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*) Journal Papers
*) Book Chapters
*) Conferences, Symposiums, and Workshops
*) Posters
*) Technical Reports
*) Thesis

Journal Papers

    2016

    1. V. Stodden, M. McNutt, D. H. Bailey, E. Deelman, Y. Gil, B. Hanson, M. A. Heroux, J. P.A. Ioannidis, and M. Taufer. Enhancing Reproducibility for Computational Methods - Data, code and workflows should be available and cited. Science, 354(6317), December 9, 2016.
    2. S. Herbein, S. McDaniel, N. Podhorszki, S. Klasky, and M. Taufer. Performance Characterization of Irregular I/O at the Extreme Scale. Journal of Parallel Computing, 51: 17 - 36, 2016.

    2015

    1. T. Johnston, B. Zhang, A. Liwo, S. Crivelli, and M. Taufer. It-Situ Data Analysis of Protein Folding Trajectories. CoRR abs/1510.08789, pp. 1 - 40, October 30, 2015.
    2. M. Taufer and A. L. Rosenberg. Scheduling DAG-based Workflows on Single Cloud Instances: High- performance and Cost Effectiveness with a Static Scheduler. International Journal of High Performance Computing Applications, pp. 1 - 10, doi: 10.1177/1094342015594518, July 22, 2015.
    3. S. Ou, D. Cui, M. Wezowicz, M. Taufer, and S. Patel. Free Energetics of Carbon Nanotube Association in Aqueous Inorganic NaI Salt Solutions: Temperature Effects using All-Atom Molecular Dynamics Simulations and High-Performance Graphical Processing Unit Based Resources. Journal of Computational Chemistry, 36(16): 1196 - 1212, 2015.

    2014

    1. S. Schlachter, S. Herbein, S. Ou, J.S. Logan, S. Patel, and M. Taufer. Pursuing Resource Utilization and Coordinated Progression in GPU-enabled Molecular Simulations. IEEE Design&Test of Computers, IEEE Design&Test of Computers, 31(1): 40 – 50, February 2014.
    2. J. F. Lawrence, E.S. Cochran, A. Chung, A. Kaiser, C.M. Christensen, R. Allen, D. Anderson, J.W. Baker, B. Fry, T. Heaton, D. Kilb, M.D. Kohler, and M. Taufer. MEMS Accelerometers and Distributed Sensing for Rapid Earthquake Characterization. Bulletin of the Seismological Society of America (BSSA), January 7, 2014

    2013

    1. K. Benson, S. Schlachter, T. Estrada, M. Taufer, E. Cochran, and J. Lawrence: On the Powerful Use of Simulations in the Quake-Catcher Network to Efficiently Position Low-cost Earthquake Sensors. Future Generation Computer Systems, 29(8): 2128-2142, 2013.
    2. B. Zhang, D. T. Yehdego, K. L. Johnson, M.-Y. Leung, and M. Taufer: Enhancement of Accuracy and Efficiency for RNA Secondary Structure Prediction by Sequence Segmentation and MapReduce. BMC Structural Biology Journal, 13(Suppl 1):S3, 2013
    3. M. Taufer, N. Ganesan, and S. Patel: GPU enabled Macromolecular Simulation: Challenges and Opportunities. IEEE Computing in Science and Engineering (CiSE), 15(1): 56 - 64, 2013.

    2012

    1. T. Estrada, B. Zhang, P. Cicotti, R. Armen, and M. 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.
    2. G. Arampatzis, M.A. Katsoulakis, P. Plechac, M. Taufer, and L. Xu: Hierarchical Fractional-step Approximations and Parallel Kinetic Monte Carlo Algorithms. J. Comput. Physics, 231(23): 7795-7814, 2012.

    2011

    1. N. Ganesan, B.A. Bauer, T. Lucas, S. Patel, and M. Taufer: Structural, Dynamic, and Electrostatic Properties of Fully Hydrated DMPC Bilayers from Molecular Dynamics Simulations Accelerated with Graphical Processing Units (GPUs). J. Computational Chemistry, 32(14): 2958 – 2973, 2011.
    2. O. Rahaman, T. Estrada, D. Doren, M. Taufer, C. L. Brooks III, R.S. Armen: Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein-Ligand Binding Geometry and Free Energy. Journal of Chemical Information and Modeling, J. Chemical Information and Modeling, 51(9): 2047 – 65, 2011.
    3. B.A. Bauer, J.E. Davis, M. Taufer, and S. Patel: Molecular Dynamics Simulations of Aqueous Ions at the Liquid-Vapor Interface Accelerated Using Graphics Processors. J. Comp. Chem., (32)3: 375–385, 2011.

    2010

    1. J.J. Rosskopf, John H. Upton, III, M.-Y. Leung, M. Taufer, and K. L. Johnson: A 3 Terminal Stem-loop Structure 
in Nodamura Virus RNA2 Forms an Essential Cis-acting Signal for RNA 
replication. Virus Research, Virus Research, 150: 12-21, 2010.

    2009

    1. T. Estrada, M. Taufer, and D. Anderson: Performance Prediction and Analysis of BOINC Projects: An Empirical Study with EmBOINC. J. Grid Computing, 7: 537–554, 2009.
    2. M. Taufer, R.S. Armen, J. Chen, P.J. Teller, and C.L. Brooks III: Computational Multi-Scale Modeling in Protein-Ligand Docking. IEEE Engineering in Medicine and Biology Magazine. (28)2: 58 - 69, 2009.
    3. M. Taufer, A. Licon, R. Araiza, D. Mireles, A. Gultyaev, F.H.D. Van Batenburg, M-Y Leung: PseudoBase++: An Extension of PseudoBase for Easy Searching, Formatting, and Visualization of Pseudoknots. Nucleic Acids Research. Database Issue, 37, 2009. D129 doi: 10.1093/nar/gkn806

    2008

    1. M. Taufer, M-Y. Leung, T. Solorio, A. Licon, D. Mireles, R. Araiza, K.L. Johnson: RNAVLab: A Virtual Laboratory for Studying RNA Secondary Structures based on Grid Computing Technology. Journal of Parallel Computing. 34: 661-680, 2008.
    2. T. Estrada, O. Fuentes, and M. Taufer: A Distributed Evolutionary Method to Design Scheduling Policies for Volunteer Computing. ACM SIGMETRICS Performance Evaluation Review Journal. (36)3: 40 – 49, December 2008.

    2006

    1. K. Bhatia, M. Taufer, B. Stearn, R. Zamudio, D. Catarino: Integrate GridFTP into Firefox - Build grid protocols into Mozilla-based tools. IBM developerWorks, 10 Oct 2006.
    2. M. Taufer, C. An, A. Kerstens , and C.L. Brooks III: Predictor@Home: A Protein Structure Prediction Supercomputer Based on Global Computing. IEEE Transactions on Parallel and Distributed Systems. (17)8: 786 - 796, August 2006.

    2005

    1. M. Taufer, M. Crowley, D. Price, A.A. Chien, and C.L. Brooks III: Study of an Accurate and Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics. Concurrency and Computation: Practice and Experience. (17)14: 1627-1641, December 2005.
    2. P. Cicotti, M. Taufer, and A.A. Chien: DGMonitor: a Performance Monitoring Tool for Sandbox-based Desktop Grid Platforms. The Journal of Supercomputing. Springer Science+Business Media B.V., Formerly Kluwer Academic Publishers B.V. (34)2: 113 - 133, November 2005.
    3. K. Baldridge, J.P. Greenberg, W. Sudholt, K. Bhatia, S. Mock, C. Amoreira, Y. Potier, and M. Taufer: The Computational Chemistry Prototyping Environment. Proceedings of the IEEE Special Issue on Grid Computing. (93)3: 512 - 521, March 2005.

    Book Chapters

    1. P. Cicotti, S. Oral, G. Kestor, R. Gioiosa, S. Strande, M. Taufer, J. H. Rogers, H. Abbasi, J. Hill, and L. Carrington. Data Movement in Data-Intensive High Performance Computing. Conquering Big Data with High Performance Computing. Springer International Publishing AG. ISBN 9783319337401. 2016.
    2. T. Estrada and M. Taufer: Scheduling on Large Scale Volatile Desktop Grids, from Greedy and Naive to Intelligent and Adaptive Policies. Chapter in "Desktop Grid Computing", Christophe Cerin and Gilles Fedak (Eds.), Chapman and Hall/CRC, 2012.
    3. R.S. Armen, E.R. May, and M. Taufer: Protein Docking. In Encyclopedia of Parallel Computing, Padua, David (Ed.),1st Edition., 2011, 2500 p. In 4 volumes, not available separately. Hardcover. ISBN: 978-0-387-09765-7.
    4. M. Taufer and C.L. Brooks III, Predictor@Home: A Protein Structure Prediction Supercomputer Based on Volunteer Computing. (2008). In: Distributed & Grid Computing – Science Made Transparent for Everyone. Principles, Applications and Supporting Communities (Weber, M.H.W., ed). Rechenkraft.net, Marburg.

    Research Papers in Refereed Conferences, Symposiums, and Workshops

    (peer-reviewed papers)

    2016

    1. T. Johnston, C. Zannin, and M. Taufer. HYPPO: A Hybrid, Piecewise Polynomial Modeling Technique for Non-Smooth Surfaces. In Proceedings of the 28th IEEEE International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD), pp. 1 – 8. Los Angeles, CA, USA. October 26 - 28, 2016. (One of four Best Paper Candidatate)
    2. J. Benson, T. Estrada, A. Rosenberg, and M. Taufer. Scheduling Matters: Area-oriented Heuristics for Resource Management. In Proceedings of the 28th IEEEE International Symposium on Computer Architecture and High Performance Computing (SBAC-PAD), pp. 1 - 8. Los Angeles, CA, USA. October 26 – 28, 2016.
    3. M. Wyatt, T. Johnston, M. Papas, and M. Taufer. Development of a Scalable Method for Creating Food Groups Using the NHANES Dataset and MapReduce. In Proceedings of the ACM Bioinformatics and Computational Biology Conference (BCB), pp. 1 - 10. Seattle, WA, USA. October 2 – 4, 2016.
    4. R. McKenna, S. Herbein, A. Moody, T. Gamblin, and M. Taufer. Machine Learning Predictions of Runtime and IO Traffic on High-end Clusters. IEEE Cluster Conference, pp. 1 - 4. Taipei, Taiwan. September 12 – 16, 2016.
    5. S. Herbein, D. H. Ahn, D. Lipari, T. R.W. Scogland, M. Stearman, M. Grondona, J. Garlick, B. Springmeyer, and M. Taufer. Scalable I/O-Aware Job Scheduling for Burst Buffer Enabled HPC Clusters. In Proceedings of the ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC), pp. 1 - 10. Kyoto, Japan. May 30 – Jun 4, 2016.
    6. S. Herbein, A. Dusia, A. Landwehr, S. McDaniel, J. Monsalve, Y. Yang, S. R. Seelam, and M. Taufer. . In Proceedings of the International Supercomputing Conference (ISC), pp. 1 – 19. Frankfurt, Germany. June 19 - 23, 2016.

    2015

    1. T. Estrada, M. R. Wyatt, and M. Taufer. . In Proceedings of the 21th IEEE International Conference on Parallel and Distributed Systems (ICPADS), pp. 372 – 379. Melbourne, Australia. December 14 - 16, 2015.
    2. D. Chapp, T. Johnston, and M. Taufer. The Strong Case for Pursuing Numerical Reproducibility through Intelligent Runtime Selection of Reduction Algorithms at the Extreme Scale. In Proceedings of the IEEE Cluster 2015, Sept. 8 - 11, 2015, Chicago, Illinois, USA. Slides
    3. R. McKenna, V. Pallipuram, R. Vargas, and M. Taufer. From HPC Performance to Weather Modeling: Transforming Methods for HPC Predictions Into Models of Extreme Climate Conditions. In the Proceedings of the Tenth IEEE International Conference on e-Science and Grid Technologies (eScience), August 31 – September 4, 2015, Munich, Germany. Slides
    4. V. Pallipuram, T. Estrada, and M. Taufer. A Resource-selection Heuristic for High-performance and Cost-effective Workflow Execution on the Cloud. In Proceedings of the International Conference on Parallel Processing (ICPP), Sept. 1-4, 2015, Beijing, China. Slides
    5. B. Zhang, T. Estrada, P. Cicotti, P. Balaji, and M. Taufer. Accurate Scoring of Drug Conformations at the Extreme Scale. In Proceedings of 8th IEEE International Scalable Computing Challenge - Co-located with IEEE/ACM CCGrid, May 2015. Slides
    6. T. Johnston, M. Alsulmi, P. Cicotti and M. Taufer. Performance Tuning of MapReduce Jobs Using Surrogate-Based Modeling. In Proceedings of the International Conference on Computational Science (ICCS), Reykjavik, Iceland, June 1-3, 2015. Slides

    2014

    1. B. Javadi, B. Zhang, and M. Taufer. Bandwidth Modeling in Large Distributed Systems for Big Data Applications. In Proceedings of International Conference on Parallel and Distributed Computing, Applications and Technologies (PDCAT). Hong Kong, December 9-11, 2014.
    2. M. Matheny, S. Herbein, N. Podhorszki, S. Klasky, M. Taufer. Using Surrogate-based Modeling to Predict Optimal I/O Parameters of Applications at the Extreme Scale. In Proceedings of the 20th IEEE International Conference on Parallel and Distributed Systems (ICPADS 2014), Hsinchu, Taiwan, December 16 – 19, 2014.
    3. V.K. Pallipuram, J. DiMarco, and M. Taufer. Applying Frequency Analysis Techniques to DAG-based Workflows to Benchmark and Predict Resource Behavior on Non-Dedicated Clusters. In Proceedings of CLUSTER 2014, Madrid, Spain, September 22-26, 2014.
    4. S Herbein, S. Klasky, and M. Taufer. Benchmarking the Performance of Scientific Applications with Irregular I/O at the Extreme Scale. In Proceedings of the Seventh International Workshop on Parallel Programming Models and Systems Software for High-End Computing (P2S2), Minneapolis, Minnesota, 2014.
    5. M. Portnoi, S. Schlachter and M. Taufer. Study the Network Impact on Earthquake Early Warning in the Quake-Catcher Network Project. In the Proceedings of the International Conference on Computational Science (ICCS), Cairns, Australia, 2014.
    6. B. Zhang, T. Estarda, P. Cicotti, M. Taufer. Enabling In-situ Data Analysis for Large Protein Folding Trajectory Datasets. In the Proceedings of the 28th IEEE International Parallel & Distributed Processing Symposium (IPDPS), Phoenix (Arizona) USA, 2014.

    2013

    1. S. Herbein, M. Matheny, M. Wezowicz, J. Kroger, J. Logan, J. Kim, S. Klasky, M. Taufer. Performance Impact of I/O on QMCPack Simulations at the Petascale and Beyond. In the Proceedings of the 16th IEEE International Conferences on Computational Science and Engineering, December 2013, Sydney, Australia. Slides
    2. B. Zhang, T. Estrada, P. Cicotti, and M. Taufer. On Efficiently Capturing Scientific Properties in Distributed Big Data without Moving the Data - A Case Study in Distributed Structural Biology using MapReduce. In the Proceedings of the 16th IEEE International Conferences on Computational Science and Engineering, December 2013, Sydney, Australia. Slides
    3. S. Schlachter, S. Herbein, S. Ou, J.S. Logan, S. Patel, and M. Taufer. Efficient Sodium dodecyl sulfate (SDS) Simulations on Multi-GPU Nodes of XSEDE High-end Clusters. In the Proceedings of the Eighth IEEE International Conference on e-Science and Grid Technologies (eScience), October 2013, Beijing, China. Slides
    4. T. Estrada, K. Pusecker, M. Torres, J. Cohoon, and M. Taufer. Benchmarking Gender Differences in Volunteer Computing Projects. In the Proceedings of the Third Workshop on Analyzing and Improving Collaborative eScience with Social Networks (eSoN). October 2013, Beijing, China. Slides
    5. M. Wezowicz, T. Estrada, S. Patel, and M. Taufer: Performance Dissection of a MD Code across CUDA and GPU Generations. In Proceedings of the 14th IEEE International Workshop on Parallel and Distributed Scientific and Engineering Computing (PDSEC-13), April 2013, Boston, Massachusetts, USA.
    6. D. Yehdego, B. Zhang, V. K. R. Kodimala, K. Johnson, M. Taufer, and M.-Y. Leung: Secondary Structure Predictions for Long RNA Sequences based on Inversion Excursions and MapReduce. In Proceedings of 12th IEEE International Workshop on High Performance Computational Biology (HiCOMB), April 2013, Boston, Massachusetts, USA.
    7. J. DiMarco and M. Taufer: Performance Impact of Dynamic Parallelism on Different Clustering Algorithms and the New GPU Architecture. In Proceedings of the DSS11 SPIE Defense, Security, and Sensing Symposium - Modeling and Simulation for Defense Systems and Applications VI, April 2013, Baltimore, Maryland, USA.

    2012

    1. T. Estrada and M. Taufer: On the effectiveness of application-aware self-management for scientific discovery in volunteer computing systems. In Proceedings of the IEEE/ACM International Conference for High Performance Computing, Networking, Storage, and Analysis (SC12). November 2012, Salt Lake City, Utah, USA. Slides
    2. M. Matheny, S. Schlachter, L. Crouse, E. Kimmel, T. Estrada, M. Schumann, R. Armen, G. Zoppetti, and M. Taufer: ExSciTecH: Expanding Volunteer Computing to Explore Science, Technology, and Health. In Proceedings of the 2nd workshop on Analyzing and Improving Collaborative eScience with Social Networks (eSoN 12), October 2012, Chicago, Illinois, USA.
    3. B. Zhang, D. Yehdego, K. Johnson, M.-Y. Leung, and M. Taufer: A modularized MapReduce framework to support RNA secondary structure prediction and analysis workflows. In Proceedings of the 2012 Computational Structural Bioinformatics Workshop (CSBW), October 2012, Philadelphia, Pennsylvanian, USA.
    4. T. Estrada, B. Zhang, P. Cicotti, R. Armen, and M. Taufer: Reengineering high-throughput molecular datasets for scalable clustering using MapReduce. In Proceedings of the 14th IEEE International Conference on High Performance Computing and Communications (HPCC-2012), June 2012, Liverpool, England, UK.
    5. M. Wezowicz, B. D. Saunders, and M. Taufer: Dealing with performance/portability and performance/accuracy trade-offs in heterogeneous computing systems: A case study with matrix multiplication modulo primes. In Proceedings of the DSS11 SPIE Defense, Security, and Sensing Symposium - Modeling and Simulation for Defense Systems and Applications VI, April 2012, Baltimore, Maryland, USA.

    2011

    1. K. Benson, T. Estrada, M. Taufer, E. Cochran, and J. Lawrence: On the Powerful Use of Simulations in the Quake-Catcher Network to Efficiently Position Low-cost Earthquake Sensors. In the Proceedings of the Seventh IEEE International Conference on e-Science and Grid Technologies (eScience), December 2011, Stockholm, Sweden.
    2. R. Riesen, K. Ferreira, M. Ruiz Varela, M. Taufer and A. Rodrigues: Simulating Application Resilience at Exascale. In Proceedings of the 4th Workshop on Resiliency in High Performance Computing (Resilience) in Clusters, Clouds, and Grids, held in conjunction with the 17th International European Conference on Parallel and Distributed Computing (Euro-Par), August 30, 2011, Bordeaux, France.
    3. T. Estrada and M. Taufer: Providing Application-Level QoS in Volunteer Computing . In the Proceedings of the 13th IEEE High Performance Computing and Communications (HPCC) Conference. September 2011, Banff, Canada.
    4. N. Ganesan, B. Bauer, S. Patel and M. Taufer: FEN ZI: GPU Enabled Molecular Dynamics Simulation of Large Membrane Regions Based on CHARMM Force Field and PME . In Proceedings of the Tenth IEEE Workshop on Hi-Performance Computational Biology (HiCOMB), May 2011, Anchorage (Alaska) USA.
    5. N. Ganesan , R.D. Chamberlain, J. Buhler and M. Taufer: Rolling Partial Prefix-Sums to Speedup Uniform and Affine Recurrence Equations. In Proceedings of SPIE, Defense, Security and Sensing Conference. April 2011, Orlando, FL, USA.

    2010

    1. T. Estrada, R. Armen, and M. Taufer: Automatic Selection of Near-Native Protein-Ligand Conformations using a Hierarchical Clustering and Volunteer Computing. In Proceedings of the International Conference On Bioinformatics and Computational Biology (ACM-BCB), August 2010, Niagara Falls, NY, USA.
    2. N. Ganesan, R.D. Chamberlain, J. Buhler, and M. Taufer: Accelerating HMMER on GPUs by Implementing Hybrid Data and Task Parallelism. In Proceedings of the International Conference On Bioinformatics and Computational Biology (ACM-BCB), August 2010, Niagara Falls, NY, USA.
    3. L. Xu, M. Taufer, S. Collins, and D. G. Vlachos: Parallelization of Tau-Leap Coarse-Grained Monte Carlo Simulations on GPUs. In Proceedings of the IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS), April 2010, Atlanta, Georgia, USA.
    4. M. Taufer, O. Padron, P. Saponaro, S. Patel: Improving Numerical Reproducibility and Stability in Large-Scale Numerical Simulations on GPUs. In Proceedings of the IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS), April 2010, Atlanta, Georgia, USA.
    5. A. Licon, M. Taufer, M.-Y. Leung, and K.L. Johnson: A Dynamic Programming Algorithm for Finding the Optimal Segmentation of an RNA Secondary Structure Prediction. In Proceedings of the International Conference on Bioinformatics and Computational Biology (BICoB), March 2010, Honolulu, Hawaii, USA.

    2009

    1. P. McClory, E. Kissel, D. M. Swany, and M. Taufer: MNEOMIC: Network Environment for Measurement and Observation for Network Interaction and Control. In Proceedings of the 1st Workshop on Grid and P2P Systems and Applications (GridPeer), held together with the 18th IEEE International Conference on Computer Communications and Networks (ICCCN), 2009.
    2. S. Kamboj, T. Estrada, M. Taufer, and K. S. Decker: Applying Organizational Self-Design to a Real-world Volunteer Computing System. In Proceedings of Agent Design: Advancing from Theory to Practice (ADAPT) Workshop, 2009.
    3. J. Atlas, T. Estrada, K. Decker, and M. Taufer: Balancing Scientist Needs and Volunteer Preferences in Volunteer Computing using Constraint Optimization. In Proceedings of the International Conference on Computational Science (ICCS), May 2009, Baton Rouge, Louisiana, USA.
    4. T. Estrada, K. Reed, D. Anderson, and M. Taufer: EmBOINC: An Emulator for Performance Analysis of BOINC Projects.In Proceedings of PCGrid 2009, May 2009, Rome, Italy
    5. T. Estrada, K. Reed, and M. Taufer:Modeling Job Lifespan Delays in Volunteer Computing Projects. In Proceedings of to the 9th IEEE International Symposium on Cluster Computing and Grid (CCGrid), May 2009, shanghai, China.
    6. J.E. Davis, A. Ozsoy, S. Patel, and M. Taufer: Towards Large-Scale Molecular Dynamics Simulations on Graphics Processors. In Proceedings of the International Conference on Bioinformatics and Computational Biology (BICoB), April 2009, New Orleans, Louisiana, USA.

    2008

    1. T. Estrada, O. Fuentes, and M. Taufer: A Distributed Evolutionary Method to Design Scheduling Policies for Volunteer Computing. In Proceedings of ACM Computing Frontiers 2008, May 2008, Ischia, Italy.
    2. M. Taufer, T. Solorio, A. Licon, D. Mireles, and M.-Y. Leung: On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks. In Proceedings of the Seventh IEEE International Workshop on High Performance Computational Biology (HiCOMB 2008), April 2008, Miami, Florida, USA.

    2007

    1. G. Lopez, M. Taufer, and P.J. Teller: Evaluation of IEEE 754 Floating-Point Arithmetic Compliance Across a Wide Range of Heterogeneous Computers. In Proceedings of the 2007 Richard Tapia Celebration of Diversity in Computing Conference, October 2007, Orlando, Florida, USA.
    2. R. Araiza, M. Taufer, and M.-Y. Leung: Towards Optimal Scheduling for Global Computing Under Probabilistic, Interval, and Fuzzy Uncertainty, with Potential Applications to Bioinformatics. In Proceedings of the 26th International Conference of the North American Fuzzy Information Processing Society (NAFIPS'2007), June 2007San Diego, California, USA.
    3. M. Taufer, A. Kerstens, T. Estrada, D.A. Flores, and P.J. Teller: SimBA: a Discrete Event Simulator for Performance Prediction of Volunteer Computing Projects. In Proceedings of the International Workshop on Principles of Advanced and Distributed Simulation 2007 (PADS'07), June 2007, San Diego, California, USA.
    4. M. Taufer, M.-Y. Leung, K. L. Johnson, A. Licon: RNAVLab: A unified environment for computational RNA structure analysis based on grid computing technology. Sixth IEEE International Workshop on High Performance Computational Biology (HiCOMB'07), in conjunction with IPDPS'07 March 2007, Long Beach, California, USA.
    5. M. Taufer, A. Kerstens, T. Estrada, D.A. Flores, R. Zamudio, P.J. Teller, R. Armen, and C.L. Brooks III: Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling. In Proceedings of the First Workshop on Large-Scale, Volatile Desktop Grids (PCGrid'07), in conjunction with IPDPS'07 March 2007, Long Beach, California, USA.
    6. R. Zamudio, D. Catarino, M. Taufer, K. Bhatia, and B. Stearn: Topaz: Extending Firefox to Accommodate the GridFTP Protocol. In Proceedings of the Fourth High-Performance Grid Computing Workshop (HPGC'07), in conjunction with IPDPS'07 March 2007, Long Beach, California, USA.

    2006

    1. T. Estrada, D. Flores, M. Taufer, P. Teller, A. Kerstens, and D. Anderson: The Effectiveness of Threshold-based Scheduling Policies in BOINC Projects. In Proceedings of the 2st IEEE International Conference on e-Science and Grid Technologies (eScience 2006). December 2006, Amsterdam, The Netherlands.
    2. T. Estrada, A. Licon, and M. Taufer: CompPknots: a Framework for Parallel Prediction and Comparison of RNA Secondary Structures with Pseudoknots. In Proceedings of 1st Frontier on High Performance Computing and Networking Workshop (FHPCN-06), in conjunction with ISPA 2006, December 2006, Sorrento, Italy.
    3. K. Bhatia, B. Stearn, M. Taufer, R. Zamudio, and D. Catarino: Extending Grid Protocols onto the Desktop using the Mozilla Framework. In Proceedings of the 2nd International Workshop on Grid Computing Environments (GCE 2006), in conjunction with SC 2006, November 2006, Tampa, Florida.
    4. G. Aguilera, P.J. Teller, M. Taufer, and F. Wolf: A Systematic Multi-step Methodology for Performance Analysis of Communication Traces of Distributed Applications based on Hierarchical Clustering. In Proceedings of 5th International Workshop on Performance Modeling, Evaluation, and Optimization of Parallel and Distributed Systems (PMEO-PDS 2006), in conjunction with IPDPS 2006, April 2006, Rhodes Island, Greece.

    2005

    1. M. Taufer, P.J. Teller, D.P. Anderson, and C.L. Brooks III: Metrics for Effective Resource Management in Global Computing Environments. In Proceedings of the 1st IEEE International Conference on e-Science and Grid Technologies (eScience 2005). December 2005, Melbourne, Australia.
    2. M. Taufer, C. An, A. Kerstens, and C.L. Brooks III: Predictor@Home: A "Protein Prediction Supercomputer" Based on Public-Resource Computing. In Proceedings Fourth IEEE International Workshop on High Performance Computational Biology 2005), in conjunction with IPDPS 2005, April 2005, Denver, Colorado.
    3. M. Taufer, D.P. Anderson, P. Cicotti, and C.L. Brooks III: Homogeneous Technique to Ensure Integrity of Molecular Simulation Results Using Public Resources. In Proceedings of the 14th Heterogeneous Computing Workshop (HCW 2005), with IPDPS 2005, April 2005, Denver, Colorado.

    2004

    1. M. Taufer, M. Crowley, D. Price, A.A. Chien, and C.L. Brooks III: Study of an Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics. In the Third IEEE International Workshop on High Performance Computational Biology 2004), in conjunction with IPDPS 2004, April 2004, Santa Fe, New Mexico.
    2. D. Kondo, M. Taufer, C.L. Brooks III, H. Casanova, and A.A. Chien: Characterizing and Evaluating Desktop Grids: An Empirical Study. In Proceedings of the IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS'04), April 2004, Santa Fe, New Mexico, USA.
    3. P. Cicotti, M. Taufer, and A.A. Chien: DGMonitor: a Performance Monitoring Tool for Sandbox-based Desktop Grid Platforms. In Proceedings of the Third International Workshop on Performance Modeling, Evaluation, and Optimization of Parallel and Distributed Systems (PMEO-PDS'04), in conjunction with IPDPS'04, April 2004, Santa Fe, New Mexico, USA.

    2003

    1. M. Taufer, and T. Stricker: A Performance Monitor based on Virtual Global Time for Clusters of PCs. In Proceedings of the IEEE International Conference on Cluster Computing 2003 (Cluster'03), December 2003, Hong Kong, China.
    2. B. Uk, M. Taufer, T. Stricker, G. Settanni, A. Cavalli, and A. Caflisch: Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform Is efficient protein folding possible with CHARMM on the United Devices MetaProcessor? In Proceedings the IEEE International Symposium on Cluster Computing and the Grid (CCGRID'03), May 2003, Tokyo, Japan.
    3. B. Uk, M. Taufer, T. Stricker, G. Settanni, and A. Cavalli: Implementation and Characterization of Protein Folding on a Desktop Computational Grid Is CHARMM a suitable candidate for the United Devices MetaProcessor? In Proceedings of the IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS'03), April 2003, Nice, France.

    2002

    1. M. Taufer, T. Stricker, and R. Weber: Scalability and Resource Usage of an OLAP Benchmark on Clusters of PCs. In Proceedings of the Fourteenth ACM Symposium on Parallel Algorithms and Architectures (SPAA'02), August 2002, Winnipeg, Manitoba, Canada.
    2. M. Taufer, T. Stricker, G. Roos, P. Guentert: On the Migration of the Scientific Code DYANA from SMPs to Clusters of PCs and on to the Grid. In Proceedings of the IEEE International Symposium on Cluster Computing and the Grid (CCGRID'02), May 2002, Berlin, Germany.
    3. M. Taufer, E. Perathoner, A. Cavalli, A. Caflisch, and T. Stricker: Performance Characterization of a Molecular Dynamics Code on PC Clusters - Is there any easy parallelism in CHARMM? In Proceedings of the IEEE/ACM International Parallel and Distributed Processing Symposium (IPDPS'02), April 2002, Fort Lauderdale, Florida, USA.

    1998

    1. M. Taufer, and T. Stricker: Accurate Performance Evaluation, Modeling and Prediction of a Message Passing Simulation Code based on Middleware. In Proceedings of the ACM/IEEE International Conference for High Performance Computing and Communications conference (SC'98), November 1998, Orlando, Florida, USA.

    1996

    1. P. Arbenz, M. Billeter, P. Guentert, P. Luginbuehl, M. Taufer, and U. von Matt: Molecular Dynamics Simulations on Cray Clusters using the Sciddle-PVM Environment. Lecture Notes in Computer Science 1156 A. Bode, J. Dongarra, T. Ludwig, V. Sunderam (Eds.) Presented at the Parallel Virtual Machine - EuroPVM 96, Third European PVM Conference, October 1996, Munich, Germany.

    Educational Papers

    1. M. Taufer, P.J. Teller, A. Kerstens, R. Romero: Collaborative Research Tools for Students, Staff, and Faculty. In Proceedings of the International SUN Conference on Teaching and Learning, March 2006, El Paso, Texas.

    Posters

    1. D.T. Yehdego, V. K. R. Kodimala, S. Viswakula, B. Zhang, R. Vegesna, K. L. Johnson, M. Taufer and M.-Y. Leung: Secondary Structure Predictions for Long RNA Sequences Based on Inversion Excursions. Poster in Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM-BCB), Orlando, FL, October 7-10, 2012.
    2. T. Estrada, K. Pusecker, M. Torres, J. Cohoon, and M. Taufer: Benchmarking Gender Differences in Voluntary Computer Projects. Poster in Proceedings of the 2012 Grace Hopper Celebration of Women in Computing (GHC12), October 2012, Baltimore, Maryland, USA.
    3. T. Estrada, B. Zhang, R.S. Armen, and M. Taufer: Study of Protein-ligand Binding Geometries using a Scalable and Accurate Octree-based Algorithm in MapReduce. Poster in Proceedings of the ACM/IEEE International Conference for High Performance Computing and Communications conference (SC), November 2011, Seattle, Washington, USA.
    4. Narayan Ganesan, Sandeep Patel, and Michela Taufer: Simulations of Large Membrane Regions using GPU-enabled Computations - Preliminary Results. 2010 Symposium on Application Accelerators in High Performance Computing (SAAHPC10). July 13-15, 2010. University of Tennessee Conference Center, Knoxville, Tennessee, USA.
    5. Lifan Xu, S. Collins, M. Taufer, and D.G. Vlachos: Parallelization of Tau-Leaping Coarse-Grained Monte Carlo Method for Efficient and Accurate Simulations on GPUs. Poster in Proceedings of the ACM/IEEE International Conference for High Performance Computing and Communications conference (SC’09), November 2009, Portland, Washington, USA.
    6. M. Taufer, P. Saponaro, and O. Padron:Improving Reproducibility and Stability of Numerically Intensive Applications on Graphics Processing Units. Poster at the NVIDIA Research Summit,Sep 30- Oct 2, San Jose, CA.
    7. T. Estrada, M. Taufer:Docking@Home: Searching for New Drugs using Volunteer’s Computers. In Proceedings of The Grace Hopper Celebration of Women in Computing 2009, September 30 – October 3, 2009, Tucson, AZ.
    8. K.S. Hogle, J.H. Upton, A. Licon, M.-Y. Leung, and K.L. Johnson: Role of RNA secondary structure in replication of Nodamura virus RNA2. Poster at the American Society for Virology, Twenty-seventh Annual Meeting, 2009, Cornell University, Ithaca, NY.
    9. T. Estrada, M. Taufer, and K. Reed: Performance Analysis of Volunteer Computing Traces. In Proceedings of the ACM/IEEE International Conference for High Performance Computing, Network, torage, and Analysis conference (SC07), November 2007, Reno, Nevada, USA.
    10. D. Flores, T. Estrada, M. Taufer, P. Teller, and A. Kerstens: SimBA: a Discrete Event Simulator for Performance Prediction of Volunteer Computing Projects. In In Proceedings of the ACM/IEEE International Conference for High Performance Computing, Network, Storage, and Analysis conference (SC06), November 2006, Tampa, Florida.
    11. C. An, M. Taufer, and C.L. Brooks III: Predictor@home: A Multiscale, Distributed Approach for Protein Structure Prediction. Poster presented at the 229th ACM National Meeting, March 2005, San Diego, California, USA.
    12. C. An, M. Taufer, and C.L. Brooks III: Predictor@home: A Multiscale, Distributed Approach for Protein Structure Prediction. Poster presented at the 6th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP6), December 2004, Gaeta, Italy.

    Technical Reports

    1. Lifan Xu, Michela Taufer, Stuart Collins, and Dionisios G. Vlachos: Parallelization of Tau-Leap Coarse-Grained Monte Carlo Simulations on GPUs. Technical Report No. 2009/338, Dept. of Computer and Information Sciences, University of Delaware, Newark, DE (November 2009).
    2. Michela Taufer, Omar Padron, Philip Saponaro, Sandeep Patel: Improving Numerical Reproducibility and Stability in Large-Scale Numerical Simulations on GPUs. Technical Report No. 2009/339, Dept. of Computer and Information Sciences, University of Delaware, Newark, DE (November 2009).
    3. R. Zamudio, D. Catarino, M. Taufer, B. Stearn, and K. Bhatia: Topaz: a Firefox Protocol Extension for GridFTP based on Data Flow Diagrams. Technical Report UTEP-CS-06-18, University of Texas, El Paso, April 2006.
    4. D. Kondo, M. Taufer, J. Karanicolas, C. L. Brooks III, H. Casanova, and A. Chien: Characterizing and Evaluating Desktop Grids: An Empirical Study. Technical Report CS2003-069. University of California, San Diego, November 2003, La Jolla, California.
    5. P. Cicotti, M. Taufer, and A. Chien: DGMonitor: a Performance Monitoring Tool for Sandbox-based Desktop Grid Platforms. Technical Report CS2003-070, University of California, San Diego, November 2003, La Jolla, California.
    6. B. Uk, M. Taufer, T. Stricker, G. Settanni, A. Cavalli, and A. Caflisch: Combining Task- and Data Parallelism to Speed up Protein Folding on a Desktop Grid Platform - Is efficient protein folding possible with CHARMM on the United Devices MetaProcessor? Technical Report 386, Department of Computer Science, Swiss Federal Institute of Technology Zurich (ETHZ), November 2002, Zurich, Switzerland.
    7. B. Uk, M. Taufer, T. Stricker, G. Settanni, and A. Cavalli: Implementation and Characterization of Protein Folding on a Desktop Computational Grid – Is CHARMM a suitable candidate for the United Devices MetaProcessor? Technical Report 385, Department of Computer Science, Swiss Federal Institute of Technology Zurich (ETHZ), October 2002, Zurich, Switzerland.
    8. M. Taufer, T. Stricker, and R. Weber: Inverting Middleware Framework: Framework for Performance Analysis of Distributed OLAP Benchmarks on Clusters of PCs by Filtering and Abstracting Low Level Resource Usage. Technical Report 367, Department of Computer Science, Swiss Federal Institute of Technology Zurich (ETHZ), March 2002, Zurich, Switzerland.
    9. P. Arbenz, T. Stricker, M. Taufer, and U. von Matt: Performance Characterization and Modeling of the Molecular Simulation Code OPAL. Technical Report 310, Department of Computer Science, Swiss Federal Institute of Technology Zurich (ETHZ), November 1998, Zurich, Switzerland.

    Thesis

    1. M. Taufer: Inverting Middleware: Performance Analysis of Layered Application Codes in High Performance Distributed Computing. Dissertation ETH No. 14845, Institute for Computer Systems, Swiss Federal Institute of Technology Zurich (ETHZ), December 2002, Zurich, Switzerland. Published by Hartung Gorre Verlag Konstanz, Germany, ISBN 3-89649-821-5 ISSN 1611-0943.
    2. M. Taufer: Development of the Parallelization of the Software Package OPAL for the Simulation of Dynamic Molecules on Supercomputers. Master Thesis, Department of Computer Science, University of Padova, December 1996, Padova, Italy.