Hana El-Samad, PhD
Professor
Biochemistry and Biophysics
School of Medicine

Awards

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• Donald P. Eckman Award, American Automatic Control Council, 2011
• Packard Fellowship, David and Lucille Packard Foundation, 2009
• Grace Boyer Junior Faculty Endowed Chair, University of California, San Francisco, 2008

Websites

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• Profile at biochemistry.ucsf.edu (biochemistry.ucsf.edu)

Grants and Projects

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• Synthetic circuits that drive infiltration of therapeutic T cells into immunologically cold tumors, NIH, 2021-2026
• Unraveling the quantitative dynamics of cAMP-PKA signaling in yeast, NIH, 2017-2021
• Exploring Design Principles of Cellular Control Circuits, NIH, 2010-2019
• Systems Biology of Molecular Noise in Yeast, NIH, 2009-2013

Publications (98)

Top publication keywords:
Computer SimulationSaccharomyces cerevisiae ProteinsStochastic ProcessesSynthetic BiologyGene Expression Regulation, FungalFeedbackCell EngineeringGene Regulatory NetworksCyclic AMP-Dependent Protein KinasesOptogeneticsFeedback, PhysiologicalSaccharomyces cerevisiaeModels, BiologicalOsmotic PressureStress, Physiological

• Measure for Measure.
  GEN Biotechnology 2024 Hana El-Samad
• Myths, Legends, and Wisdom.
  GEN Biotechnology 2024 Hana El-Samad
• De novo-designed minibinders expand the synthetic biology sensing repertoire.
  bioRxiv : the preprint server for biology 2024 Weinberg ZY, Soliman SS, Kim MS, Shah DH, Chen IP, Ott M, Lim WA, El-Samad H
• Degron-Based bioPROTACs for Controlling Signaling in CAR T Cells.
  ACS synthetic biology 2024 Kim MS, Bhargava HK, Shavey GE, Lim WA, El-Samad H, Ng AH
• AI as the New Medium of Creativity.
  GEN Biotechnology 2024 Hana El-Samad

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• “Black-box” Data as a New Paradigm.
  GEN Biotechnology 2024 Hana El-Samad
• Degron-based bioPROTACs for controlling signaling in CAR T cells.
  bioRxiv : the preprint server for biology 2024 Kim MS, Bhargava HK, Shavey GE, Lim WA, El-Samad H, Ng AH
• The Next Emergence of Synthetic Biology.
  GEN Biotechnology 2024 Hana El-Samad
• AI, Bias, and Discrimination.
  GEN Biotechnology 2023 Hana El-Samad
• Lessons from the Minimal Cell.
  GEN Biotechnology 2023 Hana El-Samad
• The Potential of Public–Private Partnerships for the Bioeconomy.
  GEN Biotechnology 2023 Hana El-Samad
• Strategic Thinking for Bold Goals.
  GEN Biotechnology 2023 Hana El-Samad
• Animal Alternatives for Drug Development.
  GEN Biotechnology 2023 Hana El-Samad
• Synthetic cytokine circuits that drive T cells into immune-excluded tumors.
  Science (New York, N.Y.) 2022 Allen GM, Frankel NW, Reddy NR, Bhargava HK, Yoshida MA, Stark SR, Purl M, Lee J, Yee JL, Yu W, Li AW, Garcia KC, El-Samad H, Roybal KT, Spitzer MH, Lim WA
• We Don't Need No Education Misinformation.
  GEN Biotechnology 2022 Hana El-Samad
• Mr. President, Mandate an Equitable Bioeconomy.
  GEN Biotechnology 2022 Hana El-Samad
• CoRa-A general approach for quantifying biological feedback control.
  Proceedings of the National Academy of Sciences of the United States of America 2022 Gómez-Schiavon M, El-Samad H
• Basic and Applied Research Are Fruits from the Same Tree.
  GEN Biotechnology 2022 Hana El-Samad
• The Human Right to Our Bodies.
  GEN Biotechnology 2022 Hana El-Samad
• Generosity of Spirit.
  GEN Biotechnology 2022 Hana El-Samad
• Competitive Displacement of De Novo Designed HeteroDimers Can Reversibly Control Protein–Protein Interactions and Implement Feedback in Synthetic Circuits.
  GEN Biotechnology 2022 Taylor H. Nguyen, Galen Dods, Mariana Gómez-Schiavon, Muziyue Wu, Zibo Chen, Ryan Kibler, David Baker, Hana El-Samad, Andrew H. Ng
• GEN Biotechnology and the New Age of Bioinnovation.
  GEN Biotechnology 2022 Hana El-Samad
• The Vision for GEN Biotechnology: From Precision Biology to Engaging a Broad Audience.
  GEN Biotechnology 2022 Hana El-Samad, Fay Lin
• De novo design of tyrosine and serine kinase-driven protein switches.
  Nature structural & molecular biology 2021 Woodall NB, Weinberg Z, Park J, Busch F, Johnson RS, Feldbauer MJ, Murphy M, Ahlrichs M, Yousif I, MacCoss MJ, Wysocki VH, El-Samad H, Baker D
• Director Lander, the time is now.
  Science (New York, N.Y.) 2021 Eniola-Adefeso O, El-Samad H
• Biological feedback control-Respect the loops.
  Cell systems 2021 El-Samad H
• Paralogs in the PKA Regulon Traveled Different Evolutionary Routes to Divergent Expression in Budding Yeast.
  Frontiers in fungal biology 2021 Heineike BM, El-Samad H
• Sentinel cells enable genetic detection of SARS-CoV-2 Spike protein.
  bioRxiv : the preprint server for biology 2021 Weinberg ZY, Hilburger CE, Kim M, Cao L, Khalid M, Elmes S, Diwanji D, Hernandez E, Lopez J, Schaefer K, Smith AM, Zhou F, QCRG Structural Biology Consortium, Kumar GR, Ott M, Baker D, El-Samad H
• Stress-induced growth rate reduction restricts metabolic resource utilization to modulate osmo-adaptation time.
  Cell reports 2021 Bonny AR, Kochanowski K, Diether M, El-Samad H
• Fund Black scientists.
  Cell 2021 Stevens KR, Masters KS, Imoukhuede PI, Haynes KA, Setton LA, Cosgriff-Hernandez E, Lediju Bell MA, Rangamani P, Sakiyama-Elbert SE, Finley SD, Willits RK, Koppes AN, Chesler NC, Christman KL, Allen JB…
• Orthogonal control of mean and variability of endogenous genes in a human cell line.
  Nature communications 2021 Bonny AR, Fonseca JP, Park JE, El-Samad H
• Multidimensional Characterization of Parts Enhances Modeling Accuracy in Genetic Circuits.
  ACS synthetic biology 2020 Gómez-Schiavon M, Dods G, El-Samad H, Ng AH
• Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics.
  Cell systems 2020 Chen SY, Osimiri LC, Chevalier M, Bugaj LJ, Nguyen TH, Greenstein RA, Ng AH, Stewart-Ornstein J, Neves LT, El-Samad H
• De novo design of protein logic gates.
  Science (New York, N.Y.) 2020 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
• Multi-kinase control of environmental stress responsive transcription.
  PloS one 2020 Mace K, Krakowiak J, El-Samad H, Pincus D
• Assembly of Genetic Circuits with the Mammalian ToolKit.
  Bio-protocol 2020 Fonseca JP, Bonny AR, Town J, El-Samad H
• Publisher Correction: Modular and tunable biological feedback control using a de novo protein switch.
  Nature 2020 Ng AH, Nguyen TH, Gómez-Schiavon M, Dods G, Langan RA, Boyken SE, Samson JA, Waldburger LM, Dueber JE, Baker D, El-Samad H
• 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 of the United States of America 2019 Dalal CK, Zuleta IA, Lohse MB, Zordan RE, El-Samad H, Johnson AD
• A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells.
  ACS synthetic biology 2019 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
• Design and Analysis of a Proportional-Integral-Derivative Controller with Biological Molecules.
  Cell systems 2019 Chevalier M, Gómez-Schiavon M, Ng AH, El-Samad H
• De novo design of bioactive protein switches.
  Nature 2019 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
• Modular and tunable biological feedback control using a de novo protein switch.
  Nature 2019 Ng AH, Nguyen TH, Gómez-Schiavon M, Dods G, Langan RA, Boyken SE, Samson JA, Waldburger LM, Dueber JE, Baker D, El-Samad H
• Synthetic transcriptional synergy.
  Science (New York, N.Y.) 2019 Ng AH, El-Samad H
• Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs.
  Nature communications 2019 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
• Control Theoretical Concepts for Synthetic and Systems Biology.
  Current Opinion in Systems Biology 2019 Ania-Ariadna Baetica, Alexandra Westbrook, Hana El-Samad
• Real-Time Genetic Compensation Defines the Dynamic Demands of Feedback Control.
  Cell 2018 Harrigan P, Madhani HD, El-Samad H
• Complexity-aware simple modeling.
  Current opinion in microbiology 2018 Gómez-Schiavon M, El-Samad H
• Robust Synthetic Circuits for Two-Dimensional Control of Gene Expression in Yeast.
  ACS synthetic biology 2016 Aranda-Díaz A, Mace K, Zuleta I, Harrigan P, El-Samad H
• Model-guided optogenetic study of PKA signaling in budding yeast.
  Molecular biology of the cell 2016 Stewart-Ornstein J, Chen S, Bhatnagar R, Weissman JS, El-Samad H
• Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression.
  eLife 2016 Dalal CK, Zuleta IA, Mitchell KF, Andes DR, El-Samad H, Johnson AD
• 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 Al-Sady B, Greenstein RA, El-Samad HJ, Braun S, Madhani HD
• TRADEOFFS IN ADAPTING BIOLOGICAL SYSTEMS.
  European journal of control 2016 Bhatnagar R, El-Samad H
• Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing.
  Cell systems 2016 Heimberg G, Bhatnagar R, El-Samad H, Thomson M
• The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks.
  PLoS computational biology 2015 Chevalier M, Venturelli O, El-Samad H
• Systematic analysis of asymmetric partitioning of yeast proteome between mother and daughter cells reveals "aging factors" and mechanism of lifespan asymmetry.
  Proceedings of the National Academy of Sciences of the United States of America 2015 Yang J, McCormick MA, Zheng J, Xie Z, Tsuchiya M, Tsuchiyama S, El-Samad H, Ouyang Q, Kaeberlein M, Kennedy BK, Li H
• Population diversification in a yeast metabolic program promotes anticipation of environmental shifts.
  PLoS biology 2015 Venturelli OS, Zuleta I, Murray RM, El-Samad H
• A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions.
  The Journal of chemical physics 2014 Chevalier MW, El-Samad H
• Delayed Ras/PKA signaling augments the unfolded protein response.
  Proceedings of the National Academy of Sciences of the United States of America 2014 Pincus D, Aranda-Díaz A, Zuleta IA, Walter P, El-Samad H
• Multicellular architecture of malignant breast epithelia influences mechanics.
  PloS one 2014 Venugopalan G, Camarillo DB, Webster KD, Reber CD, Sethian JA, Weaver VM, Fletcher DA, El-Samad H, Rycroft CH
• Using dynamic noise propagation to infer causal regulatory relationships in biochemical networks.
  ACS synthetic biology 2014 Lipinski-Kruszka J, Stewart-Ornstein J, Chevalier MW, El-Samad H
• Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry.
  Nature methods 2014 Zuleta IA, Aranda-Díaz A, Li H, El-Samad H
• Sensitivity Analysis and Model Reduction Applied to Adapting Biological Systems.
  Biophysical Journal 2014 Rajat Bhatnagar, Hana El-Samad
• Msn2 coordinates a stoichiometric gene expression program.
  Current biology : CB 2013 Stewart-Ornstein J, Nelson C, DeRisi J, Weissman JS, El-Samad H
• Building robust functionality in synthetic circuits using engineered feedback regulation.
  Current opinion in biotechnology 2013 Chen S, Harrigan P, Heineike B, Stewart-Ornstein J, El-Samad H
• Conformational biosensors reveal GPCR signalling from endosomes.
  Nature 2013 Irannejad R, Tomshine JC, Tomshine JR, Chevalier M, Mahoney JP, Steyaert J, Rasmussen SG, Sunahara RK, El-Samad H, Huang B, von Zastrow M
• Formation of subnuclear foci is a unique spatial behavior of mating MAPKs during hyperosmotic stress.
  Cell reports 2013 Vidal SE, Pincus D, Stewart-Ornstein J, El-Samad H
• Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Venturelli OS, El-Samad H, Murray RM
• Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses.
  Proceedings of the National Academy of Sciences of the United States of America 2012 Fordyce PM, Pincus D, Kimmig P, Nelson CS, El-Samad H, Walter P, DeRisi JL
• Towards a minimal stochastic model for a large class of diffusion-reactions on biological membranes.
  The Journal of chemical physics 2012 Chevalier MW, El-Samad H
• Modeling and simulation of cellular functions.
  Molecular Biology of the Cell 2012 Ewa Paluch, Hana El-Samad
• Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae.
  Molecular cell 2012 Stewart-Ornstein J, Weissman JS, El-Samad H
• Stochastic modeling of cellular networks.
  Methods in cell biology 2012 Stewart-Ornstein J, El-Samad H
• A data-integrated method for analyzing stochastic biochemical networks.
  The Journal of chemical physics 2011 Chevalier MW, El-Samad H
• Genetics: Noise rules.
  Nature 2011 El-Samad H, Weissman JS
• In silico feedback for in vivo regulation of a gene expression circuit.
  Nature biotechnology 2011 Milias-Argeitis A, Summers S, Stewart-Ornstein J, Zuleta I, Pincus D, El-Samad H, Khammash M, Lygeros J
• Can a systems perspective help us appreciate the biological meaning of small effects?
  Developmental cell 2011 El-Samad H, Madhani HD
• Homeostatic adaptation to endoplasmic reticulum stress depends on Ire1 kinase activity.
  The Journal of cell biology 2011 Rubio C, Pincus D, Korennykh A, Schuck S, El-Samad H, Walter P
• Homeostatic Regulation of the Unfolded Protein Response.
  Biophysical Journal 2011 Hana El-Samad
• Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway.
  Nature cell biology 2010 McCullagh E, Seshan A, El-Samad H, Madhani HD
• Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions.
  Genes & development 2010 Garcia JF, Dumesic PA, Hartley PD, El-Samad H, Madhani HD
• BiP binding to the ER-stress sensor Ire1 tunes the homeostatic behavior of the unfolded protein response.
  PLoS biology 2010 Pincus D, Chevalier MW, Aragón T, van Anken E, Vidal SE, El-Samad H, Walter P
• Defining network topologies that can achieve biochemical adaptation.
  The FASEB Journal 2010 Chao Tang, Wenzhe Ma, Ala Trusina, Hana El-Samad, Wendell Lim
• Discriminating between rival biochemical network models: three approaches to optimal experiment design.
  BMC systems biology 2010 Mélykúti B, August E, Papachristodoulou A, El-Samad H
• Modelling and analysis of gene regulatory network using feedback control theory.
  International Journal of Systems Science 2010 H. El-Samad, M. Khammash
• Not all quiet on the noise front.
  Nature chemical biology 2009 McCullagh E, Farlow J, Fuller C, Girard J, Lipinski-Kruszka J, Lu D, Noriega T, Rollins G, Spitzer R, Todhunter M, El-Samad H
• Defining network topologies that can achieve biochemical adaptation.
  Cell 2009 Ma W, Trusina A, El-Samad H, Lim WA, Tang C
• A rigorous framework for multiscale simulation of stochastic cellular networks.
  The Journal of chemical physics 2009 Chevalier MW, El-Samad H
• Tuning the activation threshold of a kinase network by nested feedback loops.
  Science (New York, N.Y.) 2009 Justman QA, Serber Z, Ferrell JE, El-Samad H, Shokat KM
• 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 2007 Herzmark P, Campbell K, Wang F, Wong K, El-Samad H, Groisman A, Bourne HR
• 9. Digital Filter Stepsize Control in DASPK and Its Effect on Control Optimization Performance.
  Real-Time PDE-Constrained Optimization 2007 Kirsten Meeker, Chris Homescu, Linda Petzold, Hana El-Samad, Mustafa Khammash, Gustaf Söderlind
• Module-based analysis of robustness tradeoffs in the heat shock response system.
  PLoS computational biology 2006 Kurata H, El-Samad H, Iwasaki R, Ohtake H, Doyle JC, Grigorova I, Gross CA, Khammash M
• Advanced Methods and Algorithms for Biological Networks Analysis.
  Proceedings of the IEEE 2006 Hana El-Samad, Stephen Prajna, Antonis Papachristodoulou, John Doyle, Mustafa Khammash
• Regulated degradation is a mechanism for suppressing stochastic fluctuations in gene regulatory networks.
  Biophysical journal 2006 El-Samad H, Khammash M
• Surviving heat shock: control strategies for robustness and performance.
  Proceedings of the National Academy of Sciences of the United States of America 2005 El-Samad H, Kurata H, Doyle JC, Gross CA, Khammash M
• Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System.
  PLoS Computational Biology 2005 Hiroyuki Kurata, Hana El-Samad, Rei Iwasaki, Hisao Ohtake, John C Doyle, Irina Grigorova, Carol A. Gross, Mustafa Khammash
• Systems biology: from physiology to gene regulation.
  IEEE Control Systems Magazine 2004 M. Khammash, H. El-Samad
• Feedback Regulation of the Heat Shock Response in E. coli.
  Multidisciplinary Research in Control 2003 Hana El-Samad, Mustafa Khammash, Hiroyuki Kurata, John C. Doyle
• Calcium homeostasis and parturient hypocalcemia: an integral feedback perspective.
  Journal of theoretical biology 2002 El-Samad H, Goff JP, Khammash M