- Hueschen, Christina L.; 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
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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; 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; 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
- Suresh, Pooja; 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
- Hueschen, Christina; 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
- Duarte, Ana I.; 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
- Larios, David A.; 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
- 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
- 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
- Hueschen, Christina; 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.; 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; 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; 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
- Galstyan, Vahe; 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; 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.; 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; Husain, Kabir; et el. (2020) Proofreading
through spatial gradients; eLife; Vol. 9; Art. No. e60415; 10.7554/eLife.60415
- Ireland, William T.; 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; 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; 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.; 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.; 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
- Banks, Rachel; 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
- McCarty, Nicholas S.; 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
- Galstyan, Vahe; 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
- 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
- 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
- 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 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
- Einav, Tal; 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; 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.; 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; 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
- Phillips, Rob; 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; 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.; 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.; 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.; 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
- Forcier, Talitha L.; 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
- Chure, Griffin; 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
- Einav, Tal; 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
- Bar-On, Yinon M.; 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.; 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; 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; 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
- Belliveau, Nathan M.; 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
- 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
- Hirokawa, Soichi; 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
- Einav, Tal; 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
- Culkin, Jamie; 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; 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
- Mahmoudabadi, Gita; 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
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great ideas of biology: Exploration through experimentation in an
undergraduate lab course; Molecular Biology of the Cell; Vol. 27;
Art. No. P830
- Einav, Tal; 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; 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.; 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; 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
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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.; 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.; 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
- Bialecka-Fornal, Maja; 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; 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.; 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.; 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; 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; 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; 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.; 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.; 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
- 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
- Chen, Yi-Ju; 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
- Barnes, Stephanie; 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
- Lindén, Martin; 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
- Jones, Daniel L.; 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
- Lovely, Geoffrey; 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
- Lee, Heun Jin; 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
- Weinert, Franz M.; 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; 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
- Rydenfelt, Mattias; 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.; 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
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Feynman Lectures on Physics; Nature; Vol. 504; No. 7478; 30-31; 10.1038/504030a
- Boedicker, James Q.; 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; 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; 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
- Lindén, Martin; 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
- 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
- Boedicker, James Q.; 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.; 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.; 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; 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.; 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
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Single-Molecule Hershey-Chase Experiment; Current Biology; Vol. 22;
No. 14; 1339-1343; PMCID PMC3462812; 10.1016/j.cub.2012.05.023
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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; 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
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Tension in Crowded Membranes; PLoS Computational Biology; Vol. 8;
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Bilayer Mechanics in a Pipette with Glass-Bilayer Adhesion;
Biophysical Journal; Vol. 101; No. 8; 1913-1920; 10.1016/j.bpj.2011.08.057
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Channels: What Can They Do and How Do They Do It?; Structure; Vol.
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Widom (1955–2011); Nature; Vol. 476; No. 7361; 400-400; 10.1038/476400a
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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
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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
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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
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Individual Environmental Bacteria for Viruses by Using Microfluidic
Digital PCR; Science; Vol. 333; No. 6038; 58-62; PMCID PMC3261838;
10.1126/science.1200758
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energy of polyhedral bilayer vesicles; Physical Review E; Vol. 83;
No. 6; Art. No. 061901; PMCID PMC3236088; 10.1103/PhysRevE.83.061901
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of Promoter Architecture on the Cell-to-Cell Variability in Gene
Expression; PLoS Computational Biology; Vol. 7; No. 3; Art.
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Phase Diagram for Lipid Membrane Domains with Entropic Tension;
Physical Review Letters; Vol. 106; No. 5; 57801; 10.1103/PhysRevLett.106.057801
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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
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Bending Energies of Bilayer Polyhedra; Physical Review Letters; Vol.
105; No. 22; Art. No. 228101; PMCID PMC3169433; 10.1103/PhysRevLett.105.228101
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fluctuations in biochemical reactions and cycles; Physical Review E;
Vol. 82; No. 3; Art. No. 031905; 10.1103/PhysRevE.82.031905
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Dynamics of DNA Ejections for Bacteriophage λ; Biophysical Journal;
Vol. 99; No. 4; 1101-1109; PMCID PMC2920739; 10.1016/j.bpj.2010.06.024
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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
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binding kinetics in an automated microfluidic reactor; Nucleic Acids
Research; Vol. 37; No. 21; e142-e142; PMCID PMC2790880; 10.1093/nar/gkp733
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binding kinetics in an automated microfluidic reactor; Nucleic Acids
Research; Vol. 37; No. 21; Art. e142; 10.1093/nar/gkp733
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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
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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
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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
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calculation of DNA looping in tethered particle experiments;
Physical Biology; Vol. 6; No. 2; Art. No. 025001; 10.1088/1478-3975/6/2/025001
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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
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roles for lipids in shaping membrane-protein function; Nature; Vol.
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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
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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
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mechanics as a probe of ion-channel gating mechanisms; Physical
Review E; Vol. 78; No. 4; Art. No. 041901; 10.1103/PhysRevE.78.041901
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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
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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
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Flux Distributions for Diffusion in the Small-Numbers Limit; Journal
of Physical Chemistry B; Vol. 111; No. 9; 2288-2292; PMCID PMC3261839;
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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
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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
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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
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Biological Frontier of Physics; Physics Today; Vol. 59; No. 5;
38-43
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effects in tethered-particle experiments: bead size matters;
Physical Review Letters; Vol. 96; No. 8; Art. No. 088306; PMCID
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Quasicontinuum: Molecular Dynamics without All the Atoms; Physical
Review Letters; Vol. 95; No. 6; Art. No. 060202; 10.1103/PhysRevLett.95.060202
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of kinkable elastic polymers; Physical Review E; Vol. 71; No. 2;
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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
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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
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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
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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
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representations of atomic-scale mechanics: From proteins to
dislocations; Annual Review of Materials Research; Vol. 32; 219-233;
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plasticity in thin metal films; MRS Bulletin; Vol. 27; No. 1; 30-37;
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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
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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
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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
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atomistic structure and energy of nascent dislocation loops;
Modelling and Simulation in Materials Science and Engineering; Vol. 7;
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and incipient plasticity; Journal of Materials Research; Vol. 14;
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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
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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
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models of fracture and plasticity; Engineering Fracture Mechanics;
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Models of Interfacial Structure and Deformation; Physical Review
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Atomistic and Continuum Models of Deformation in Solids; Langmuir;
Vol. 12; No. 19; 4529-4534; 10.1021/la9508912
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analysis of defects in solids; Philosophical Magazine A; Vol. 73;
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