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Type
Number of Years Citation(s) in RCA
1
Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K. Scalable molecular dynamics with NAMD. J Comput Chem 2005;26:1781-802. [PMID: 16222654 PMCID: PMC2486339 DOI: 10.1002/jcc.20289] [Citation(s) in RCA: 12624] [Impact Index Per Article: 631.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Research Support, N.I.H., Extramural 20 12624
2
Davison AP, Brüderle D, Eppler J, Kremkow J, Muller E, Pecevski D, Perrinet L, Yger P. PyNN: A Common Interface for Neuronal Network Simulators. Front Neuroinform 2009;2:11. [PMID: 19194529 PMCID: PMC2634533 DOI: 10.3389/neuro.11.011.2008] [Citation(s) in RCA: 236] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2008] [Accepted: 12/22/2008] [Indexed: 11/13/2022]  Open
Journal Article 16 236
3
Kutzner C, Páll S, Fechner M, Esztermann A, de Groot BL, Grubmüller H. Best bang for your buck: GPU nodes for GROMACS biomolecular simulations. J Comput Chem 2015;36:1990-2008. [PMID: 26238484 PMCID: PMC5042102 DOI: 10.1002/jcc.24030] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 07/05/2015] [Indexed: 11/11/2022]
Research Support, Non-U.S. Gov't 10 153
4
Murphy M, Alley M, Demmel J, Keutzer K, Vasanawala S, Lustig M. Fast l₁-SPIRiT compressed sensing parallel imaging MRI: scalable parallel implementation and clinically feasible runtime. IEEE TRANSACTIONS ON MEDICAL IMAGING 2012;31:1250-62. [PMID: 22345529 PMCID: PMC3522122 DOI: 10.1109/tmi.2012.2188039] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Research Support, N.I.H., Extramural 13 145
5
Ayres DL, Cummings MP, Baele G, Darling AE, Lewis PO, Swofford DL, Huelsenbeck JP, Lemey P, Rambaut A, Suchard MA. BEAGLE 3: Improved Performance, Scaling, and Usability for a High-Performance Computing Library for Statistical Phylogenetics. Syst Biol 2019;68:1052-1061. [PMID: 31034053 PMCID: PMC6802572 DOI: 10.1093/sysbio/syz020] [Citation(s) in RCA: 140] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 04/10/2019] [Accepted: 04/10/2019] [Indexed: 11/12/2022]  Open
Research Support, N.I.H., Extramural 6 140
6
Flouri T, Izquierdo-Carrasco F, Darriba D, Aberer AJ, Nguyen LT, Minh BQ, Von Haeseler A, Stamatakis A. The phylogenetic likelihood library. Syst Biol 2014;64:356-62. [PMID: 25358969 PMCID: PMC4380035 DOI: 10.1093/sysbio/syu084] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Research Support, Non-U.S. Gov't 11 104
7
Xi NM, Li JJ. Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data. Cell Syst 2021;12:176-194.e6. [PMID: 33338399 PMCID: PMC7897250 DOI: 10.1016/j.cels.2020.11.008] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 10/06/2020] [Accepted: 11/19/2020] [Indexed: 12/29/2022]
Research Support, N.I.H., Extramural 4 102
8
Plank G, Burton RAB, Hales P, Bishop M, Mansoori T, Bernabeu MO, Garny A, Prassl AJ, Bollensdorff C, Mason F, Mahmood F, Rodriguez B, Grau V, Schneider JE, Gavaghan D, Kohl P. Generation of histo-anatomically representative models of the individual heart: tools and application. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2009;367:2257-92. [PMID: 19414455 PMCID: PMC2881535 DOI: 10.1098/rsta.2009.0056] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
research-article 16 100
9
Winslow RL, Scollan DF, Holmes A, Yung CK, Zhang J, Jafri MS. Electrophysiological modeling of cardiac ventricular function: from cell to organ. Annu Rev Biomed Eng 2000;2:119-55. [PMID: 11701509 PMCID: PMC1403490 DOI: 10.1146/annurev.bioeng.2.1.119] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
research-article 25 84
10
Bellec P, Lavoie-Courchesne S, Dickinson P, Lerch JP, Zijdenbos AP, Evans AC. The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows. Front Neuroinform 2012;6:7. [PMID: 22493575 PMCID: PMC3318188 DOI: 10.3389/fninf.2012.00007] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 03/05/2012] [Indexed: 11/20/2022]  Open
Journal Article 13 82
11
Parallel computation with molecular-motor-propelled agents in nanofabricated networks. Proc Natl Acad Sci U S A 2016;113:2591-6. [PMID: 26903637 DOI: 10.1073/pnas.1510825113] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Research Support, Non-U.S. Gov't 9 72
12
van Albada SJ, Rowley AG, Senk J, Hopkins M, Schmidt M, Stokes AB, Lester DR, Diesmann M, Furber SB. Performance Comparison of the Digital Neuromorphic Hardware SpiNNaker and the Neural Network Simulation Software NEST for a Full-Scale Cortical Microcircuit Model. Front Neurosci 2018;12:291. [PMID: 29875620 PMCID: PMC5974216 DOI: 10.3389/fnins.2018.00291] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 04/13/2018] [Indexed: 01/12/2023]  Open
Journal Article 7 57
13
Yuan J, Xu G, Yu Y, Zhou Y, Carson PL, Wang X, Liu X. Real-time photoacoustic and ultrasound dual-modality imaging system facilitated with graphics processing unit and code parallel optimization. JOURNAL OF BIOMEDICAL OPTICS 2013;18:86001. [PMID: 23907277 PMCID: PMC3733419 DOI: 10.1117/1.jbo.18.8.086001] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Revised: 05/31/2013] [Accepted: 06/21/2013] [Indexed: 05/18/2023]
Research Support, N.I.H., Extramural 12 54
14
Rossant C, Goodman DFM, Fontaine B, Platkiewicz J, Magnusson AK, Brette R. Fitting neuron models to spike trains. Front Neurosci 2011;5:9. [PMID: 21415925 PMCID: PMC3051271 DOI: 10.3389/fnins.2011.00009] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Accepted: 01/13/2011] [Indexed: 11/30/2022]  Open
research-article 14 51
15
Vitay J, Dinkelbach HÜ, Hamker FH. ANNarchy: a code generation approach to neural simulations on parallel hardware. Front Neuroinform 2015;9:19. [PMID: 26283957 PMCID: PMC4521356 DOI: 10.3389/fninf.2015.00019] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 07/13/2015] [Indexed: 11/22/2022]  Open
Journal Article 10 49
16
Kunkel S, Schmidt M, Eppler JM, Plesser HE, Masumoto G, Igarashi J, Ishii S, Fukai T, Morrison A, Diesmann M, Helias M. Spiking network simulation code for petascale computers. Front Neuroinform 2014;8:78. [PMID: 25346682 PMCID: PMC4193238 DOI: 10.3389/fninf.2014.00078] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 08/27/2014] [Indexed: 11/13/2022]  Open
Journal Article 11 45
17
Jordan J, Ippen T, Helias M, Kitayama I, Sato M, Igarashi J, Diesmann M, Kunkel S. Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers. Front Neuroinform 2018;12:2. [PMID: 29503613 PMCID: PMC5820465 DOI: 10.3389/fninf.2018.00002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/18/2018] [Indexed: 11/13/2022]  Open
Journal Article 7 45
18
Helias M, Kunkel S, Masumoto G, Igarashi J, Eppler JM, Ishii S, Fukai T, Morrison A, Diesmann M. Supercomputers ready for use as discovery machines for neuroscience. Front Neuroinform 2012;6:26. [PMID: 23129998 PMCID: PMC3486988 DOI: 10.3389/fninf.2012.00026] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 10/08/2012] [Indexed: 11/16/2022]  Open
Journal Article 13 44
19
Kozloski J, Wagner J. An Ultrascalable Solution to Large-scale Neural Tissue Simulation. Front Neuroinform 2011;5:15. [PMID: 21954383 PMCID: PMC3175572 DOI: 10.3389/fninf.2011.00015] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2011] [Accepted: 08/10/2011] [Indexed: 11/29/2022]  Open
Journal Article 14 34
20
Li C, Li L, Zhang J, Alexov E. Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi. J Comput Chem 2012;33:1960-6. [PMID: 22674480 PMCID: PMC3412928 DOI: 10.1002/jcc.23033] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Revised: 04/20/2012] [Accepted: 05/11/2012] [Indexed: 11/07/2022]
Research Support, N.I.H., Extramural 13 33
21
Tyka MD, Jung K, Baker D. Efficient sampling of protein conformational space using fast loop building and batch minimization on highly parallel computers. J Comput Chem 2012;33:2483-91. [PMID: 22847521 PMCID: PMC3760475 DOI: 10.1002/jcc.23069] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 05/30/2012] [Accepted: 06/24/2012] [Indexed: 12/22/2022]
research-article 13 32
22
Ahmad K, Rizzi A, Capelli R, Mandelli D, Lyu W, Carloni P. Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective. Front Mol Biosci 2022;9:899805. [PMID: 35755817 PMCID: PMC9216551 DOI: 10.3389/fmolb.2022.899805] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 05/09/2022] [Indexed: 12/12/2022]  Open
Review 3 30
23
Zenke F, Gerstner W. Limits to high-speed simulations of spiking neural networks using general-purpose computers. Front Neuroinform 2014;8:76. [PMID: 25309418 PMCID: PMC4160969 DOI: 10.3389/fninf.2014.00076] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2014] [Accepted: 08/25/2014] [Indexed: 11/13/2022]  Open
Journal Article 11 28
24
Chattopadhyay A, Lu TP. Gene-gene interaction: the curse of dimensionality. ANNALS OF TRANSLATIONAL MEDICINE 2019;7:813. [PMID: 32042829 DOI: 10.21037/atm.2019.12.87] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Review 6 26
25
Meng J, Wang B, Wei Y, Feng S, Balaji P. SWAP-Assembler: scalable and efficient genome assembly towards thousands of cores. BMC Bioinformatics 2014;15 Suppl 9:S2. [PMID: 25253533 PMCID: PMC4168705 DOI: 10.1186/1471-2105-15-s9-s2] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
abstract 11 26
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