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Hana El-Samad, PhD

Title(s)Professor, Biochemistry and Biophysics
SchoolSchool of Medicine
Address1700 4th St
San Francisco CA 94158
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 - Jun 30, 2016
    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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. De novo design of protein logic gates. Science. 2020 04 03; 368(6486):78-84. Chen Z, Kibler RD, Hunt A, Busch F, Pearl J, Jia M, VanAernum ZL, Wicky BIM, Dods G, Liao H, Wilken MS, Ciarlo C, Green S, El-Samad H, Stamatoyannopoulos J, Wysocki VH, Jewett MC, Boyken SE, Baker D. PMID: 32241946.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    2. Multi-kinase control of environmental stress responsive transcription. PLoS One. 2020; 15(3):e0230246. Mace K, Krakowiak J, El-Samad H, Pincus D. PMID: 32160258.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    3. Publisher Correction: Modular and tunable biological feedback control using a de novo protein switch. Nature. 2020 03; 579(7798):E8. Ng AH, Nguyen TH, Gómez-Schiavon M, Dods G, Langan RA, Boyken SE, Samson JA, Waldburger LM, Dueber JE, Baker D, El-Samad H. PMID: 32094663.
      View in: PubMed   Mentions:    Fields:    
    4. A population shift between two heritable cell types of the pathogen Candida albicans is based both on switching and selective proliferation. Proceedings of the National Academy of Sciences. 2019 Dec 10; 201908986. Chiraj K. Dalal, Ignacio A. Zuleta, Matthew B. Lohse, Rebecca E. Zordan, Hana El-Samad, Alexander D. Johnson. .
      View in: Publisher Site   Mentions:
    5. A population shift between two heritable cell types of the pathogen Candida albicans is based both on switching and selective proliferation. Proc Natl Acad Sci U S A. 2019 Dec 10. Dalal CK, Zuleta IA, Lohse MB, Zordan RE, El-Samad H, Johnson AD. PMID: 31822605.
      View in: PubMed   Mentions:    Fields:    
    6. A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells. ACS Synth Biol. 2019 11 15; 8(11):2593-2606. 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. PMID: 31686495.
      View in: PubMed   Mentions:    Fields:    
    7. Design and Analysis of a Proportional-Integral-Derivative Controller with Biological Molecules. Cell Syst. 2019 10 23; 9(4):338-353.e10. Chevalier M, Gómez-Schiavon M, Ng AH, El-Samad H. PMID: 31563473.
      View in: PubMed   Mentions:    Fields:    
    8. De novo design of bioactive protein switches. Nature. 2019 08; 572(7768):205-210. 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. PMID: 31341284.
      View in: PubMed   Mentions: 2     Fields:    Translation:HumansAnimalsCells
    9. Modular and tunable biological feedback control using a de novo protein switch. Nature. 2019 08; 572(7768):265-269. Ng AH, Nguyen TH, Gómez-Schiavon M, Dods G, Langan RA, Boyken SE, Samson JA, Waldburger LM, Dueber JE, Baker D, El-Samad H. PMID: 31341280.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    10. Synthetic transcriptional synergy. Science. 2019 05 10; 364(6440):531-532. Ng AH, El-Samad H. PMID: 31073055.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    11. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun. 2019 05 09; 10(1):2127. 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. PMID: 31073154.
      View in: PubMed   Mentions: 4     Fields:    
    12. Control Theoretical Concepts for Synthetic and Systems Biology. Current Opinion in Systems Biology. 2019 Apr 1; 14(ACS Synthetic Biology 7 5 2018):50-57. Ania-Ariadna Baetica, Alexandra Westbrook, Hana El-Samad. .
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    13. Real-Time Genetic Compensation Defines the Dynamic Demands of Feedback Control. Cell. 2018 10 18; 175(3):877-886.e10. Harrigan P, Madhani HD, El-Samad H. PMID: 30340045.
      View in: PubMed   Mentions:    Fields:    Translation:Animals
    14. Complexity-aware simple modeling. Curr Opin Microbiol. 2018 10; 45:47-52. Gómez-Schiavon M, El-Samad H. PMID: 29494832.
      View in: PubMed   Mentions: 1     Fields:    
    15. Robust Synthetic Circuits for Two-Dimensional Control of Gene Expression in Yeast. ACS Synth Biol. 2017 03 17; 6(3):545-554. Aranda-Díaz A, Mace K, Zuleta I, Harrigan P, El-Samad H. PMID: 27930885.
      View in: PubMed   Mentions: 3     Fields:    Translation:AnimalsCells
    16. Model-guided optogenetic study of PKA signaling in budding yeast. Mol Biol Cell. 2017 01 01; 28(1):221-227. Stewart-Ornstein J, Chen S, Bhatnagar R, Weissman JS, El-Samad H. PMID: 28035051.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    17. Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression. Elife. 2016 09 10; 5. Dalal CK, Zuleta IA, Mitchell KF, Andes DR, El-Samad H, Johnson AD. PMID: 27614020.
      View in: PubMed   Mentions: 15     Fields:    Translation:HumansAnimalsCells
    18. 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. Al-Sady B, Greenstein RA, El-Samad HJ, Braun S, Madhani HD. PMID: 27479698.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    19. Tradeoffs in adapting biological systems. European Journal of Control. 2016 Jul 1; 30:68-75. Rajat Bhatnagar, Hana El-Samad. .
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    20. 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. Heimberg G, Bhatnagar R, El-Samad H, Thomson M. PMID: 27135536.
      View in: PubMed   Mentions: 21     Fields:    Translation:HumansAnimals
    21. The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks. PLoS Comput Biol. 2015 Oct; 11(10):e1004462. Chevalier M, Venturelli O, El-Samad H. PMID: 26484538.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    22. 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. Yang J, McCormick MA, Zheng J, Xie Z, Tsuchiya M, Tsuchiyama S, El-Samad H, Ouyang Q, Kaeberlein M, Kennedy BK, Li H. PMID: 26351681.
      View in: PubMed   Mentions: 7     Fields:    Translation:Animals
    23. Population diversification in a yeast metabolic program promotes anticipation of environmental shifts. PLoS Biol. 2015 Jan; 13(1):e1002042. Venturelli OS, Zuleta I, Murray RM, El-Samad H. PMID: 25626086.
      View in: PubMed   Mentions: 29     Fields:    Translation:AnimalsCells
    24. 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. Chevalier MW, El-Samad H. PMID: 25481130.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    25. Delayed Ras/PKA signaling augments the unfolded protein response. Proc Natl Acad Sci U S A. 2014 Oct 14; 111(41):14800-5. Pincus D, Aranda-Díaz A, Zuleta IA, Walter P, El-Samad H. PMID: 25275008.
      View in: PubMed   Mentions: 12     Fields:    Translation:AnimalsCells
    26. Multicellular architecture of malignant breast epithelia influences mechanics. PLoS One. 2014; 9(8):e101955. Venugopalan G, Camarillo DB, Webster KD, Reber CD, Sethian JA, Weaver VM, Fletcher DA, El-Samad H, Rycroft CH. PMID: 25111489.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    27. Using dynamic noise propagation to infer causal regulatory relationships in biochemical networks. ACS Synth Biol. 2015 Mar 20; 4(3):258-64. Lipinski-Kruszka J, Stewart-Ornstein J, Chevalier MW, El-Samad H. PMID: 24967515.
      View in: PubMed   Mentions: 5     Fields:    Translation:Animals
    28. Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry. Nat Methods. 2014 Apr; 11(4):443-8. Zuleta IA, Aranda-Díaz A, Li H, El-Samad H. PMID: 24608180.
      View in: PubMed   Mentions: 16     Fields:    Translation:Animals
    29. Sensitivity Analysis and Model Reduction Applied to Adapting Biological Systems. Biophysical Journal. 2014 Jan 1; 106(2):377a. Rajat Bhatnagar, Hana El-Samad. .
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    30. Msn2 coordinates a stoichiometric gene expression program. Curr Biol. 2013 Dec 02; 23(23):2336-45. Stewart-Ornstein J, Nelson C, DeRisi J, Weissman JS, El-Samad H. PMID: 24210615.
      View in: PubMed   Mentions: 17     Fields:    Translation:AnimalsCells
    31. Building robust functionality in synthetic circuits using engineered feedback regulation. Curr Opin Biotechnol. 2013 Aug; 24(4):790-6. Chen S, Harrigan P, Heineike B, Stewart-Ornstein J, El-Samad H. PMID: 23566378.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimals
    32. Conformational biosensors reveal GPCR signalling from endosomes. Nature. 2013 Mar 28; 495(7442):534-8. Irannejad R, Tomshine JC, Tomshine JR, Chevalier M, Mahoney JP, Steyaert J, Rasmussen SG, Sunahara RK, El-Samad H, Huang B, von Zastrow M. PMID: 23515162.
      View in: PubMed   Mentions: 209     Fields:    Translation:HumansCells
    33. Formation of subnuclear foci is a unique spatial behavior of mating MAPKs during hyperosmotic stress. Cell Rep. 2013 Feb 21; 3(2):328-34. Vidal SE, Pincus D, Stewart-Ornstein J, El-Samad H. PMID: 23416049.
      View in: PubMed   Mentions:    Fields:    Translation:AnimalsCells
    34. 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. Venturelli OS, El-Samad H, Murray RM. PMID: 23150580.
      View in: PubMed   Mentions: 16     Fields:    Translation:Animals
    35. 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. Fordyce PM, Pincus D, Kimmig P, Nelson CS, El-Samad H, Walter P, DeRisi JL. PMID: 23054834.
      View in: PubMed   Mentions: 19     Fields:    Translation:AnimalsCells
    36. Towards a minimal stochastic model for a large class of diffusion-reactions on biological membranes. J Chem Phys. 2012 Aug 28; 137(8):084103. Chevalier MW, El-Samad H. PMID: 22938214.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    37. Modeling and simulation of cellular functions. Molecular Biology of the Cell. 2012 Mar 15; 23(6):972-972. Ewa Paluch, Hana El-Samad. .
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    38. Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae. Mol Cell. 2012 Feb 24; 45(4):483-93. Stewart-Ornstein J, Weissman JS, El-Samad H. PMID: 22365828.
      View in: PubMed   Mentions: 58     Fields:    Translation:AnimalsCells
    39. Stochastic modeling of cellular networks. Methods Cell Biol. 2012; 110:111-37. Stewart-Ornstein J, El-Samad H. PMID: 22482947.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansCells
    40. Genetics: Noise rules. Nature. 2011 Dec 07; 480(7376):188-9. El-Samad H, Weissman JS. PMID: 22158239.
      View in: PubMed   Mentions: 1     Fields:    Translation:Animals
    41. A data-integrated method for analyzing stochastic biochemical networks. J Chem Phys. 2011 Dec 07; 135(21):214110. Chevalier MW, El-Samad H. PMID: 22149782.
      View in: PubMed   Mentions: 2     Fields:    
    42. In silico feedback for in vivo regulation of a gene expression circuit. Nat Biotechnol. 2011 Nov 06; 29(12):1114-6. Milias-Argeitis A, Summers S, Stewart-Ornstein J, Zuleta I, Pincus D, El-Samad H, Khammash M, Lygeros J. PMID: 22057053.
      View in: PubMed   Mentions: 47     Fields:    Translation:Animals
    43. Can a systems perspective help us appreciate the biological meaning of small effects? Dev Cell. 2011 Jul 19; 21(1):11-3. El-Samad H, Madhani HD. PMID: 21763599.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansCells
    44. Homeostatic adaptation to endoplasmic reticulum stress depends on Ire1 kinase activity. J Cell Biol. 2011 Apr 04; 193(1):171-84. Rubio C, Pincus D, Korennykh A, Schuck S, El-Samad H, Walter P. PMID: 21444684.
      View in: PubMed   Mentions: 61     Fields:    Translation:AnimalsCells
    45. Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway. Nat Cell Biol. 2010 Oct; 12(10):954-62. McCullagh E, Seshan A, El-Samad H, Madhani HD. PMID: 20852627.
      View in: PubMed   Mentions: 32     Fields:    Translation:AnimalsCells
    46. Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions. Genes Dev. 2010 Aug 15; 24(16):1758-71. Garcia JF, Dumesic PA, Hartley PD, El-Samad H, Madhani HD. PMID: 20675407.
      View in: PubMed   Mentions: 27     Fields:    Translation:AnimalsCells
    47. 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. Pincus D, Chevalier MW, Aragón T, van Anken E, Vidal SE, El-Samad H, Walter P. PMID: 20625545.
      View in: PubMed   Mentions: 136     Fields:    Translation:AnimalsCells
    48. Discriminating between rival biochemical network models: three approaches to optimal experiment design. BMC Syst Biol. 2010 Apr 01; 4:38. Mélykúti B, August E, Papachristodoulou A, El-Samad H. PMID: 20356406.
      View in: PubMed   Mentions: 18     Fields:    Translation:AnimalsCells
    49. Modelling and analysis of gene regulatory network using feedback control theory. International Journal of Systems Science. 2010 Jan 1; 41(1):17-33. H. El-Samad, M. Khammash. .
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    50. Not all quiet on the noise front. Nat Chem Biol. 2009 Oct; 5(10):699-704. McCullagh E, Farlow J, Fuller C, Girard J, Lipinski-Kruszka J, Lu D, Noriega T, Rollins G, Spitzer R, Todhunter M, El-Samad H. PMID: 19763097.
      View in: PubMed   Mentions: 5     Fields:    
    51. Defining network topologies that can achieve biochemical adaptation. Cell. 2009 Aug 21; 138(4):760-73. Ma W, Trusina A, El-Samad H, Lim WA, Tang C. PMID: 19703401.
      View in: PubMed   Mentions: 250     Fields:    Translation:Cells
    52. A rigorous framework for multiscale simulation of stochastic cellular networks. J Chem Phys. 2009 Aug 07; 131(5):054102. Chevalier MW, El-Samad H. PMID: 19673546.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    53. Tuning the activation threshold of a kinase network by nested feedback loops. Science. 2009 Apr 24; 324(5926):509-12. Justman QA, Serber Z, Ferrell JE, El-Samad H, Shokat KM. PMID: 19390045.
      View in: PubMed   Mentions: 22     Fields:    Translation:AnimalsCells
    54. 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. Herzmark P, Campbell K, Wang F, Wong K, El-Samad H, Groisman A, Bourne HR. PMID: 17684096.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
    55. 9. Digital Filter Stepsize Control in DASPK and Its Effect on Control Optimization Performance. Real-Time PDE-Constrained Optimization. 2007 Jan 1; 183-195. Kirsten Meeker, Chris Homescu, Linda Petzold, Hana El-Samad, Mustafa Khammash, Gustaf Söderlind. .
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    56. Module-based analysis of robustness tradeoffs in the heat shock response system. PLoS Comput Biol. 2006 Jul 28; 2(7):e59. Kurata H, El-Samad H, Iwasaki R, Ohtake H, Doyle JC, Grigorova I, Gross CA, Khammash M. PMID: 16863396.
      View in: PubMed   Mentions: 27     Fields:    Translation:Cells
    57. Advanced Methods and Algorithms for Biological Networks Analysis. Proceedings of the IEEE. 2006 Apr 1; 94(4):832-853. Hana El-Samad, Stephen Prajna, Antonis Papachristodoulou, John Doyle, Mustafa Khammash. .
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    58. Regulated degradation is a mechanism for suppressing stochastic fluctuations in gene regulatory networks. Biophys J. 2006 May 15; 90(10):3749-61. El-Samad H, Khammash M. PMID: 16500958.
      View in: PubMed   Mentions: 20     Fields:    Translation:Cells
    59. Surviving heat shock: control strategies for robustness and performance. Proc Natl Acad Sci U S A. 2005 Feb 22; 102(8):2736-41. El-Samad H, Kurata H, Doyle JC, Gross CA, Khammash M. PMID: 15668395.
      View in: PubMed   Mentions: 68     Fields:    Translation:Cells
    60. Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System. PLoS Computational Biology. 2005 Jan 1; preprint(2006):e59. Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash. .
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    61. Systems biology: from physiology to gene regulation. IEEE Control Systems Magazine. 2004 Aug 1; 24(4):62-76. M. Khammash, H. El-Samad. .
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    62. Feedback Regulation of the Heat Shock Response in E. coli. Multidisciplinary Research in Control. 2003 Jan 1; 289:115-128. Hana El-Samad, Mustafa Khammash, Hiroyuki Kurata, John C. Doyle. .
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    63. Calcium homeostasis and parturient hypocalcemia: an integral feedback perspective. J Theor Biol. 2002 Jan 07; 214(1):17-29. El-Samad H, Goff JP, Khammash M. PMID: 11786029.
      View in: PubMed   Mentions: 45     Fields:    Translation:Animals