Bonny, A.R., Kochanowski, K., Deither, M., El-Samad, H. Stress-Induced Transient Cell Cycle Arrest Coordinates Metabolic Resource Allocation to Balance Adaptive Tradeoffs. BioRxiv doi:https://doi.org/10.1101/2020.04.08.033035

Chen, Z., Kibler, R.D., Hunt, A., Busch, F., Pearl, J., Jia, M., VanAernum, Z.L., Wicky, B.I.M., Dods, G., Liao, H., Wilken, M.S., Ciarlo, C., Green, S., El-Samad, H., Stamatoyannopoulos, J., Wysocki, V.H., Jewett, M.C., Boyken, S.E., Baker, D. De novo design of protein logic gates. Science. 2020; doi:10.1126/science.aay2790

Mace, K., Krakowiak, J., El-Samad, H., Pincus, D. Multi-kinase control of environmental stress responsive transcription. Plos One. doi:https://doi.org/10.1371/journal.pone.0230246


Dalal, C.K., Zuleta, I.A., Lohse, M.B., Zordan, R.E., El-Samad, H, Johnson, A.D. A population shift between two heritable cell types of the pathogen Candida albicans is based both on switching and selective proliferation. PNAS. 2019; doi: https://doi.org/10.1073/pnas.1908986116

Heineike, B.M., El-Samad, H. Paralogs in the PKA regulon traveled different evolutionary routes to divergent expression in budding yeast. BioRxiv doi:https://doi.org/10.1101/860981

Fonseca, J.P., Aslankoohi, E., El-Samad, H. Biphasic Response of Protein Kinase A to Cyclic Adenosine Monophosphate Triggers Distinct Epithelial Phenotypes. BioRxiv doi:https://doi.org/10.1101/747030

Langan, R.A., Boyken, S.E., Ng, A.H., Samson, J.A., , Dods, G., Westbrook, A., Nguyen, T.H., Lajoie, M.J., Chen, Z., Berger, S., Khipple Mulligan, V., Dueber, J.E., Novak, W.R.P., El-Samad, H., Baker, D. De novo design of bioactive protein switches. Nature. 2019; doi:https://doi.org/10.1038/s41586-019-1432-8

Ng, A.H., Nguyen, T.H., Gómez-Schiavon, M., Dods, G., Langan, R.A., Boyken, S.E., Samson, J.A., Waldburger, L.M., Dueber, J.E., Baker, D., El-Samad, H. Modular and tunable bioloical feedback control using a de novo protein switch. Nature. 2019; doi:https://doi.org/10.1038/s41586-019-1425-7

Kundert, K., Lucas, J.E., Watters, K.E., Fellmann, C., Ng, A., Heineike, B.M., Fitzsimmons, C.M., Oakes, B.L., Savage, D.F., El-Samad, H., Doudna, J.A., Kortemme, T. Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs. Nat Commun 2019. doi:https://doi.org/10.1038/s41467-019-09985-2.

Ng, A.H., El-Samad, H. Synthetic transcriptional synergy. Science. 2019; doi:https://doi.org/10.1126/science.aax4556

Baetica, A.A., Westbrook, A.,El-Samad, H. Control Theoretical Concepts for Synthetic and Systems Biology. Curr Opin Syst Biol. 2019; doi:https://doi.org/10.1016/j.coisb.2019.02.010

Chen, S.Y., Osimiri, L.C., Chevalier, M.W., Bugaj, L.J., Ng. A.H, Stewart-Ornstein, J., Neves, L.T., El-Samad, H. Optogenetic control reveals differential promoter interpretation of transcription factor nuclear translocation dynamics. BioRxiv. doi:https://doi.org/10.1101/548255

Mace, K., Krakowiak, J., El-Samad, H., Pincus, D. A dataset to explore kinase control of environmental stress responsive transcription. BioRxiv. doi:https://doi.org/10.1101/547356

Fonseca, J.P., Bonny, A.R.,Kumar, G.R., Ng. A.H., Town, J., Wu, Q.C., Aslankoohi, E., Chen, S.Y., Dods, G., Harrigan, P., Osimiri, L.C., Kistler, A.K., El-Samad, H. A Toolkit for Rapid Modular Construction of Biological Circuits in Mammalian Cells. BioRxiv. doi:https://doi.org/10.1101/506188


Harrigan, P., Madhani, H., El-Samad, H. Real-Time Genetic Compensation Defines the Dynamic Demands of Feedback Control. Cell. 2018;175(3):877-86. doi: https://doi.org/10.1016/j.cell.2018.09.044

Blanchini, F., El-Samad, H., Giordano, G., Sontag, E.D. Control-theoretic methods for biological networks. Submitted to the proceedings of CDC 2018.

Chevalier, M., Gómez-Schiavon, M., Ng, A., El-Samad, H. Design and analysis of a Proportional-Integral-Derivative controller with biological molecules. BioRxiv. doi: https://doi.org/10.1101/303545 .

Gómez-Schiavon, M., El-Samad, H. Complexity-aware simple modeling. Curr Opin Microbiol. 2018;45:47-52. doi: https://doi.org/10.1016/j.mib.2018.01.004.


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 Jan 1;28(1):221-227. doi: 10.1091/mbc.E16-06-0354. PMID: 28035051


Aranda-Diaz 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. 2016 Dec 27;doi: 1021/acssynbio.6b00251. PMID: 27930885

Dalal CK, Zuleta IA, Mitchell KF, Andes DR, El-Samad HJ, Johnson AD. Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression. eLife. 2016;10.7554/eLife.18981.

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.

Bhatnagar R, El-Samad H. Tradeoffs in adapting biological systems European Journal of Control. 2016 May 13. doi:10.1016/j.ejcon.2016.04.010

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 Systems. 2016 Apr 27; 2(4):239-250. DOI: http://dx.doi.org/10.1016/j.cels.2016.04.001. *co-first authors


Chevalier MW, Venturelli OS, El-Samad H. The Impact of Different Sources of Fluctuations on Mutual Information in Biochemical Networks. PLoS Comput Biol. 2015 Oct 20; 11(10):e1004462. DOI:10.1371/journal.pcbi.1004462.

Yang, J, McCormick MA, Zheng J, Xie Z, Tsuchiya M, Tsuchiyama, 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 USA. 2015 Sept 22;112(38)11977-82. DOI: 10.1073/pnas.1506054112. Epub 2015 Sept 8. Pubmed PMID: 26351681; PubMed Central PMCID: PMC4586869.

Venturelli OS, Zuleta IA, Murray RM, El-Samad H. Population diversification in a metabolic program promotes anticipation of environmental shifts. PLoS Biology. 2015 Jan 27; 13(1):e1002042. DOI:10.1371/journal.pbio.1002042.


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 7;141(21):214108. doi: 10.1063/1.4902239. PubMed PMID: 25481130.

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. doi: 10.1073/pnas.1409588111. Epub 2014 Oct 1. PubMed PMID: 25275008; PubMed Central PMCID: PMC4205644.

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 Aug 11;9(8):e101955. doi: 10.1371/journal.pone.0101955. eCollection 2014. PubMed PMID: 25111489; PubMed Central PMCID: PMC4128597.

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. 2014 Jul 11. [Epub ahead of print] PubMed PMID: 24967515.

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. doi: 10.1038/nmeth.2879. Epub 2014 Mar 9. PubMed PMID: 24608180; PubMed Central PMCID: PMC4016179.


Stewart-Ornstein J, Nelson C, DeRisi J, Weissman JS, El-Samad H. Msn2 coordinates a stoichiometric gene expression program. Curr Biol. 2013 Dec 2;23(23):2336-45.

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. *Co-first authors

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. doi: 10.1038/nature12000. Epub 2013 Mar 20. PubMed PMID: 23515162; PubMed Central PMCID: PMC3835555.

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. doi: 10.1016/j.celrep.2013.01.022. Epub 2013 Feb 14. PubMed PMID: 23416049; PubMed Central PMCID: PMC3616637.


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. doi: 10.1073/pnas.1211902109. Epub 2012 Nov 12. PubMed PMID: 23150580; PubMed Central PMCID: PMC3511703.

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 6;109(45):E3084-93. doi: 10.1073/pnas.1212457109. Epub 2012 Oct 10. PubMed PMID: 23054834; PubMed Central PMCID: PMC3494901.

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. doi: 10.1063/1.4746692. PubMed PMID: 22938214; PubMed Central PMCID: PMC3436915.

Stewart-Ornstein J, El-Samad H. Stochastic modeling of cellular networks. Methods Cell Biol. 2012;110:111-37. doi: 10.1016/B978-0-12-388403-9.00005-9. PubMed PMID: 22482947.

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. doi: 10.1016/j.molcel.2011.11.035. PubMed PMID: 22365828; PubMed Central PMCID: PMC3327736.


El-Samad H, Weissman JS. Genetics: Noise rules. Nature. 2011 Dec 7;480(7376):188-9. doi: 10.1038/480188a. PubMed PMID: 22158239.

Chevalier MW, El-Samad H. A data-integrated method for analyzing stochastic biochemical networks. J Chem Phys. 2011 Dec 7;135(21):214110. doi: 10.1063/1.3664126. PubMed PMID: 22149782; PubMed Central PMCID: PMC3324259.

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 6;29(12):1114-6. doi: 10.1038/nbt.2018. PubMed PMID: 22057053. *Co-first authors **Corresponding authors, in alphabetical order.

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. doi: 10.1016/j.devcel.2011.06.005. PubMed PMID: 21763599; PubMed Central PMCID: PMC3615985.

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 4;193(1):171-84. doi: 10.1083/jcb.201007077. Epub 2011 Mar 28. PubMed PMID: 21444684; PubMed Central PMCID: PMC3082176.


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. doi: 10.1038/ncb2097. Epub 2010 Sep 19. PubMed PMID: 20852627; PubMed Central PMCID: PMC2948760.

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. doi: 10.1101/gad.1946410. Epub 2010 Jul 30. PubMed PMID: 20675407; PubMed Central PMCID: PMC2922504.

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 6;8(7):e1000415. doi: 10.1371/journal.pbio.1000415. PubMed PMID: 20625545; PubMed Central PMCID: PMC2897766. *Corresponding authors

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 1;4:38. doi: 10.1186/1752-0509-4-38. PubMed PMID: 20356406; PubMed Central PMCID: PMC2873315.


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. doi: 10.1038/nchembio.222. PubMed PMID: 19763097.

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. doi: 10.1016/j.cell.2009.06.013. PubMed PMID: 19703401; PubMed Central PMCID: PMC3068210.

Chevalier MW, El-Samad H. A rigorous framework for multiscale simulation of stochastic cellular networks. J Chem Phys. 2009 Aug 7;131(5):054102. doi: 10.1063/1.3190327. PubMed PMID: 19673546; PubMed Central PMCID: PMC2736569.

Justman QA, Serber Z, Ferrell JE Jr, 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. doi: 10.1126/science.1169498. PubMed PMID: 19390045; PubMed Central PMCID: PMC2880456. *Corresponding authors

Before 2009

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. Epub 2007 Aug 7. PubMed PMID: 17684096; PubMed Central PMCID: PMC1940227.

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. Epub 2006 Apr 13. PubMed PMID: 16863396; PubMed Central PMCID: PMC1523291.

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. Epub 2006 Feb 24. PubMed PMID: 16500958; PubMed Central PMCID: PMC1440756.

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. Epub 2005 Jan 24. PubMed PMID: 15668395; PubMed Central PMCID: PMC549435.

El-Samad H, Goff JP, Khammash M. Calcium homeostasis and parturient hypocalcemia: an integral feedback perspective. J Theor Biol. 2002 Jan 7;214(1):17-29. PubMed PMID: 11786029.