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Items: 41

1.

Complexity-aware simple modeling.

Gómez-Schiavon M, El-Samad H.

Curr Opin Microbiol. 2018 Feb 26;45:47-52. doi: 10.1016/j.mib.2018.01.004. [Epub ahead of print] Review.

PMID:
29494832
2.

Model-guided optogenetic study of PKA signaling in budding yeast.

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

Mol Biol Cell. 2017 Jan 1;28(1):221-227. doi: 10.1091/mbc.E16-06-0354. Epub 2016 Nov 9.

3.

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

Aranda-Díaz A, Mace K, Zuleta I, Harrigan P, El-Samad H.

ACS Synth Biol. 2017 Mar 17;6(3):545-554. doi: 10.1021/acssynbio.6b00251. Epub 2016 Dec 27.

4.

Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression.

Dalal CK, Zuleta IA, Mitchell KF, Andes DR, El-Samad H, Johnson AD.

Elife. 2016 Sep 10;5. pii: e18981. doi: 10.7554/eLife.18981.

5.

Sensitive and Quantitative Three-Color Protein Imaging in Fission Yeast Using Spectrally Diverse, Recoded Fluorescent Proteins with Experimentally-Characterized In Vivo Maturation Kinetics.

Al-Sady B, Greenstein RA, El-Samad HJ, Braun S, Madhani HD.

PLoS One. 2016 Aug 1;11(8):e0159292. doi: 10.1371/journal.pone.0159292. eCollection 2016.

6.

Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing.

Heimberg G, Bhatnagar R, El-Samad H, Thomson M.

Cell Syst. 2016 Apr 27;2(4):239-250. doi: 10.1016/j.cels.2016.04.001. Epub 2016 Apr 27.

7.

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

Chevalier M, Venturelli O, El-Samad H.

PLoS Comput Biol. 2015 Oct 20;11(10):e1004462. doi: 10.1371/journal.pcbi.1004462. eCollection 2015 Oct.

8.

Systematic analysis of asymmetric partitioning of yeast proteome between mother and daughter cells reveals "aging factors" and mechanism of lifespan asymmetry.

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

Proc Natl Acad Sci U S A. 2015 Sep 22;112(38):11977-82. doi: 10.1073/pnas.1506054112. Epub 2015 Sep 8.

9.

Population diversification in a yeast metabolic program promotes anticipation of environmental shifts.

Venturelli OS, Zuleta I, Murray RM, El-Samad H.

PLoS Biol. 2015 Jan 27;13(1):e1002042. doi: 10.1371/journal.pbio.1002042. eCollection 2015 Jan.

10.

A master equation and moment approach for biochemical systems with creation-time-dependent bimolecular rate functions.

Chevalier MW, El-Samad H.

J Chem Phys. 2014 Dec 7;141(21):214108. doi: 10.1063/1.4902239.

11.

Delayed Ras/PKA signaling augments the unfolded protein response.

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

Proc Natl Acad Sci U S A. 2014 Oct 14;111(41):14800-5. doi: 10.1073/pnas.1409588111. Epub 2014 Oct 1.

12.

Multicellular architecture of malignant breast epithelia influences mechanics.

Venugopalan G, Camarillo DB, Webster KD, Reber CD, Sethian JA, Weaver VM, Fletcher DA, El-Samad H, Rycroft CH.

PLoS One. 2014 Aug 11;9(8):e101955. doi: 10.1371/journal.pone.0101955. eCollection 2014.

13.

Using dynamic noise propagation to infer causal regulatory relationships in biochemical networks.

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

ACS Synth Biol. 2015 Mar 20;4(3):258-64. doi: 10.1021/sb5000059. Epub 2014 Jul 11.

14.

Dynamic characterization of growth and gene expression using high-throughput automated flow cytometry.

Zuleta IA, Aranda-Díaz A, Li H, El-Samad H.

Nat Methods. 2014 Apr;11(4):443-8. doi: 10.1038/nmeth.2879. Epub 2014 Mar 9.

15.

Msn2 coordinates a stoichiometric gene expression program.

Stewart-Ornstein J, Nelson C, DeRisi J, Weissman JS, El-Samad H.

Curr Biol. 2013 Dec 2;23(23):2336-45. doi: 10.1016/j.cub.2013.09.043. Epub 2013 Nov 7.

16.

Building robust functionality in synthetic circuits using engineered feedback regulation.

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

Curr Opin Biotechnol. 2013 Aug;24(4):790-6. doi: 10.1016/j.copbio.2013.02.025. Epub 2013 Apr 6. Review.

17.

Conformational biosensors reveal GPCR signalling from endosomes.

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

Nature. 2013 Mar 28;495(7442):534-8. doi: 10.1038/nature12000. Epub 2013 Mar 20.

18.

Formation of subnuclear foci is a unique spatial behavior of mating MAPKs during hyperosmotic stress.

Vidal SE, Pincus D, Stewart-Ornstein J, El-Samad H.

Cell Rep. 2013 Feb 21;3(2):328-34. doi: 10.1016/j.celrep.2013.01.022. Epub 2013 Feb 14.

19.

Synergistic dual positive feedback loops established by molecular sequestration generate robust bimodal response.

Venturelli OS, El-Samad H, Murray RM.

Proc Natl Acad Sci U S A. 2012 Nov 27;109(48):E3324-33. doi: 10.1073/pnas.1211902109. Epub 2012 Nov 12.

20.

Basic leucine zipper transcription factor Hac1 binds DNA in two distinct modes as revealed by microfluidic analyses.

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

Proc Natl Acad Sci U S A. 2012 Nov 6;109(45):E3084-93. doi: 10.1073/pnas.1212457109. Epub 2012 Oct 10.

21.

Towards a minimal stochastic model for a large class of diffusion-reactions on biological membranes.

Chevalier MW, El-Samad H.

J Chem Phys. 2012 Aug 28;137(8):084103. doi: 10.1063/1.4746692.

22.

Stochastic modeling of cellular networks.

Stewart-Ornstein J, El-Samad H.

Methods Cell Biol. 2012;110:111-37. doi: 10.1016/B978-0-12-388403-9.00005-9.

PMID:
22482947
23.

Cellular noise regulons underlie fluctuations in Saccharomyces cerevisiae.

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

Mol Cell. 2012 Feb 24;45(4):483-93. doi: 10.1016/j.molcel.2011.11.035.

24.

Genetics: Noise rules.

El-Samad H, Weissman JS.

Nature. 2011 Dec 7;480(7376):188-9. doi: 10.1038/480188a. No abstract available.

PMID:
22158239
25.

A data-integrated method for analyzing stochastic biochemical networks.

Chevalier MW, El-Samad H.

J Chem Phys. 2011 Dec 7;135(21):214110. doi: 10.1063/1.3664126.

26.

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

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

Nat Biotechnol. 2011 Nov 6;29(12):1114-6. doi: 10.1038/nbt.2018.

27.

Can a systems perspective help us appreciate the biological meaning of small effects?

El-Samad H, Madhani HD.

Dev Cell. 2011 Jul 19;21(1):11-3. doi: 10.1016/j.devcel.2011.06.005.

28.

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

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

J Cell Biol. 2011 Apr 4;193(1):171-84. doi: 10.1083/jcb.201007077. Epub 2011 Mar 28.

29.

Coordinate control of gene expression noise and interchromosomal interactions in a MAP kinase pathway.

McCullagh E, Seshan A, El-Samad H, Madhani HD.

Nat Cell Biol. 2010 Oct;12(10):954-62. doi: 10.1038/ncb2097. Epub 2010 Sep 19.

30.

Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions.

Garcia JF, Dumesic PA, Hartley PD, El-Samad H, Madhani HD.

Genes Dev. 2010 Aug 15;24(16):1758-71. doi: 10.1101/gad.1946410. Epub 2010 Jul 30.

31.

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

Pincus D, Chevalier MW, Aragón T, van Anken E, Vidal SE, El-Samad H, Walter P.

PLoS Biol. 2010 Jul 6;8(7):e1000415. doi: 10.1371/journal.pbio.1000415.

32.

Discriminating between rival biochemical network models: three approaches to optimal experiment design.

Mélykúti B, August E, Papachristodoulou A, El-Samad H.

BMC Syst Biol. 2010 Apr 1;4:38. doi: 10.1186/1752-0509-4-38.

33.

Not all quiet on the noise front.

McCullagh E, Farlow J, Fuller C, Girard J, Lipinski-Kruszka J, Lu D, Noriega T, Rollins G, Spitzer R, Todhunter M, El-Samad H.

Nat Chem Biol. 2009 Oct;5(10):699-704. doi: 10.1038/nchembio.222.

PMID:
19763097
34.

Defining network topologies that can achieve biochemical adaptation.

Ma W, Trusina A, El-Samad H, Lim WA, Tang C.

Cell. 2009 Aug 21;138(4):760-73. doi: 10.1016/j.cell.2009.06.013.

35.

A rigorous framework for multiscale simulation of stochastic cellular networks.

Chevalier MW, El-Samad H.

J Chem Phys. 2009 Aug 7;131(5):054102. doi: 10.1063/1.3190327.

36.

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

Justman QA, Serber Z, Ferrell JE Jr, El-Samad H, Shokat KM.

Science. 2009 Apr 24;324(5926):509-12. doi: 10.1126/science.1169498.

37.

Bound attractant at the leading vs. the trailing edge determines chemotactic prowess.

Herzmark P, Campbell K, Wang F, Wong K, El-Samad H, Groisman A, Bourne HR.

Proc Natl Acad Sci U S A. 2007 Aug 14;104(33):13349-54. Epub 2007 Aug 7.

38.

Module-based analysis of robustness tradeoffs in the heat shock response system.

Kurata H, El-Samad H, Iwasaki R, Ohtake H, Doyle JC, Grigorova I, Gross CA, Khammash M.

PLoS Comput Biol. 2006 Jul 28;2(7):e59. Epub 2006 Apr 13.

39.

Regulated degradation is a mechanism for suppressing stochastic fluctuations in gene regulatory networks.

El-Samad H, Khammash M.

Biophys J. 2006 May 15;90(10):3749-61. Epub 2006 Feb 24.

40.

Surviving heat shock: control strategies for robustness and performance.

El-Samad H, Kurata H, Doyle JC, Gross CA, Khammash M.

Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2736-41. Epub 2005 Jan 24.

41.

Calcium homeostasis and parturient hypocalcemia: an integral feedback perspective.

El-Samad H, Goff JP, Khammash M.

J Theor Biol. 2002 Jan 7;214(1):17-29.

PMID:
11786029

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