Publications by authors named "Hernan G Garcia"

35Publications

A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting.

Curr Opin Cell Biol 2020 Nov 23;67:147-157. Epub 2020 Nov 23.

Biophysics Graduate Group, University of California at Berkeley, Berkeley, CA, USA; Department of Physics, University of California at Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Institute for Quantitative Biosciences-QB3, University of California at Berkeley, Berkeley, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ceb.2020.08.001DOI Listing
November 2020

Quantitative dissection of transcription in development yields evidence for transcription factor-driven chromatin accessibility.

Elife 2020 Oct 19;9. Epub 2020 Oct 19.

Molecular and Cell Biology, Physics, University of California, Berkeley, Berkeley, United States.

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http://dx.doi.org/10.7554/eLife.56429DOI Listing
October 2020

Genetically Encoded Fluorescent Biosensor for Rapid Detection of Protein Expression.

ACS Synth Biol 2020 11 12;9(11):2955-2963. Epub 2020 Oct 12.

Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada.

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http://dx.doi.org/10.1021/acssynbio.0c00407DOI Listing
November 2020

Lighting up the central dogma for predictive developmental biology.

Curr Top Dev Biol 2020 22;137:1-35. Epub 2019 Nov 22.

Department of Physics, University of California at Berkeley, Berkeley, CA, United States.

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http://dx.doi.org/10.1016/bs.ctdb.2019.10.010DOI Listing
November 2019

Multimodal transcriptional control of pattern formation in embryonic development.

Proc Natl Acad Sci U S A 2020 01 27;117(2):836-847. Epub 2019 Dec 27.

Biophysics Graduate Group, University of California, Berkeley, CA 94720;

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http://dx.doi.org/10.1073/pnas.1912500117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6969519PMC
January 2020

Mandatory notifications of type 1 diabetes incident cases in Chilean children, 2006 to 2014: A population-based study.

Pediatr Diabetes 2020 02 11;21(1):48-52. Epub 2019 Nov 11.

Division of Pediatrics, Pontificia Universidad Católica de Chile School of Medicine, Santiago, Chile.

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https://onlinelibrary.wiley.com/doi/abs/10.1111/pedi.12937
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http://dx.doi.org/10.1111/pedi.12937DOI Listing
February 2020

Enhancer Priming Enables Fast and Sustained Transcriptional Responses to Notch Signaling.

Dev Cell 2019 08 1;50(4):411-425.e8. Epub 2019 Aug 1.

Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, UK. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2019.07.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706658PMC
August 2019

LlamaTags: A Versatile Tool to Image Transcription Factor Dynamics in Live Embryos.

Cell 2018 06 10;173(7):1810-1822.e16. Epub 2018 May 10.

Department of Molecular & Cell Biology, UC Berkeley, Berkeley, CA 94720, USA; Department of Physics, UC Berkeley, Berkeley, CA 94720, USA; Biophysics Graduate Group, UC Berkeley, Berkeley, CA 94720, USA; Institute for Quantitative Biosciences-QB3, University of California, Berkeley, CA 94720, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674183040
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http://dx.doi.org/10.1016/j.cell.2018.03.069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6003873PMC
June 2018

Live Imaging of mRNA Synthesis in Drosophila.

Methods Mol Biol 2018 ;1649:349-357

Department of Physics, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.

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http://dx.doi.org/10.1007/978-1-4939-7213-5_23DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909709PMC
June 2018

Using synthetic biology to make cells tomorrow's test tubes.

Integr Biol (Camb) 2016 Apr 8;8(4):431-50. Epub 2016 Mar 8.

Department of Molecular and Cell Biology, Department of Physics, Biophysics Graduate Group, and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley CA 94720, USA.

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http://dx.doi.org/10.1039/c6ib00006aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837077PMC
April 2016

Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo.

Elife 2015 Aug 12;4. Epub 2015 Aug 12.

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.

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https://elifesciences.org/articles/07956
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http://dx.doi.org/10.7554/eLife.07956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532966PMC
August 2015

The influence of promoter architectures and regulatory motifs on gene expression in Escherichia coli.

PLoS One 2014 30;9(12):e114347. Epub 2014 Dec 30.

Department of Applied Physics, California Institute of Technology, Pasadena, CA, United States of America; Division of Biology, California Institute of Technology, Pasadena, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114347PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4280137PMC
January 2016

The embryo as a laboratory: quantifying transcription in Drosophila.

Trends Genet 2014 Aug 6;30(8):364-75. Epub 2014 Jul 6.

Department of Molecular Biology, Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1016/j.tig.2014.06.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4129518PMC
August 2014

Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos.

Proc Natl Acad Sci U S A 2014 Jul 3;111(29):10598-603. Epub 2014 Jul 3.

Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720; and

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http://www.pnas.org/cgi/doi/10.1073/pnas.1410022111
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http://dx.doi.org/10.1073/pnas.1410022111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115566PMC
July 2014

The transcription factor titration effect dictates level of gene expression.

Cell 2014 Mar 6;156(6):1312-1323. Epub 2014 Mar 6.

Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

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http://www.rpgroup.caltech.edu/publications/brewster2014_SI_
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http://linkinghub.elsevier.com/retrieve/pii/S009286741400221
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http://dx.doi.org/10.1016/j.cell.2014.02.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4080642PMC
March 2014

The plasma membrane flattens out to fuel cell-surface growth during Drosophila cellularization.

Dev Cell 2013 Dec 5;27(6):648-55. Epub 2013 Dec 5.

Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2013.11.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3888437PMC
December 2013

DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation.

Phys Biol 2013 Dec 15;10(6):066005. Epub 2013 Nov 15.

Departments of Applied Physics and Biology, California Institute of Technology, 1200 California Boulevard, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1088/1478-3975/10/6/066005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3915735PMC
December 2013

Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning.

Curr Biol 2013 Nov 17;23(21):2140-5. Epub 2013 Oct 17.

Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ 08544, USA.

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http://dx.doi.org/10.1016/j.cub.2013.08.054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3828032PMC
November 2013

Statistical mechanics of Monod-Wyman-Changeux (MWC) models.

J Mol Biol 2013 May 14;425(9):1433-60. Epub 2013 Mar 14.

Department of Physics, University of California Berkeley, Berkeley, CA 94720-7300, USA.

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http://dx.doi.org/10.1016/j.jmb.2013.03.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3786005PMC
May 2013

Theoretical and experimental dissection of DNA loop-mediated repression.

Phys Rev Lett 2013 Jan 2;110(1):018101. Epub 2013 Jan 2.

Department of Applied Physics, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3716456PMC
http://dx.doi.org/10.1103/PhysRevLett.110.018101DOI Listing
January 2013

Operator sequence alters gene expression independently of transcription factor occupancy in bacteria.

Cell Rep 2012 Jul 12;2(1):150-61. Epub 2012 Jul 12.

Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.celrep.2012.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616187PMC
July 2012

Comparison and calibration of different reporters for quantitative analysis of gene expression.

Biophys J 2011 Aug;101(3):535-44

Department of Physics, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1016/j.bpj.2011.06.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145315PMC
August 2011

Quantitative dissection of the simple repression input-output function.

Proc Natl Acad Sci U S A 2011 Jul 5;108(29):12173-8. Epub 2011 Jul 5.

Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1073/pnas.1015616108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141941PMC
July 2011

Building enhancers from the ground up: a synthetic biology approach.

Cell 2011 Jul;146(1):105-18

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.cell.2011.06.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155781PMC
July 2011

Effect of promoter architecture on the cell-to-cell variability in gene expression.

PLoS Comput Biol 2011 Mar 3;7(3):e1001100. Epub 2011 Mar 3.

Graduate Program in Biophysics and Structural Biology, Brandeis University, Waltham, Massachusetts,USA.

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http://dx.doi.org/10.1371/journal.pcbi.1001100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048382PMC
March 2011

Thermodynamics of biological processes.

Methods Enzymol 2011 ;492:27-59

Department of Physics, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1016/B978-0-12-381268-1.00014-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264492PMC
March 2011

First-principles calculation of DNA looping in tethered particle experiments.

Phys Biol 2009 Jul 1;6(2):025001. Epub 2009 Jul 1.

Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1088/1478-3975/6/2/025001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3298194PMC
July 2009

Concentration and length dependence of DNA looping in transcriptional regulation.

PLoS One 2009 May 25;4(5):e5621. Epub 2009 May 25.

Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0005621PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682762PMC
May 2009

Transcriptional regulation by the numbers: models.

Curr Opin Genet Dev 2005 Apr;15(2):116-24

Physics Department, Brandeis University, Waltham, MA 02454, USA.

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http://dx.doi.org/10.1016/j.gde.2005.02.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3482385PMC
April 2005