Hana El-Samad, PhD

ADJ PROF-FY
Biochemistry And Biophysics
[email protected]
+1 415 476-2596

Our lab is interested in interdisciplinary research at the interface of cellular biology, dynamical systems modeling, and control theory.

Publications: 

Measure for Measure.

GEN Biotechnology

Hana El-Samad

Myths, Legends, and Wisdom.

GEN Biotechnology

Hana El-Samad

De novo-designed minibinders expand the synthetic biology sensing repertoire.

bioRxiv : the preprint server for biology

Weinberg ZY, Soliman SS, Kim MS, Chen IP, Ott M, El-Samad H

Degron-Based bioPROTACs for Controlling Signaling in CAR T Cells.

ACS synthetic biology

Kim MS, Bhargava HK, Shavey GE, Lim WA, El-Samad H, Ng AH

AI as the New Medium of Creativity.

GEN Biotechnology

Hana El-Samad

“Black-box” Data as a New Paradigm.

GEN Biotechnology

Hana El-Samad

Degron-based bioPROTACs for controlling signaling in CAR T cells.

bioRxiv : the preprint server for biology

Kim MS, Bhargava HK, Shavey GE, Lim WA, El-Samad H, Ng AH

The Next Emergence of Synthetic Biology.

GEN Biotechnology

Hana El-Samad

AI, Bias, and Discrimination.

GEN Biotechnology

Hana El-Samad

Lessons from the Minimal Cell.

GEN Biotechnology

Hana El-Samad

Strategic Thinking for Bold Goals.

GEN Biotechnology

Hana El-Samad

Animal Alternatives for Drug Development.

GEN Biotechnology

Hana El-Samad

Synthetic cytokine circuits that drive T cells into immune-excluded tumors.

Science (New York, N.Y.)

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

Hana El-Samad

Mr. President, Mandate an Equitable Bioeconomy.

GEN Biotechnology

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

G?mez-Schiavon M, El-Samad H

The Human Right to Our Bodies.

GEN Biotechnology

Hana El-Samad

Generosity of Spirit.

GEN Biotechnology

Hana El-Samad

Competitive Displacement of De Novo Designed HeteroDimers Can Reversibly Control Protein–Protein Interactions and Implement Feedback in Synthetic Circuits.

GEN Biotechnology

Taylor H. Nguyen, Galen Dods, Mariana Gómez-Schiavon, Muziyue Wu, Zibo Chen, Ryan Kibler, David Baker, Hana El-Samad, Andrew H. Ng

De novo design of tyrosine and serine kinase-driven protein switches.

Nature structural & molecular biology

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.)

Eniola-Adefeso O, El-Samad H

Fund Black scientists.

Cell

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, Wong JY, El-Samad H, Desai TA, Eniola-Adefeso O

Orthogonal control of mean and variability of endogenous genes in a human cell line.

Nature communications

Bonny AR, Fonseca JP, Park JE, El-Samad H

Multidimensional Characterization of Parts Enhances Modeling Accuracy in Genetic Circuits.

ACS synthetic biology

Gómez-Schiavon M, Dods G, El-Samad H, Ng AH

Optogenetic Control Reveals Differential Promoter Interpretation of Transcription Factor Nuclear Translocation Dynamics.

Cell systems

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.)

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

Mace K, Krakowiak J, El-Samad H, Pincus D

Assembly of Genetic Circuits with the Mammalian ToolKit.

Bio-protocol

Fonseca JP, Bonny AR, Town J, El-Samad H

Publisher Correction: Modular and tunable biological feedback control using a de novo protein switch.

Nature

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

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

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

Chevalier M, Gómez-Schiavon M, Ng AH, El-Samad H

De novo design of bioactive protein switches.

Nature

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

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.)

Ng AH, El-Samad H

Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs.

Nature communications

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

Ania-Ariadna Baetica, Alexandra Westbrook, Hana El-Samad

Complexity-aware simple modeling.

Current opinion in microbiology

Gómez-Schiavon M, El-Samad H

Robust Synthetic Circuits for Two-Dimensional Control of Gene Expression in Yeast.

ACS synthetic biology

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

Stewart-Ornstein J, Chen S, Bhatnagar R, Weissman JS, El-Samad H

TRADEOFFS IN ADAPTING BIOLOGICAL SYSTEMS.

European Journal of Control

Bhatnagar R, El-Samad H

The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks.

PLoS computational biology

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

Yang J, McCormick MA, Zheng J, Xie Z, Tsuchiya M, Tsuchiyama S, El-Samad H, Ouyang Q, Kaeberlein M, Kennedy BK, Li H

Delayed Ras/PKA signaling augments the unfolded protein response.

Proceedings of the National Academy of Sciences of the United States of America

Pincus D, Aranda-Díaz A, Zuleta IA, Walter P, El-Samad H

Multicellular architecture of malignant breast epithelia influences mechanics.

PloS one

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

Lipinski-Kruszka J, Stewart-Ornstein J, Chevalier MW, El-Samad H

Msn2 coordinates a stoichiometric gene expression program.

Current biology : CB

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

Chen S, Harrigan P, Heineike B, Stewart-Ornstein J, El-Samad H

Conformational biosensors reveal GPCR signalling from endosomes.

Nature

Irannejad R, Tomshine JC, Tomshine JR, Chevalier M, Mahoney JP, Steyaert J, Rasmussen SG, Sunahara RK, El-Samad H, Huang B, von Zastrow M

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

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

Fordyce PM, Pincus D, Kimmig P, Nelson CS, El-Samad H, Walter P, DeRisi JL

Modeling and simulation of cellular functions.

Molecular biology of the cell

Ewa Paluch, Hana El-Samad

Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae.

Molecular cell

Stewart-Ornstein J, Weissman JS, El-Samad H

Stochastic modeling of cellular networks.

Methods in cell biology

Stewart-Ornstein J, El-Samad H

A data-integrated method for analyzing stochastic biochemical networks.

The Journal of chemical physics

Chevalier MW, El-Samad H

Genetics: Noise rules.

Nature

El-Samad H, Weissman JS

In silico feedback for in vivo regulation of a gene expression circuit.

Nature biotechnology

Milias-Argeitis A, Summers S, Stewart-Ornstein J, Zuleta I, Pincus D, El-Samad H, Khammash M, Lygeros J

Homeostatic adaptation to endoplasmic reticulum stress depends on Ire1 kinase activity.

The Journal of cell biology

Rubio C, Pincus D, Korennykh A, Schuck S, El-Samad H, Walter P

BiP binding to the ER-stress sensor Ire1 tunes the homeostatic behavior of the unfolded protein response.

PLoS biology

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

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

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

H. El-Samad, M. Khammash

Not all quiet on the noise front.

Nature chemical biology

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

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

Chevalier MW, El-Samad H

Tuning the activation threshold of a kinase network by nested feedback loops.

Science (New York, N.Y.)

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

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

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

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

Hana El-Samad, Stephen Prajna, Antonis Papachristodoulou, John Doyle, Mustafa Khammash

Surviving heat shock: control strategies for robustness and performance.

Proceedings of the National Academy of Sciences of the United States of America

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

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

M. Khammash, H. El-Samad

Feedback Regulation of the Heat Shock Response in E. coli.

Multidisciplinary Research in Control

Hana El-Samad, Mustafa Khammash, Hiroyuki Kurata, John C. Doyle

Calcium homeostasis and parturient hypocalcemia: an integral feedback perspective.

Journal of theoretical biology

El-Samad H, Goff JP, Khammash M