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Hana El-Samad, PhD

Title(s)Professor, Biochemistry and Biophysics
SchoolSchool of Medicine
Phone415-476-2596
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    Collapse Biography 
    Collapse Awards and Honors
    American Automatic Control Council2011Donald P. Eckman Award
    David and Lucille Packard Foundation2009Packard Fellowship
    University of California, San Francisco2008Grace Boyer Junior Faculty Endowed Chair

    Collapse Research 
    Collapse Research Activities and Funding
    Unraveling the quantitative dynamics of cAMP-PKA signaling in yeast
    NIH/NIGMS R01GM119033Feb 1, 2017 - Jan 31, 2021
    Role: Principal Investigator
    Exploring Design Principles of Cellular Control Circuits
    NIH/NIGMS P50GM081879Aug 1, 2010 - Jul 31, 2018
    Role: Co-Investigator
    Systems Biology of Molecular Noise in Yeast
    NIH/NIGMS R01GM086379May 1, 2009 - Jun 28, 2013
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Websites

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Fonseca JP, Bonny AR, Kumar GR, Ng AH, Town J, Wu QC, Aslankoohi E, Chen SY, Dods G, Harrigan P, Osimiri LC, Kistler AL, El-Samad H. A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells. ACS Synth Biol. 2019 Nov 15; 8(11):2593-2606. PMID: 31686495.
      View in: PubMed
    2. Chevalier M, Gómez-Schiavon M, Ng AH, El-Samad H. Design and Analysis of a Proportional-Integral-Derivative Controller with Biological Molecules. Cell Syst. 2019 Sep 23. PMID: 31563473.
      View in: PubMed
    3. Langan RA, Boyken SE, Ng AH, Samson JA, Dods G, Westbrook AM, Nguyen TH, Lajoie MJ, Chen Z, Berger S, Mulligan VK, Dueber JE, Novak WRP, El-Samad H, Baker D. De novo design of bioactive protein switches. Nature. 2019 Aug; 572(7768):205-210. PMID: 31341284.
      View in: PubMed
    4. Ng AH, Nguyen TH, Gómez-Schiavon M, Dods G, Langan RA, Boyken SE, Samson JA, Waldburger LM, Dueber JE, Baker D, El-Samad H. Modular and tunable biological feedback control using a de novo protein switch. Nature. 2019 Aug; 572(7768):265-269. PMID: 31341280.
      View in: PubMed
    5. Ng AH, El-Samad H. Synthetic transcriptional synergy. Science. 2019 05 10; 364(6440):531-532. PMID: 31073055.
      View in: PubMed
    6. Kundert K, Lucas JE, Watters KE, Fellmann C, Ng AH, Heineike BM, Fitzsimmons CM, Oakes BL, Qu J, Prasad N, Rosenberg OS, Savage DF, El-Samad H, Doudna JA, Kortemme T. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun. 2019 05 09; 10(1):2127. PMID: 31073154.
      View in: PubMed
    7. Harrigan P, Madhani HD, El-Samad H. Real-Time Genetic Compensation Defines the Dynamic Demands of Feedback Control. Cell. 2018 10 18; 175(3):877-886.e10. PMID: 30340045.
      View in: PubMed
    8. Gómez-Schiavon M, El-Samad H. Complexity-aware simple modeling. Curr Opin Microbiol. 2018 10; 45:47-52. PMID: 29494832.
      View in: PubMed
    9. Aranda-Díaz A, Mace K, Zuleta I, Harrigan P, El-Samad H. Robust Synthetic Circuits for Two-Dimensional Control of Gene Expression in Yeast. ACS Synth Biol. 2017 03 17; 6(3):545-554. PMID: 27930885.
      View in: PubMed
    10. Stewart-Ornstein J, Chen S, Bhatnagar R, Weissman JS, El-Samad H. Model-guided optogenetic study of PKA signaling in budding yeast. Mol Biol Cell. 2017 01 01; 28(1):221-227. PMID: 28035051.
      View in: PubMed
    11. Dalal CK, Zuleta IA, Mitchell KF, Andes DR, El-Samad H, Johnson AD. Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression. Elife. 2016 09 10; 5. PMID: 27614020.
      View in: PubMed
    12. Al-Sady B, Greenstein RA, El-Samad HJ, Braun S, Madhani HD. Sensitive and Quantitative Three-Color Protein Imaging in Fission Yeast Using Spectrally Diverse, Recoded Fluorescent Proteins with Experimentally-Characterized In Vivo Maturation Kinetics. PLoS One. 2016; 11(8):e0159292. PMID: 27479698.
      View in: PubMed
    13. Heimberg G, Bhatnagar R, El-Samad H, Thomson M. Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing. Cell Syst. 2016 04 27; 2(4):239-250. PMID: 27135536.
      View in: PubMed
    14. Chevalier M, Venturelli O, El-Samad H. The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks. PLoS Comput Biol. 2015 Oct; 11(10):e1004462. PMID: 26484538.
      View in: PubMed
    15. Yang J, McCormick MA, Zheng J, Xie Z, Tsuchiya M, Tsuchiyama S, El-Samad H, Ouyang Q, Kaeberlein M, Kennedy BK, Li H. Systematic analysis of asymmetric partitioning of yeast proteome between mother and daughter cells reveals "aging factors" and mechanism of lifespan asymmetry. Proc Natl Acad Sci U S A. 2015 Sep 22; 112(38):11977-82. PMID: 26351681.
      View in: PubMed
    16. Venturelli OS, Zuleta I, Murray RM, El-Samad H. Population diversification in a yeast metabolic program promotes anticipation of environmental shifts. PLoS Biol. 2015 Jan; 13(1):e1002042. PMID: 25626086.
      View in: PubMed
    17. Chevalier MW, El-Samad H. A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions. J Chem Phys. 2014 Dec 07; 141(21):214108. PMID: 25481130.
      View in: PubMed
    18. Pincus D, Aranda-Díaz A, Zuleta IA, Walter P, El-Samad H. Delayed Ras/PKA signaling augments the unfolded protein response. Proc Natl Acad Sci U S A. 2014 Oct 14; 111(41):14800-5. PMID: 25275008.
      View in: PubMed
    19. Venugopalan G, Camarillo DB, Webster KD, Reber CD, Sethian JA, Weaver VM, Fletcher DA, El-Samad H, Rycroft CH. Multicellular architecture of malignant breast epithelia influences mechanics. PLoS One. 2014; 9(8):e101955. PMID: 25111489.
      View in: PubMed
    20. Lipinski-Kruszka J, Stewart-Ornstein J, Chevalier MW, El-Samad H. Using dynamic noise propagation to infer causal regulatory relationships in biochemical networks. ACS Synth Biol. 2015 Mar 20; 4(3):258-64. PMID: 24967515.
      View in: PubMed
    21. Zuleta IA, Aranda-Díaz A, Li H, El-Samad H. Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry. Nat Methods. 2014 Apr; 11(4):443-8. PMID: 24608180.
      View in: PubMed
    22. Stewart-Ornstein J, Nelson C, DeRisi J, Weissman JS, El-Samad H. Msn2 coordinates a stoichiometric gene expression program. Curr Biol. 2013 Dec 02; 23(23):2336-45. PMID: 24210615.
      View in: PubMed
    23. Chen S, Harrigan P, Heineike B, Stewart-Ornstein J, El-Samad H. Building robust functionality in synthetic circuits using engineered feedback regulation. Curr Opin Biotechnol. 2013 Aug; 24(4):790-6. PMID: 23566378.
      View in: PubMed
    24. Irannejad R, Tomshine JC, Tomshine JR, Chevalier M, Mahoney JP, Steyaert J, Rasmussen SG, Sunahara RK, El-Samad H, Huang B, von Zastrow M. Conformational biosensors reveal GPCR signalling from endosomes. Nature. 2013 Mar 28; 495(7442):534-8. PMID: 23515162.
      View in: PubMed
    25. Vidal SE, Pincus D, Stewart-Ornstein J, El-Samad H. Formation of subnuclear foci is a unique spatial behavior of mating MAPKs during hyperosmotic stress. Cell Rep. 2013 Feb 21; 3(2):328-34. PMID: 23416049.
      View in: PubMed
    26. Venturelli OS, El-Samad H, Murray RM. Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response. Proc Natl Acad Sci U S A. 2012 Nov 27; 109(48):E3324-33. PMID: 23150580.
      View in: PubMed
    27. Fordyce PM, Pincus D, Kimmig P, Nelson CS, El-Samad H, Walter P, DeRisi JL. Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses. Proc Natl Acad Sci U S A. 2012 Nov 06; 109(45):E3084-93. PMID: 23054834.
      View in: PubMed
    28. Chevalier MW, El-Samad H. Towards a minimal stochastic model for a large class of diffusion-reactions on biological membranes. J Chem Phys. 2012 Aug 28; 137(8):084103. PMID: 22938214.
      View in: PubMed
    29. Stewart-Ornstein J, Weissman JS, El-Samad H. Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae. Mol Cell. 2012 Feb 24; 45(4):483-93. PMID: 22365828.
      View in: PubMed
    30. Stewart-Ornstein J, El-Samad H. Stochastic modeling of cellular networks. Methods Cell Biol. 2012; 110:111-37. PMID: 22482947.
      View in: PubMed
    31. El-Samad H, Weissman JS. Genetics: Noise rules. Nature. 2011 Dec 07; 480(7376):188-9. PMID: 22158239.
      View in: PubMed
    32. Chevalier MW, El-Samad H. A data-integrated method for analyzing stochastic biochemical networks. J Chem Phys. 2011 Dec 07; 135(21):214110. PMID: 22149782.
      View in: PubMed
    33. Milias-Argeitis A, Summers S, Stewart-Ornstein J, Zuleta I, Pincus D, El-Samad H, Khammash M, Lygeros J. In silico feedback for in vivo regulation of a gene expression circuit. Nat Biotechnol. 2011 Nov 06; 29(12):1114-6. PMID: 22057053.
      View in: PubMed
    34. El-Samad H, Madhani HD. Can a systems perspective help us appreciate the biological meaning of small effects? Dev Cell. 2011 Jul 19; 21(1):11-3. PMID: 21763599.
      View in: PubMed
    35. Rubio C, Pincus D, Korennykh A, Schuck S, El-Samad H, Walter P. Homeostatic adaptation to endoplasmic reticulum stress depends on Ire1 kinase activity. J Cell Biol. 2011 Apr 04; 193(1):171-84. PMID: 21444684.
      View in: PubMed
    36. McCullagh E, Seshan A, El-Samad H, Madhani HD. Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway. Nat Cell Biol. 2010 Oct; 12(10):954-62. PMID: 20852627.
      View in: PubMed
    37. Garcia JF, Dumesic PA, Hartley PD, El-Samad H, Madhani HD. Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions. Genes Dev. 2010 Aug 15; 24(16):1758-71. PMID: 20675407.
      View in: PubMed
    38. Pincus D, Chevalier MW, Aragón T, van Anken E, Vidal SE, El-Samad H, Walter P. BiP binding to the ER-stress sensor Ire1 tunes the homeostatic behavior of the unfolded protein response. PLoS Biol. 2010 Jul 06; 8(7):e1000415. PMID: 20625545.
      View in: PubMed
    39. Mélykúti B, August E, Papachristodoulou A, El-Samad H. Discriminating between rival biochemical network models: three approaches to optimal experiment design. BMC Syst Biol. 2010 Apr 01; 4:38. PMID: 20356406.
      View in: PubMed
    40. McCullagh E, Farlow J, Fuller C, Girard J, Lipinski-Kruszka J, Lu D, Noriega T, Rollins G, Spitzer R, Todhunter M, El-Samad H. Not all quiet on the noise front. Nat Chem Biol. 2009 Oct; 5(10):699-704. PMID: 19763097.
      View in: PubMed
    41. Ma W, Trusina A, El-Samad H, Lim WA, Tang C. Defining network topologies that can achieve biochemical adaptation. Cell. 2009 Aug 21; 138(4):760-73. PMID: 19703401.
      View in: PubMed
    42. Chevalier MW, El-Samad H. A rigorous framework for multiscale simulation of stochastic cellular networks. J Chem Phys. 2009 Aug 07; 131(5):054102. PMID: 19673546.
      View in: PubMed
    43. Justman QA, Serber Z, Ferrell JE, El-Samad H, Shokat KM. Tuning the activation threshold of a kinase network by nested feedback loops. Science. 2009 Apr 24; 324(5926):509-12. PMID: 19390045.
      View in: PubMed
    44. Herzmark 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. Proc Natl Acad Sci U S A. 2007 Aug 14; 104(33):13349-54. PMID: 17684096.
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    45. Kurata H, El-Samad H, Iwasaki R, Ohtake H, Doyle JC, Grigorova I, Gross CA, Khammash M. Module-based analysis of robustness tradeoffs in the heat shock response system. PLoS Comput Biol. 2006 Jul 28; 2(7):e59. PMID: 16863396.
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    46. El-Samad H, Khammash M. Regulated degradation is a mechanism for suppressing stochastic fluctuations in gene regulatory networks. Biophys J. 2006 May 15; 90(10):3749-61. PMID: 16500958.
      View in: PubMed
    47. El-Samad H, Kurata H, Doyle JC, Gross CA, Khammash M. Surviving heat shock: control strategies for robustness and performance. Proc Natl Acad Sci U S A. 2005 Feb 22; 102(8):2736-41. PMID: 15668395.
      View in: PubMed
    48. El-Samad H, Goff JP, Khammash M. Calcium homeostasis and parturient hypocalcemia: an integral feedback perspective. J Theor Biol. 2002 Jan 07; 214(1):17-29. PMID: 11786029.
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