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


2026

  • Elizabeth Eck, Bruno Moretti, Brandon H. Schlomann, Jordão Bragantini, Merlin Lange, Xiang Zhao, Shruthi VijayKumar, Guillaume Valentin, Cristina Loureiro, Pablo Perez Franco, Chloé Jollivet, Virginie Braman, Baldemar Motomochi, Loïc A. Royer, Andrew C. Oates, Hernan G. Garcia : Single-cell transcriptional dynamics in a living vertebrate . Cell Systems 17, 101708 | DOI: https://doi.org/10.1016/j.cels.2026.101708 | PDF full text | Supplemental information |

  • Doruk Efe Gökmen, Rosalind Wenshan Pan, Tom Röschinger, Stephen Quake, Hernan G Garcia, Rob Phillips, Vincenzo Vitelli : Informational blueprints reveal condition-dependent gene regulatory architectures . preprint on bioRxiv 2026.05.18.726006 | DOI: https://www.biorxiv.org/content/10.64898/2026.05.18.726006v1 |

  • Jane Kondev, Marc Kirschner, Hernan G. Garcia, Gabriel L. Salmon, Rob Phillips : Biological Processes as Exploratory Dynamics . Biophysical Journal 125 | DOI: https://doi.org/10.1016/j.bpj.2025.09.009 | PDF full text |

  • Zitao Yang, Rebecca J. Rousseau, Sara D. Mahdavi, Hernan G. Garcia, Rob Phillips : The Dynamics of Inducible Genetic Circuits . Physical Review E 113 | DOI: https://doi.org/10.1103/kzdj-53jf | PDF full text |

  • Arman Karshenas, Tom Röschinger, Hernan G. Garcia : Predictive Modeling of Gene Expression and Localization of DNA Binding Site Using Deep Convolutional Neural Networks . PLOS Computational Biology 22 (4), e1014092 | DOI: https://doi.org/10.1371/journal.pcbi.1014092 | PDF full text |

2025

  • Ofri Axelrod, Udi Binshtok, Brian Gebelein, Hernan G. Garcia, David Sprinzak : A model of transcriptional bursting dynamics based on coupling between chromatin and enhancer states . preprint on bioRxiv | DOI: https://doi.org/10.1101/2025.11.29.691276 | PDF full text |

  • Julia Ainsworth, Yunchong Zhao, Ke Gao, Nicholas M. Gravina, Zachary H. Goldberg, Coleman Pinkerton, Scott A. Rifkin, Andreas M. Ernst, Hernan G. Garcia, Michael W. Perry : Cell fate ratios are encoded by transcriptional dynamics in the Drosophila retina . Current Biology 35 (12) | DOI: https://doi.org/10.1016/j.cub.2025.05.037 | PDF full text |

  • Meghan A. Turner, Nicholas M. Gravina, Bruno Moretti, Sadia Siddika Dima, Gabriella Martini, Gregory T. Reeves, and Hernan G. Garcia : Novel Fluorescent and Photoconvertible Fusions Reveal Dorsal Activator Dynamics . prepring on bioRxiv 2025.05.12.653543 | DOI: https://doi.org/10.1101/2025.05.12.653543 | PDF full text |

  • Samantha Fallacaro, Manya Kapoor, Lillian Encarnation, Apratim Mukherjee, Meghan A. Turner, Hernan G. Garcia, and Mustafa Mir : Enhancer binding kinetics explain transcription factor hub formation . preprint on bioRxiv 2025.04.07.647578 | DOI: https://doi.org/10.1101/2025.04.07.647578 | PDF full text |

  • Sadia Siddika Dima, Meghan A. Turner, Hernan G. Garcia, and Gregory T. Reeves : Global maps of transcription factor properties reveal threshold-based formation of DNA-bound and mobile clusters . Science Advances 12 (9) | DOI: https://doi.org/10.1126/sciadv.ady3909 | PDF full text |

2024

  • Jiaxi Zhao, Nicholas C. Lammers, Simon Alamos, Yang Joon Kim, Gabriella Martini, and Hernan G. Garcia : Optogenetic dissection of transcriptional repression in a multicellular organism . Nature Communications 15, Article number 9263 | DOI: https://doi.org/10.1038/s41467-024-53539-0 | PDF full text |

  • Erik Kubaczka, Maximilian Gehri, Jérémie J. M. Marlhens, Tobias Schwarz, Maik Molderings, Nicolai Engelmann, Hernan G. Garcia, Christian Hochberger, Heinz Koeppl : Energy Aware Technology Mapping of Genetic Logic Circuits . ACS Synthetic Biology 13/Issue 10 | DOI: https://doi.org/10.1021/acssynbio.4c00395 | PDF |

  • Shuyao Kong, Mingyuan Zhu, M. Regina Scarpin, David Pan, Longfei Jia, Ryan E. Martinez, Simon Alamos, Batthula Vijaya Lakshmi Vadde, Hernan G. Garcia, Shu-Bing Qian, Jacob O. Brunkard, and Adrienne H.K. Roeder : DRMY1 promotes robust morphogenesis in Arabidopsis by sustaining the translation of cytokinin-signaling inhibitor proteins . Developmental Cell In press | DOI: https://doi.org/10.1016/j.devcel.2024.08.010 | PDF |

  • Brandon H. Schlomann, Ting-Wei Pai, Jazmin Sandhu, Genesis Ferrer Imbert, Thomas G.W. Graham, Hernan G Garcia : Spatial microenvironments tune immune response dynamics in the Drosophila larval fat body . preprint on bioRxiv 2024.09.12.612587 | DOI: https://www.biorxiv.org/content/10.1101/2024.09.12.612587v1 | PDF full text |

  • Julia Falo-Sanjuan, Yuliana Diaz-Tirado, Meghan A. Turner, Julian Davis, Claudia Medrano, Jenna Haines, Joey McKenna, Arman Karshenas, Michael B. Eisen, Hernan G. Garcia : Targeted mutagenesis of specific genomic DNA sequences in animals for the in vivo generation of variant libraries . preprint on bioRxiv 2024.06.10.598328 | DOI: https://doi.org/10.1101/2024.06.10.598328 | PDF full text |

2023

  • Kirstin Meyer, Nicholas C. Lammers, Lukasz J. Bugaj, Hernan G. Garcia, and Orion D. Weiner : Optogenetic control of YAP reveals a dynamic communication code for stem cell fate and proliferation . Nature Communications 14 | DOI: https://doi.org/10.1038/s41467-023-42643-2 | PDF full text |

  • Gabriella Martini, and Hernan G. Garcia : Temperature variation drives coordinated scaling of temporal and dynamic features of transcription in embryonic development . preprint on bioRxiv 2023.08.09.552666 | |

  • Jiaxi Zhao, Mindy Liu Perkins, Matthew Norstad, and Hernan G. Garcia : A bistable autoregulatory module in the developing embryo commits cells to binary fates . Current Biology Volume 33 Issue 14 | DOI: https://doi.org/10.1016/j.cub.2023.06.060 | PDF full text |

  • Sara Mahdavi, Gabriel L. Salmon, Patill Daghlian, Hernan G. Garcia, and Robert Phillips : Flexibility and sensitivity in gene regulation out of equilibrium . PNAS 121 (46) e2411395121 | DOI: https://www.pnas.org/doi/10.1073/pnas.2411395121 | PDF |

  • Simon Alamos, Armando Reimer, 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 . Cell Systems Cell Systems 14, 1-17 | DOI: https://doi.org/10.1016/j.cels.2022.12.008 | PDF |

  • Augusto Berrocal, Nicholas C Lammers, Hernan G Garcia, Michael B Eisen : Unified bursting strategies in ectopic and endogenous even-skipped expression patterns . eLife Developmental Biology, Chromosomes and Gene Expression | DOI: https://doi.org/10.7554/eLife.88671.2 | PDF |

  • Nicholas C. Lammers, Avi I. Flamholz, and Hernan G. Garcia : Competing constraints shape the non-equilibrium limits of cellular decision making . PNAS 120 - No. 10 | DOI: https://doi.org/10.1073/pnas.2211203120 | PDF full text |

2022

  • Eduardo González-Grandío, Simón Álamos, Yu Zhang, Jutta Dalton-Roesler, Krishna K. Niyogi, Hernan G. Garcia, and Peter H. Quail : Chromatin changes in Phytochrome Interacting Factor-regulated genes parallel their rapid transcriptional response to light . Frontiers in Plant Science 13:803441 | DOI: https://doi.org/10.3389/fpls.2022.803441 | PDF full text |

  • 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 . eLife 11:e73395 | DOI: https://doi.org/10.7554/eLife.73395 | PDF full text |

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 |

  • Tatsuya Nobori: Real time quantitative imaging of transcriptional activity at the single cell level . | Article Link | Article Snapshot |

  • 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 |