models: three approaches to optimal experiment design , BMC Systems Biology, Vol. 4, No. 38, 2010.|
|- Chevalier M and El-Samad H, A rigorous framework for multi-scale simulation of stochastic cellular networks , Journal of Chemical Physics, Vol. 131, No. 5, 054102, 2009. PMCID: PMC2736569.|
|- Rathinam M and El-Samad H, Reversible-equivalent-monomolecular tau: A leaping method for "small number and stiff" stochastic chemical systems, J. of Computational Physics 224 (2): 897-923 JUN 10 2007|
|- Hana El-Samad, Stephen Prajna, Antonis Papachristodoulou, John Doyle, and Mustafa Khammash, Advanced Methods and Algorithms for Biological Networks Analysis Proceedings of the IEEE, VOL. 94, NO. 4, APRIL 2006 [PDF].|
|- Hana El Samad, Mustafa Khammash, Linda Petzold, and Dan Gillespie, Stochastic modelling of gene regulatory networks ,Int. J. Robust Nonlinear Control 2005; 15:691–711 [PDF].|
|- H. El-Samad, and M.Khammash, Stochastic Stability and its Applications to the Study of Gene Regulatory Networks , Proceedings of the 43d IEEE Conference on Decision and Control, Paradise Island, Bahamas, 2004 [PDF].|
|- El-Samad H, S. Prajna, A. Papachristodoulou, M. H. Khammash, and J. C. Doyle. 2003. Model Validation and Robust Stability Analysis of the Bacterial Heat Shock Response Using SOSTOOLS. In Proc. of the IEEE Conference on Decision and Control. Maui, HI. 2003 [PDF]|
Biological System Analysis
|- J. Stewart-Ornstein, C. Nelson, J. DeRisi, J. S. Weissman, H El-Samad Msn2 Coordinates a Stoichiometric Gene Expression Program, Current Biology, November 2013.
|- S. Chen*, P. Harrigan*, B. Heineike*, J. Stewart-Ornstein, H. El-Samad Building robust functionality in synthetic circuits using engineered feedback regulation, Current Opinion in Biotechnology, ISSN 0958-1669, April 2013.
*: Co-first authors
|- R. Iannejad, R., J. C. Tomshine, J. R. Tomshine, M. Chevalier, H. El-Samad, B. Huang, and M. von Zastrow Conformational Biosensors Reveal GPCR Signaling from Endosomes, Nature, Volume 495,534–538, 28 March 2013.|
|- S. Vidal, D Pincus, J. Stewart-Ornstein, H. El-Samad Formation of Subnuclear Foci Is a Unique Spatial Behavior of Mating MAPKs during Hyperosmotic Stress, Cell Reports, Volume 3, Issue 2, 238-334, January 2013.|
|- O. S. Venturelli, H. El-Samad and R.M. Murray Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response., PNAS, E3324-33, November 2012.|
|- P.M. Fordyce, D. Pincus, P. Kimming, C.S. Nelson, H. El-Samad, P. Walter, J. L. Derisi The Basic Leucine Zipper Transcription Factor Hac1 binds DNA in Two Distinct Modes as Revealed by Microfluidic Analyses, PNAS, E3084–E3093, Published online October 10, 2012.|
|- J. Stewart-Ornstein, J.S. Weissman, and H. El-Samad Cellular Noise Regulons Underlie Fluctuations in Saccharomyces cerevisiae, Molecular Cell, Volume 45, Issue 4, 483-493, 24 February 2012.|
|- A.M. Argeitis*, S. Summers*, J. Stewart-Ornstein*, I. Zuleta, D. Pincus, H. El-Samad**, M. Khammash** and J. Lygeros** In silico Feedback fro in vivo Regulation of a gene Expression Circuit, Advanced Online Publication Nov6th 2011.
*: Co-first authors
**: Corresponding authors, listed in alphabetical order.
|- H. El-Samad, HD. Madhani Can a Systems Perspective Help Us Appreciate the Biological Meaning of Small Effects?, Developmental Cell, 21(1): 11-13, 2011.|
|- C. Rubio, D. Pincus, A. Korrennykh, S. Shuck, H. El-Samad, P. Walter Homeostatic adaptation to endoplasmic reticulum stress depends on Ire1 kinase activity, Journal of Cell Biology, 193(1): 171-184, 2011|
|- E. McCullagh, A. Seshan, H. El-Samad* and H. D. Madhani* , Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway , Nature Cell Biology, 12(10):954-62, 2010
* Co-corresponding authors.
|- J.F. Garcia, P.A. Dumesic, P.D. Hartley, H. El-Samad, and H.D. Madhani , Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions , Genes & Development, 24: 1758-1771, 2010.|
|- D. Pincus, M.W. Chevalier, T. Aragon, E. Van Anken, S.E. Vidal, H. El-Samad* and P. Walter ,BiP Binding to the ER-Stress Sensor Ire1 Tunes the Homeostatic Behavior of the Unfolded Protein Response , PloS Biology, Vol. 8, No. 7, 2010.*Corresponding author.|
|- E. McCullagh, J. Farlow, C. Fuller, J. Girard, J. Lipinski-Kruszka, D. Lu, T. Noriega, G. Rollins, R. Spitzer, M. Todhunter, and H. El-Samad ,Not all Quiet on the Noise Front , Nature Chemical Biology, Vol. 5, No. 10, 699-704, 2009.|
|- Wenzhe Ma, Ala Trusina,
Hana El-Samad, Wendell Lim and Chao Tang , Design
Principles of Biochemical Adaptation: Enumerating Solutions in Network
Space , Cell, Vol. 138, No. 4, 760-773, 2009.
|- Q.A. Justman, Z. Server, J.E. Ferrell Jr., H. El-Samad*, and K.M. Shokat*, Tuning the Activation Threshold of a Kinase Network by Nested Feedback Loops, Science,Vol. 324. no. 5926, pp. 509 - 512, 2009. *Co-corresponding authors.|
|- Herzmar P, Campbell K, Wang F, Wong K, El-Samad H, Groisman A, Bourne HR, Bound attractant at the leading vs. the trailing edge determines chemotactic prowess, Proceedings of the National Academy of Sciences of the United States of America 104 (33): 13349-13354 AUG 14 2007.|
|- Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A Gross, and Mustafa Khammash, Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System , PLoS Comput Biol. 2006 July; 2(7): e59 [PDF] .|
|H. El-Samad, H. Kurata, J. Doyle, C. Gross, and M. Khammash, Surviving heat-shock: control strategies for robustness and performance , Proceedings of the National Academy of Sciences (PNAS), 2005; 102:2736-2741 [PDF]|
|Hana El-Samad and Mustafa Khammash, Regulated Degradation Is a Mechanism for Suppressing Stochastic Fluctuations in Gene Regulatory Networks , Biophysical Journal, Vol 90, (2006) 3749–3761 [PDF].|
|H. El Samad, M. Khammash, C. Homescu, and L. Petzold, Optimal Performance of the Heat-Shock Gene Regulatory Network, Proceedings 16th IFAC World Congress to be held in Prague, Czech Republic, July 2005.|
|M. Khammash and H. El Samad, Systems Biology: From Physiology to Gene Regulation , IEEE Control Systems Magazine, vol. 24, No. 4, pp. 62-76, 2004 [PDF].|
|H. El-Samad, J. Goff, and M. Khammash, Calcium Homeostasis and Parturient Hypocalcemia: An Integral Feedback Perspective , Journal of Theoretical Biology, pp. 214, 17-29, 2002 [PDF].|