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Hernan G. Garcia, Ph.D. - Publications

Affiliations: 
Physics Princeton University, Princeton, NJ 
 Molecular and Cell Biology University of California, Berkeley, Berkeley, CA, United States 
Area:
Physical biology. Transcriptional regulation. Development of the fruit fly Drosophila melanogaster
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57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Eck E, Moretti B, Schlomann BH, Bragantini J, Lange M, Zhao X, VijayKumar S, Valentin G, Loureiro C, Soroldoni D, Royer LA, Oates AC, Garcia HG. Single-cell transcriptional dynamics in a living vertebrate. Biorxiv : the Preprint Server For Biology. PMID 38260569 DOI: 10.1101/2024.01.03.574108  0.362
2023 Lammers NC, Flamholz AI, Garcia HG. Competing constraints shape the nonequilibrium limits of cellular decision-making. Proceedings of the National Academy of Sciences of the United States of America. 120: e2211203120. PMID 36862689 DOI: 10.1073/pnas.2211203120  0.362
2023 Berrocal A, Lammers NC, Garcia HG, Eisen MB. Unified bursting strategies in ectopic and endogenous expression patterns. Biorxiv : the Preprint Server For Biology. PMID 36798351 DOI: 10.1101/2023.02.09.527927  0.345
2023 Alamos S, Reimer A, Westrum C, Turner MA, Talledo P, Zhao J, Luu E, Garcia HG. Minimal synthetic enhancers reveal control of the probability of transcriptional engagement and its timing by a morphogen gradient. Cell Systems. PMID 36696901 DOI: 10.1016/j.cels.2022.12.008  0.433
2022 Kim YJ, Rhee K, Liu J, Jeammet P, Turner MA, Small SJ, Garcia HG. Predictive modeling reveals that higher-order cooperativity drives transcriptional repression in a synthetic developmental enhancer. Elife. 11. PMID 36503705 DOI: 10.7554/eLife.73395  0.426
2020 Lammers NC, Kim YJ, Zhao J, Garcia HG. A matter of time: Using dynamics and theory to uncover mechanisms of transcriptional bursting. Current Opinion in Cell Biology. 67: 147-157. PMID 33242838 DOI: 10.1016/j.ceb.2020.08.001  0.354
2020 Eck E, Liu J, Kazemzadeh-Atoufi M, Ghoreishi S, Blythe SA, Garcia HG. Quantitative dissection of transcription in development yields evidence for transcription factor-driven chromatin accessibility. Elife. 9. PMID 33074101 DOI: 10.7554/eLife.56429  0.377
2020 Garcia HG, Berrocal A, Kim YJ, Martini G, Zhao J. Lighting up the central dogma for predictive developmental biology. Current Topics in Developmental Biology. 137: 1-35. PMID 32143740 DOI: 10.1016/Bs.Ctdb.2019.10.010  0.402
2019 Lammers NC, Galstyan V, Reimer A, Medin SA, Wiggins CH, Garcia HG. Multimodal transcriptional control of pattern formation in embryonic development. Proceedings of the National Academy of Sciences of the United States of America. PMID 31882445 DOI: 10.1073/Pnas.1912500117  0.489
2019 Falo-Sanjuan J, Lammers NC, Garcia HG, Bray SJ. Enhancer Priming Enables Fast and Sustained Transcriptional Responses to Notch Signaling. Developmental Cell. PMID 31378591 DOI: 10.1016/J.Devcel.2019.07.002  0.459
2019 Phillips R, Belliveau NM, Chure G, Garcia HG, Razo-Mejia M, Scholes C. Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression. Annual Review of Biophysics. 48: 121-163. PMID 31084583 DOI: 10.1146/Annurev-Biophys-052118-115525  0.462
2019 Yamada S, Whitney PH, Huang SK, Eck EC, Garcia HG, Rushlow CA. The Drosophila Pioneer Factor Zelda Modulates the Nuclear Microenvironment of a Dorsal Target Enhancer to Potentiate Transcriptional Output. Current Biology : Cb. PMID 30982648 DOI: 10.1016/J.Cub.2019.03.019  0.478
2019 DePace AH, Garcia H. Decision letter: Multi-enhancer transcriptional hubs confer phenotypic robustness Elife. DOI: 10.7554/Elife.45325.016  0.334
2018 Mir M, Reimer A, Stadler M, Tangara A, Hansen AS, Hockemeyer D, Eisen MB, Garcia H, Darzacq X. Single Molecule Imaging in Live Embryos Using Lattice Light-Sheet Microscopy. Methods in Molecular Biology (Clifton, N.J.). 1814: 541-559. PMID 29956254 DOI: 10.1007/978-1-4939-8591-3_32  0.363
2018 Bothma JP, Norstad MR, Alamos S, Garcia HG. LlamaTags: A Versatile Tool to Image Transcription Factor Dynamics in Live Embryos. Cell. PMID 29754814 DOI: 10.1016/J.Cell.2018.03.069  0.464
2018 Garcia HG, Gregor T. Live Imaging of mRNA Synthesis in Drosophila. Methods in Molecular Biology (Clifton, N.J.). 1649: 349-357. PMID 29130209 DOI: 10.1007/978-1-4939-7213-5_23  0.625
2018 Alamos S, Joon Kim Y, Xiao JY, Earley E, Garcia HG. Uncovering Dynamical Mechanisms of Transcription Factor Readout in Development using Optogenetics Biophysical Journal. 114: 249a. DOI: 10.1016/J.Bpj.2017.11.1386  0.415
2018 Eck E, Liu J, Garcia H. Transcriptional Dynamics and the Regulation of Chromatin Accessibility in Drosophila Embryonic Development Biophysical Journal. 114: 249a. DOI: 10.1016/J.Bpj.2017.11.1384  0.447
2018 Child M, Reimer A, Luu E, Garcia H. Using Minimal Synthetic Enhancers to Reach a Predictive Understanding of Transcriptional Regulation in Development Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.1380  0.424
2017 Mir M, Reimer A, Haines JE, Li XY, Stadler M, Garcia H, Eisen MB, Darzacq X. Dense Bicoid hubs accentuate binding along the morphogen gradient. Genes & Development. 31: 1784-1794. PMID 28982761 DOI: 10.1101/Gad.305078.117  0.437
2016 Garcia HG, Brewster RC, Phillips R. Using synthetic biology to make cells tomorrow's test tubes. Integrative Biology : Quantitative Biosciences From Nano to Macro. PMID 26952708 DOI: 10.1039/C6Ib00006A  0.321
2015 Bothma JP, Garcia HG, Ng S, Perry MW, Gregor T, Levine M. Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo. Elife. 4. PMID 26267217 DOI: 10.7554/Elife.07956  0.554
2015 Bothma JP, Garcia HG, Ng S, Perry MW, Gregor T, Levine M. Author response: Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo Elife. DOI: 10.7554/Elife.07956.013  0.543
2015 Bothma JP, Garcia HG, Ng S, Perry MW, Gregor T, Levine M. Enhancer additivity and non-additivity are determined by enhancer strength in the Drosophila embryo Elife. 4. DOI: 10.7554/eLife.07956.001  0.519
2014 Rydenfelt M, Garcia HG, Cox RS, Phillips R. The influence of promoter architectures and regulatory motifs on gene expression in Escherichia coli. Plos One. 9: e114347. PMID 25549361 DOI: 10.1371/Journal.Pone.0114347  0.472
2014 Gregor T, Garcia HG, Little SC. The embryo as a laboratory: quantifying transcription in Drosophila. Trends in Genetics : Tig. 30: 364-75. PMID 25005921 DOI: 10.1016/J.Tig.2014.06.002  0.718
2014 Bothma JP, Garcia HG, Esposito E, Schlissel G, Gregor T, Levine M. Dynamic regulation of eve stripe 2 expression reveals transcriptional bursts in living Drosophila embryos. Proceedings of the National Academy of Sciences of the United States of America. 111: 10598-603. PMID 24994903 DOI: 10.1073/Pnas.1410022111  0.639
2014 Brewster RC, Weinert FM, Garcia HG, Song D, Rydenfelt M, Phillips R. The transcription factor titration effect dictates level of gene expression. Cell. 156: 1312-23. PMID 24612990 DOI: 10.1016/J.Cell.2014.02.022  0.469
2014 Rydenfelt M, Cox RS, Garcia H, Phillips R. Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 89: 012702. PMID 24580252 DOI: 10.1103/Physreve.89.012702  0.505
2014 Rydenfelt M, Garcia HG, Cox RS, Phillips R. Predicted RNAP binding energy to promoters in the simple activation (1,0) and simple repression architecture (0,1). Plos One. DOI: 10.1371/Journal.Pone.0114347.G015  0.331
2014 Rydenfelt M, Garcia HG, Cox RS, Phillips R. Predicted RNAP binding energy [26] for promoters in RegulonDB 8.5 and DNA sequences randomly chosen from the E. coli genome. Plos One. DOI: 10.1371/Journal.Pone.0114347.G014  0.313
2014 Rydenfelt M, Garcia HG, Cox RS, Phillips R. DNA binding site size (in base pairs) for all TF-DNA interactions (RegulonDB 8.5). Plos One. DOI: 10.1371/Journal.Pone.0114347.G012  0.338
2014 Rydenfelt M, Garcia HG, Cox RS, Phillips R. Probability of TF binding site overlap. Plos One. DOI: 10.1371/Journal.Pone.0114347.G011  0.303
2014 Rydenfelt M, Garcia HG, Cox RS, Phillips R. Distribution of activating and repressing binding sites bound by global TFs and specific TFs, respectively. Plos One. DOI: 10.1371/Journal.Pone.0114347.G010  0.344
2014 Rydenfelt M, Garcia HG, Cox RS, Phillips R. Measured protein copy number vs. number of TF binding sites regulating the transcription of the protein. Plos One. DOI: 10.1371/Journal.Pone.0114347.G007  0.391
2014 Rydenfelt M, Garcia HG, Cox RS, Phillips R. TF copy number plotted as a function of the total number of TF binding sites (RegulonDB 8.5) for that particular TF. Plos One. DOI: 10.1371/Journal.Pone.0114347.G006  0.334
2014 Rydenfelt M, Garcia HG, Cox RS, Phillips R. Number of binding sites and TF types regulating each operon (RegulonDB 8.5). Plos One. DOI: 10.1371/Journal.Pone.0114347.G003  0.35
2014 Rydenfelt M, Garcia HG, Cox RS, Phillips R. Number of operons, genes and binding sites regulated per TF (RegulonDB 8.5.) Plos One. DOI: 10.1371/Journal.Pone.0114347.G002  0.395
2013 Boedicker JQ, Garcia HG, Johnson S, Phillips R. DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation. Physical Biology. 10: 066005. PMID 24231252 DOI: 10.1088/1478-3975/10/6/066005  0.397
2013 Garcia HG, Tikhonov M, Lin A, Gregor T. Quantitative imaging of transcription in living Drosophila embryos links polymerase activity to patterning. Current Biology : Cb. 23: 2140-5. PMID 24139738 DOI: 10.1016/J.Cub.2013.08.054  0.703
2013 Marzen S, Garcia HG, Phillips R. Statistical mechanics of Monod-Wyman-Changeux (MWC) models. Journal of Molecular Biology. 425: 1433-60. PMID 23499654 DOI: 10.1016/J.Jmb.2013.03.013  0.307
2013 Boedicker JQ, Garcia HG, Phillips R. Theoretical and experimental dissection of DNA loop-mediated repression. Physical Review Letters. 110: 018101. PMID 23383841 DOI: 10.1103/Physrevlett.110.018101  0.406
2013 Garcia HG, Lin A, Tikhonov M, Gregor T. Novel Mechanism for Noise Reduction between Nuclear Transcriptional Activity and Cytoplasmic MRNA Distributions Living Fly Embryos Biophysical Journal. 104: 552a. DOI: 10.1016/J.Bpj.2012.11.3062  0.635
2012 Garcia HG, Sanchez A, Boedicker JQ, Osborne M, Gelles J, Kondev J, Phillips R. Operator sequence alters gene expression independently of transcription factor occupancy in bacteria. Cell Reports. 2: 150-61. PMID 22840405 DOI: 10.1016/J.Celrep.2012.06.004  0.405
2011 Garcia HG, Lee HJ, Boedicker JQ, Phillips R. Comparison and calibration of different reporters for quantitative analysis of gene expression. Biophysical Journal. 101: 535-44. PMID 21806921 DOI: 10.1016/J.Bpj.2011.06.026  0.378
2011 Garcia HG, Phillips R. Quantitative dissection of the simple repression input-output function. Proceedings of the National Academy of Sciences of the United States of America. 108: 12173-8. PMID 21730194 DOI: 10.1073/Pnas.1015616108  0.464
2011 Amit R, Garcia HG, Phillips R, Fraser SE. Building enhancers from the ground up: a synthetic biology approach. Cell. 146: 105-18. PMID 21729783 DOI: 10.1016/J.Cell.2011.06.024  0.607
2011 Sanchez A, Garcia HG, Jones D, Phillips R, Kondev J. Effect of promoter architecture on the cell-to-cell variability in gene expression. Plos Computational Biology. 7: e1001100. PMID 21390269 DOI: 10.1371/Journal.Pcbi.1001100  0.446
2011 Garcia HG, Kondev J, Orme N, Theriot JA, Phillips R. Thermodynamics of biological processes. Methods in Enzymology. 492: 27-59. PMID 21333788 DOI: 10.1016/B978-0-12-381268-1.00014-8  0.301
2010 Garcia HG, Sanchez A, Kuhlman T, Kondev J, Phillips R. Transcription by the numbers redux: experiments and calculations that surprise. Trends in Cell Biology. 20: 723-33. PMID 20801657 DOI: 10.1016/J.Tcb.2010.07.002  0.436
2009 Towles KB, Beausang JF, Garcia HG, Phillips R, Nelson PC. First-principles calculation of DNA looping in tethered particle experiments. Physical Biology. 6: 025001. PMID 19571369 DOI: 10.1088/1478-3975/6/2/025001  0.313
2009 Han L, Garcia HG, Blumberg S, Towles KB, Beausang JF, Nelson PC, Phillips R. Concentration and length dependence of DNA looping in transcriptional regulation. Plos One. 4: e5621. PMID 19479049 DOI: 10.1371/Journal.Pone.0005621  0.553
2009 Garcia HG, Phillips R. DNA Architecture and Transcriptional Regulation Exploring DNA's Mechanical Code Biophysical Journal. 96: 306. DOI: 10.1016/J.Bpj.2008.12.1525  0.444
2007 Garcia HG, Grayson P, Han L, Inamdar M, Kondev J, Nelson PC, Phillips R, Widom J, Wiggins PA. Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity. Biopolymers. 85: 115-30. PMID 17103419 DOI: 10.1002/Bip.20627  0.637
2005 Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R. Transcriptional regulation by the numbers: applications. Current Opinion in Genetics & Development. 15: 125-35. PMID 15797195 DOI: 10.1016/J.Gde.2005.02.006  0.458
2005 Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R. Transcriptional regulation by the numbers: models. Current Opinion in Genetics & Development. 15: 116-24. PMID 15797194 DOI: 10.1016/J.Gde.2005.02.007  0.462
2005 Garcia HG. Transcriptional Regulation by the Numbers Bulletin of the American Physical Society. DOI: 10.7907/63Rg-8P84.  0.461
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