Phillips, Rob
Mahmoudabadi, Gita and Homyk, Kelsey, et el. (2024) Machine learning models can identify individuals based on a resident oral bacteriophage family ; Frontiers in Microbiomes; Vol. 3; 1408203; 10.3389/frmbi.2024.1408203
Flamholz, Avi I. and Goyal, Akshit, et el. (2024) The proteome is a terminal electron acceptor ; PMCID PMC10862836; 10.1101/2024.01.31.578293
Hueschen, Christina L. and Dunn, Alexander R., et el. (2023) Wildebeest herds on rolling hills: Flocking on arbitrary curved surfaces ; Physical Review E; Vol. 108; No. 2; 024610; 10.1103/physreve.108.024610
Choe, Mangyu and Einav, Tal, et el. (2023) Data-driven model of glycolysis identifies the role of allostery in maintaining ATP homeostasis ; 10.1101/2022.12.28.522046
Banks, Rachel A. and Galstyan, Vahe, et el. (2023) Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies ; eLife; Vol. 12; Art. No. e79402; PMCID PMC10014072; 10.7554/elife.79402
Suresh, Pooja and Galstyan, Vahe, et el. (2022) Modeling and mechanical perturbations reveal how spatially regulated anchorage gives rise to spatially distinct mechanics across the mammalian spindle ; eLife; Vol. 11; Art. No. e79558; PMCID PMC9642996; 10.7554/elife.79558
Chure, Griffin and Banks, Rachel A., et el. (2022) Anthroponumbers.org: A quantitative database of human impacts on Planet Earth ; Patterns; Vol. 3; No. 9; Art. No. 100552; PMCID PMC9481956; 10.1016/j.patter.2022.100552
Hueschen, Christina L. and Dunn, Alexander R., et el. (2022) Wildebeest Herds on Rolling Hills: Flocking on Arbitrary Curved Surfaces ; 10.1101/2022.06.22.497052
Hueschen, Christina L. and Segev Zarko, Li-av, et el. (2022) Emergent Actin Flows Explain Diverse Parasite Gliding Modes ; 10.1101/2022.06.08.495399
Suresh, Pooja and Galstyan, Vahe, et el. (2022) Modeling and mechanical perturbations reveal how spatially regulated anchorage gives rise to spatially distinct mechanics across the mammalian spindle ; 10.1101/2022.04.08.487649
Chure, Griffin and Banks, Rachel A., et el. (2022) Anthroponumbers.org: A Quantitative Database Of Human Impacts on Planet Earth ; 10.1101/2022.03.04.483053
Salmon, Gabe and Phillips, Rob (2022) Reproducibility, stochasticity, and geometry in a lattice of cross-feeding microbial cells ; Biophysical Journal; Vol. 121; No. 3; 120a; 10.1016/j.bpj.2021.11.2086
Larios, David A. and Phillips, Rob, et el. (2022) Reconstituting the nonequilibrium biophysics of the LECA cytoskeleton in active matter ; Biophysical Journal; Vol. 121; No. 3; 521a; 10.1016/j.bpj.2021.11.2744
Suresh, Pooja and Galstyan, Vahe, et el. (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; 448a-449a; 10.1016/j.bpj.2021.11.536
Duarte, Ana I. and Jin Lee, Heun, et el. (2022) Measuring energy consumption through space and time in an active matter system of cytoskeletal motors and filaments ; Biophysical Journal; Vol. 121; No. 3; 521a-522a; 10.1016/j.bpj.2021.11.2745
Hueschen, Christina and Segev Zarko, Li-av, et el. (2022) Distinct self-organized actin patterns explain diverse parasite gliding modes ; Biophysical Journal; Vol. 121; No. 3; 314a; 10.1016/j.bpj.2021.11.1183
Tadmor, Arbel D. and 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; 631-647; PMCID PMC10060711; 10.1093/bioinformatics/btab703
Banks, Rachel A. and Galstyan, Vahe, et el. (2021) Motor processivity and speed determine structure and dynamics of microtubule-motor assemblies ; 10.1101/2021.10.22.465381
Hueschen, Christina and Segev Zarko, Li-Av, et el. (2021) Actin Organization and Dynamics in Motile Toxoplasma Gondii Parasites ; American Journal of Tropical Medicine and Hygiene; Vol. 105; No. 5; 448-449; 10.4269/ajtmh.abstract2021
Belliveau, Nathan M. and Chure, Griffin, et el. (2021) Fundamental limits on the rate of bacterial growth and their influence on proteomic composition ; Cell Systems; Vol. 12; No. 9; 924-944; PMCID PMC8460600; 10.1016/j.cels.2021.06.002
Qu, Zijie and Schildknecht, Dominik, et el. (2021) Persistent fluid flows defined by active matter boundaries ; Communications Physics; Vol. 4; Art. No. 198; 10.1038/s42005-021-00703-3
Sender, Ron and Bar-On, Yinon M., et el. (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; Art. No. e2024815118; PMCID PMC8237675; 10.1073/pnas.2024815118
Phillips, Rob (2021) Schrödinger's What Is Life? at 75 ; Cell Systems; Vol. 12; No. 6; 465-476; 10.1016/j.cels.2021.05.013
Chure, Griffin and Banks, Rachel A., et el. (2021) The Anthropocene by the Numbers: A Quantitative Snapshot of Humanity's Influence on the Planet ; 10.48550/arXiv.2101.09620
Qu, Zijie and Jiang, Jialong, et el. (2021) Programming Boundary Deformation Patterns in Active Networks ; 10.48550/arXiv.2101.08464
Galstyan, Vahe and Suresh, Pooja, et el. (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; 347A; 10.1016/j.bpj.2020.11.2158
Morrison, Muir and Razo-Mejia, Manuel, et el. (2021) Reconciling kinetic and thermodynamic models of bacterial transcription ; PLOS Computational Biology; Vol. 17; No. 1; Art. No. e1008572; PMCID PMC7845990; 10.1371/journal.pcbi.1008572
Yu, Timothy C. and Liu, Winnie L., et el. (2021) Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems ; Nature Communications; Vol. 12; Art. No. 325; PMCID PMC7804116; 10.1038/s41467-020-20094-3
Galstyan, Vahe and Husain, Kabir, et el. (2020) Proofreading through spatial gradients ; eLife; Vol. 9; Art. No. e60415; 10.7554/eLife.60415
Ireland, William T. and Beeler, Suzannah M., et el. (2020) Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time ; eLife; Vol. 2020; No. 9; Art. No. e55308; PMCID PMC7567609; 10.7554/eLife.55308
Razo-Mejia, Manuel and Marzen, Sarah, et el. (2020) First-principles prediction of the information processing capacity of a simple genetic circuit ; Physical Review E; Vol. 102; No. 2; Art. No. 022404; 10.1103/PhysRevE.102.022404
Hirokawa, Soichi and Chure, Griffin, et el. (2020) Sequence-Dependent Dynamics of Synthetic and Endogenous RSSs in V(D)J Recombination ; Nucleic Acids Research; Vol. 48; No. 12; 6726-6739; PMCID PMC7337519; 10.1093/nar/gkaa418
Laxhuber, Kathrin S. and Morrison, Muir J., et el. (2020) Theoretical investigation of a genetic switch for metabolic adaptation ; PLoS ONE; Vol. 15; No. 5; Art. No. e0226453; PMCID PMC7205307; 10.1371/journal.pone.0226453
Bar-On, Yinon M. and Flamholz, Avi, et el. (2020) SARS-CoV-2 (COVID-19) by the numbers ; eLife; Vol. 9; Art. No. e57309; PMCID PMC7224694; 10.7554/elife.57309
Salmon, Gabe and Phillips, Rob (2020) Modeling Microbial Interactions across Nutritional Environments using Maximum Entropy ; Biophysical Journal; Vol. 118; No. 3; 347a; 10.1016/j.bpj.2019.11.2004
McCarty, Nicholas S. and Razo-Mejia, Manuel, et el. (2020) Genetic Barcodes Enable Quantitative Mapping of Operator Mutants to Gene Expression ; Biophysical Journal; Vol. 118; No. 3; 611a; 10.1016/j.bpj.2019.11.3298
Chure, Griffin and Phillips, Rob (2020) The Molecular Biophysics of Adaptation ; Biophysical Journal; Vol. 118; No. 3; 545a; 10.1016/j.bpj.2019.11.2983
Galstyan, Vahe and Husain, Kabir, et el. (2020) Kinetic Proofreading using Substrate Gradients and Enzyme Diffusion ; Biophysical Journal; Vol. 118; No. 3; 573a-574a; 10.1016/j.bpj.2019.11.3118
Phillips, Rob (2020) Schrodinger's "What is Life" At 75: The Physical Aspects of the Living Cell Revisited ; Biophysical Journal; Vol. 118; No. 3; 2a; 10.1016/j.bpj.2019.11.204
Banks, Rachel and Lee, Heun Jin, et el. (2020) Bridging Kinesin Properties with System-scale Characteristics of Microtubule-Motor Assemblies ; Biophysical Journal; Vol. 118; No. 3; 176a-177a; 10.1016/j.bpj.2019.11.1081
Einav, Tal and Yazdi, Shahrzad, et el. (2020) Harnessing Avidity: Quantifying Entropic and Energetic Effects of Linker Length and Rigidity Required for Multivalent Binding of Antibodies to HIV-1 Spikes ; 10.1101/406454
Galstyan, Vahe and Phillips, Rob (2019) Allostery and Kinetic Proofreading ; Journal of Physical Chemistry B; Vol. 123; No. 51; 10990-11002; PMCID PMC6995354; 10.1021/acs.jpcb.9b08380
Chure, Griffin and Kaczmarek, Zofii A., et el. (2019) Physiological Adaptability and Parametric Versatility in a Simple Genetic Circuit
Einav, Tal and Yazdi, Shahrzad, et el. (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; 466-474; PMCID PMC6892280; 10.1016/j.cels.2019.09.007
Chure, Griffin and Razo-Mejia, Manuel, et el. (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; 18275-18284; PMCID PMC6744869; 10.1073/pnas.1907869116
Ross, Tyler D. and Lee, Heun Jin, et el. (2019) Controlling Organization and Forces in Active Matter Through Optically-Defined Boundaries ; Nature; Vol. 572; No. 7768; 224-229; PMCID PMC6719720; 10.1038/s41586-019-1447-1
Einav, Tal and 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; 13340-13345; PMCID PMC6613100; 10.1073/pnas.1905615116
Wadhwa, Navish and Phillips, Rob, et el. (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; 11764-11769; PMCID PMC6576217; 10.1073/pnas.1904577116
Mahmoudabadi, Gita and Phillips, Rob, et el. (2019) Defining the Energetic Costs of Cellular Structures ; 10.1101/666040
Chure, Griffin and Razo-Mejia, Manuel, et el. (2019) The Energetics of Molecular Adaptation in Transcriptional Regulation ; 10.48550/arXiv.1905.06360
Phillips, Rob and Belliveau, Nathan M., et el. (2019) Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression ; Annual Review of Biophysics; Vol. 48; 121-163; 10.1146/annurev-biophys-052118-115525
Galstyan, Vahe and Funk, Luke, et el. (2019) Combinatorial Control through Allostery ; Journal of Physical Chemistry B; Vol. 123; No. 13; 2792-2800; PMCID PMC6467274; 10.1021/acs.jpcb.8b12517
Foster, Peter J. and Razo-Mejia, Manuel, et el. (2019) Measuring the Energetic Costs of Embryonic Development ; Developmental Cell; Vol. 48; No. 5; 591-592; 10.1016/j.devcel.2019.02.016
Hueschen, Christina L. and Galstyan, Vahe, et el. (2019) Microtubule End-Clustering Maintains a Steady-State Spindle Shape ; Current Biology; Vol. 29; No. 4; 700-708; PMCID PMC6383811; 10.1016/j.cub.2019.01.016
Barnes, Stephanie L. and Belliveau, Nathan M., et el. (2019) Mapping DNA sequence to transcription factor binding energy in vivo ; PLoS Computational Biology; Vol. 15; No. 2; Art. No. e1006226; PMCID PMC6375646; 10.1371/journal.pcbi.1006226
Mahmoudabadi, Gita and Homyk, Kelsey, et el. (2019) Human Phageprints: A high-resolution exploration of oral phages reveals globally-distributed phage families with individual-specific and temporally-stable community compositions ; 10.1101/516864
Forcier, Talitha L. and Ayaz, Andalus, et el. (2018) Measuring cis-regulatory energetics in living cells using allelic manifolds ; eLife; Vol. 7; Art. No. e40618; 10.7554/eLife.40618
Einav, Tal and Gnanapragasam, Priyanthi N. P., et el. (2018) Modeling Entropic and Energetic Effects of Linker Length and Rigidity within Synthetic HIV-1 Antibodies designed to Bind Bivalently to Env Spikes ; 10.1101/406454
Chure, Griffin and Lee, Heun Jin, et el. (2018) Connecting the dots between mechanosensitive channel abundance, osmotic shock, and survival at single-cell resolution ; Journal of Bacteriology; Vol. 200; No. 23; Art. No. e00460-18; PMCID PMC6222198; 10.1128/jb.00460-18
Forcier, Talitha and Ayaz, Andalus, et el. (2018) Precision measurement of cis-regulatory energetics in living cells ; 10.1101/380972
Galimidi, Rachel P. and Einav, Tal, et el. (2018) Quantifying the Entropic and Energetic Effects of Linker Length and Rigidity within Synthetic HIV-1 Antibodies designed to Bind Bivalently to Env Spikes ; 10.1101/406454
Einav, Tal and Duque, Julia, et el. (2018) Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants ; PLoS ONE; Vol. 13; No. 9; Art. No. e0204275; PMCID PMC6157895; 10.1371/journal.pone.0204275
Phillips, Rob (2018) Membranes by the Numbers ; 10.48550/arXiv.1703.02066
Bar-On, Yinon M. and Phillips, Rob, et el. (2018) The biomass distribution on Earth ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 115; No. 25; 6506-6511; PMCID PMC6016768; 10.1073/pnas.1711842115
Belliveau, Nathan M. and Barnes, Stephanie L., et el. (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; E4796-E4805; PMCID PMC6003448; 10.1073/pnas.1722055115
Razo-Mejia, Manuel and Barnes, Stephanie L., et el. (2018) Tuning transcriptional regulation through signaling: A predictive theory of allosteric induction ; Cell Systems; Vol. 6; No. 4; 456-469; PMCID PMC5991102; 10.1016/j.cels.2018.02.004
Mahmoudabadi, Gita and Phillips, Rob (2018) Research: A comprehensive and quantitative exploration of thousands of viral genomes ; eLife; Vol. 7; Art. No. e31955; PMCID PMC5908442; 10.7554/eLife.31955
Chen, Yi-Ju and Wu, David, et el. (2018) Two-Stage Dynamics of In Vivo Bacteriophage Genome Ejection ; Physical Review X; Vol. 8; No. 2; Art. No. 021029; 10.1103/PhysRevX.8.021029
Einav, Tal and Duque, Julia, et el. (2018) Theoretical Analysis of Allosteric and Operator Binding for Cyclic-AMP Receptor Protein Mutants ; Biophysical Journal; Vol. 114; No. 3; 420A-421A; 10.1016/j.bpj.2017.11.2330
Hirokawa, Soichi and Belliveau, Nathan M., et el. (2018) Skewing the Playing Field: A Single-Molecule Study on how RSS Sequence Influences Gene Segment Selection ; Biophysical Journal; Vol. 114; No. 3; 86a; 10.1016/j.bpj.2017.11.511
Phillips, Rob (2018) Membrane Tension and the Charge State of Cells ; Biophysical Journal; Vol. 114; No. 3; 29a; 10.1016/j.bpj.2017.11.203
Belliveau, Nathan M. and Barnes, Stephanie L., et el. (2018) A Systematic and Scalable Approach for Dissecting the Molecular Mechanisms of Transcriptional Regulation in Bacteria ; Biophysical Journal; Vol. 114; No. 3; 151A; 10.1016/j.bpj.2017.11.849
Culkin, Jamie and de Bruin, Lennart, et el. (2017) The role of DNA sequence in nucleosome breathing ; European Physical Journal E; Vol. 40; No. 11; Art. No. 106; PMCID PMC7001874; 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; 4207-4215; 10.1096/fj.201700594
Landman, Jasper and Brewster, Robert C., et el. (2017) Self-consistent theory of transcriptional control in complex regulatory architectures ; PLOS ONE; Vol. 12; No. 7; Art. No. e0179235; PMCID PMC5501422; 10.1371/journal.pone.0179235
Razo-Mejia, Manuel and Barnes, Stephanie L., et el. (2017) An allosteric theory of transcription factor induction ; 10.1101/111013
Mahmoudabadi, Gita and Milo, Ron, et el. (2017) Energetic cost of building a virus ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 114; No. 22; E4324-E4333; PMCID PMC5465929; 10.1073/pnas.1701670114
Einav, Tal and Phillips, Rob (2017) Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants ; Journal of Physical Chemistry B; Vol. 121; No. 15; 3813-3824; PMCID PMC5551692; 10.1021/acs.jpcb.6b12672
Finch, L. and Horii, C. V., et el. (2016) The great ideas of biology: Exploration through experimentation in an undergraduate lab course ; Molecular Biology of the Cell; Vol. 27; Art. No. P830
Einav, Tal and Mazutis, Linas, et el. (2016) Statistical Mechanics of Allosteric Enzymes ; Journal of Physical Chemistry B; Vol. 120; No. 26; 6021-6037; PMCID PMC5452729; 10.1021/acs.jpcb.6b01911
Mohapatra, Lishibanya and Goode, Bruce L., et el. (2016) Design Principles of Length Control of Cytoskeletal Structures ; Annual Review of Biophysics; Vol. 45; 85-116; PMCID PMC5466818; 10.1146/annurev-biophys-070915-094206
Garcia, Hernan G. and Brewster, Robert C., et el. (2016) Using synthetic biology to make cells tomorrow's test tubes ; Integrative Biology; Vol. 8; No. 4; 431-450; PMCID PMC4837077; 10.1039/C6IB00006A
Shamir, Maya and Bar-On, Yinon, et el. (2016) SnapShot: Timescales in Cell Biology ; Cell; Vol. 164; No. 6; 1302-1302.e1; 10.1016/j.cell.2016.02.058
Kreamer, Naomi N. and Phillips, Rob, et el. (2015) Predicting the impact of promoter variability on regulatory outputs ; Scientific Reports; Vol. 5; Art. No. 18238; PMCID PMC4682146; 10.1038/srep18238
Phillips, Rob (2015) Theory in Biology: Figure 1 or Figure 7? ; Trends in Cell Biology; Vol. 25; No. 12; 723-729; PMCID PMC4666001; 10.1016/j.tcb.2015.10.007
Mulligan, Peter J. and Chen, Yi-Ju, et el. (2015) Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics ; Biophysical Journal; Vol. 109; No. 3; 618-629; 10.1016/j.bpj.2015.06.054
Lovely, Geoffrey A. and Brewster, Robert C., et el. (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; E1715-E1723; PMCID PMC4394307; 10.1073/pnas.1503477112
Phillips, Rob (2015) Napoleon Is in Equilibrium ; Annual Review of Condensed Matter Physics; Vol. 6; 85-111; PMCID PMC4946674; 10.1146/annurev-conmatphys-031214-014558
Tadmor, Arbel D. and Phillips, Rob (2015) Host-Virus Interaction: From Metagenomics to Single-Cell Genomics ; ISBN 978-1-4899-7477-8; Encyclopedia of Metagenomics; 257-265; 10.1007/978-1-4899-7478-5_792
Bialecka-Fornal, Maja and Lee, Heun Jin, et el. (2015) The Rate of Osmotic Downshock Determines the Survival Probability of Bacterial Mechanosensitive Channel Mutants ; Journal of Bacteriology; Vol. 197; No. 1; 231-237; PMCID PMC4288683; 10.1128/JB.02175-14
Rydenfelt, Mattias and Garcia, Hernan G., et el. (2014) The Influence of Promoter Architectures and Regulatory Motifs on Gene Expression in Escherichia coli ; PLoS ONE; Vol. 9; No. 12; Art. No. e114347; PMCID PMC4280137; 10.1371/journal.pone.0114347
Jones, Daniel L. and Brewster, Robert C., et el. (2014) Promoter architecture dictates cell-to-cell variability in gene expression ; Science; Vol. 346; No. 6216; 1533-1536; PMCID PMC4388425; 10.1126/science.1255301
Weinert, Franz M. and Brewster, Robert C., et el. (2014) Scaling of Gene Expression with Transcription-Factor Fugacity ; Physical Review Letters; Vol. 113; No. 25; Art. No. 258101; PMCID PMC4386862; 10.1103/PhysRevLett.113.258101
Chen, Yi-Ju and Johnson, Stephanie, et el. (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; 17396-17401; PMCID PMC4267329; 10.1073/pnas.1415685111
Flamholz, Avi and Phillips, Rob, et el. (2014) The quantified cell ; Molecular Biology of the Cell; Vol. 25; No. 22; 3497-3500; PMCID PMC4230611; 10.1091/mbc.E14-09-1347
Johnson, Stephanie and van de Meent, Jan-Willem, et el. (2014) Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion ; Nucleic Acids Research; Vol. 42; No. 16; 10265-10277; PMCID PMC4176382; 10.1093/nar/gku563
Razo-Mejia, M. and Boedicker, J. Q., et el. (2014) Comparison of the theoretical and real-world evolutionary potential of a genetic circuit ; Physical Biology; Vol. 11; No. 2; Art. No. 026005; PMCID PMC4051709; 10.1088/1478-3975/11/2/026005
Brewster, Robert C. and Weinert, Franz M., et el. (2014) The Transcription Factor Titration Effect Dictates Level of Gene Expression ; Cell; Vol. 156; No. 6; 1312-1323; PMCID PMC4080642; 10.1016/j.cell.2014.02.022
Lindén, Martin and Johnson, Stephanie, et el. (2014) Multiple Lac-Mediated Loops Revealed by Bayesian Statistics and Tethered Particle Motion ; Biophysical Journal; Vol. 106; No. 2; 22A; 10.1016/j.bpj.2013.11.174
Weinert, Franz M. and Brewster, Robert C., et el. (2014) The Transcription Factor Titration Effect Dictates Level of Gene Expression ; Biophysical Journal; Vol. 106; No. 2; 489A; 10.1016/j.bpj.2013.11.4483
Brewster, Robert and Weinert, Franz, et el. (2014) Time-Resolved Plasmid Counting by Way of Transcription Factor Sequestration ; Biophysical Journal; Vol. 106; No. 2; 274A; 10.1016/j.bpj.2013.11.1606
Jones, Daniel L. and Brewster, Robert, et el. (2014) Promoter Architecture Dictates Variability in Gene Expression ; Biophysical Journal; Vol. 106; No. 2; 489A; 10.1016/j.bpj.2013.11.4481
Lee, Heun Jin and Bialecka-Fornal, Maja, et el. (2014) The Rate of Osmotic Shock Determines Bacterial Survival ; Biophysical Journal; Vol. 106; No. 2; 554A; 10.1016/j.bpj.2013.11.3084
Chen, Yi-Ju and Zhiyentayev, Timur, et el. (2014) Dynamic Gene Expression and Design Principles of Viral Infection Pathway ; Biophysical Journal; Vol. 106; No. 2; 373A; 10.1016/j.bpj.2013.11.2111
Boedicker, James and Phillips, Rob (2014) Dissecting the Role of Ferrous Iron in Pseudomonas Aeruginosa Gene Regulation ; Biophysical Journal; Vol. 106; No. 2; 374A; 10.1016/j.bpj.2013.11.2115
Lovely, Geoffrey and Lindén, Martin, et el. (2014) Single Molecule Dynamics Governing the Initiation of V(D)J Recombination ; Biophysical Journal; Vol. 106; No. 2; 692A; 10.1016/j.bpj.2013.11.3826
Barnes, Stephanie and Jones, Daniel, et el. (2014) Identification and Analysis of the Transcriptional Regulatory Networks Governing Mechanosensitive Channels in E. coli ; Biophysical Journal; Vol. 106; No. 2; 487A; 10.1016/j.bpj.2013.11.4472
Rydenfelt, Mattias and Cox, Robert Sidney, III, et el. (2014) Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration ; Physical Review E; Vol. 89; No. 1; Art. No. 012702; PMCID PMC4043999; 10.1103/PhysRevE.89.012702
Ngo, Huu B. and Lovely, Geoffrey A., et el. (2014) Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation ; Nature Communications; Vol. 5; No. 1; Art. No. 3077; PMCID PMC3936014; 10.1038/ncomms4077
Phillips, Rob (2013) The Feynman Lectures on Physics ; Nature; Vol. 504; No. 7478; 30-31; 10.1038/504030a
Boedicker, James Q. and Garcia, Hernan G., et el. (2013) DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation ; Physical Biology; Vol. 10; No. 6; Art. No. 066005; PMCID PMC3915735; 10.1088/1478-3975/10/6/066005
Johnson, Stephanie and Chen, Yi-Ju, et el. (2013) Poly(dA:dT)-Rich DNAs Are Highly Flexible in the Context
of DNA Looping ; PLOS ONE; Vol. 8; No. 10; Art. No. e75799; PMCID PMC3795714; 10.1371/journal.pone.0075799
Marzen, Sarah and Garcia, Hernan G., et el. (2013) Statistical Mechanics of Monod–Wyman–Changeux (MWC) Models ; Journal of Molecular Biology; Vol. 425; No. 9; 1433-1460; PMCID PMC3786005; 10.1016/j.jmb.2013.03.013
Haselwandter, Christoph A. and Phillips, Rob (2013) Connection between Oligomeric State and Gating Characteristics of Mechanosensitive Ion Channels ; PLoS Computational Biology; Vol. 9; No. 5; Art. No. e1003055; PMCID PMC3656111; 10.1371/journal.pcbi.1003055
Haselwandter, Christoph A. and Phillips, Rob (2013) Directional interactions and cooperativity between mechanosensitive membrane proteins ; Europhysics Letters; Vol. 101; No. 6; Art. No. 68002; PMCID PMC4193682; 10.1209/0295-5075/101/68002
Phillips, Rob (2013) Bacteria are Stressed Out Too: The Physics of Mechanosensation ; Biophysical Journal; Vol. 104; No. 2; 8A-8A; 10.1016/j.bpj.2012.11.072
Lindén, Martin and Johnson, Stephanie, et el. (2013) Analysis of DNA Looping Kinetics in Tethered Particle Motion Experiments using Hidden Markov Models ; Biophysical Journal; Vol. 104; No. 2; 418A-418A; 10.1016/j.bpj.2012.11.2329
Boedicker, James Q. and Garcia, Hernan G., et el. (2013) Theoretical and Experimental Dissection of DNA Loop-Mediated Repression ; Physical Review Letters; Vol. 110; No. 1; Art. No. 018101; PMCID PMC3716456; 10.1103/PhysRevLett.110.018101
Vale, Ronald D. and DeRisi, Joseph, et el. (2012) Interdisciplinary Graduate Training in Teaching Labs ; Science; Vol. 338; No. 6114; 1542-1543; PMCID PMC3810400; 10.1126/science.1216570
Brewster, Robert C. and Jones, Daniel L., et el. (2012) Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli ; PLoS Computational Biology; Vol. 8; No. 12; Art. No. e1002811; PMCID PMC3521663; 10.1371/journal.pcbi.1002811
Johnson, Stephanie and Lindén, Martin, et el. (2012) Sequence Dependence of Transcription Factor-Mediated DNA Looping ; Nucleic Acids Research; Vol. 40; No. 16; 7728-7738; PMCID PMC3439888; 10.1093/nar/gks473
Phillips, Rob (2012) A single-molecule view of protein action at a distance ; Protein Science; Vol. 21; No. S1; 65
Garcia, Hernan G. and Sanchez, Alvaro, et el. (2012) Operator Sequence Alters Gene Expression Independently of Transcription Factor Occupancy in Bacteria ; Cell Reports; Vol. 2; No. 1; 150-161; PMCID PMC3616187; 10.1016/j.celrep.2012.06.004
Van Valen, David and Wu, David, et el. (2012) A Single-Molecule Hershey-Chase Experiment ; Current Biology; Vol. 22; No. 14; 1339-1343; PMCID PMC3462812; 10.1016/j.cub.2012.05.023
Bassereau, Patricia and Phillips, Rob, et el. (2012) Focus on the physics of the cell membrane ; New Journal of Physics; Vol. 14; Art. No. 055021; 10.1088/1367-2630/14/5/055021
Bialecka-Fornal, Maja and Lee, Heun Jin, et el. (2012) Single-Cell Census of Mechanosensitive Channels in Living Bacteria ; PLoS ONE; Vol. 7; No. 3; Art. No. e33077; PMCID PMC3302805; 10.1371/journal.pone.0033077
Lindén, Martin and Sens, Pierre, et el. (2012) Entropic Tension in Crowded Membranes ; PLoS Computational Biology; Vol. 8; No. 3; Art. no. e1002431; PMCID PMC3305330; 10.1371/journal.pcbi.1002431
Ursell, Tristan and Agrawal, Ashutosh, et el. (2011) Lipid Bilayer Mechanics in a Pipette with Glass-Bilayer Adhesion ; Biophysical Journal; Vol. 101; No. 8; 1913-1920; 10.1016/j.bpj.2011.08.057
Haswell, Elizabeth S. and Phillips, Rob, et el. (2011) Mechanosensitive Channels: What Can They Do and How Do They Do It? ; Structure; Vol. 19; No. 10; 1356-1369; PMCID PMC3203646; 10.1016/j.str.2011.09.005
Phillips, Rob (2011) Jonathan Widom (1955–2011) ; Nature; Vol. 476; No. 7361; 400-400; 10.1038/476400a
Garcia, Hernan G. and Lee, Heun Jin, et el. (2011) Comparison and Calibration of Different Reporters for Quantitative Analysis of Gene Expression ; Biophysical Journal; Vol. 101; No. 3; 535-544; 10.1016/j.bpj.2011.06.026
Garcia, Hernan G. and 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; 12173-12178; PMCID PMC3141941; 10.1073/pnas.1015616108
Amit, Roee and Garcia, Hernan G., et el. (2011) Building Enhancers from the Ground Up: A Synthetic Biology Approach ; Cell; Vol. 146; No. 1; 105-118; PMCID PMC3155781; 10.1016/j.cell.2011.06.024
Tadmor, Arbel D. and Ottesen, Elizabeth A., et el. (2011) Probing Individual Environmental Bacteria for Viruses by Using Microfluidic Digital PCR ; Science; Vol. 333; No. 6038; 58-62; PMCID PMC3261838; 10.1126/science.1200758
Haselwandter, Christoph A. and Phillips, Rob (2011) Elastic energy of polyhedral bilayer vesicles ; Physical Review E; Vol. 83; No. 6; Art. No. 061901; PMCID PMC3236088; 10.1103/PhysRevE.83.061901
Sanchez, Alvaro and Garcia, Hernan G., et el. (2011) Effect of Promoter Architecture on the Cell-to-Cell Variability in Gene Expression ; PLoS Computational Biology; Vol. 7; No. 3; Art. No. e1001100; PMCID PMC3048382; 10.1371/journal.pcbi.1001100
Rim, J. E. and Ursell, T. S., et el. (2011) Morphological Phase Diagram for Lipid Membrane Domains with Entropic Tension ; Physical Review Letters; Vol. 106; No. 5; 057801; 10.1103/PhysRevLett.106.057801
Garcia, Hernan G. and Kondev, Jane, et el. (2011) Thermodynamics of Biological Processes ; ISBN 9780123860033; Biothermodynamics. Part D; 27-59; 10.1016/B978-0-12-381268-1.00014-8
Garcia, Hernan G. and Sanchez, Alvaro, et el. (2010) Transcription by the numbers redux: experiments and calculations that surprise ; Trends in Cell Biology; Vol. 20; No. 12; 723-733; PMCID PMC3174145; 10.1016/j.tcb.2010.07.002
Haselwandter, Christoph A. and Phillips, Rob (2010) Minimal Bending Energies of Bilayer Polyhedra ; Physical Review Letters; Vol. 105; No. 22; Art. No. 228101; PMCID PMC3169433; 10.1103/PhysRevLett.105.228101
Pressé, S. and Ghosh, K., et el. (2010) Dynamical fluctuations in biochemical reactions and cycles ; Physical Review E; Vol. 82; No. 3; Art. No. 031905; 10.1103/PhysRevE.82.031905
Wu, David and Van Valen, David, et el. (2010) Ion-Dependent Dynamics of DNA Ejections for Bacteriophage λ ; Biophysical Journal; Vol. 99; No. 4; 1101-1109; PMCID PMC2920739; 10.1016/j.bpj.2010.06.024
Phillips, Rob and 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; 21465-21471; PMCID PMC2799844; 10.1073/pnas.0907732106
Ridgeway, William K. and Seitaridou, Effrosyni, et el. (2009) RNA-protein binding kinetics in an automated microfluidic reactor ; Nucleic Acids Research; Vol. 37; No. 21; e142-e142; PMCID PMC2790880; 10.1093/nar/gkp733
Ridgeway, William K. and Seitaridou, Effrosyni, et el. (2009) RNA–protein binding kinetics in an automated microfluidic reactor ; Nucleic Acids Research; Vol. 37; No. 21; Art. e142; 10.1093/nar/gkp733
Ursell, Tristan S. and Klug, William S., et el. (2009) Morphology and interaction between lipid domains ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 106; No. 32; 13301-13306; PMCID PMC2726347; 10.1073/pnas.0903825106
Wu, David and Ghosh, Kingshuk, et el. (2009) Trajectory Approach to Two-State Kinetics of Single Particles on Sculpted Energy Landscapes ; Physical Review Letters; Vol. 103; No. 5; Art. No. 050603; PMCID PMC3273425; 10.1103/PhysRevLett.103.050603
Peterson, Eric L. and Kondev, Jané, et el. (2009) Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment ; Bioinformatics; Vol. 25; No. 11; 1356-1362; PMCID PMC2732308; 10.1093/bioinformatics/btp164
Towles, Kevin B. and Beausang, John F, et el. (2009) First-principles calculation of DNA looping in tethered particle experiments ; Physical Biology; Vol. 6; No. 2; Art. No. 025001; 10.1088/1478-3975/6/2/025001
Han, Lin and Garcia, Hernan G., et el. (2009) Concentration and Length Dependence of DNA Looping in Transcriptional Regulation ; PLoS ONE; Vol. 4; No. 5; Art. No. e5621; PMCID PMC2682762; 10.1371/journal.pone.0005621
Phillips, Rob and Ursell, Tristan, et el. (2009) Emerging roles for lipids in shaping membrane-protein function ; Nature; Vol. 459; No. 7245; 379-385; PMCID PMC3169427; 10.1038/nature08147
Van Valen, David and Haataja, Mikko, et el. (2009) Biochemistry on a Leash: The Roles of Tether Length and Geometry in Signal Integration Proteins ; Biophysical Journal; Vol. 96; No. 4; 1275-1292; PMCID PMC2717227; 10.1016/j.bpj.2008.10.052
Han, Lin and Lui, Bertrand H., et el. (2009) Calibration of Tethered Particle Motion Experiments ; ISBN 978-1-4419-0670-0; Mathematics of DNA structure, function and interactions; 123-138; 10.1007/978-1-4419-0670-0_6
Lee, Heun Jin and Peterson, Eric-L, et el. (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; 19252-19256; PMCID PMC2614748; 10.1073/pnas.0806814105
Reeves, Daniel and Ursell, Tristan, et el. (2008) Membrane mechanics as a probe of ion-channel gating mechanisms ; Physical Review E; Vol. 78; No. 4; Art. No. 041901; 10.1103/PhysRevE.78.041901
Grayson, Paul and Han, Lin, et el. (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; 14652-14657; PMCID PMC1976217; 10.1073/pnas.0703274104
Ursell, Tristan and Huang, Kerwin Casey, et el. (2007) Cooperative Gating and Spatial Organization of Membrane Proteins through Elastic Interactions ; PLOS Computational Biology; Vol. 3; No. 5; 803-812; PMCID PMC1864995; 10.1371/journal.pcbi.0030081
Seitaridou, Effrosyni and Inamdar, Mandar M., et el. (2007) Measuring Flux Distributions for Diffusion in the Small-Numbers Limit ; Journal of Physical Chemistry B; Vol. 111; No. 9; 2288-2292; PMCID PMC3261839; 10.1021/jp067036j
Garcia, Hernan G. and Grayson, Paul, et el. (2007) Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity ; Biopolymers; Vol. 85; No. 2; 115-130; PMCID PMC3496788; 10.1002/bip.20627
Wiggins, Paul A. and van der Heijden, Thijn, et el. (2006) High flexibility of DNA on short length scales probed by atomic force microscopy ; Nature Nanotechnology; Vol. 1; No. 2; 137-141; 10.1038/nnano.2006.63
Grayson, Paul and Evilevitch, Alex, et el. (2006) The effect of genome length on ejection forces in bacteriophage lambda ; Virology; Vol. 348; No. 2; 430-436; PMCID PMC3178461; 10.1016/j.virol.2006.01.003
Phillips, Rob and Quake, Stephen R. (2006) The Biological Frontier of Physics ; Physics Today; Vol. 59; No. 5; 38-43
Segall, Darren E. and Nelson, Philip C., et el. (2006) Volume-exclusion effects in tethered-particle experiments: bead size matters ; Physical Review Letters; Vol. 96; No. 8; Art. No. 088306; PMCID PMC3261840; 10.1103/PhysRevLett.96.088306
Dupuy, L. M. and Tadmor, E. B., et el. (2005) Finite-Temperature Quasicontinuum: Molecular Dynamics without All the Atoms ; Physical Review Letters; Vol. 95; No. 6; Art. No. 060202; 10.1103/PhysRevLett.95.060202
Wiggins, Paul A. and Phillips, Rob, et el. (2005) Exact theory of kinkable elastic polymers ; Physical Review E; Vol. 71; No. 2; Art. No. 021909; PMCID PMC3496790; 10.1103/PhysRevE.71.021909
Olmsted, David L. and Phillips, Rob, et el. (2004) Modelling diffusion in crystals under high internal stress gradients ; Modelling and Simulation in Materials Science and Engineering; Vol. 12; No. 5; 781-797; 10.1088/0965-0393/12/5/003
Wiggins, Paul and 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; 4071-4076; PMCID PMC384697; 10.1073/pnas.0307804101
Purohit, Prashant K. and Kondev, Jané, et el. (2003) Force steps during viral DNA packaging? ; Journal of the Mechanics and Physics of Solids; Vol. 51; No. 11-12; 2239-2257; 10.1016/j.jmps.2003.09.016
Purohit, Prashant K. and Kondev, Jané, et el. (2003) Mechanics of DNA packaging in viruses ; Proceedings of the National Academy of Sciences of the United States of America; Vol. 100; No. 6; 3173-3178; PMCID PMC404299; 10.1073/pnas.0737893100
Phillips, Rob and Dittrich, Markus, et el. (2002) Quasicontinuum representations of atomic-scale mechanics: From proteins to dislocations ; Annual Review of Materials Research; Vol. 32; 219-233; 10.1146/annurev.matsci.32.122001.102202
Bhate, N. and Clifton, R. J., et el. (2002) Atomistic Simulations of the Motion of an Edge Dislocation in Aluminum Using the Embedded Atom Method ; ISBN 0-7354-0068-7; Shock Compression of Condensed Matter 2001; 339-342; 10.1063/1.1483548
Kraft, O. and Freund, L. B., et el. (2002) Dislocation plasticity in thin metal films ; MRS Bulletin; Vol. 27; No. 1; 30-37; 10.1557/mrs2002.17
Olmsted, David L. and Hardikar, Kedar Y., et el. (2001) Lattice resistance and Peierls stress in finite size atomistic dislocation simulations ; Modelling and Simulation in Materials Science and Engineering; Vol. 9; No. 3; 215-247; 10.1088/0965-0393/9/3/308
Tadmor, E. B. and Phillips, R., et el. (2000) Hierarchical modeling in the mechanics of materials ; International Journal of Solids and Structures; Vol. 37; No. 1-2; 379-389; 10.1016/S0020-7683(99)00095-5
Phillips, Rob and Rodney, David, et el. (1999) Hierarchical models of plasticity: dislocation nucleation and interaction ; Modelling and Simulation in Materials Science and Engineering; Vol. 7; No. 5; 769-780; 10.1088/0965-0393/7/5/309
Shenoy, V. B. and Ortiz, M., et el. (1999) The atomistic structure and energy of nascent dislocation loops ; Modelling and Simulation in Materials Science and Engineering; Vol. 7; No. 4; 603-619; 10.1088/0965-0393/7/4/309
Tadmor, E.B. and Miller, R., et el. (1999) Nanoindentation and incipient plasticity ; Journal of Materials Research; Vol. 14; No. 6; 2233-2250
Miller, Ron and Phillips, Rob, et el. (1998) A non-local formulation of the Peierls dislocation model ; Journal of the Mechanics and Physics of Solids; Vol. 46; No. 10; 1845-1867; 10.1016/S0022-5096(98)00057-X
Miller, R. and Tadmor, E. B., et el. (1998) Quasicontinuum simulation of fracture at the atomic scale ; Modelling and Simulation in Materials Science and Engineering; Vol. 6; No. 5; 607-638; 10.1088/0965-0393/6/5/008
Miller, R. and Ortiz, M., et el. (1998) Quasicontinuum models of fracture and plasticity ; Engineering Fracture Mechanics; Vol. 61; No. 3-4; 427-444; 10.1016/S0013-7944(98)00047-2
Shenoy, V. B. and Miller, R., et el. (1998) Quasicontinuum Models of Interfacial Structure and Deformation ; Physical Review Letters; Vol. 08; No. 4; 742-745; 10.1103/PhysRevLett.80.742
Ortiz, Michael and Phillips, Rob (1998) Nanomechanics of Defects in Solids ; ISBN 978-0-12-002036-2; Advances in Applied Mechanics; 1-79; 10.1016/S0065-2156(08)70184-4
Tadmor, E. B. and Phillips, Rob, et el. (1996) Mixed Atomistic and Continuum Models of Deformation in Solids ; Langmuir; Vol. 12; No. 19; 4529-4534; 10.1021/la9508912
Tadmor, E. B. and Ortiz, M., et el. (1996) Quasicontinuum analysis of defects in solids ; Philosophical Magazine A; Vol. 73; No. 6; 1529-1563; 10.1080/01418619608243000
