Phillips, Rob

(orcid 0000-0003-3082-2809)

Article(s) from CaltechAUTHORS

• Suresh, Pooja; Galstyan, Vahe et al. (2022) Modeling and mechanical perturbations reveal how spatially regulated anchorage gives rise to spatially distinct mechanics across the mammalian spindle eLife; Vol. 11; https://doi.org/10.7554/elife.79558

• Chure, Griffin; Banks, Rachel A. et al. (2022) Anthroponumbers.org: A quantitative database of human impacts on Planet Earth Patterns; Vol. 3; No. 9; https://doi.org/10.1016/j.patter.2022.100552

• Suresh, Pooja; Galstyan, Vahe et al. (2022) Connections distributed within 3 μm of chromosomes are necessary and sufficient for the kinetochore-fiber’s robust anchorage in the mammalian spindle Biophysical Journal; Vol. 121; No. 3; In: 66th Biophysical Society Annual Meeting, 19-23 February 2022, San Francisco, CA https://doi.org/10.1016/j.bpj.2021.11.536

• Hueschen, Christina; Segev Zarko, Li-av et al. (2022) Distinct self-organized actin patterns explain diverse parasite gliding modes Biophysical Journal; Vol. 121; No. 3; In: 66th Biophysical Society Annual Meeting, 19-23 February 2022, San Francisco, CA https://doi.org/10.1016/j.bpj.2021.11.1183

• Duarte, Ana I.; Jin Lee, Heun et al. (2022) Measuring energy consumption through space and time in an active matter system of cytoskeletal motors and filaments Biophysical Journal; Vol. 121; No. 3; In: 66th Biophysical Society Annual Meeting, 19-23 February 2022, San Francisco, CA https://doi.org/10.1016/j.bpj.2021.11.2745

• Larios, David A.; Phillips, Rob et al. (2022) Reconstituting the nonequilibrium biophysics of the LECA cytoskeleton in active matter Biophysical Journal; Vol. 121; No. 3; In: 66th Biophysical Society Annual Meeting, 19-23 February 2022, San Francisco, CA https://doi.org/10.1016/j.bpj.2021.11.2744

• Salmon, Gabe; Phillips, Rob (2022) Reproducibility, stochasticity, and geometry in a lattice of cross-feeding microbial cells Biophysical Journal; Vol. 121; No. 3; In: 66th Biophysical Society Annual Meeting, 19-23 February 2022, San Francisco, CA https://doi.org/10.1016/j.bpj.2021.11.2086

• Tadmor, Arbel D.; Phillips, Rob (2022) MCRL: using a reference library to compress a metagenome into a non-redundant list of sequences, considering viruses as a case study Bioinformatics; Vol. 38; No. 3; https://doi.org/10.1093/bioinformatics/btab703

• Hueschen, Christina; Segev Zarko, Li-Av et al. (2021) Actin Organization and Dynamics in Motile Toxoplasma Gondii Parasites American Journal of Tropical Medicine and Hygiene; Vol. 105; No. 5; In: 2021 ASTMH Annual Meeting, 17-21 November 2021, [Online Only] https://doi.org/10.4269/ajtmh.abstract2021

• Belliveau, Nathan M.; Chure, Griffin et al. (2021) Fundamental limits on the rate of bacterial growth and their influence on proteomic composition Cell Systems; Vol. 12; No. 9; https://doi.org/10.1016/j.cels.2021.06.002

• Qu, Zijie; Schildknecht, Dominik et al. (2021) Persistent fluid flows defined by active matter boundaries Communications Physics; Vol. 4; https://doi.org/10.1038/s42005-021-00703-3

• Sender, Ron; Bar-On, Yinon M. et al. (2021) The total number and mass of SARS-CoV-2 virions Proceedings of the National Academy of Sciences of the United States of America; Vol. 118; No. 25; https://doi.org/10.1073/pnas.2024815118

• Phillips, Rob (2021) Schrödinger’s What Is Life? at 75 Cell Systems; Vol. 12; No. 6; https://doi.org/10.1016/j.cels.2021.05.013

• Galstyan, Vahe; Suresh, Pooja et al. (2021) Understanding the Mechanisms that Give Rise to the Mammalian Spindle's Response to Force using Theory and Microneedle Manipulation Biophysical Journal; Vol. 120; No. 3; In: 65th Biophysical Society Annual Meeting, 22-26 February 2021, [Online Only] https://doi.org/10.1016/j.bpj.2020.11.2158

• Morrison, Muir; Razo-Mejia, Manuel et al. (2021) Reconciling kinetic and thermodynamic models of bacterial transcription PLOS Computational Biology; Vol. 17; No. 1; https://doi.org/10.1371/journal.pcbi.1008572

• Yu, Timothy C.; Liu, Winnie L. et al. (2021) Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems Nature Communications; Vol. 12; https://resolver.caltech.edu/CaltechAUTHORS:20200203-092359628

• Galstyan, Vahe; Husain, Kabir et al. (2020) Proofreading through spatial gradients eLife; Vol. 9; https://resolver.caltech.edu/CaltechAUTHORS:20200526-121021095

• Ireland, William T.; Beeler, Suzannah M. et al. (2020) Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time eLife; Vol. 2020; No. 9; https://resolver.caltech.edu/CaltechAUTHORS:20200121-102719123

• Razo-Mejia, Manuel; Marzen, Sarah et al. (2020) First-principles prediction of the information processing capacity of a simple genetic circuit Physical Review E; Vol. 102; No. 2; https://resolver.caltech.edu/CaltechAUTHORS:20190402-080512452

• Hirokawa, Soichi; Chure, Griffin et al. (2020) Sequence-Dependent Dynamics of Synthetic and Endogenous RSSs in V(D)J Recombination Nucleic Acids Research; Vol. 48; No. 12; https://resolver.caltech.edu/CaltechAUTHORS:20191007-074542895

• Laxhuber, Kathrin S.; Morrison, Muir J. et al. (2020) Theoretical investigation of a genetic switch for metabolic adaptation PLoS ONE; Vol. 15; No. 5; https://resolver.caltech.edu/CaltechAUTHORS:20191202-142214486

• Bar-On, Yinon M.; Flamholz, Avi et al. (2020) SARS-CoV-2 (COVID-19) by the numbers eLife; Vol. 9; https://doi.org/10.7554/elife.57309

• Banks, Rachel; Lee, Heun Jin et al. (2020) Bridging Kinesin Properties with System-scale Characteristics of Microtubule-Motor Assemblies Biophysical Journal; Vol. 118; No. 3; In: 64th Annual Meeting of the Biophysical Society, 15-19 February 2020, San Diego, CA https://doi.org/10.1016/j.bpj.2019.11.1081

• McCarty, Nicholas S.; Razo-Mejia, Manuel et al. (2020) Genetic Barcodes Enable Quantitative Mapping of Operator Mutants to Gene Expression Biophysical Journal; Vol. 118; No. 3; In: 64th Annual Meeting of the Biophysical Society, 15-19 February 2020, San Diego, CA https://doi.org/10.1016/j.bpj.2019.11.3298

• Galstyan, Vahe; Husain, Kabir et al. (2020) Kinetic Proofreading using Substrate Gradients and Enzyme Diffusion Biophysical Journal; Vol. 118; No. 3; In: 64th Annual Meeting of the Biophysical Society, 15-19 February 2020, San Diego, CA https://doi.org/10.1016/j.bpj.2019.11.3118

• Salmon, Gabe; Phillips, Rob (2020) Modeling Microbial Interactions across Nutritional Environments using Maximum Entropy Biophysical Journal; Vol. 118; No. 3; In: 64th Annual Meeting of the Biophysical Society, 15-19 February 2020, San Diego, CA https://doi.org/10.1016/j.bpj.2019.11.2004

• Phillips, Rob (2020) Schrodinger's “What is Life” At 75: The Physical Aspects of the Living Cell Revisited Biophysical Journal; Vol. 118; No. 3; In: 64th Annual Meeting of the Biophysical Society, 15-19 February 2020, San Diego, CA https://doi.org/10.1016/j.bpj.2019.11.204

• Chure, Griffin; Phillips, Rob (2020) The Molecular Biophysics of Adaptation Biophysical Journal; Vol. 118; No. 3; In: 64th Annual Meeting of the Biophysical Society, 15-19 February 2020, San Diego, CA https://doi.org/10.1016/j.bpj.2019.11.2983

• Galstyan, Vahe; Phillips, Rob (2019) Allostery and Kinetic Proofreading Journal of Physical Chemistry B; Vol. 123; No. 51; https://doi.org/10.1021/acs.jpcb.9b08380

• Einav, Tal; Yazdi, Shahrzad et al. (2019) Harnessing Avidity: Quantifying the Entropic and Energetic Effects of Linker Length and Rigidity for Multivalent Binding of Antibodies to HIV-1 Cell Systems; Vol. 9; No. 5; https://doi.org/10.1016/j.cels.2019.09.007

• Chure, Griffin; Razo-Mejia, Manuel et al. (2019) Predictive shifts in free energy couple mutations to their phenotypic consequences Proceedings of the National Academy of Sciences of the United States of America; Vol. 116; No. 37; https://doi.org/10.1073/pnas.1907869116

• Ross, Tyler D.; Lee, Heun Jin et al. (2019) Controlling Organization and Forces in Active Matter Through Optically-Defined Boundaries Nature; Vol. 572; No. 7768; https://doi.org/10.1038/s41586-019-1447-1

• Einav, Tal; Phillips, Rob (2019) How the avidity of polymerase binding to the –35/–10 promoter sites affects gene expression Proceedings of the National Academy of Sciences of the United States of America; Vol. 116; No. 27; https://doi.org/10.1073/pnas.1905615116

• Wadhwa, Navish; Phillips, Rob et al. (2019) Torque-dependent remodeling of the bacterial flagellar motor Proceedings of the National Academy of Sciences of the United States of America; Vol. 116; No. 24; https://doi.org/10.1073/pnas.1904577116

• Phillips, Rob; Belliveau, Nathan M. et al. (2019) Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression Annual Review of Biophysics; Vol. 48; https://doi.org/10.1146/annurev-biophys-052118-115525

• Galstyan, Vahe; Funk, Luke et al. (2019) Combinatorial Control through Allostery Journal of Physical Chemistry B; Vol. 123; No. 13; https://doi.org/10.1021/acs.jpcb.8b12517

• Foster, Peter J.; Razo-Mejia, Manuel et al. (2019) Measuring the Energetic Costs of Embryonic Development Developmental Cell; Vol. 48; No. 5; https://doi.org/10.1016/j.devcel.2019.02.016

• Hueschen, Christina L.; Galstyan, Vahe et al. (2019) Microtubule End-Clustering Maintains a Steady-State Spindle Shape Current Biology; Vol. 29; No. 4; https://doi.org/10.1016/j.cub.2019.01.016

• Barnes, Stephanie L.; Belliveau, Nathan M. et al. (2019) Mapping DNA sequence to transcription factor binding energy in vivo PLoS Computational Biology; Vol. 15; No. 2; https://resolver.caltech.edu/CaltechAUTHORS:20181030-132608570

• Forcier, Talitha L.; Ayaz, Andalus et al. (2018) Measuring cis-regulatory energetics in living cells using allelic manifolds eLife; Vol. 7; https://resolver.caltech.edu/CaltechAUTHORS:20181128-093526476

• Chure, Griffin; Lee, Heun Jin et al. (2018) Connecting the dots between mechanosensitive channel abundance, osmotic shock, and survival at single-cell resolution Journal of Bacteriology; Vol. 200; No. 23; https://resolver.caltech.edu/CaltechAUTHORS:20180917-125104010

• Einav, Tal; Duque, Julia et al. (2018) Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants PLoS ONE; Vol. 13; No. 9; https://resolver.caltech.edu/CaltechAUTHORS:20181009-105623284

• Bar-On, Yinon M.; Phillips, Rob et al. (2018) The biomass distribution on Earth Proceedings of the National Academy of Sciences of the United States of America; Vol. 115; No. 25; https://doi.org/10.1073/pnas.1711842115

• Belliveau, Nathan M.; Barnes, Stephanie L. et al. (2018) Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria Proceedings of the National Academy of Sciences of the United States of America; Vol. 115; No. 21; https://doi.org/10.1073/pnas.1722055115

• Razo-Mejia, Manuel; Barnes, Stephanie L. et al. (2018) Tuning transcriptional regulation through signaling: A predictive theory of allosteric induction In: Tuning transcriptional regulation through signaling: A predictive theory of allosteric induction; Cell Systems; Vol. 6; No. 4; https://doi.org/10.1016/j.cels.2018.02.004

• Mahmoudabadi, Gita; Phillips, Rob (2018) Research: A comprehensive and quantitative exploration of thousands of viral genomes eLife; Vol. 7; https://doi.org/10.7554/eLife.31955

• Chen, Yi-Ju; Wu, David et al. (2018) Two-Stage Dynamics of In Vivo Bacteriophage Genome Ejection Physical Review X; Vol. 8; No. 2; https://doi.org/10.1103/PhysRevX.8.021029

• Belliveau, Nathan M.; Barnes, Stephanie L. et al. (2018) A Systematic and Scalable Approach for Dissecting the Molecular Mechanisms of Transcriptional Regulation in Bacteria Biophysical Journal; Vol. 114; No. 3; In: 62nd Annual Meeting of the Biophysical-Society, 17-21 February 2018, San Francisco, CA https://doi.org/10.1016/j.bpj.2017.11.849

• Phillips, Rob (2018) Membrane Tension and the Charge State of Cells Biophysical Journal; Vol. 114; No. 3; In: 62nd Annual Meeting of the Biophysical-Society, February 17-21, 2018, San Francisco, CA https://doi.org/10.1016/j.bpj.2017.11.203

• Hirokawa, Soichi; Belliveau, Nathan M. et al. (2018) Skewing the Playing Field: A Single-Molecule Study on how RSS Sequence Influences Gene Segment Selection Biophysical Journal; Vol. 114; No. 3; In: 62nd Annual Meeting of the Biophysical-Society, February 17-21, 2018, San Francisco, CA https://doi.org/10.1016/j.bpj.2017.11.511

• Einav, Tal; Duque, Julia et al. (2018) Theoretical Analysis of Allosteric and Operator Binding for Cyclic-AMP Receptor Protein Mutants Biophysical Journal; Vol. 114; No. 3; In: 62nd Annual Meeting of the Biophysical-Society, February 17-21, 2018, San Francisco, CA https://doi.org/10.1016/j.bpj.2017.11.2330

• Culkin, Jamie; de Bruin, Lennart et al. (2017) The role of DNA sequence in nucleosome breathing European Physical Journal E; Vol. 40; No. 11; https://doi.org/10.1140/epje/i2017-11596-2

• Phillips, Rob (2017) Musings on mechanism: quest for a quark theory of proteins? FASEB Journal; Vol. 31; No. 10; https://doi.org/10.1096/fj.201700594

• Landman, Jasper; Brewster, Robert C. et al. (2017) Self-consistent theory of transcriptional control in complex regulatory architectures PLOS ONE; Vol. 12; No. 7; https://doi.org/10.1371/journal.pone.0179235

• Mahmoudabadi, Gita; Milo, Ron et al. (2017) Energetic cost of building a virus Proceedings of the National Academy of Sciences of the United States of America; Vol. 114; No. 22; https://doi.org/10.1073/pnas.1701670114

• Einav, Tal; Phillips, Rob (2017) Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants Journal of Physical Chemistry B; Vol. 121; No. 15; https://doi.org/10.1021/acs.jpcb.6b12672

• Finch, L.; Horii, C. V. et al. (2016) The great ideas of biology: Exploration through experimentation in an undergraduate lab course Molecular Biology of the Cell; Vol. 27; In: 2016 Annual Meeting of the American-Society-for-Cell-Biology (ASCB), 3-7 December 2016, San Francisco, CA https://resolver.caltech.edu/CaltechAUTHORS:20170331-134057165

• Einav, Tal; Mazutis, Linas et al. (2016) Statistical Mechanics of Allosteric Enzymes Journal of Physical Chemistry B; Vol. 120; No. 26; https://doi.org/10.1021/acs.jpcb.6b01911

• Mohapatra, Lishibanya; Goode, Bruce L. et al. (2016) Design Principles of Length Control of Cytoskeletal Structures Annual Review of Biophysics; Vol. 45; https://doi.org/10.1146/annurev-biophys-070915-094206

• Garcia, Hernan G.; Brewster, Robert C. et al. (2016) Using synthetic biology to make cells tomorrow's test tubes Integrative Biology; Vol. 8; No. 4; https://doi.org/10.1039/C6IB00006A

• Shamir, Maya; Bar-On, Yinon et al. (2016) SnapShot: Timescales in Cell Biology Cell; Vol. 164; No. 6; https://doi.org/10.1016/j.cell.2016.02.058

• Kreamer, Naomi N.; Phillips, Rob et al. (2015) Predicting the impact of promoter variability on regulatory outputs Scientific Reports; Vol. 5; https://doi.org/10.1038/srep18238

• Phillips, Rob (2015) Theory in Biology: Figure 1 or Figure 7? Trends in Cell Biology; Vol. 25; No. 12; https://doi.org/10.1016/j.tcb.2015.10.007

• Mulligan, Peter J.; Chen, Yi-Ju et al. (2015) Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics Biophysical Journal; Vol. 109; No. 3; https://doi.org/10.1016/j.bpj.2015.06.054

• Lovely, Geoffrey A.; Brewster, Robert C. et al. (2015) Single-molecule analysis of RAG-mediated V(D)J DNA cleavage Proceedings of the National Academy of Sciences of the United States of America; Vol. 112; No. 14; https://doi.org/10.1073/pnas.1503477112

• Phillips, Rob (2015) Napoleon Is in Equilibrium Annual Review of Condensed Matter Physics; Vol. 6; https://doi.org/10.1146/annurev-conmatphys-031214-014558

• Bialecka-Fornal, Maja; Lee, Heun Jin et al. (2015) The Rate of Osmotic Downshock Determines the Survival Probability of Bacterial Mechanosensitive Channel Mutants Journal of Bacteriology; Vol. 197; No. 1; https://doi.org/10.1128/JB.02175-14

• Rydenfelt, Mattias; Garcia, Hernan G. et al. (2014) The Influence of Promoter Architectures and Regulatory Motifs on Gene Expression in Escherichia coli PLoS ONE; Vol. 9; No. 12; https://doi.org/10.1371/journal.pone.0114347

• Jones, Daniel L.; Brewster, Robert C. et al. (2014) Promoter architecture dictates cell-to-cell variability in gene expression Science; Vol. 346; No. 6216; https://doi.org/10.1126/science.1255301

• Weinert, Franz M.; Brewster, Robert C. et al. (2014) Scaling of Gene Expression with Transcription-Factor Fugacity Physical Review Letters; Vol. 113; No. 25; https://doi.org/10.1103/PhysRevLett.113.258101

• Chen, Yi-Ju; Johnson, Stephanie et al. (2014) Modulation of DNA loop lifetimes by the free energy of loop formation Proceedings of the National Academy of Sciences of the United States of America; Vol. 111; No. 49; https://doi.org/10.1073/pnas.1415685111

• Flamholz, Avi; Phillips, Rob et al. (2014) The quantified cell Molecular Biology of the Cell; Vol. 25; No. 22; https://doi.org/10.1091/mbc.E14-09-1347

• Johnson, Stephanie; van de Meent, Jan-Willem et al. (2014) Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion Nucleic Acids Research; Vol. 42; No. 16; https://doi.org/10.1093/nar/gku563

• Razo-Mejia, M.; Boedicker, J. Q. et al. (2014) Comparison of the theoretical and real-world evolutionary potential of a genetic circuit Physical Biology; Vol. 11; No. 2; https://resolver.caltech.edu/CaltechAUTHORS:20140509-111341446

• Brewster, Robert C.; Weinert, Franz M. et al. (2014) The Transcription Factor Titration Effect Dictates Level of Gene Expression Cell; Vol. 156; No. 6; https://doi.org/10.1016/j.cell.2014.02.022

• Boedicker, James; Phillips, Rob (2014) Dissecting the Role of Ferrous Iron in Pseudomonas Aeruginosa Gene Regulation Biophysical Journal; Vol. 106; No. 2; In: 58th Annual Meeting of the Biophysical-Society, February 15-19, 2014, San Francisco, CA https://doi.org/10.1016/j.bpj.2013.11.2115

• Chen, Yi-Ju; Zhiyentayev, Timur et al. (2014) Dynamic Gene Expression and Design Principles of Viral Infection Pathway Biophysical Journal; Vol. 106; No. 2; In: 58th Annual Meeting of the Biophysical-Society, February 15-19, 2014, San Francisco, CA https://doi.org/10.1016/j.bpj.2013.11.2111

• Barnes, Stephanie; Jones, Daniel et al. (2014) Identification and Analysis of the Transcriptional Regulatory Networks Governing Mechanosensitive Channels in E. coli Biophysical Journal; Vol. 106; No. 2; In: 58th Annual Meeting of the Biophysical-Society, February 15-19, 2014, San Francisco, CA https://doi.org/10.1016/j.bpj.2013.11.4472

• Lindén, Martin; Johnson, Stephanie et al. (2014) Multiple Lac-Mediated Loops Revealed by Bayesian Statistics and Tethered Particle Motion Biophysical Journal; Vol. 106; No. 2; In: 58th Annual Meeting of the Biophysical-Society, February 15-19, 2014, San Francisco, CA https://doi.org/10.1016/j.bpj.2013.11.174

• Jones, Daniel L.; Brewster, Robert et al. (2014) Promoter Architecture Dictates Variability in Gene Expression Biophysical Journal; Vol. 106; No. 2; In: 58th Annual Meeting of the Biophysical-Society, February 15-19, 2014, San Francisco, CA https://doi.org/10.1016/j.bpj.2013.11.4481

• Lovely, Geoffrey; Lindén, Martin et al. (2014) Single Molecule Dynamics Governing the Initiation of V(D)J Recombination Biophysical Journal; Vol. 106; No. 2; In: 58th Annual Meeting of the Biophysical-Society, February 15-19, 2014, San Francisco, CA https://doi.org/10.1016/j.bpj.2013.11.3826

• Lee, Heun Jin; Bialecka-Fornal, Maja et al. (2014) The Rate of Osmotic Shock Determines Bacterial Survival Biophysical Journal; Vol. 106; No. 2; In: 58th Annual Meeting of the Biophysical-Society, February 15-19, 2014, San Francisco, CA https://doi.org/10.1016/j.bpj.2013.11.3084

• Weinert, Franz M.; Brewster, Robert C. et al. (2014) The Transcription Factor Titration Effect Dictates Level of Gene Expression Biophysical Journal; Vol. 106; No. 2; In: 58th Annual Meeting of the Biophysical-Society, February 15-19, 2014, San Francisco, CA https://doi.org/10.1016/j.bpj.2013.11.4483

• Brewster, Robert; Weinert, Franz et al. (2014) Time-Resolved Plasmid Counting by Way of Transcription Factor Sequestration Biophysical Journal; Vol. 106; No. 2; In: 58th Annual Meeting of the Biophysical-Society, February 15-19, 2014, San Francisco, CA https://doi.org/10.1016/j.bpj.2013.11.1606

• Rydenfelt, Mattias; Cox, Robert Sidney, III et al. (2014) Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration Physical Review E; Vol. 89; No. 1; https://doi.org/10.1103/PhysRevE.89.012702

• Ngo, Huu B.; Lovely, Geoffrey A. et al. (2014) Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation Nature Communications; Vol. 5; No. 1; https://doi.org/10.1038/ncomms4077

• Phillips, Rob (2013) The Feynman Lectures on Physics Nature; Vol. 504; No. 7478; https://doi.org/10.1038/504030a

• Boedicker, James Q.; Garcia, Hernan G. et al. (2013) DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation Physical Biology; Vol. 10; No. 6; https://doi.org/10.1088/1478-3975/10/6/066005

• Johnson, Stephanie; Chen, Yi-Ju et al. (2013) Poly(dA:dT)-Rich DNAs Are Highly Flexible in the Context of DNA Looping PLOS ONE; Vol. 8; No. 10; https://doi.org/10.1371/journal.pone.0075799

• Marzen, Sarah; Garcia, Hernan G. et al. (2013) Statistical Mechanics of Monod–Wyman–Changeux (MWC) Models Journal of Molecular Biology; Vol. 425; No. 9; https://doi.org/10.1016/j.jmb.2013.03.013

• Haselwandter, Christoph A.; Phillips, Rob (2013) Connection between Oligomeric State and Gating Characteristics of Mechanosensitive Ion Channels PLoS Computational Biology; Vol. 9; No. 5; https://doi.org/10.1371/journal.pcbi.1003055

• Haselwandter, Christoph A.; Phillips, Rob (2013) Directional interactions and cooperativity between mechanosensitive membrane proteins Europhysics Letters; Vol. 101; No. 6; https://doi.org/10.1209/0295-5075/101/68002

• Lindén, Martin; Johnson, Stephanie et al. (2013) Analysis of DNA Looping Kinetics in Tethered Particle Motion Experiments using Hidden Markov Models Biophysical Journal; Vol. 104; No. 2; In: 57th Annual Meeting of the Biophysical-Society, Feb. 02-06, 2013, Philadelphia, PA https://doi.org/10.1016/j.bpj.2012.11.2329

• Phillips, Rob (2013) Bacteria are Stressed Out Too: The Physics of Mechanosensation Biophysical Journal; Vol. 104; No. 2; In: 57th Annual Meeting of the Biophysical-Society, Feb. 02-06, 2013, Philadelphia, PA https://doi.org/10.1016/j.bpj.2012.11.072

• Boedicker, James Q.; Garcia, Hernan G. et al. (2013) Theoretical and Experimental Dissection of DNA Loop-Mediated Repression Physical Review Letters; Vol. 110; No. 1; https://doi.org/10.1103/PhysRevLett.110.018101

• Vale, Ronald D.; DeRisi, Joseph et al. (2012) Interdisciplinary Graduate Training in Teaching Labs Science; Vol. 338; No. 6114; https://doi.org/10.1126/science.1216570

• Brewster, Robert C.; Jones, Daniel L. et al. (2012) Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli PLoS Computational Biology; Vol. 8; No. 12; https://doi.org/10.1371/journal.pcbi.1002811

• Johnson, Stephanie; Lindén, Martin et al. (2012) Sequence Dependence of Transcription Factor-Mediated DNA Looping Nucleic Acids Research; Vol. 40; No. 16; https://doi.org/10.1093/nar/gks473

• Phillips, Rob (2012) A single-molecule view of protein action at a distance Protein Science; Vol. 21; No. S1; In: 26th Annual Symposium of the Protein-Society , Aug. 05-08, 2012 , San Diego, CA https://resolver.caltech.edu/CaltechAUTHORS:20120827-142257698

• Garcia, Hernan G.; Sanchez, Alvaro et al. (2012) Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria Cell Reports; Vol. 2; No. 1; https://doi.org/10.1016/j.celrep.2012.06.004

• Van Valen, David; Wu, David et al. (2012) A Single-Molecule Hershey-Chase Experiment Current Biology; Vol. 22; No. 14; https://doi.org/10.1016/j.cub.2012.05.023

• Bassereau, Patricia; Phillips, Rob et al. (2012) Focus on the physics of the cell membrane New Journal of Physics; Vol. 14; https://doi.org/10.1088/1367-2630/14/5/055021

• Bialecka-Fornal, Maja; Lee, Heun Jin et al. (2012) Single-Cell Census of Mechanosensitive Channels in Living Bacteria PLoS ONE; Vol. 7; No. 3; https://doi.org/10.1371/journal.pone.0033077

• Lindén, Martin; Sens, Pierre et al. (2012) Entropic Tension in Crowded Membranes PLoS Computational Biology; Vol. 8; No. 3; https://doi.org/10.1371/journal.pcbi.1002431

• Ursell, Tristan; Agrawal, Ashutosh et al. (2011) Lipid Bilayer Mechanics in a Pipette with Glass-Bilayer Adhesion Biophysical Journal; Vol. 101; No. 8; https://doi.org/10.1016/j.bpj.2011.08.057

• Haswell, Elizabeth S.; Phillips, Rob et al. (2011) Mechanosensitive Channels: What Can They Do and How Do They Do It? Structure; Vol. 19; No. 10; https://doi.org/10.1016/j.str.2011.09.005

• Phillips, Rob (2011) Jonathan Widom (1955–2011) Nature; Vol. 476; No. 7361; https://doi.org/10.1038/476400a

• Garcia, Hernan G.; Lee, Heun Jin et al. (2011) Comparison and Calibration of Different Reporters for Quantitative Analysis of Gene Expression Biophysical Journal; Vol. 101; No. 3; https://doi.org/10.1016/j.bpj.2011.06.026

• Garcia, Hernan G.; Phillips, Rob (2011) Quantitative dissection of the simple repression input–output function Proceedings of the National Academy of Sciences of the United States of America; Vol. 108; No. 29; https://doi.org/10.1073/pnas.1015616108

• Amit, Roee; Garcia, Hernan G. et al. (2011) Building Enhancers from the Ground Up: A Synthetic Biology Approach Cell; Vol. 146; No. 1; https://doi.org/10.1016/j.cell.2011.06.024

• Tadmor, Arbel D.; Ottesen, Elizabeth A. et al. (2011) Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR Science; Vol. 333; No. 6038; https://doi.org/10.1126/science.1200758

• Haselwandter, Christoph A.; Phillips, Rob (2011) Elastic energy of polyhedral bilayer vesicles Physical Review E; Vol. 83; No. 6; https://doi.org/10.1103/PhysRevE.83.061901

• Sanchez, Alvaro; Garcia, Hernan G. et al. (2011) Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression PLoS Computational Biology; Vol. 7; No. 3; https://doi.org/10.1371/journal.pcbi.1001100

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• Haselwandter, Christoph A.; Phillips, Rob (2010) Minimal Bending Energies of Bilayer Polyhedra Physical Review Letters; Vol. 105; No. 22; https://doi.org/10.1103/PhysRevLett.105.228101

• Pressé, S.; Ghosh, K. et al. (2010) Dynamical fluctuations in biochemical reactions and cycles Physical Review E; Vol. 82; No. 3; https://doi.org/10.1103/PhysRevE.82.031905

• Wu, David; Van Valen, David et al. (2010) Ion-Dependent Dynamics of DNA Ejections for Bacteriophage λ Biophysical Journal; Vol. 99; No. 4; https://doi.org/10.1016/j.bpj.2010.06.024

• Phillips, Rob; Milo, Ron (2009) A feeling for the numbers in biology Proceedings of the National Academy of Sciences of the United States of America; Vol. 106; No. 51; https://doi.org/10.1073/pnas.0907732106

• Ridgeway, William K.; Seitaridou, Effrosyni et al. (2009) RNA-protein binding kinetics in an automated microfluidic reactor Nucleic Acids Research; Vol. 37; No. 21; https://doi.org/10.1093/nar/gkp733

• Ridgeway, William K.; Seitaridou, Effrosyni et al. (2009) RNA–protein binding kinetics in an automated microfluidic reactor Nucleic Acids Research; Vol. 37; No. 21; https://doi.org/10.1093/nar/gkp733

• Ursell, Tristan S.; Klug, William S. et al. (2009) Morphology and interaction between lipid domains Proceedings of the National Academy of Sciences of the United States of America; Vol. 106; No. 32; https://doi.org/10.1073/pnas.0903825106

• Wu, David; Ghosh, Kingshuk et al. (2009) Trajectory Approach to Two-State Kinetics of Single Particles on Sculpted Energy Landscapes Physical Review Letters; Vol. 103; No. 5; https://doi.org/10.1103/PhysRevLett.103.050603

• Peterson, Eric L.; Kondev, Jané et al. (2009) Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment Bioinformatics; Vol. 25; No. 11; https://doi.org/10.1093/bioinformatics/btp164

• Towles, Kevin B.; Beausang, John F et al. (2009) First-principles calculation of DNA looping in tethered particle experiments Physical Biology; Vol. 6; No. 2; https://doi.org/10.1088/1478-3975/6/2/025001

• Han, Lin; Garcia, Hernan G. et al. (2009) Concentration and Length Dependence of DNA Looping in Transcriptional Regulation PLoS ONE; Vol. 4; No. 5; https://doi.org/10.1371/journal.pone.0005621

• Phillips, Rob; Ursell, Tristan et al. (2009) Emerging roles for lipids in shaping membrane-protein function Nature; Vol. 459; No. 7245; https://doi.org/10.1038/nature08147

• Van Valen, David; Haataja, Mikko et al. (2009) Biochemistry on a Leash: The Roles of Tether Length and Geometry in Signal Integration Proteins Biophysical Journal; Vol. 96; No. 4; https://doi.org/10.1016/j.bpj.2008.10.052

• Lee, Heun Jin; Peterson, Eric-L et al. (2008) Membrane shape as a reporter for applied forces Proceedings of the National Academy of Sciences of the United States of America; Vol. 105; No. 49; https://doi.org/10.1073/pnas.0806814105

• Reeves, Daniel; Ursell, Tristan et al. (2008) Membrane mechanics as a probe of ion-channel gating mechanisms Physical Review E; Vol. 78; No. 4; https://doi.org/10.1103/PhysRevE.78.041901

• Grayson, Paul; Han, Lin et al. (2007) Real-time observations of single bacteriophage λ DNA ejections in vitro Proceedings of the National Academy of Sciences of the United States of America; Vol. 104; No. 37; https://resolver.caltech.edu/CaltechAUTHORS:GRApnas07

• Ursell, Tristan; Huang, Kerwin Casey et al. (2007) Cooperative Gating and Spatial Organization of Membrane Proteins through Elastic Interactions PLOS Computational Biology; Vol. 3; No. 5; https://doi.org/10.1371/journal.pcbi.0030081

• Seitaridou, Effrosyni; Inamdar, Mandar M. et al. (2007) Measuring Flux Distributions for Diffusion in the Small-Numbers Limit Journal of Physical Chemistry B; Vol. 111; No. 9; https://doi.org/10.1021/jp067036j

• Garcia, Hernan G.; Grayson, Paul et al. (2007) Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity Biopolymers; Vol. 85; No. 2; https://doi.org/10.1002/bip.20627

• Wiggins, Paul A.; van der Heijden, Thijn et al. (2006) High flexibility of DNA on short length scales probed by atomic force microscopy Nature Nanotechnology; Vol. 1; No. 2; https://doi.org/10.1038/nnano.2006.63

• Grayson, Paul; Evilevitch, Alex et al. (2006) The effect of genome length on ejection forces in bacteriophage lambda Virology; Vol. 348; No. 2; https://doi.org/10.1016/j.virol.2006.01.003

• Phillips, Rob; Quake, Stephen R. (2006) The Biological Frontier of Physics Physics Today; Vol. 59; No. 5; https://resolver.caltech.edu/CaltechAUTHORS:PHIpt06

• Segall, Darren E.; Nelson, Philip C. et al. (2006) Volume-exclusion effects in tethered-particle experiments: bead size matters Physical Review Letters; Vol. 96; No. 8; https://doi.org/10.1103/PhysRevLett.96.088306

• Dupuy, L. M.; Tadmor, E. B. et al. (2005) Finite-Temperature Quasicontinuum: Molecular Dynamics without All the Atoms Physical Review Letters; Vol. 95; No. 6; https://doi.org/10.1103/PhysRevLett.95.060202

• Wiggins, Paul A.; Phillips, Rob et al. (2005) Exact theory of kinkable elastic polymers Physical Review E; Vol. 71; No. 2; https://doi.org/10.1103/PhysRevE.71.021909

• Olmsted, David L.; Phillips, Rob et al. (2004) Modelling diffusion in crystals under high internal stress gradients Modelling and Simulation in Materials Science and Engineering; Vol. 12; No. 5; https://doi.org/10.1088/0965-0393/12/5/003

• Wiggins, Paul; Phillips, Rob (2004) Analytic models for mechanotransduction: gating a mechanosensitive channel Proceedings of the National Academy of Sciences of the United States of America; Vol. 101; No. 12; https://resolver.caltech.edu/CaltechAUTHORS:WIGpnas04

• Purohit, Prashant K.; Kondev, Jané et al. (2003) Force steps during viral DNA packaging? Journal of the Mechanics and Physics of Solids; Vol. 51; No. 11-12; https://doi.org/10.1016/j.jmps.2003.09.016

• Purohit, Prashant K.; Kondev, Jané et al. (2003) Mechanics of DNA packaging in viruses Proceedings of the National Academy of Sciences of the United States of America; Vol. 100; No. 6; https://resolver.caltech.edu/CaltechAUTHORS:PURpnas03

• Phillips, Rob; Dittrich, ­Markus et al. (2002) Quasicontinuum representations of atomic-scale mechanics: From proteins to dislocations Annual Review of Materials Research; Vol. 32; https://doi.org/10.1146/annurev.matsci.32.122001.102202

• Kraft, O.; Freund, L. B. et al. (2002) Dislocation plasticity in thin metal films MRS Bulletin; Vol. 27; No. 1; https://doi.org/10.1557/mrs2002.17

• Olmsted, David L.; Hardikar, Kedar Y. et al. (2001) Lattice resistance and Peierls stress in finite size atomistic dislocation simulations Modelling and Simulation in Materials Science and Engineering; Vol. 9; No. 3; https://doi.org/10.1088/0965-0393/9/3/308

• Tadmor, E. B.; Phillips, R. et al. (2000) Hierarchical modeling in the mechanics of materials International Journal of Solids and Structures; Vol. 37; No. 1-2; https://doi.org/10.1016/S0020-7683(99)00095-5

• Phillips, Rob; Rodney, David et al. (1999) Hierarchical models of plasticity: dislocation nucleation and interaction Modelling and Simulation in Materials Science and Engineering; Vol. 7; No. 5; https://doi.org/10.1088/0965-0393/7/5/309

• Shenoy, V. B.; Ortiz, M. et al. (1999) The atomistic structure and energy of nascent dislocation loops Modelling and Simulation in Materials Science and Engineering; Vol. 7; No. 4; https://doi.org/10.1088/0965-0393/7/4/309

• Tadmor, E.B.; Miller, R. et al. (1999) Nanoindentation and incipient plasticity Journal of Materials Research; Vol. 14; No. 6; https://resolver.caltech.edu/CaltechAUTHORS:TADjmr99

• Miller, Ron; Phillips, Rob et al. (1998) A non-local formulation of the Peierls dislocation model Journal of the Mechanics and Physics of Solids; Vol. 46; No. 10; https://doi.org/10.1016/S0022-5096(98)00057-X

• Miller, R.; Ortiz, M. et al. (1998) Quasicontinuum models of fracture and plasticity Engineering Fracture Mechanics; Vol. 61; No. 3-4; https://doi.org/10.1016/S0013-7944(98)00047-2

• Miller, R.; Tadmor, E. B. et al. (1998) Quasicontinuum simulation of fracture at the atomic scale Modelling and Simulation in Materials Science and Engineering; Vol. 6; No. 5; https://doi.org/10.1088/0965-0393/6/5/008

• Shenoy, V. B.; Miller, R. et al. (1998) Quasicontinuum Models of Interfacial Structure and Deformation Physical Review Letters; Vol. 08; No. 4; https://doi.org/10.1103/PhysRevLett.80.742

• Tadmor, E. B.; Phillips, Rob et al. (1996) Mixed Atomistic and Continuum Models of Deformation in Solids Langmuir; Vol. 12; No. 19; In: Workshop on Physical and Chemical Mechanisms in Tribology, August 27-September 1, 1995, Bar Harbor, ME https://doi.org/10.1021/la9508912

• Tadmor, E. B.; Ortiz, M. et al. (1996) Quasicontinuum analysis of defects in solids Philosophical Magazine A; Vol. 73; No. 6; https://doi.org/10.1080/01418619608243000