Publications
Books
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
Publications
2024
- Arman Karshenas , Tom Röschinger , Hernan G. Garcia
: Predictive Modeling of Gene Expression and Localization of DNA Binding Site Using Deep Convolutional Neural Networks
. preprint on bioRxiv 2024.12.17.629042 | DOI: https://doi.org/10.1101/2024.12.17.629042 | PDF full text |
- 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 |
- Elizabeth Eck, Bruno Moretti, Brandon H Schlomann, Jordão Bragantini, Merlin Lange, Xiang Zhao, Shruthi VijayKumar, Guillaume Valentin, Cristina Loureiro, Daniele Soroldoni, Loic Alain Royer, Andrew C. Oates, Hernan H Garcia
: Single-cell transcriptional dynamics in a living vertebrate
. preprint on bioRxiv 2024.01.03.574108 | DOI: https://doi.org/10.1101/2024.01.03.574108 | 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 |
- by Simon Alamos, Armando Reimer, Krishna K. Niyogi, and Hernan G. Garcia in 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 |
- News and Views by Katey Abley and James C.W. Locke in Noisy transcription under the spotlight . Nature Plants 7:996 (2021) | DOI: https://doi.org/10.1038/s41477-021-00987-x | 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 |
- Highlighted by Caroline Vissers and Ryoichiro Kageyama in Bursting the notch bubble: New insights into in vivo transcriptional dynamics . Dev Cell 50:393 (2019) | DOI: https://doi.org/10.1016/j.devcel.2019.07.028 | 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 |
- Highlighted by Dimitrios Papadopoulos and Pavel Tomancak in Gene regulation: Analog to digital conversion of transcription factor gradients . Current Biology 29:R403 (2019) | DOI: https://doi.org/10.1016/j.cub.2019.04.052 | 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 |
- Highlighted by Ruth Williams in Ready, Set, Glow . The Scientist (2018) | Article Link |
- Recommended by Adrienne Roeder and Mingyuan Zhu in . F1000Prime (2018) | DOI: https://doi.org/10.3410/f.733205368.793548141 |
- 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 |
- Highlighted by Florian A. Karreth, Yvonne Tay, and Pier Paolo Pandolfi in Target competition: transcription factors enter the limelight . Genome Biology 15:114 (2014) | DOI: https://doi.org/10.1186/gb4174 | PDF full text |
- Highlighted by Methods in Brief in Synthetic biology: Tuning expression by numbers . Nature Methods 11, 475 (2014) | DOI: https://doi.org/10.1038/nmeth.2942 | PDF full text |
- 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 |
- Highlighted by Jacques Bothma and Michael Levine in Development: Lights, Camera, Action -- The Drosophila Embryo Goes Live! . Current Biology 23:R965 (2013) | DOI: https://doi.org/10.1016/j.cub.2013.09.054 | PDF full text |
- Highlighted by Isabel Lokody in Seeing the pattern . Nature Review Genetics 14, 823 (2013) | DOI: https://doi.org/10.1038/nrg3619 | PDF full text |
- Highlighted by Sarah C.P. Williams in Measuring transcription to follow embryo development . BioTechniques News (2013) | Article Snapshot |
- 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 |