Publications



Physical Biology of the Cell, Second Edition
by Rob Phillips, Jané Kondev, Julie Theriot, Hernan Garcia,
and illustrated by Nigel Orme. Garland Science, 2012.
Book Website | Erratum


2021

  • Jennifer Cable, Michael B Elowitz, Ana I Domingos, Naomi Habib, Shalev Itzkovitz, Homaira Hamidzada, Michael S Balzer, Itai Yanai, Prisca Liberali, Jessica Whited, Aaron Streets, Long Cai, Andrew B Stergachis, Clarice Kit Yee Hong, Leeat Keren, Martin Guilliams, Uri Alon, Alex K. Shalek, Regan Hamel, Sarah J Pfau, Arjun Raj, Stephen R Quake, Nancy R Zhang, Jean Fan, Cole Trapnell, Bo Wang, Noah F Greenwald, Roser Vento-Tormo, Silvia DM Santos, Sabrina L Spencer, Hernan G Garcia, Geethika Arekatla, Federico Gaiti, Rinat Arbel-Goren, Steffen Rulands, Jan Philipp Junker, Allon M Klein, Samantha A Morris, John I Murray, Kate E Galloway, Michael Ratz, and Merrit Romeike : Single cell biology—a Keystone Symposia report . Annals of the New York Academy of Sciences ISSN 0077-8923 | DOI: http://doi.org/10.1111/nyas.14692 | PDF full text |

  • Eduardo González-Grandío, Simón Álamos, Yu Zhang, Jutta Dalton-Roesler, Krishna K. Niyogi, Hernan G. Garcia, and Peter H. Quail : Chromatin changes in PIF-regulated genes parallel their rapid transcriptional response to light . preprint on bioRxiv 2021.10.04.463089 | DOI: https://doi.org/10.1101/2021.10.04.463089 | PDF full text |

  • Simon Alamos, Armando Reimer, Krishna K. Niyogi, and Hernan G. Garcia: Quantitative imaging of RNA polymerase II activity in plants reveals the single-cell basis of tissue-wide transcriptional dynamics . Nature Plants 7 | DOI: https://doi.org/10.1038/s41477-021-00976-0 | PDF full text | Supporting Information |

  • Armando Reimer, Simon Alamos, Clay Westrum, Meghan A. Turner, Paul Talledo, Jiaxi Zhao, and Hernan G Garcia : Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen . preprint on bioRxiv 2021.07.10.451524 | DOI: https://doi.org/10.1101/2021.07.10.451524 |

  • Yang Joon Kim, Kaitlin Rhee, Jonathan Liu, Paul Jeammet, Meghan A. Turner, Stephen Small, and Hernan G. Garcia : Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental . preprint on bioRxiv 2021.07.28.454075 | DOI: https://doi.org/10.1101/2021.07.28.454075 |

  • Myron Child VI, Jack R. Bateman, Amir Jahangiri, Armando Reimer, Nicholas C. Lammers Nica Sbouni, Diego Villamarin, Grace C. McKenzie-Smith, Justine E. Johnson, Daniel Jost, and Hernan G. Garcia : Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila . eLife 2021;10:e64412 | DOI: https://doi.org/10.7554/eLife.64412 | PDF full text |

  • Jonathan Liu, Donal Hansen, Elizabeth Eck, Yang Joon Kim, Meghan A. Turner, Simon Alamos, and Hernan G. Garcia : Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage . PLOS Computational Biology 17(5):e1008999 | DOI: https://doi.org/10.1371/journal.pcbi.1008999 | PDF full text |

  • Nathan Belliveau, Griffin Chure, Christina L Hueschen, Hernan G. Garcia, Jane Kondev, Daniel S Fisher, Julie Theriot, and Rob Phillips : Fundamental limits on the rate of bacterial growth and their influence on proteomic composition . Cell Systems 129 | DOI: https://doi.org/10.1016/j.cels.2021.06.002 | PDF full text |

2020

  • Nicholas C. Lammers, Yang Joon Kim, Jiaxi Zhao, and Hernan G. Garcia: A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting . Current Opinion in Cell Biology 67 | DOI: https://doi.org/10.1016/j.ceb.2020.08.001 | PDF full text |

  • Matthew G. Eason, Antonia T. Pandelieva, Marc M. Mayer, Safwat T. Khan, Hernan G. Garcia, and Roberto A. Chica : Genetically-encoded fluorescent biosensor for rapid detection of protein expression. ACS Synthetic Biology | DOI: https://doi.org/10.1021/acssynbio.0c00407 | PDF full text |

  • Elizabeth Eck, Jonathan Liu, Maryam Kazemzadeh-Atoufi, Sydney Ghoreishi, Shelby A. Blythe, and Hernan G. Garcia: Quantitative dissection of transcription in development yields evidence for transcription factor-driven chromatin accessibility . eLife Oct 9;e56429 | DOI: https://doi.org/10.7554/eLife.56429 | PDF full text |

  • Hernan G. Garcia, Augusto Berrocal, Yang Joon Kim, Gabriella Martini, and Jiaxi Zhao : Lighting up the central dogma for predictive developmental biology . Current Topics in Developmental Biology 137 | PDF full text |

  • Augusto Berrocal, Nicholas Lammers, Hernan G. Garcia, and Michael Eisen: Kinetic sculpting of the seven stripes of the Drosophila even-skipped gene. eLife 2020;9:e61635 | DOI: https://doi.org/10.7554/eLife.61635 | PDF full text |

  • Nicholas C. Lammers, Vahe Galstyan, Armando Reimer, Sean A. Medin, Christopher H. Wiggins, and Hernan G. Garcia : Multimodal transcriptional control of pattern formation in embryonic development . PNAS 117(2) | DOI: https://doi.org/10.1073/PNAS.1912500117 | PDF full text | Supporting Information |

2019

  • Julia Falo-Sanjuan, Nicholas C. Lammers, Hernan G. Garcia, and Sarah Bray : Enhancer priming enables fast and sustained transcriptional responses to Notch signaling . Developmental Cell 50 | DOI: https://doi.org/10.1016/j.devcel.2019.07.002 | PDF Full Text |

  • Rob Phillips, Nathan M. Belliveau, Griffin Chure, Hernan G. Garcia, Manuel Razo-Mejia, and Clarissa Scholes : Figure 1 theory meets Figure 2 experiments in the study of gene expression. Annual Review of Biophysics 48 | PDF full text |

  • Shigehiro Yamada, Peter H. Whitney, Shao-Kuei Huang, Elizabeth C. Eck, Hernan G. Garcia, and Christine A. Rushlow : The Drosophila pioneer factor Zelda modulates the nuclear microenvironment of a Dorsal target enhancer to potentiate transcriptional output . Current Biology 29(8) | DOI: https://doi.org/10.1016/j.cub.2019.03.019 | PDF Full Text |

2018

  • Mustafa Mir, Armando Reimer, Michael Stadler, Astou Tangara, Anders S. Hansen, Dirk Hockemeyr, Michael B. Eisen, Hernan G. Garcia, and Xavier Darzacq. : Single molecule imaging in live embryos using lattice light-sheet microscopy . Nanoscale Imaging, Methods in Molecular Biology 1814 | DOI: https://doi.org/10.1007/978-1-4939-8591-3_32 | PDF Full Text |

  • Vincent Bourdreau, James Hazel, Jake Sellinger, Pan Chen, Kathryn Manakova, Rochell Radzyminski, Hernan G. Garcia, Jun Allard, Jesse Gatlin, and Paul Maddox : Nucleo-cytoplasmic trafficking regulates nuclear surface area during nuclear organogenesis. preprint on bioRxiv | DOI: https://doi.org/10.1101/326140 | PDF full text |

  • Jacques P. Bothma, Matthew R. Norstad, Simon Alamos, and Hernan G. Garcia : LlamaTags: A versatile tool to image transcription factor dynamics in live embryos . Cell 173(1) | PDF full text | SI Movies |

  • Hernan G. Garcia and Thomas Gregor: Live imaging of mRNA synthesis in Drosophila. RNA Detection: Methods in Molecular Biology 1649 | PDF full text |

2017

  • Mustafa Mir, Armando Reimer, Jenna E. Haines, Xiao-Yong Li, Michael Stadler, Hernan G. Garcia, Michael E. Eisen, and Xavier Darzacq : Dense Bicoid hubs accentuate binding along the morphogen gradient. Genes & Development 37(1784) | PDF full text | SI | Videos |

2016

  • Hernan G. Garcia, Robert C. Brewster, and Rob Phillips: Using synthetic biology to make cells tomorrow's test tubes. Integrative Biology 8(431) | PDF full text |

2015

  • Jacques P. Bothma*, Hernan G. Garcia*, Samuel Ng, Michael Perry, Thomas Gregor, and Michael Levine : Enhancer additivity and non-additivity in the early Drosophila embryo are determined by enhancer strength . eLife 4e07956 | PDF Full Text |

2014

  • Mattias Rydenfelt, Hernan G. Garcia, Robert Sidney Cox III, and Rob Phillips : The influence of promoter architectures and regulatory motifs on gene expression in Escherichia coli . PLOS One 10(3) | PDF full text | SI figures | SI tables |

  • Thomas Gregor, Hernan G. Garcia, and Shawn C. Little: The embryo as a laboratory: quantifying transcription in Drosophila. Trends in Genetics 30(364) | PDF full text |

  • Jacques P. Bothma*, Hernan G. Garcia*, Emilia Esposito, Gavin Schlissel, Thomas Gregor, and Michael Levine : Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos . PNAS 111(29) | PDF full text |

  • Robert C. Brewster, Franz Weinert, Hernan G. Garcia, Linda Song, Mattias Rydenfelt, and Rob Phillips : The transcription factor titration effect dictates level of gene expression . Cell 156 | PDF Full Text | Supporting Information |

  • Mattias Rydenfelt, Robert Sidney Cox III, Hernan G. Garcia, and Rob Phillips : The transcription factor titration effect: Statistical mechanical model of coupled transcription from multiple promoters . Physical Review E 89 | PDF Full Text |

2013

  • Lauren Figard, Heng Zu, Hernan G. Garcia, Ido Golding, and Anna Marie Sokac : The plasma membrane flattens out to fuel cell surface growth during Drosophila cellularization . Developmental Cell 27 | PDF Full Text | Supporting Information |

  • James Q. Boedicker, Hernan G. Garcia, Stephanie Johnson, and Rob Phillips : DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated DNA loop formation . Physical Biology 10 | PDF Full Text | Supporting Information |

  • Hernan G. Garcia, Mikhail Tikhonov, Albert Lin, and Thomas Gregor : Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning . Current Biology 23 | PDF Full Text | Supporting Information |

  • Sarah Marzen, Hernan G. Garcia, and Rob Phillips : Statistical Mechanics of Mnod-Wyman-Changeux (MWC) Models . Journal of Molecular Biology 23 | PDF Full Text | Supporting Information |

  • James Q. Boedicker*, Hernan G. Garcia*, and Rob Phillips: Theoretical and experimental dissection of DNA loop-mediated repression . Physical Review Lettes 110 | PDF Full Text | Supporting Information |

2012

  • Hernan G. Garcia*, Alvaro Sanchez*, James Q. Boedicker*, Melisa Osborne, Jeff Gelles, Jané Kondev, and Rob Phillips : Operator sequence alters gene expression independently of transcription factor occupancy . Cell Reports 2 | PDF Full Text |

2011

  • Hernan G. Garcia and Rob Phillips: Quantitative dissection of the simple repression input-output function . PNAS 108 | PDF Full Text | Supporting Information |

  • Hernan G. Garcia, Heun Jin Lee, James Q. Boedicker, and Rob Phillips : The limits and validity of methods of measuring gene expression for the testing of quantitative models . Biophysical Journal 101 | PDF Full Text | Supporting Information |

  • Roee Amit, Hernan G. Garcia, Rob Phillips, and Scott E. Fraser: Precision computational features in synthetic enhancers. Cell 7 | PDF Full Text | Supporting Information |

  • Alvaro Sanchez, Hernan G. Garcia, Daniel Jones, Rob Phillips, and Jané Kondev : Effect of promoter architecture on the cell-to-cell variability in gene expression . PLoS Computational Biology 7 | PDF Full Text | Supporting Information |

  • Hernan G. Garcia, Jané Kondev, Nigel Orme, Julie A. Theriot, and Rob Phillips : Thermodynamics of biological processes. Methods in Enzymology 492 | PDF Full Text |

2010

  • Hernan G. Garcia, Alvaro Sanchez, Thomas Kuhlman, Jané Kondev, and Rob Phillips. : Transcription by the numbers redux: experiments and calculations that surprise . Trends in Cell Biology 20 | PDF Full Text |

2009

  • Kevin B. Towles, John F. Beausang, Hernan G. Garcia, Rob PHillips, and PHilip C. Nelson. : First principles calculation of DNA looping in tethered particle experiments . Physical Biology 6 | PDF Full Text |

  • Lin Han, Hernan G. Garcia, Seth BLumberg, Kevin B. Towles, John F. Beausang, Philip C. Nelson, and Rob Phillips : Concentration and length dependence of DNA looping in transcriptional regulation . PLoS One 4(5) | PDF Full Text | Supporting Information |

2007

  • Hernan G. Garcia, Jané Kondev, Nigel Orme, Julie Theriot, and Rob Phillips: A first exposure to statistical mechanics for life scientists. arXiv 0708.1899v1 | PDF Full Text |

  • Hernan G. Garcia, Paul Grayson, Lin Han, Mandar Inamdar, Jane Kondev, Philip C. Nelson, Rob Phillips, Jonathan Widom, and Paul A. Wiggins : Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity . Biopolymers 85(2) | PDF full text |

2005

  • Lacramioara Bintu, Nicolas E. Buchler, Hernan G. Garcia, Ulrich Gerland, Terence Hwa, Jane Kondev, Thomas Kuhlman, and Rob Phillips : Transcriptional regulation by the numbers 2: Applications. Current Opinion in Genetics and Development 15(2) | PDF full text |

  • Lacramioara Bintu, Nicolas E. Buchler, Hernan G. Garcia, Ulrich Gerland, Terence Hwa, Jane Kondev, and Rob Phillips : Transcriptional regulation by the numbers 1: Models. Current Opinion in Genetics and Development 15(2) | PDF full text |