Publications by authors named "Rob Phillips"

100Publications

First-principles prediction of the information processing capacity of a simple genetic circuit.

Phys Rev E 2020 Aug;102(2-1):022404

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1103/PhysRevE.102.022404DOI Listing
August 2020

Correction to: Maternal Hypertension, Advanced Doppler Haemodynamics and Therapeutic Precision: Principles and Illustrative Cases.

Curr Hypertens Rep 2020 Aug 24;22(8):59. Epub 2020 Aug 24.

Department of Maternal Intensive Care Medicine Unit, Shandong Maternal and Child Health Hospital, Jinan, Shandong, China.

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http://dx.doi.org/10.1007/s11906-020-01095-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7645491PMC
August 2020

Maternal Hypertension, Advanced Doppler Haemodynamics and Therapeutic Precision: Principles and Illustrative Cases.

Curr Hypertens Rep 2020 Jul 13;22(7):49. Epub 2020 Jul 13.

Department of Maternal Intensive Care Medicine Unit, Shandong Maternal and Child Health Hospital, Jinan, Shandong, China.

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http://dx.doi.org/10.1007/s11906-020-01060-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7359153PMC
July 2020

Sequence-dependent dynamics of synthetic and endogenous RSSs in V(D)J recombination.

Nucleic Acids Res 2020 07;48(12):6726-6739

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1093/nar/gkaa418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337519PMC
July 2020

Theoretical investigation of a genetic switch for metabolic adaptation.

PLoS One 2020 7;15(5):e0226453. Epub 2020 May 7.

Department of Physics, California Institute of Technology, Pasadena, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0226453PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7205307PMC
August 2020

SARS-CoV-2 (COVID-19) by the numbers.

Elife 2020 04 2;9. Epub 2020 Apr 2.

Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.7554/eLife.57309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7224694PMC
April 2020

Allostery and Kinetic Proofreading.

J Phys Chem B 2019 12 13;123(51):10990-11002. Epub 2019 Dec 13.

Department of Physics , California Institute of Technology , Pasadena , California 91125 , United States.

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http://dx.doi.org/10.1021/acs.jpcb.9b08380DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995354PMC
December 2019

Harnessing Avidity: Quantifying the Entropic and Energetic Effects of Linker Length and Rigidity for Multivalent Binding of Antibodies to HIV-1.

Cell Syst 2019 11 23;9(5):466-474.e7. Epub 2019 Oct 23.

Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2019.09.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6892280PMC
November 2019

Predictive shifts in free energy couple mutations to their phenotypic consequences.

Proc Natl Acad Sci U S A 2019 09 26;116(37):18275-18284. Epub 2019 Aug 26.

Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;

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http://dx.doi.org/10.1073/pnas.1907869116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6744869PMC
September 2019

Controlling organization and forces in active matter through optically defined boundaries.

Nature 2019 08 7;572(7768):224-229. Epub 2019 Aug 7.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.

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http://dx.doi.org/10.1038/s41586-019-1447-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6719720PMC
August 2019

How the avidity of polymerase binding to the -35/-10 promoter sites affects gene expression.

Proc Natl Acad Sci U S A 2019 07 13;116(27):13340-13345. Epub 2019 Jun 13.

Department of Physics, California Institute of Technology, Pasadena, CA 91125;

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http://dx.doi.org/10.1073/pnas.1905615116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6613100PMC
July 2019

Torque-dependent remodeling of the bacterial flagellar motor.

Proc Natl Acad Sci U S A 2019 06 29;116(24):11764-11769. Epub 2019 May 29.

Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138.

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http://dx.doi.org/10.1073/pnas.1904577116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6576217PMC
June 2019

Measuring the Energetic Costs of Embryonic Development.

Dev Cell 2019 03;48(5):591-592

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S15345807193013
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http://dx.doi.org/10.1016/j.devcel.2019.02.016DOI Listing
March 2019

Combinatorial Control through Allostery.

J Phys Chem B 2019 04 4;123(13):2792-2800. Epub 2019 Mar 4.

Harvard-MIT Division of Health Sciences and Technology and the Broad Institute of MIT and Harvard , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States.

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http://dx.doi.org/10.1021/acs.jpcb.8b12517DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6467274PMC
April 2019

Microtubule End-Clustering Maintains a Steady-State Spindle Shape.

Curr Biol 2019 02 7;29(4):700-708.e5. Epub 2019 Feb 7.

Department of Cell and Tissue Biology, UCSF, San Francisco, CA 94143, USA; Biomedical Sciences Graduate Program, UCSF, San Francisco, CA 94143, USA; Department of Cellular and Molecular Pharmacology, UCSF, San Francisco, CA 94143, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cub.2019.01.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6383811PMC
February 2019

Mapping DNA sequence to transcription factor binding energy in vivo.

PLoS Comput Biol 2019 02 4;15(2):e1006226. Epub 2019 Feb 4.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1006226DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6375646PMC
February 2019

Measuring cis-regulatory energetics in living cells using allelic manifolds.

Elife 2018 12 20;7. Epub 2018 Dec 20.

Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, United States.

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https://elifesciences.org/articles/40618
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http://dx.doi.org/10.7554/eLife.40618DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6301791PMC
December 2018

Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants.

PLoS One 2018 26;13(9):e0204275. Epub 2018 Sep 26.

Department of Physics, California Institute of Technology, Pasadena, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0204275PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6157895PMC
March 2019

Connecting the Dots between Mechanosensitive Channel Abundance, Osmotic Shock, and Survival at Single-Cell Resolution.

J Bacteriol 2018 12 6;200(23). Epub 2018 Nov 6.

Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA

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http://dx.doi.org/10.1128/JB.00460-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6222198PMC
December 2018

The biomass distribution on Earth.

Proc Natl Acad Sci U S A 2018 06 21;115(25):6506-6511. Epub 2018 May 21.

Department of Plant and Environmental Sciences, Weizmann Institute of Science, 76100 Rehovot, Israel;

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http://dx.doi.org/10.1073/pnas.1711842115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6016768PMC
June 2018

Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria.

Proc Natl Acad Sci U S A 2018 05 4;115(21):E4796-E4805. Epub 2018 May 4.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125;

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http://dx.doi.org/10.1073/pnas.1722055115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6003448PMC
May 2018

A comprehensive and quantitative exploration of thousands of viral genomes.

Elife 2018 04 19;7. Epub 2018 Apr 19.

Department of Bioengineering, California Institute of Technology, Pasadena, United States.

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http://dx.doi.org/10.7554/eLife.31955DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5908442PMC
April 2018

Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction.

Cell Syst 2018 Apr 21;6(4):456-469.e10. Epub 2018 Mar 21.

Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA; Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.02.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991102PMC
April 2018

The role of DNA sequence in nucleosome breathing.

Eur Phys J E Soft Matter 2017 Nov 30;40(11):106. Epub 2017 Nov 30.

Institute Lorentz for Theoretical Physics, Leiden University, Niels Bohrweg 2, 2333 CA, Leiden, The Netherlands.

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http://dx.doi.org/10.1140/epje/i2017-11596-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7001874PMC
November 2017

Musings on mechanism: quest for a quark theory of proteins?

Authors:
Rob Phillips

FASEB J 2017 10;31(10):4207-4215

Department of Applied Physics and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA

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http://dx.doi.org/10.1096/fj.201700594DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6207179PMC
October 2017

Self-consistent theory of transcriptional control in complex regulatory architectures.

PLoS One 2017 7;12(7):e0179235. Epub 2017 Jul 7.

Van 't Hoff Laboratory for Physical & Colloid Chemistry, Utrecht University, Utrecht, the Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0179235PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5501422PMC
October 2017

Energetic cost of building a virus.

Proc Natl Acad Sci U S A 2017 05 16;114(22):E4324-E4333. Epub 2017 May 16.

Department of Bioengineering, California Institute of Technology, Pasadena, CA 91125;

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http://dx.doi.org/10.1073/pnas.1701670114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5465929PMC
May 2017

Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants.

J Phys Chem B 2017 04 21;121(15):3813-3824. Epub 2017 Feb 21.

Department of Applied Physics and Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, California 91125, United States.

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http://dx.doi.org/10.1021/acs.jpcb.6b12672DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5551692PMC
April 2017

Design Principles of Length Control of Cytoskeletal Structures.

Annu Rev Biophys 2016 07 29;45:85-116. Epub 2016 Apr 29.

Department of Physics, Brandeis University, Waltham, Massachusetts 02454; email:

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http://dx.doi.org/10.1146/annurev-biophys-070915-094206DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466818PMC
July 2016

Statistical Mechanics of Allosteric Enzymes.

J Phys Chem B 2016 07 29;120(26):6021-37. Epub 2016 Apr 29.

Department of Applied Physics and Division of Biology, California Institute of Technology , Pasadena, California 91125, United States.

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http://dx.doi.org/10.1021/acs.jpcb.6b01911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5452729PMC
July 2016

SnapShot: Timescales in Cell Biology.

Cell 2016 Mar;164(6):1302-1302.e1

Weizmann Institute of Science, Rehovot 7610001, Israel.

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http://dx.doi.org/10.1016/j.cell.2016.02.058DOI Listing
March 2016

Using synthetic biology to make cells tomorrow's test tubes.

Integr Biol (Camb) 2016 Apr 8;8(4):431-50. Epub 2016 Mar 8.

Department of Molecular and Cell Biology, Department of Physics, Biophysics Graduate Group, and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley CA 94720, USA.

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http://dx.doi.org/10.1039/c6ib00006aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4837077PMC
April 2016

Predicting the impact of promoter variability on regulatory outputs.

Sci Rep 2015 Dec 17;5:18238. Epub 2015 Dec 17.

Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA.

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http://dx.doi.org/10.1038/srep18238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4682146PMC
December 2015

Theory in Biology: Figure 1 or Figure 7?

Authors:
Rob Phillips

Trends Cell Biol 2015 Dec 13;25(12):723-729. Epub 2015 Nov 13.

Department of Applied Physics and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.tcb.2015.10.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666001PMC
December 2015

Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics.

Biophys J 2015 Aug;109(3):618-29

Department of Chemical Engineering, Stanford University, Stanford, California; Biophysics Program, Stanford University, Stanford, California; Department of Materials Science and Engineering, Stanford University, Stanford, California; Department of Applied Physics, Stanford University, Stanford, California. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2015.06.054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4572505PMC
August 2015

Single-molecule analysis of RAG-mediated V(D)J DNA cleavage.

Proc Natl Acad Sci U S A 2015 Apr 23;112(14):E1715-23. Epub 2015 Mar 23.

Biochemistry and Molecular Biophysics Option, Division of Biology and Biological Engineering, and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125; and

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http://dx.doi.org/10.1073/pnas.1503477112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394307PMC
April 2015

Napoleon Is in Equilibrium.

Authors:
Rob Phillips

Annu Rev Condens Matter Phys 2015 Mar;6:85-111

Department of Applied Physics and Division of Biology, California Institute of Technology, Pasadena, California 91125; Laboratoire de Physico-Chimie Théorique, CNRS/UMR 7083-ESPCI, 75231 Paris Cedex 05, France.

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http://www.annualreviews.org/doi/10.1146/annurev-conmatphys-
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http://dx.doi.org/10.1146/annurev-conmatphys-031214-014558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4946674PMC
March 2015

Scaling of gene expression with transcription-factor fugacity.

Phys Rev Lett 2014 Dec 16;113(25):258101. Epub 2014 Dec 16.

Van 't Hoff Laboratory for Physical and Colloid Chemistry, Debye Research Institute, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

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https://link.aps.org/doi/10.1103/PhysRevLett.113.258101
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4386862PMC
http://dx.doi.org/10.1103/PhysRevLett.113.258101DOI Listing
December 2014

The influence of promoter architectures and regulatory motifs on gene expression in Escherichia coli.

PLoS One 2014 30;9(12):e114347. Epub 2014 Dec 30.

Department of Applied Physics, California Institute of Technology, Pasadena, CA, United States of America; Division of Biology, California Institute of Technology, Pasadena, CA, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0114347PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4280137PMC
January 2016

Promoter architecture dictates cell-to-cell variability in gene expression.

Science 2014 Dec 18;346(6216):1533-6. Epub 2014 Dec 18.

Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA. Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1126/science.1255301DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4388425PMC
December 2014

Modulation of DNA loop lifetimes by the free energy of loop formation.

Proc Natl Acad Sci U S A 2014 Dec 19;111(49):17396-401. Epub 2014 Nov 19.

Applied Physics, and Biology, California Institute of Technology, Pasadena, CA 91125;

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http://dx.doi.org/10.1073/pnas.1415685111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267329PMC
December 2014

The quantified cell.

Mol Biol Cell 2014 Nov;25(22):3497-500

Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot 76100, Israel

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http://dx.doi.org/10.1091/mbc.E14-09-1347DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230611PMC
November 2014

The rate of osmotic downshock determines the survival probability of bacterial mechanosensitive channel mutants.

J Bacteriol 2015 Jan 27;197(1):231-7. Epub 2014 Oct 27.

Departments of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California, USA Department of Applied Physics, California Institute of Technology, Pasadena, California, USA Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA

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http://dx.doi.org/10.1128/JB.02175-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4288683PMC
January 2015

Multiple LacI-mediated loops revealed by Bayesian statistics and tethered particle motion.

Nucleic Acids Res 2014 12;42(16):10265-77. Epub 2014 Aug 12.

Center for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, Svante Arrhenius väg 16C, SE-106 91 Stockholm, Sweden Department of Cell and Molecular Biology, Uppsala University, Box 256, SE-751 05 Uppsala, Sweden

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http://dx.doi.org/10.1093/nar/gku563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4176382PMC
January 2015

Fluid responsiveness is about stroke volume, and not pulse pressure Yogi: the power of Doppler fluid management and cardiovascular monitoring.

J Clin Monit Comput 2015 Feb 22;29(1):197-200. Epub 2014 Jul 22.

The School of Medicine, The University of Queensland, Brisbane, Australia,

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http://dx.doi.org/10.1007/s10877-014-9598-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4309918PMC
February 2015

A national investigation of the prevalence and diversity of thermophilic Campylobacter species in agricultural watersheds in Canada.

Water Res 2014 Sep 28;61:243-52. Epub 2014 May 28.

Watershed Hydrology and Ecology Research Division (WHERD), Canada Centre for Inland Waters (CCIW), Environment Canada, 867 Lakeshore Road, Burlington L7R 4A6, Ontario, Canada.

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http://dx.doi.org/10.1016/j.watres.2014.05.027DOI Listing
September 2014

The transcription factor titration effect dictates level of gene expression.

Cell 2014 Mar 6;156(6):1312-1323. Epub 2014 Mar 6.

Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA. Electronic address:

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http://www.rpgroup.caltech.edu/publications/brewster2014_SI_
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http://linkinghub.elsevier.com/retrieve/pii/S009286741400221
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http://dx.doi.org/10.1016/j.cell.2014.02.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4080642PMC
March 2014

Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration.

Phys Rev E Stat Nonlin Soft Matter Phys 2014 Jan 6;89(1):012702. Epub 2014 Jan 6.

Department of Applied Physics, California Institute of Technology, Pasadena, California 91125, USA and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4043999PMC
http://dx.doi.org/10.1103/PhysRevE.89.012702DOI Listing
January 2014

Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation.

Nat Commun 2014 ;5:3077

1] Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA [2] Howard Hughes Medical Institute, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1038/ncomms4077DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3936014PMC
November 2015

In retrospect: The Feynman Lectures on Physics.

Authors:
Rob Phillips

Nature 2013 Dec;504(7478):30-1

California Institute of Technology.

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http://dx.doi.org/10.1038/504030aDOI Listing
December 2013

DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation.

Phys Biol 2013 Dec 15;10(6):066005. Epub 2013 Nov 15.

Departments of Applied Physics and Biology, California Institute of Technology, 1200 California Boulevard, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1088/1478-3975/10/6/066005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3915735PMC
December 2013

Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping.

PLoS One 2013 11;8(10):e75799. Epub 2013 Oct 11.

Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, California, United States of America ; Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America.

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http://www.rpgroup.caltech.edu/publications/journal.pone.007
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http://dx.plos.org/10.1371/journal.pone.0075799
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075799PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3795714PMC
July 2014

Connection between oligomeric state and gating characteristics of mechanosensitive ion channels.

PLoS Comput Biol 2013 16;9(5):e1003055. Epub 2013 May 16.

Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1003055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3656111PMC
March 2014

Statistical mechanics of Monod-Wyman-Changeux (MWC) models.

J Mol Biol 2013 May 14;425(9):1433-60. Epub 2013 Mar 14.

Department of Physics, University of California Berkeley, Berkeley, CA 94720-7300, USA.

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http://dx.doi.org/10.1016/j.jmb.2013.03.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3786005PMC
May 2013

Directional interactions and cooperativity between mechanosensitive membrane proteins.

Europhys Lett 2013 Mar;101(6):68002p1-68002p6

Department of Applied Physics, California Institute of Technology - Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1209/0295-5075/101/68002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4193682PMC
March 2013

Theoretical and experimental dissection of DNA loop-mediated repression.

Phys Rev Lett 2013 Jan 2;110(1):018101. Epub 2013 Jan 2.

Department of Applied Physics, California Institute of Technology, 1200 East California Boulevard, Pasadena, California 91125, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3716456PMC
http://dx.doi.org/10.1103/PhysRevLett.110.018101DOI Listing
January 2013

Tuning promoter strength through RNA polymerase binding site design in Escherichia coli.

PLoS Comput Biol 2012 13;8(12):e1002811. Epub 2012 Dec 13.

Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3521663PMC
May 2013

Operator sequence alters gene expression independently of transcription factor occupancy in bacteria.

Cell Rep 2012 Jul 12;2(1):150-61. Epub 2012 Jul 12.

Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.celrep.2012.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3616187PMC
July 2012

A single-molecule Hershey-Chase experiment.

Curr Biol 2012 Jul 21;22(14):1339-43. Epub 2012 Jun 21.

Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.cub.2012.05.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3462812PMC
July 2012

Sequence dependence of transcription factor-mediated DNA looping.

Nucleic Acids Res 2012 Sep 19;40(16):7728-38. Epub 2012 Jun 19.

Department of Biochemistry and Molecular Biophysics, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1093/nar/gks473DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3439888PMC
September 2012

Entropic tension in crowded membranes.

PLoS Comput Biol 2012 15;8(3):e1002431. Epub 2012 Mar 15.

Department of Applied Physics, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1371/journal.pcbi.1002431DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3305330PMC
June 2012

Single-cell census of mechanosensitive channels in living bacteria.

PLoS One 2012 13;7(3):e33077. Epub 2012 Mar 13.

Biochemistry and Molecular Biophysics Option, California Institute of Technology, Pasadena, California, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3302805PMC
August 2012

Lipid bilayer mechanics in a pipette with glass-bilayer adhesion.

Biophys J 2011 Oct;101(8):1913-20

Department of Applied Physics, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1016/j.bpj.2011.08.057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192956PMC
October 2011

Mechanosensitive channels: what can they do and how do they do it?

Structure 2011 Oct;19(10):1356-69

Department of Biology, Washington University, St. Louis, MO 63130, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3203646PMC
October 2011

Jonathan Widom (1955-2011).

Authors:
Rob Phillips

Nature 2011 Aug 24;476(7361):400. Epub 2011 Aug 24.

California Institute of Technology, Pasadena, California 91125, USA.

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August 2011

Comparison and calibration of different reporters for quantitative analysis of gene expression.

Biophys J 2011 Aug;101(3):535-44

Department of Physics, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1016/j.bpj.2011.06.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3145315PMC
August 2011

Elastic energy of polyhedral bilayer vesicles.

Phys Rev E Stat Nonlin Soft Matter Phys 2011 Jun 1;83(6 Pt 1):061901. Epub 2011 Jun 1.

Department of Applied Physics, California Institute of Technology, Pasadena, California 91125, USA.

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June 2011

Quantitative dissection of the simple repression input-output function.

Proc Natl Acad Sci U S A 2011 Jul 5;108(29):12173-8. Epub 2011 Jul 5.

Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1073/pnas.1015616108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3141941PMC
July 2011

Building enhancers from the ground up: a synthetic biology approach.

Cell 2011 Jul;146(1):105-18

Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1016/j.cell.2011.06.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3155781PMC
July 2011

Probing individual environmental bacteria for viruses by using microfluidic digital PCR.

Science 2011 Jul;333(6038):58-62

Department of Biochemistry and Molecular Biophysics, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1126/science.1200758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3261838PMC
July 2011

Effect of promoter architecture on the cell-to-cell variability in gene expression.

PLoS Comput Biol 2011 Mar 3;7(3):e1001100. Epub 2011 Mar 3.

Graduate Program in Biophysics and Structural Biology, Brandeis University, Waltham, Massachusetts,USA.

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http://dx.doi.org/10.1371/journal.pcbi.1001100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3048382PMC
March 2011

Challenges in comparison of Doppler CO measurement methods and the importance of understanding ultrasound theory and practice.

J Clin Monit Comput 2011 Apr 1;25(2):91-3. Epub 2011 Mar 1.

School of Medicine, The University of Queensland, Brisbane, QLD, Australia.

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http://dx.doi.org/10.1007/s10877-011-9275-3DOI Listing
April 2011

Thermodynamics of biological processes.

Methods Enzymol 2011 ;492:27-59

Department of Physics, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1016/B978-0-12-381268-1.00014-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3264492PMC
March 2011

Minimal bending energies of bilayer polyhedra.

Phys Rev Lett 2010 Nov 24;105(22):228101. Epub 2010 Nov 24.

Department of Applied Physics, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1103/PhysRevLett.105.228101DOI Listing
November 2010

Ion-dependent dynamics of DNA ejections for bacteriophage lambda.

Biophys J 2010 Aug;99(4):1101-9

Division of Engineering and Applied Sciences, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1016/j.bpj.2010.06.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2920739PMC
August 2010

SnapShot: key numbers in biology.

Cell 2010 Jun;141(7):1262-1262.e1

Weizmann Institute of Science, Rehovot, Israel.

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http://dx.doi.org/10.1016/j.cell.2010.06.019DOI Listing
June 2010

A feeling for the numbers in biology.

Proc Natl Acad Sci U S A 2009 Dec 14;106(51):21465-71. Epub 2009 Dec 14.

Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2799844PMC
December 2009

A methods comparison for the isolation and detection of thermophilic Campylobacter in agricultural watersheds.

J Microbiol Methods 2009 Dec 6;79(3):307-13. Epub 2009 Oct 6.

Aquatic Ecosystem Protection Research Division, Water Science & Technology Directorate, National Water Research Institute (NWRI), Environment Canada, Burlington, Ontario, Canada L7R 4A6.

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http://dx.doi.org/10.1016/j.mimet.2009.09.024DOI Listing
December 2009

Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes.

Phys Rev Lett 2009 Jul 31;103(5):050603. Epub 2009 Jul 31.

California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1103/PhysRevLett.103.050603DOI Listing
July 2009

RNA-protein binding kinetics in an automated microfluidic reactor.

Nucleic Acids Res 2009 Nov;37(21):e142

Department of Molecular Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd, MB33, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/nar/gkp733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790880PMC
November 2009

Morphology and interaction between lipid domains.

Proc Natl Acad Sci U S A 2009 Aug 20;106(32):13301-6. Epub 2009 Jul 20.

Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1073/pnas.0903825106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2726347PMC
August 2009

First-principles calculation of DNA looping in tethered particle experiments.

Phys Biol 2009 Jul 1;6(2):025001. Epub 2009 Jul 1.

Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1088/1478-3975/6/2/025001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3298194PMC
July 2009

Concentration and length dependence of DNA looping in transcriptional regulation.

PLoS One 2009 May 25;4(5):e5621. Epub 2009 May 25.

Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2682762PMC
May 2009

Emerging roles for lipids in shaping membrane-protein function.

Nature 2009 May;459(7245):379-85

Department of Applied Physics, California Institute of Technology, Pasadena, California 91125, USA.

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http://dx.doi.org/10.1038/nature08147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3169427PMC
May 2009

Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment.

Bioinformatics 2009 Jun 7;25(11):1356-62. Epub 2009 Apr 7.

Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp164DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732308PMC
June 2009

Noninvasive cardiac output measurement in heart failure subjects on circulatory support.

Anesth Analg 2009 Mar;108(3):881-6

Department of Medicine, The University of Queensland, Brisbane, Australia.

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http://dx.doi.org/10.1213/ane.0b013e318193174bDOI Listing
March 2009

Biochemistry on a leash: the roles of tether length and geometry in signal integration proteins.

Biophys J 2009 Feb;96(4):1275-92

Department of Applied Physics, California Institute of Technology, Pasadena, California, USA.

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http://dx.doi.org/10.1016/j.bpj.2008.10.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2717227PMC
February 2009

Membrane shape as a reporter for applied forces.

Proc Natl Acad Sci U S A 2008 Dec 1;105(49):19253-7. Epub 2008 Dec 1.

Department of Applied Physics, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1073/pnas.0806814105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614748PMC
December 2008

Membrane mechanics as a probe of ion-channel gating mechanisms.

Phys Rev E Stat Nonlin Soft Matter Phys 2008 Oct 1;78(4 Pt 1):041901. Epub 2008 Oct 1.

Department of Physics, Brandeis University, Waltham, Massachusetts 02454, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3496789PMC
http://dx.doi.org/10.1103/PhysRevE.78.041901DOI Listing
October 2008

High flexibility of DNA on short length scales probed by atomic force microscopy.

Nat Nanotechnol 2006 Nov 3;1(2):137-41. Epub 2006 Nov 3.

Whitehead Institute, Cambridge Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nnano.2006.63DOI Listing
November 2006

Real-time observations of single bacteriophage lambda DNA ejections in vitro.

Proc Natl Acad Sci U S A 2007 Sep 5;104(37):14652-7. Epub 2007 Sep 5.

Department of Physics, California Institute of Technology, Pasadena, CA 91125, USA.

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http://dx.doi.org/10.1073/pnas.0703274104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1976217PMC
September 2007

Cooperative gating and spatial organization of membrane proteins through elastic interactions.

PLoS Comput Biol 2007 May;3(5):e81

Department of Applied Physics, California Institute of Technology, Pasadena, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0030081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1864995PMC
May 2007