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Items: 1 to 50 of 111


Long-Term Safety and Efficacy in Continued Access Left Atrial Appendage Closure Registries.

Holmes DR Jr, Reddy VY, Gordon NT, Delurgio D, Doshi SK, Desai AJ, Stone JE Jr, Kar S.

J Am Coll Cardiol. 2019 Dec 10;74(23):2878-2889. doi: 10.1016/j.jacc.2019.09.064.


Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism.

Singharoy A, Maffeo C, Delgado-Magnero KH, Swainsbury DJK, Sener M, Kleinekathöfer U, Vant JW, Nguyen J, Hitchcock A, Isralewitz B, Teo I, Chandler DE, Stone JE, Phillips JC, Pogorelov TV, Mallus MI, Chipot C, Luthey-Schulten Z, Tieleman DP, Hunter CN, Tajkhorshid E, Aksimentiev A, Schulten K.

Cell. 2019 Nov 14;179(5):1098-1111.e23. doi: 10.1016/j.cell.2019.10.021.


The Society for Maternal-Fetal Medicine (SMFM) Fetal Anomalies Consult Series.

Society for Maternal-Fetal Medicine, Stone JE, Kuller JA, Norton ME, Abuhamad A.

Am J Obstet Gynecol. 2019 Nov;221(5):B2-B24. doi: 10.1016/j.ajog.2019.08.014. Epub 2019 Aug 20. No abstract available.


High-Performance Analysis of Biomolecular Containers to Measure Small-Molecule Transport, Transbilayer Lipid Diffusion, and Protein Cavities.

Bryer AJ, Hadden-Perilla JA, Stone JE, Perilla JR.

J Chem Inf Model. 2019 Oct 28;59(10):4328-4338. doi: 10.1021/acs.jcim.9b00324. Epub 2019 Oct 3.


Application of a Limit-Cycle Oscillator Model for Prediction of Circadian Phase in Rotating Night Shift Workers.

Stone JE, Aubert XL, Maass H, Phillips AJK, Magee M, Howard ME, Lockley SW, Rajaratnam SMW, Sletten TL.

Sci Rep. 2019 Jul 30;9(1):11032. doi: 10.1038/s41598-019-47290-6.


Generalizability of A Neural Network Model for Circadian Phase Prediction in Real-World Conditions.

Stone JE, Phillips AJK, Ftouni S, Magee M, Howard M, Lockley SW, Sletten TL, Anderson C, Rajaratnam SMW, Postnova S.

Sci Rep. 2019 Jul 29;9(1):11001. doi: 10.1038/s41598-019-47311-4.


Sleepiness and driving events in shift workers: the impact of circadian and homeostatic factors.

Mulhall MD, Sletten TL, Magee M, Stone JE, Ganesan S, Collins A, Anderson C, Lockley SW, Howard ME, Rajaratnam SMW.

Sleep. 2019 Jun 11;42(6). pii: zsz074. doi: 10.1093/sleep/zsz074.


The Impact of Shift Work on Sleep, Alertness and Performance in Healthcare Workers.

Ganesan S, Magee M, Stone JE, Mulhall MD, Collins A, Howard ME, Lockley SW, Rajaratnam SMW, Sletten TL.

Sci Rep. 2019 Mar 15;9(1):4635. doi: 10.1038/s41598-019-40914-x.


Temporal dynamics of circadian phase shifting response to consecutive night shifts in healthcare workers: role of light-dark exposure.

Stone JE, Sletten TL, Magee M, Ganesan S, Mulhall MD, Collins A, Howard M, Lockley SW, Rajaratnam SMW.

J Physiol. 2018 Jun;596(12):2381-2395. doi: 10.1113/JP275589. Epub 2018 Apr 6.


NAMD goes quantum: an integrative suite for hybrid simulations.

Melo MCR, Bernardi RC, Rudack T, Scheurer M, Riplinger C, Phillips JC, Maia JDC, Rocha GB, Ribeiro JV, Stone JE, Neese F, Schulten K, Luthey-Schulten Z.

Nat Methods. 2018 May;15(5):351-354. doi: 10.1038/nmeth.4638. Epub 2018 Mar 26.


Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations.

Earnest TM, Watanabe R, Stone JE, Mahamid J, Baumeister W, Villa E, Luthey-Schulten Z.

J Phys Chem B. 2017 Apr 20;121(15):3871-3881. doi: 10.1021/acs.jpcb.7b00672. Epub 2017 Mar 30.


Immersive Molecular Visualization with Omnidirectional Stereoscopic Ray Tracing and Remote Rendering.

Stone JE, Sherman WR, Schulten K.

IEEE Int Symp Parallel Distrib Process Workshops Phd Forum. 2016 May;2016:1048-1057. Epub 2016 Aug 4.


High Performance Molecular Visualization: In-Situ and Parallel Rendering with EGL.

Stone JE, Messmer P, Sisneros R, Schulten K.

IEEE Int Symp Parallel Distrib Process Workshops Phd Forum. 2016 May;2016:1014-1023. Epub 2016 Aug 4.


Evaluation of Emerging Energy-Efficient Heterogeneous Computing Platforms for Biomolecular and Cellular Simulation Workloads.

Stone JE, Hallock MJ, Phillips JC, Peterson JR, Luthey-Schulten Z, Schulten K.

IEEE Int Symp Parallel Distrib Process Workshops Phd Forum. 2016 May;2016:89-100.


Molecular dynamics-based refinement and validation for sub-5 Å cryo-electron microscopy maps.

Singharoy A, Teo I, McGreevy R, Stone JE, Zhao J, Schulten K.

Elife. 2016 Jul 7;5. pii: e16105. doi: 10.7554/eLife.16105.


Atomic Detail Visualization of Photosynthetic Membranes with GPU-Accelerated Ray Tracing.

Stone JE, Sener M, Vandivort KL, Barragan A, Singharoy A, Teo I, Ribeiro JV, Isralewitz B, Liu B, Goh BC, Phillips JC, MacGregor-Chatwin C, Johnson MP, Kourkoutis LF, Hunter CN, Schulten K.

Parallel Comput. 2016 Jul;55:17-27.


Early Experiences Porting the NAMD and VMD Molecular Simulation and Analysis Software to GPU-Accelerated OpenPOWER Platforms.

Stone JE, Hynninen AP, Phillips JC, Schulten K.

High Perform Comput (2016). 2016 Jun;9945:188-206. doi: 10.1007/978-3-319-46079-6_14. Epub 2016 Oct 6.


QwikMD - Integrative Molecular Dynamics Toolkit for Novices and Experts.

Ribeiro JV, Bernardi RC, Rudack T, Stone JE, Phillips JC, Freddolino PL, Schulten K.

Sci Rep. 2016 May 24;6:26536. doi: 10.1038/srep26536.


TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

Vermaas JV, Hardy DJ, Stone JE, Tajkhorshid E, Kohlmeyer A.

J Chem Inf Model. 2016 Jun 27;56(6):1112-6. doi: 10.1021/acs.jcim.6b00103. Epub 2016 Jun 1.


Runtime and Architecture Support for Efficient Data Exchange in Multi-Accelerator Applications.

Cabezas J, Gelado I, Stone JE, Navarro N, Kirk DB, Hwu WM.

IEEE Trans Parallel Distrib Syst. 2015 May 1;26(5):1405-1418.


Aboriginal vascular health and insights into atherosclerosis.

Stone JA, Stone JE.

J Hum Hypertens. 2016 Apr;30(4):223-4. doi: 10.1038/jhh.2015.54. Epub 2015 May 28. No abstract available.


Multilevel summation method for electrostatic force evaluation.

Hardy DJ, Wu Z, Phillips JC, Stone JE, Skeel RD, Schulten K.

J Chem Theory Comput. 2015 Feb 10;11(2):766-79. doi: 10.1021/ct5009075.


Statins to protect against cancer chemotherapy cardiotoxicity.

Stone JA, Stone JE.

Can J Cardiol. 2015 Mar;31(3):244-6. doi: 10.1016/j.cjca.2015.01.017. Epub 2015 Jan 24. No abstract available.


Methodologies for the analysis of instantaneous lipid diffusion in MD simulations of large membrane systems.

Chavent M, Reddy T, Goose J, Dahl AC, Stone JE, Jobard B, Sansom MS.

Faraday Discuss. 2014;169:455-75. doi: 10.1039/c3fd00145h. Epub 2014 Jun 17.


GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting.

Stone JE, McGreevy R, Isralewitz B, Schulten K.

Faraday Discuss. 2014;169:265-83. doi: 10.1039/c4fd00005f. Epub 2014 Jun 30.


Stable small quantum dots for synaptic receptor tracking on live neurons.

Cai E, Ge P, Lee SH, Jeyifous O, Wang Y, Liu Y, Wilson KM, Lim SJ, Baird MA, Stone JE, Lee KY, Davidson MW, Chung HJ, Schulten K, Smith AM, Green WN, Selvin PR.

Angew Chem Int Ed Engl. 2014 Nov 10;53(46):12484-8. doi: 10.1002/anie.201405735. Epub 2014 Sep 26.


Simulation of reaction diffusion processes over biologically relevant size and time scales using multi-GPU workstations.

Hallock MJ, Stone JE, Roberts E, Fry C, Luthey-Schulten Z.

Parallel Comput. 2014 May 1;40(5-6):86-99.


Assembly of Nsp1 nucleoporins provides insight into nuclear pore complex gating.

Gamini R, Han W, Stone JE, Schulten K.

PLoS Comput Biol. 2014 Mar 13;10(3):e1003488. doi: 10.1371/journal.pcbi.1003488. eCollection 2014 Mar.


Promoting collaborative interdisciplinary research at the Duke Center for Systems Biology.

Stone JE, Benfey PN, You L.

ACS Synth Biol. 2012 May 18;1(5):153-5. doi: 10.1021/sb300036z. No abstract available.


Lattice Microbes: high-performance stochastic simulation method for the reaction-diffusion master equation.

Roberts E, Stone JE, Luthey-Schulten Z.

J Comput Chem. 2013 Jan 30;34(3):245-55. doi: 10.1002/jcc.23130. Epub 2012 Sep 25.


DNA polymerase zeta generates clustered mutations during bypass of endogenous DNA lesions in Saccharomyces cerevisiae.

Stone JE, Lujan SA, Kunkel TA, Kunkel TA.

Environ Mol Mutagen. 2012 Dec;53(9):777-86. doi: 10.1002/em.21728. Epub 2012 Sep 11.


RNase H and postreplication repair protect cells from ribonucleotides incorporated in DNA.

Lazzaro F, Novarina D, Amara F, Watt DL, Stone JE, Costanzo V, Burgers PM, Kunkel TA, Plevani P, Muzi-Falconi M.

Mol Cell. 2012 Jan 13;45(1):99-110. doi: 10.1016/j.molcel.2011.12.019.


Lesion bypass by S. cerevisiae Pol ζ alone.

Stone JE, Kumar D, Binz SK, Inase A, Iwai S, Chabes A, Burgers PM, Kunkel TA.

DNA Repair (Amst). 2011 Aug 15;10(8):826-34. doi: 10.1016/j.dnarep.2011.04.032. Epub 2011 May 31.


OpenCL: A Parallel Programming Standard for Heterogeneous Computing Systems.

Stone JE, Gohara D, Shi G.

Comput Sci Eng. 2010 May;12(3):66-72.


GPU-accelerated molecular modeling coming of age.

Stone JE, Hardy DJ, Ufimtsev IS, Schulten K.

J Mol Graph Model. 2010 Sep;29(2):116-25. doi: 10.1016/j.jmgm.2010.06.010. Epub 2010 Jul 8.


Multilevel Summation of Electrostatic Potentials Using Graphics Processing Units.

Hardy DJ, Stone JE, Schulten K.

Parallel Comput. 2009 Mar 1;35(3):164-177.


Visualisation of cyclic and multi-branched molecules with VMD.

Cross S, Kuttel MM, Stone JE, Gain JE.

J Mol Graph Model. 2009 Sep;28(2):131-9. doi: 10.1016/j.jmgm.2009.04.010. Epub 2009 May 4.


Cardiolipin and monolysocardiolipin analysis in fibroblasts, lymphocytes, and tissues using high-performance liquid chromatography-mass spectrometry as a diagnostic test for Barth syndrome.

Houtkooper RH, Rodenburg RJ, Thiels C, van Lenthe H, Stet F, Poll-The BT, Stone JE, Steward CG, Wanders RJ, Smeitink J, Kulik W, Vaz FM.

Anal Biochem. 2009 Apr 15;387(2):230-7. doi: 10.1016/j.ab.2009.01.032. Epub 2009 Jan 31.


Low-fidelity DNA synthesis by the L979F mutator derivative of Saccharomyces cerevisiae DNA polymerase zeta.

Stone JE, Kissling GE, Lujan SA, Rogozin IB, Stith CM, Burgers PM, Kunkel TA.

Nucleic Acids Res. 2009 Jun;37(11):3774-87. doi: 10.1093/nar/gkp238. Epub 2009 Apr 20.


Using VMD: an introductory tutorial.

Hsin J, Arkhipov A, Yin Y, Stone JE, Schulten K.

Curr Protoc Bioinformatics. 2008 Dec;Chapter 5:Unit 5.7. doi: 10.1002/0471250953.bi0507s24.


Evaluation of risk factors associated with suture-nidus cystoliths in dogs and cats: 176 cases (1999-2006).

Appel SL, Lefebvre SL, Houston DM, Holmberg DL, Stone JE, Moore AE, Weese JS.

J Am Vet Med Assoc. 2008 Dec 15;233(12):1889-95. doi: 10.2460/javma.233.12.1889.


Role of proliferating cell nuclear antigen interactions in the mismatch repair-dependent processing of mitotic and meiotic recombination intermediates in yeast.

Stone JE, Ozbirn RG, Petes TD, Jinks-Robertson S.

Genetics. 2008 Mar;178(3):1221-36. doi: 10.1534/genetics.107.085415. Epub 2008 Feb 3.


Bloodspot assay using HPLC-tandem mass spectrometry for detection of Barth syndrome.

Kulik W, van Lenthe H, Stet FS, Houtkooper RH, Kemp H, Stone JE, Steward CG, Wanders RJ, Vaz FM.

Clin Chem. 2008 Feb;54(2):371-8. Epub 2007 Dec 10.


Accelerating molecular modeling applications with graphics processors.

Stone JE, Phillips JC, Freddolino PL, Hardy DJ, Trabuco LG, Schulten K.

J Comput Chem. 2007 Dec;28(16):2618-40.


Mutator alleles of yeast DNA polymerase zeta.

Sakamoto AN, Stone JE, Kissling GE, McCulloch SD, Pavlov YI, Kunkel TA.

DNA Repair (Amst). 2007 Dec 1;6(12):1829-38. Epub 2007 Aug 21.


Shirt designs for sun protection.

Song K, Stone JE.

J Environ Health. 2005 Jun;67(10):50-6.


Intratumoral oxygenation of invasive squamous cell carcimoma of the vulva is not correlated with regional lymph node metastasis.

Stone JE, Parker R, Gilks CB, Stanbridge EJ, Liao SY, Aquino-Parsons C.

Eur J Gynaecol Oncol. 2005;26(1):31-5.


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