Michela Taufer

Michela Taufer, Narayan Ganesan, Sandeep Patel: GPU-Enabled Macromolecular Simulation: Challenges and Opportunities. Computing in Science and Engineering 15(1): 56-65 (2013)

Trilce Estrada, Boyu Zhang, Pietro Cicotti, Roger Armen, Michela Taufer: A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach. Comp. in Bio. and Med. 42(7): 758-771 (2012)

Giorgos Arampatzis, Markos A. Katsoulakis, Petr Plechác, Michela Taufer, Lifan Xu: Hierarchical fractional-step approximations and parallel kinetic Monte Carlo algorithms. J. Comput. Physics 231(23): 7795-7814 (2012)

Daniel T. Yehdego, Boyu Zhang, Michela Taufer, Vikram Kumar Reddy Kodimala, Rahulsimham Vegesna, Sameera Viswakula, Kyle L. Johnson, Ming-Ying Leung: Secondary structure predictions for long RNA sequences based on inversion excursions: preliminary results. BCB 2012: 545-547

Boyu Zhang, Daniel T. Yehdego, Kyle L. Johnson, Ming-Ying Leung, Michela Taufer: A modularized MapReduce framework to support RNA secondary structure prediction and analysis workflows. BIBM Workshops 2012: 86-93

M. Matheny, S. Schlachter, L. M. Crouse, E. T. Kimmel, Trilce Estrada, M. Schumann, Roger Armen, Gary M. Zoppetti, Michela Taufer: ExSciTecH: Expanding volunteer computing to Explore Science, Technology, and Health. eScience 2012: 1-8

Trilce Estrada, Boyu Zhang, Michela Taufer, Pietro Cicotti, Roger Armen: Reengineering High-throughput Molecular Datasets for Scalable Clustering Using MapReduce. HPCC-ICESS 2012: 351-359

Trilce Estrada, Michela Taufer: On the effectiveness of application-aware self-management for scientific discovery in volunteer computing systems. SC 2012: 80

Matthew Wezowicz, Michela Taufer: On the Cost of a General GPU Framework: The Strange Case of CUDA 4.0 vs. CUDA 5.0. SC Companion 2012: 1535-1536

Jong Hyuk Park, Sheikh Iqbal Ahamed, Willy Susilo, Michela Taufer: Special issue of computer communications on information and future communication security. Computer Communications 34(3): 223-225 (2011)

Brad A. Bauer, Joseph E. Davis, Michela Taufer, Sandeep Patel: Molecular dynamics simulations of aqueous ions at the liquid-vapor interface accelerated using graphics processors. Journal of Computational Chemistry 32(3): 375-385 (2011)

Narayan Ganesan, Brad A. Bauer, Timothy R. Lucas, Sandeep Patel, Michela Taufer: Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs). Journal of Computational Chemistry 32(14): 2958-2973 (2011)

K. Benson, Trilce Estrada, Michela Taufer, J. Lawrence, E. Cochran: On the Powerful Use of Simulations in the Quake-Catcher Network to Efficiently Position Low-cost Earthquake Sensors. eScience 2011: 77-84

Rolf Riesen, Kurt B. Ferreira, Maria Ruiz Varela, Michela Taufer, Arun Rodrigues: Simulating Application Resilience at Exascale. Euro-Par Workshops (2) 2011: 221-230

Trilce Estrada, Michela Taufer: Providing Quality of Science in Volunteer Computing. HPCC 2011: 68-77

Narayan Ganesan, Michela Taufer, Brad A. Bauer, Sandeep Patel: FENZI: GPU-Enabled Molecular Dynamics Simulations of Large Membrane Regions Based on the CHARMM Force Field and PME. IPDPS Workshops 2011: 472-480

Trilce Estrada, Boyu Zhang, Pietro Cicotti, Roger Armen, Michela Taufer: Poster: study of protein-ligand binding geometries using a scalable and accurate octree-based algorithm in mapReduce. SC Companion 2011: 39-40

Roger Armen, Eric R. May, Michela Taufer: Protein Docking. Encyclopedia of Parallel Computing 2011: 1638-1647

Trilce Estrada, Roger Armen, Michela Taufer: Automatic selection of near-native protein-ligand conformations using a hierarchical clustering and volunteer computing. BCB 2010: 204-213

Narayan Ganesan, Roger D. Chamberlain, Jeremy Buhler, Michela Taufer: Accelerating HMMER on GPUs by implementing hybrid data and task parallelism. BCB 2010: 418-421

Abel Licon, Michela Taufer, Ming-Ying Leung, Kyle L. Johnson: A Dynamic Programming Algorithm for Finding the Optimal Segmentation of an RNA Sequence in Secondary Structure Predictions. BICoB 2010: 165-170

Michela Taufer, Omar Padron, Philip Saponaro, Sandeep Patel: Improving numerical reproducibility and stability in large-scale numerical simulations on GPUs. IPDPS 2010: 1-9

Lifan Xu, Michela Taufer, Stuart Collins, Dionisios G. Vlachos: Parallelization of tau-leap coarse-grained Monte Carlo simulations on GPUs. IPDPS 2010: 1-9

Trilce Estrada, Michela Taufer, David P. Anderson: Performance Prediction and Analysis of BOINC Projects: An Empirical Study with EmBOINC. J. Grid Comput. 7(4): 537-554 (2009)

Michela Taufer, Abel Licon, Roberto Araiza, David Mireles, F. H. D. van Batenburg, Alexander P. Gultyaev, Ming-Ying Leung: PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots. Nucleic Acids Research 37(Database-Issue): 127-135 (2009)

Joseph E. Davis, Adnan Ozsoy, Sandeep Patel, Michela Taufer: Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors. BICoB 2009: 176-186

Trilce Estrada, Michela Taufer, Kevin Reed: Modeling Job Lifespan Delays in Volunteer Computing Projects. CCGRID 2009: 331-338

James Atlas, Trilce Estrada, Keith Decker, Michela Taufer: Balancing Scientist Needs and Volunteer Preferences in Volunteer Computing Using Constraint Optimization. ICCS (1) 2009: 143-152

Patrick McClory, Ezra Kissel, D. Martin Swany, Michela Taufer: MNEMONIC: A Network Environment for Automatic Optimization and Tuning of Data Movement over Advanced Networks. ICCCN 2009: 1-7

Trilce Estrada, Michela Taufer, Kevin Reed, David P. Anderson: EmBOINC: An emulator for performance analysis of BOINC projects. IPDPS 2009: 1-8

Michela Taufer, Ming-Ying Leung, Thamar Solorio, Abel Licon, David Mireles, Roberto Araiza, Kyle L. Johnson: RNAVLab: A virtual laboratory for studying RNA secondary structures based on grid computing technology. Parallel Computing 34(11): 661-680 (2008)

Trilce Estrada, Olac Fuentes, Michela Taufer: A distributed evolutionary method to design scheduling policies for volunteer computing. SIGMETRICS Performance Evaluation Review 36(3): 40-49 (2008)

Trilce Estrada, Olac Fuentes, Michela Taufer: A distributed evolutionary method to design scheduling policies for volunteer computing. Conf. Computing Frontiers 2008: 313-322

Michela Taufer, Thamar Solorio, Abel Licon, David Mireles, Ming-Ying Leung: On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks. IPDPS 2008: 1-8

Michela Taufer, Andre Kerstens, Trilce Estrada, David A. Flores, Richard Zamudio, Patricia J. Teller, Roger Armen, Charles L. Brooks III: Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling. IPDPS 2007: 1-8

Michela Taufer, Ming-Ying Leung, Kyle L. Johnson, Abel Licon: RNAVLab: A unified environment for computational RNA structure analysis based on grid computing technology. IPDPS 2007: 1-8

Richard Zamudio, Daniel Catarino, Michela Taufer, Brent Stearn, Karan Bhatia: Topaz: Extending Firefox to Accommodate the GridFTP Protocol. IPDPS 2007: 1-8

Michela Taufer, Andre Kerstens, Trilce Estrada, David A. Flores, Patricia J. Teller: SimBA: A Discrete Event Simulator for Performance Prediction of Volunteer Computing Projects. PADS 2007: 189-197

Guillermo A. Lopez, Michela Taufer, Patricia J. Teller: Evaluation of IEEE 754 floating-point arithmetic compliance across a wide range of heterogeneous computers. Richard Tapia Celebration of Diversity in Computing Conference 2007: 1-4

Michela Taufer, Chahm An, Andreas Kerstens, Charles L. Brooks III: Predictor@Home: A "Protein Structure Prediction Supercomputer' Based on Global Computing. IEEE Trans. Parallel Distrib. Syst. 17(8): 786-796 (2006)

Trilce Estrada, David A. Flores, Michela Taufer, Patricia J. Teller, Andre Kerstens, David P. Anderson: The Effectiveness of Threshold-Based Scheduling Policies in BOINC Projects. e-Science 2006: 88

Maria Gabriel Aguilera, Patricia J. Teller, Michela Taufer, F. Wolf: A systematic multi-step methodology for performance analysis of communication traces of distributed applications based on hierarchical clustering. IPDPS 2006

Trilce Estrada, Abel Licon, Michela Taufer: compPknots: A Framework for Parallel Prediction and Comparison of RNA Secondary Structures with Pseudoknots. ISPA Workshops 2006: 677-686

David A. Flores, Trilce Estrada, Michela Taufer, Patricia J. Teller, Andre Kerstens: Poster reception - SimBA: a discrete event simulator for performance prediction of volunteer computing projects. SC 2006: 168

Michela Taufer, Michael Crowley, Daniel J. Price, Andrew A. Chien, Charles L. Brooks III: Study of a highly accurate and fast protein-ligand docking method based on molecular dynamics. Concurrency and Computation: Practice and Experience 17(14): 1627-1641 (2005)

Pietro Cicotti, Michela Taufer, Andrew A. Chien: DGMonitor: A Performance Monitoring Tool for Sandbox-Based Desktop Grid Platforms. The Journal of Supercomputing 34(2): 113-133 (2005)

Michela Taufer, Patricia J. Teller, David P. Anderson, Charles L. Brooks III: Metrics for Effective Resource Management in Global Computing Environments. e-Science 2005: 204-211

Michela Taufer, David P. Anderson, Pietro Cicotti, Charles L. Brooks III: Homogeneous Redundancy: a Technique to Ensure Integrity of Molecular Simulation Results Using Public Computing. IPDPS 2005

Michela Taufer, Chahm An, Andreas Kerstens, Charles L. Brooks III: Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing. IPDPS 2005

Pietro Cicotti, Michela Taufer, Andrew A. Chien: DGMonitor: A Performance Monitoring Tool for Sandbox-Based Desktop Grid Platforms. IPDPS 2004

Derrick Kondo, Michela Taufer, Charles L. Brooks III, Henri Casanova, Andrew A. Chien: Characterizing and Evaluating Desktop Grids: An Empirical Study. IPDPS 2004

Michela Taufer, Michael Crowley, Daniel J. Price, Andrew A. Chien, Charles L. Brooks III: Study of a Highly Accurate and Fast Protein-Ligand Docking Algorithm Based on Molecular Dynamics. IPDPS 2004

Bennet Uk, Michela Taufer, Thomas Stricker, Giovanni Settanni, Andrea Cavalli, Amedeo Caflisch: Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform. CCGRID 2003: 240-247

Michela Taufer, Thomas Stricker: A Performance Monitor Based on Virtual Global Time for Clusters of PCs. CLUSTER 2003: 64-72

Bennet Uk, Michela Taufer, Thomas Stricker, Giovanni Settanni, Andrea Cavalli: Implementation and Characterization of Protein Folding on a Desktop Computational Grid - Is CHARMM a Suitable Candidate for the United Devices MetaProcessor? IPDPS 2003: 50

Michela Taufer: Inverting middleware: performance analysis of layered application codes in high performance distributed computing. ETH Zurich 2002, isbn 3-89649-821-5, pp. 1-137

Michela Taufer, Thomas Stricker, Gerard Roos, Peter Güntert: On the Migration of the Scientific Code Dyana from SMPs to Clusters of PCs and on to the Grid. CCGRID 2002: 93-101

Michela Taufer, Egon Perathoner, Andrea Cavalli, Amedeo Caflisch, Thomas Stricker: Performance Characterization of a Molecular Dynamics Code on PC Clusters: Is There Any Easy Parallelism in CHARMM?. IPDPS 2002

Michela Taufer, Thomas Stricker, Roger Weber: Scalability and resource usage of an OLAP benchmark on clusters of PCs. SPAA 2002: 83-94

Michela Taufer, Thomas Stricker: Accurate Performance Evaluation, Modelling and Prediction of a Message Passing Simulation Code based on Middleware. SC 1998: 52

Peter Arbenz, Martin Billeter, Peter Güntert, Peter Luginbühl, Michela Taufer, Urs von Matt: Molecular Dynamics Simulations on Cray Clusters using the SCIDDLE-PVM environment. PVM 1996: 142-149