Scienza e ricerca

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Scienze Cognitive

(Cognitive science)

 

mindmodelling

Mind Modelling

 

Moore L. R., Gunzelmann G. - "An interpolation approach for fitting computationally intensive models". Cognitive Systems Research 19, 2014. Link

Moore L.R. - "Cognitive model exploration and optimization: a new challenge for computational science". Computational and Mathematical Organization Theory 17(3), 2011. Link

Harris J., Gluck K.A., Moore L.R. - "MindModeling@Home. . . and Anywhere Else You Have Idle Processors". 9th International Conference on Cognitive Modelling, 2009. Link

Moore L.R., Kopala M., Mielke T. et al. - "Simultaneous performance exploration and optimized search with volunteer computing". 19th ACM International Symposium on High Perfomance Distribuited Computing, 2010. Link

Harris J. - "MindModeling@Home: a large-scale computational cognitive modeling infrastructure". CSER 2008. Link

 


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Progetti Non Boinc - Citizen Science

(Not-Boinc)

 

CosmoQuest ° Dizeez ° Dimes ° EteRNA ° EyeWired ° Folding ° Fold.It ° Gimps ° HashClash ° LifeMaper ° Muon1 ° Phylo ° SetiLive ° SeventeenOrBurst ° Stardust ° The Cure ° ZooUniverse

 

 

CosmoQuest

 

Moon Mapper

Robbins S.J. - "New crater calibrations for the lunar crater-age chronology". Earth and Planetary Science Letters 403, 2014. Link
    
Robbins S.J, Antonenko I., Kirchoff M.R. et al. - "The variability of crater identification among expert and community crater analysts". Icarus 234 (109). Link

Antonenko I., Robbins S.J., Gay P. et al. - "Effects of Incidence Angle on Crater Detection and the Lunar Isochron System: Preliminary Results from the CosmoQuest MoonMappers Citizen Science Project”. 44th Lunar and Planetary Science Conference, 2013. Link
    
Robbins S.J, Antonenko I., Lehan C., Moore J. - "CosmoQuest Moon Mappers: Cataloguing the Moon”. National Lunar Sciences Forum, 2012. Link
   
Gay P., Antonenko I., Robbins S. J. et al. - "CosmoQuest MoonMappers: Citizen Lunar Exploration." European Planetary Science Congress 2012. Link


Education

Gugliucci N., Gay P., Bracey G., CosmoQuest Team - "Evaluating Motivations of Citizen Science and Impacts of Guerilla Outreach". Meeting of the Astronomical Society of the Pacific, 2014. Link

Gugliucci N., Bracey G., Costello K. et al. - "Designing Lessons for NGSS Using Citizen Science". Meeting of the Astronomical Society of the Pacific, 2014. Link

Bracey, G. "Evaluation of a Virtual Citizen Science Facility: A Comprehensive Mixed-Methods Approach". Astronomical Society of the Pacific Conference Series, 2014. Link

Gugliucci N. , Gay, P. , Bracey, G. , Antonenko, I. et al. - "Citizen Science with CosmoQuest: Science and Strategies". Astronomical Society of the Pacific Conference Series, 2014. Link

Gugliucci N. , Gay, P. , Bracey, G. - "Citizen Science Motivations as Discovered with CosmoQuest". Astronomical Society of the Pacific Conference Series, 2014. Link

Gay P., Lehan C. , Moore, J. et al. - "CosmoQuest: A Cyber-Infrastructure for Crowdsourcing Planetary Surface Mapping and More". 45th Lunar and Planetary Science Conference, 2014. Link

Gugliucci N., Gay P., Antonenko I. et al. - "CosmoQuest Collaboration. CosmoQuest Year 2: Citizen Science Progress, Motivations, and Education". Poster at the American Astronomical Society, AAS Meeting #223, 2014 (ADS abstract). Link

Gay P., Bracey G., Gugliucci N. - "TerraLuna: A CosmoQuest Adventure in Geology". 40th COSPAR Scientific Assembly, 2014. Link

Gay P. - "Designing a Virtual Research Facility to motivate Professional-Citizen Collaboration". 40th COSPAR Scientific Assembly, 2014. Link

Gay, P. - "Taking Science On-air with Google+". Communicating Astronomy with the Public Journal 14, 2014. Link

Gay, P. - "Collaborative Cyberinfrastructure: Crowdsourcing of Knowledge and Discoveries." Invited Talk at American Geophysical Union, 2013. Link

Gibbs M.G., Buxner S., Gay P., Crown D.A. et al. - "Collaboration in teacher workshops and citizen science." American Geophysical Union, 2013. Link

Gugliucci N., Gay P., Bracey G., CosmoQuest Team - "CosmoQuest Year 1.5: Citizen Scientist Behaviors and Site Usage Across Multiple Projects." Poster at the American Astronomical Society, AAS Meeting #222, 2013. Link

Gay P., Gugliucci N., Bracey G. et al. - "The CosmoQuest Virtual Research Facility for the Public." 44th Lunar and Planetary Science Conference, 2013. Link

Gugliucci N., Gay P., Bracey G., et al. - "Study of Citizen Scientist Motivations and Effectiveness of Social Media Campaigns". Poster at the American Astronomical Society, AAS Meeting #221, 2013. Link

Gay P., Lehan C., Bracey G., Gugliucci N. - "CosmoQuest: A Virtual Facility for Learning and Doing Science". European Planetary Science Congress 2012. Link

Lewis S., Gugliucci N., Amateur Astronomer Team et al. - "CosmoQuest: Virtual Star Parties as a Conduit to Citizen Science Research". American Astronomical Society Meeting #221, 2013. Link

Gugliucci N., Gay P., Bracey G. et al.- "Citizen Science and Planetary Science Education through CosmoQuest." American Geophysical Union, 2012. Link


Vesta

Wise J., Schmidt B.E., Cobb W.H. et al. - "The Dawn Mission’s Use of Google + Hangout for Professional Development and Product Assessment." 44th Lunar and Planetary Science Conference, 2013. Link

Scully J.E.C., Schmidt B.E., Gay P. et al. - "The Dawn Mission and Asteroid Mappers: Vesta Edition: The Impact of Crowd-Sourced Crater Counting". 44th Lunar and Planetary Science Conference, 2013. Link

 

 


 

Dizeez

 

Loquercio S., Good B.M., Al S. - "Dizeez: an online game for human gene-disease annotation". PloS One 8(8), 2013. Link

 


dimes

DIMES Project

 

Shavitt Y., Zilberman N. - "Arabian Nights: Measuring the Arab Internet During the 2011 Events". IEEE Network 26(6), 2012. Link

Feldman D., Shavitt Y., Zilberman N. - "A structural approach for PoP geo-location". Computer Networks 56(3), 2012. Link

Marcus D., Shavitt Y. - "RAGE – A rapid graphlet enumerator for large networks". Computer Networks 56(2), 2012. Link

Shavitt Y., Weinsberg U. - "Quantifying the Importance of Vantage Point Distribution in Internet Topology Mapping". IEEE Journal on Selected Areas in Communications 29(8), 2011. Link

Gonen M., Shavitt Y. - "Approximating the Number of Network Motifs". Internet Mathematics 6(3), 2009. Link

Shavitt Y., Weinsberg U. - "Quantifying the Importance of Vantage Points Distribution in Internet Topology Measurements". IEEE INFOCOM, 2009. Link

Weinsberg U., Shavitt Y., Shir E. - "Near-Deterministic Inference of AS Relationships". INFOCOM Workshops, 2009. Link

Allalouf M., Kaplan E., Shavitt Y. - "On the Feasibility of a Large Scale Distributed Testbed for Measuring Quality of Path Characteristics in the Internet". 5th International Conf on Testbeds and Research Infrastr for the Development of Networks & Communities and Workshops, 2009. Link

Almog A., Goldberger J., Shavitt Y. - "Unifying Unknown Nodes in the Internet Graph Using Semisupervised Spectral Clustering". International Conference on Data Mining Workshops, 2008. Link

Shavitt Y., Singer Y. - "Trading Potatoes in Distributed Multi-Tier Routing Systems". 3rd International Workshop on Economics of Networked Systems, 2008. Link

Feldman D., Shavitt Y. - "Automatic Large Scale Generation of Internet PoP Level Maps". Global Telecommunications Conference, 2008. Link

Shavitt Y., Tankel T. - "Hyperbolic Embedding of Internet Graph for Distance Estimation and Overlay Construction". IEEE Transactions on Networking, 16(1), 2008. Link

Carmi S., Havlin S., Kirkpatrick S., Shavitt Y., Shir E. - "From the Cover: A Model of Internet Topology Using K-Shell Decomposition". National Academy of Sciences 104(27), 2007. Link

Shavitt Y., Singer Y. - "Beyond Centrality - Classifying Topological Significance Using Backup Efficiency and Alternative Paths". New Journal of Physics 9, 2007. Link

Shavitt Y., Shir E. - "DIMES: Let the Internet Measure Itself". ACM SIGCOMM Computer Communication Review 35(5), 2005. Link

Buchanan M. - "DISTRIBUTED COMPUTING: Data-Bots Chart the Internet". Science 308(5723), 2005. Link

Shavitt Y., Tankel T. - "On the Curvature of the Internet and Its Usage for Overlay Construction and Distance Estimation". 23th Conference IEEE Computer and Communications Societies, 2004. Link

Shavitt Y., Sun X., Wool A., Yener B. - "Computing the Unmeasured: An Algebraic Approach to Internet Mapping". IEEE Journal on Selected Areas in Communications 22(1), 2004. Link

Raz D., Shavitt Y., Zhang L. - "Distributed Council Election". IEEE Transactions on Networking 12(3), 2004. Link

Shavitt Y., Tankel T. - "Big-Bang Simulation for Embedding Network Distances in Euclidean Space". IEEE Transactions on Networking 12(6), 2004. Link

 


 eterna

EteRNA Project

 

Portela F. - "Eterna: Towards a More Complete Crowdsourcing of Experimental Sciences". AAAS Annual Meeting 2016. Link

Anderson L., Fisker E., Treuille A. et al. - "Principles for Predicting RNA Secondary Structure Design Difficulty". J of Molec Biol 428(5), 2016. Link

Kosaraju V.S. - "Towards Rational RNA Therapeutics: 3D RNA Engineering in a Massive Open Laboratory". California State Science Fair, 2015. Link

Treuille A, Das R. - "Scientific rigor through videogames". Cell Press 39(11), 2014. Link

Rowles T.A. - "Power to the people: does Eterna signal the arrival of a new wave of crowd-sourced projects?".  BCM Biochem 14(26), 2013. Link

Lee J., Lee M., Kladwang W, Cantu D. et al. - "RNA design rules from a massive open laboratory". National Academy of Science of the USA, 2013. Link

 


eyewire-logo-blue

EyeWired

 

Green M.J, Seung H.S., EyeWirers et al. - "Analogous Convergence of Sustained and Transient Inputs in Parallel On and Off Pathways for Retinal Motion Computation". Cell Reports 14, 2015. Link

Kim J.S., Green M.J, Seung H.S., EyeWirers et al. - "Space-time wiring specificity supports direction selectivity in the retina". Nature 509(7500), 2014.Link

 


folding

Folding@Home

 

Mukherjee S., Pantelopulos G.A., Voelz V. - "Markov models of the apo-MDM2 lid region reveal diffuse yet two-state binding dynamics and receptor poses for computational docking". Sci Rep 19(6), 2016. Link

Zhou G., Voelz V. - "Using Kinetic Network Models To Probe Non-Native Salt-Bridge Effects on a-Helix Folding". J. Phys. Chem. B 120(5), 2016. Link

McGibbon R.T., Pande V. - "Efficient maximum likelihood parameterization of continuous-time Markov processes". J of Chem Phys 143(3), 2015. Link

Qi R., Wang L.P., Pande V. et al. - "United polarizable multipole water model for molecular mechanics simulation". J of Chem Phys 143(1), 2015. Link

Weber J.K., Shukla D., Pande V. - "Heat dissipation guides activation in signaling proteins". Proceeding Nation Acad of Science 112(33), 2015. Link

McGibbon R.T., Beauchamp K.A., Pande V. et al. - "MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories". Biophys J. 109(8), 2015. Link

Eastman P., Pande V. - "OpenMM: A Hardware Independent Framework for Molecular Simulations". Comput Sci Eng. 12(4), 2015.
Link

Vanatta D.K., Shukla D., Pande V. - "A network of molecular switches controls the activation of the two-component response regulator NtrC". Nature Communic 6(7283), 2015. Link

Shukla D., Lawrenz M, Pande V. - "Elucidating Ligand-Modulated Conformational Landscape of GPCRs Using Cloud-Computing Approaches". Methods in Enzymol 557, 2015. Link

McGibbon R.T., Pande V. - "Variational cross-validation of slow dynamical modes in molecular kinetics". J of Chem Phys 142(12), 2015. Link

Laury M.L., Wang L-P., Pande V. et al. - "Revised Parameters for the AMOEBA Polarizable Atomic Multipole Water Model". J Phys Chem B 119(29), 2015. Link

Shukla D., Pande V. et al. - "Markov state models provide insights into dynamic modulation of protein function". Acc Chem Res. 48(2), 2015. Link

Lawrenz M, Shukla D., Pande V. - "Cloud computing approaches for prediction of ligand binding poses and pathways". Scient Reports 5(7918), 2015. Link

Shukla D., Roux B., Meng Y., Pande V. - "Activation pathway of Src kinase reveals intermediate states as targets for drug design". Nature Communications 5 (3397), 2014. Link

McGibbon R.T., Shwantes C.R., Pande V. - "Statistical Model Selection for Markov Models of Biomolecular Dynamics". J. Phys Chem B. 118(24), 2014. Link

Shukla D., Meng Y, Roux B, Pande V. - "Activation pathway of Src kinase reveals intermediate states as targets for drug design". Nature Communications 5(3397), 2014. Link

Weber J.K., Jack R.L., Schwantes C.R., Pande V. - "Dynamical Phase Transitions Reveal Amyloid-like States on Protein Folding Landscapes". Biophys J. 107(4), 2014. Link

Baiz C.R., Lin Y.S, Peng C.S, Pande V. et al. - "A Molecular Interpretation of 2D IR Protein Folding Experiments with Markov State Models". Biophys J. 106(6), 2014. Link

Kohlhoff K.J., Shukla D., Lawrenz M, Pande V. et al. - "Cloud-based simulations on Google Exacycle reveal ligand-modulation of GPCR activation pathways". Nature Chemistry 6, 2013. Link

Mc Gibbon R., Pande V. - "Learning Kinetic Distance Metrics for Markov State Models of Protein Conformational Dynamics". J.Chem. Theory Comput. 9(7), 2013. Link

Gu C., Chang H.W., Maibaum L., Pande V. et al. - "Building Markov State Models with Solvent Dynamics". Bioinfomatics 14(2), 2013. Link

Schwantes C.R., Pande V. - "Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9". J.Chem. Theory Comput. 9(4), 2013. Link

Weber J.K., Jack R., Pande V. - "Emergence of Glass-like Behavior in Markov State Models of Protein Folding Dynamics". J. Americ. Chem. Soc 135(15), 2013. Link

Lane T.J., Shukla D., Pande V. - "To milliseconds and beyond: challenges in the simulation of protein folding". Curr. Opin. Struct. Biol. 23(1), 2013. Link

Eastman P., Friedrichs M.S., Chodera J.D., Radmer R.J, Pande V. et al. - "OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation". J.Chem. Theory Comput. 9(1), 2013. Link

Cronkite-Ratcliff B., Pande V. - "MSMExplorer: Visualizing Markov State Models for Biomolecule Folding Simulations". Bioinformatics 29(7), 2013. Link

Lin Y.S., Pande V. - "Effects of familial mutations on the monomer structure of AlfaBeta42". Biophys J. 103(12), 2012. Link

Ring A.M., Lin J.X., Feng D., Mitra S., Pande V. et al. - "Mechanistic and structural insight into the functional dichotomy between IL-2 and IL-15". Nature Immunol. 13(12), 2012. Link

Walker J.R., Novick P.A., Parsons W.H., Pande V. et al. - "Marked difference in saxitoxin and tetrodotoxin affinity for the human nociceptive voltage-gated sodium channel (Nav1.7)". National Academic of Science of USA 109(44), 2012. Link

Beauchamp K.A., Mc Gibbon R., Lin Y., Pande V. - "Simple few-state models reveal hidden complexity in protein folding". PNAS 109(44), 2012. Link

Voelz V.A., Jager M., Yao S., Pande V. et al. - "Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment". J. Americ. Chem. Soc 134(30), 2012. Link

Levin A.M., Bates D.L., Ring A.M., Krieg C., Pande V. et al. - "Exploiting a natural conformational switch to engineer an interleukin-2 ‘superkine’". Nature 484 (7395), 2012. Link

Lin Y.S., Bowman G.R., Beauchamp K.A., Pande V. - "Investigating how peptide length and a pathogenic mutation modify the structural ensemble of amyloid beta monomer". Biophys J. 102(2), 2012. Link

Lane J.T., Pande V. - "A Simple Model Predicts Experimental Folding Rates and a Hub-Like Topology". J. Phys.Chem. B 116(23), 2012. Link

Novick P.A., Lopes D.H., Branson K.M. et al. - "Design of Beta-Amyloid Aggregation Inhibitors from a Predicted Structural Motif". J. Medical Chem. 55(7), 2012. Link

Rajadas J., Liu C.W., Novick P. et al. - "Rationally designed turn promoting mutation in the amyloid beta-peptide sequence to stabilize oligomers in solution". Plos One 6(7), 2011. Link

Pronk S., Larsson P., Pouya I. et al - "Copernicus: A new paradigm for parallel adaptive molecular dynamics". Conference on High Performance Computing, 2011. Link

Beauchamp K.A., Ensign D.L., Das R., Pande V. - "Quantitative comparison of villin headpiece subdomain simulations and triplet–triplet energy transfer experiments". National Academic of Science of USA 108(31), 2012. Link

Wagoner J.A., Pande V. - "A smoothly decoupled particle interface (SDPI): new methods for coupling explicit and implicit solvent". J. Chem Phys 134(21), 2011. Link

Bowman G.R., Voelz V.A., Pande V. - "Taming the complexity of protein folding". Curr. Opin. Struct. Biol. 21(1), 2011. Link

Bowman G.R., Voelz V.A., Pande V. - "Atomistic folding simulations of the five helix bundle protein Lambda6-85". J. Chem Phys 133(4), 2011. Link

Snow C.D., Aitken C.E., Pande V. - "Non-Bulk-Like Solvent Behavior in the Ribosome Exit Tunnel". PloS Comput Biol. 6(10), 2011. Link

Eastman P., Pande V. - "Speeding development and execution speed with Just In Time GPU code development approaches". Gpu Computing Gems Emerald Edition Book, 2011. Link

Haque I., Pande V. - "Large-scale Chemical Informatics on the GPU". Gpu Computing Gems Emerald Edition Book, 2011. Link

Kasson P.M., Lindahl E., Pande V. - "Water Ordering at Membrane Interfaces Controls Fusion Dynamics". J of American Chem. Society 133(11), 2011. Link

Haque I., Pande V. - "Hard Data on Soft Errors: A Large-Scale Assessment of Real-World Error Rates in GPGPU". 10th Cluster, Cloud and Grid Computing Conference, 2010. Link

Pande V., Beauchamp K., Bowman G.R. - "Everything you wanted to know about Markov State Models but were afraid to ask". Methods 52(1), 2010. Link

Bowman G.R, Pande V. - "Protein folded states are kinetic hubs". National Acad of Science of USA 107(38), 2010. Link

Bowman G.R, Ensign D.L., Pande V. - "Enhanced Modeling via Network Theory: Adaptive Sampling of Markov State Models". J of Chem Theory and Comput 6(3). Link

Eastman P, Pande V. - "OpenMM: A Hardware Abstraction Layer for Molecular Simulations". Computing in Science and Engineering 12, 2010. Link

Ponder J.W., Chuanjie W., Ren P., Pande V. et al. - "Current Status of the AMOEBA Polarizable Force Field". J. of Physical Chem. B. 114(8), 2010. Link

Voelz V.A., Singh V.R., Lapidus L.J., Pande V. - "Unfolded state dynamics and structure of protein L characterized by simulation and experiment". J of American Chem. Society 132(13), 2010. Link

Bowman G.R., Pande V. - "Network models for molecular kinetics and their initial applications to human health". Cell Res. 20(6), 2010. Link

DePaul A.J., Thompson E., Pande V et al. - "Equilibrium conformational dynamics in an RNA tetraloop from massively parallel molecular dynamics". Nucleic Acid Res. 38(14), 2010. Link

DePaul A.J., Thompson E., Patel S.S., Sorin E.J. - "Evaluating Molecular Mechanical Potentials for Helical Peptides and Proteins". PloS One 5(4), 2010. Link

Pande V. - "A simple theory of protein folding kinetics". Phys Rev Lett. 105(19), 2010. Link

Bowman G.R., Pande V. - "Protein folded states are kinetic hubs". National Acad of Science of USA 107(38), 2010. Link

Kasson P.M., Lindahl E., Pande V. - "Atomic-Resolution Simulations Predict a Transition State for Vesicle Fusion Defined by Contact of a Few Lipid Tails". PloS One 6(6), 2010. Link

Voelz V.A., Bowman G.R., Beauchamp K., Pande V. - "Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1-39)". J. of American Chem Society 132(5), 2010. Link

Bacallado S., Chodera J.D., Pande V. - "Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint". J. Chem Phys. 131(4), 2009. Link

Kasson P.M., Ensign D.L., Pande V. - "Combining Molecular Dynamics with Bayesian Analysis To Predict and Evaluate Ligand-Binding Mutations in Influenza Hemagglutinin".  J. of American Chem Society 131(32), 2009. Link

Bowman G.R., Pande V. - "The Roles of Entropy and Kinetics in Structure Prediction". PloS One 4(6), 2009. Link

Larson S.M., Snow C.D., Shirts M., Pande V. - "Folding@home and Genome@Home: Using distributed computing to tackle previously intractable problems in computational biology". ArXiv, 2009. Link

Bowman G.R., Pande V., Huang X. - "Using generalized ensemble simulations and Markov state models to identify conformational states". Methods 49(2), 2009. Link

Beberg A.L., Ensign D.L., Pande V. et al. - "Folding@home: lessons from eight years of distributed computing". IEEE Symposium on Parallel and Distribuited Processing, 2009. Link

Voelz V.A., Luttmann E., Pande V. et al. - "Probing the nanosecond dynamics of a designed three-stranded beta-sheet with massively parallel molecular dynamics simulation". Int. J. Mol. Sci. 10(3), 2009. Link

Voelz V.A., Petrone P., Pande V. - "A multiscale approach to sampling nascent peptide chains in the ribosomal exit tunnel". Pac. Symp. Biocomputing, 2009. Link

Ensign D.L., Pande V. - "The Fip35 WW Domain Folds with Structural and Mechanistic Heterogeneity in Molecular Dynamics Simulations". Biophys J. 96(8), 2009. Link

Friedrichs M.S, Eastman P., Pande V. et al. - "Accelerating Molecular Dynamic Simulation on Graphics Processing Units". J. Comput. Chem. 30(6), 2009. Link

Kelley N.W., Huang X., Frydman J, Pande V. - "The predicted structure of the headpiece of the Huntingtin protein and its implications on Huntingtin aggregation". J. Molec. Biol. 388(5), 2009. Link

Kasson P.M., Pande V. - "Combining Mutual Information with Structural Analysis to Screen for Functionally Important Residues in Influenza Hemagglutinin". Pac. Symp. Biocomputing, 2009. Link

Luttmann E., Ensign D.L., Pande V. et al. - "Accelerating Molecular Dynamic Simulation on the Cell processor and PlayStation 3". J. Comput. Chem. 30(2), 2009. Link

Petrone P.M., Snow C.D., Pande V. - "Side-chain recognition and gating in the ribosome exit tunnel". National Acad. of Science of USA 105(43), 2009. Link

Kelley N.W., Vishal V., Krafft G.A., Pande V. - "Simulating oligomerization at experimental concentrations and long timescales: A Markov state model approach".  J. Chem Phys. 129(21), 2008. Link

Bowman G.R., Huang X., Yao Y., Pande V. et al. - "Structural Insight into RNA Hairpin Folding Intermediates". J. of American Chem Society 130(30), 2008. Link

Huang X, Bowman G.R., Pande V. - "Convergence of folding free energy landscapes via application of enhanced sampling methods in a distributed computing environment". J. Chem Phys. 128(20), 2008. Link

Elsen E., Vishal V., Houston M., Pande V. et al. - "N-Body simulation on GPUs". ArXiv, 2007. Link

Hinrichs N.S., Pande V. - "Calculation of the distribution of eigenvalues and eigenvectors in Markovian state models for molecular dynamics". J. Chem Phys. 126(24), 2007.  Link

Ensign D.L., Kasson P.M., Pande V. - "Heterogeneity Even at the Speed Limit of Folding: Large-scale Molecular Dynamics Study of a Fast-folding Variant of the Villin Headpiece". J. Molec. Biol. 374(3), 2007. Link

Kasson P.M., Pande V. - "Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics". PloS Comput. Biol. 3(11), 2007.  Link

Kasson P.M., Zomorodian A., Park S., Pande V. et al. - "Persistent voids: a new structural metric for membrane fusion". Bioinformatics 23(14), 2007. Link

Del Lucent, Vishal V., Pande V. - "Protein folding under confinement: a role for solvent". National Acad. of Science of USA 104(25), 2007. Link

Chodera J.D., Singhal N., Pande V. et al. - "Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics". J. Chem Phys. 126(15), 2007. Link

Beberg A.L., Pande V. - "Storage@home: Petascale Distributed Storage". IEEE International Parallel and Distributed Processing Symposium, 2007. Link

Kasson P.M., Pande V. - "Predicting structure and dynamics of loosely-ordered protein complexes: influenza hemagglutinin fusion peptide". Pac Symp Biocomp 2007. Link

Park S., Ensign D.L., Pande V. - "A Bayesian Update Method for Adaptive Weighted Sampling". Phys. Rev. E 74, 2006. Link

Jayachandran G., Vishal V, Garcia A.E., Pande V. - "Local structure formation in simulations of two small proteins". J. Struct. Biol. 157(3), 2006. Link

Snow C.D., Rhee Y.M., Pande V. - "Kinetic Definition of Protein Folding Transition State Ensembles and Reaction Coordinates". Biophys J. 91(1), 2006. Link

Jayachandran G., Shirts M.R., Pande V. - "Parallelized Over Parts Computation of Absolute Binding Free Energy with Docking and Molecular Dynamics". J. of Chem Phys 125, 2006. Link

Jayachandran G., Shirts M.R., Pande V. - "Folding Simulations of the Villin Headpiece in All-Atom Detail". J. of Chem Phys 124, 2006. Link

Kasson P.M., Kelley N.W., Pande V. et al. - "Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion". National Acad of Science of USA 103(32), 2006. Link

Suydam I.T., Snow C.D., Boxer S.G, Pande V. - "Electric Fields at the Active Site of an Enzyme: Direct Comparison of Experiment with Theory". Science 313(5784), 2006. Link

Chong L.T., Swope W.C., Pitera J.W, Pande V. - "Kinetic Computational Alanine Scanning: Application to p53 Oligomerization". J. Molec. Biol. 357(3), 2006. Link

Park S., Pande V. - "Validation of Markov state models using Shannon’s entropy". J. Chem. Phys 124(5), 2006. Link

Rhee Y.M., Pande V. - "On the role of chemical detail in simulating protein folding kinetics". Chem Phys 323, 2006. Link

Sorin E.J., Pande V. - "Nanotube confinement denatures protein helices". J. of American Chem Society 128(19), 2006. Link

Sorin E.J., Rhee Y.M., Shirts M.R., Pande V. - "The solvation interface is a determining factor in peptide conformational preferences". J. Molec. Biol. 356(1), 2005. Link

Petrone P., Pande V. - "Can conformational change be described by only a few normal modes?". Biophys J. 90(5), 2005. Link

Zagrovic B., Jayach G., Millet I.S., Doniach S., Pande V. - "How large is alpha-helix in solution? Studies of the radii of gyration of helical peptides by SAXS and MD". J. Molec. Biol. 353(2), 2005. Link

Singhal N., Pande V. - "Error Analysis in Markovian State Models for protein folding". J. Chem. Phys 123(12), 2005. Link

Fujitani H., Tanida Y., Ito M., Pande V. et al. - "Direct calculation of the binding free energies of FKBP ligands". J. Chem. Phys 123(8), 2005. Link

Park S., Radmer R.J., Klein T.E., Pande V. - "A New Set of Molecular Mechanics Parameters for Hydroxyproline and Its Use in Molecular Dynamics Simulations of Collagen-Like Peptides". J. Comput. Chem. 26(15), 2005. Link

Shirts M.R., Pande V. - "Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration". J. Chem. Phys 122(14), 2005. Link

Shirts M.R., Pande V. - "Solvation free energies of amino acid side chain analogs for common molecular mechanics water models". J. Chem. Phys 122(13), 2005. Link

Elmer S.P., Park S., Pande V. - "Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water". J. Chem. Phys 123(11), 2005. Link

Elmer S.P., Park S., Pande V. - "Foldamer dynamics expressed via Markov state models. II. State space decomposition". J. Chem. Phys 123(11), 2005. Link

Zagrovic B., Lipfert J., Sorin E.J., Pande V. et al. - "Unusual compactness of a polyproline type II structure". National Acad of Science of USA 102(33), 2005. Link

Snow C.D., Sorin E.J., Rhee Y.M., Pande V. - "How well can simulation predict protein folding kinetics and thermodynamics?". Annual Review of Biophy and Biomolec Struct 34, 2005. Link

Sorin E.J., Pande V. - "Empirical Force-Field Assessment: The Interplay Between Backbone Torsions and Noncovalent Term Scaling". J. Comput. Chem. 26(7), 2005. Link

Sorin E.J., Pande V. - "Exploring the Helix-Coil Transition via All-atom Equilibrium Ensemble Simulations". Biophys J. 88(4), 2005. Link

Sorin E.J., Rhee Y.M., Pande V. - "Does Water Play a Structural Role in the Folding of Small Nucleic Acids?". Biophys J. 88(4), 2005. Link

Chong L.T., Snow C.D., Rhee Y.M., Pande V. - "Dimerization of the p53 Oligomerization Domain: Identification of a Folding Nucleus by Molecular Dynamics Simulations". J. Molec. Biol. 345(4), 2005. Link

Singhal N., Snow C.D., Pande V. - "Using path sampling to build better Markovian state models: Predicting the folding rate and mechanism of a tryptophan zipper beta hairpin". J. Chem. Phys 121(1), 2004. Link

Sorin E.J., Rhee Y.M., Pande V. et al. - "Simulations of the role of water in the protein-folding mechanism". National Acad of Science of USA 101 (17), 2004. Link

Snow C.D., Qiu L., Du D., Gai F., Hagen S.J., Pande V. - "Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy". National Acad of Science of USA 101(12), 2004. Link

Sorin E.J., Rhee Y.M., Vishal V., Pande V. et al. - "Does Native State Topology Determine the RNA Folding Mechanism?". J. Molec. Biol. 337(4), 2004. Link

Zagrovic B., Pande V. - "Structural correspondence between the alpha-helix and the random-flight chain resolves how unfolded proteins can have native-like properties". Nat. Struc. Biol. 10(11), 2003. Link

Shirts M.R., Bair E., Hooker G., Pande V. - "Equilibrium Free Energies from Nonequilibrium Measurements Using Maximum-Likelihood Methods". Phys. Rev. Lett. 91(14), 2003. Link

Shirts M.R., Pitera J.W., Swope W:C., Pande V. - "Extremely precise free energy calculations of amino acid side chain analogs: Comparison of common molecular mechanics force fields for proteins". J. Chem. Phys. 119(11), 2003. Link

Zagrovic B., Pande V. - "Solvent Viscosity Dependence of the Folding Rate of a Small Protein: Distributed Computing Study". J. Comput. Chem. 24(12), 2003. Link

Sorin E.J., Rhee Y.M., Nakatani B.J., Pande V. - "Insights Into Nucleic Acid Conformational Dynamics from Massively Parallel Stochastic Simulations". Biophys. J. 85(2), 2003. Link

Pande V., Baker I, Chapma J., Elmer S.P. et al. - "Atomistic protein folding simulations on the submillisecond timescale using worldwide distributed computing". Biopolymers 68(1), 2003. Link

Rhee Y.M., Pande V. - "Multiplexed-Replica Exchange Molecular Dynamics Method for Protein Folding Simulation". Biophys. J. 84(2 pt1), 2003. Link

Snow C.D., Zagrovic B., Pande V. - "The Trp Cage: Folding Kinetics and Unfolded State Topology via Molecular Dynamics Simulations". J. of American Chem Society 124(49), 2002. Link

Snow C.D., Nguyen H., Pande V., Grubele M. - "Absolute comparison of simulated and experimental protein-folding dynamics". Nature 420(6911), 2002. Link

Zagrovic B., Snow C.D., Khaliq S., Shirts M.R., Pande V. - "Native-like Mean Structure in the Unfolded Ensemble of Small Proteins". J. Molec. Biol. 323(1), 2002. Link

 Zagrovic B., Snow C.D., Shirts M.R., Pande V. - "Simulation of Folding of a Small Alpha-helical Protein in Atomistic Detail using Worldwidedistributed Computing". J. Molec. Biol. 323(5), 2002. Link

Zagrovic B., Sorin E.J., Pande V. - "Beta-Hairpin Folding Simulations in Atomistic Detail Using an Implicit Solvent Model". J. Molec. Biol. 313(1), 2001. Link

Shirts M.R., Pande V. - "Mathematical Foundations of ensemble dynamics". Phys. Rev. Lett. 86, 2001. Link

Shirts M.R., Pande V. - "Screen savers of the world, Unite!". Science 290(5498), 2000. Link

 

 


foldit

Fold.it

 

Horowitz S., Koepnick B., Foldit playest et al. - "Determining crystal structures through crowdsourcing and coursework". Nature Comunic 7(12549), 2016. Link

Khoury G.A., Liwo A., Khatib F., Zhou H., Foldit players et al. - "WeFold: A Coopetition for Protein Structure Prediction". Proteins:Structure,Function and Bioinformatics 82, 2014.  Link

Cooper S., Khatib F., Baker D. - "Increasing Public Involvement in Structural Biology". Structure 21(9), 2013. Link

Eiben C.B., Siegel J.B., Bale J.B., Cooper S., Baker D., Foldit players et al. - "Increased Diels-Alderase activity through backbone remodeling guided by Foldit players". Nature Biotechnology 30(2), 2012. Link

Khoury G.A., Khatib F., Zhou H, Foldit players et al. - "Hybrid Human Protein Structure Prediction via the Online Multiplayer Game Foldit Coupled with an Iterative Clustering Approach for Selection of Near-Native Structures, Knowledge-Based Refinement, and State-of-the-Art Scoring Functions". CASP10, 2012. Link

Bortot L.O., Faccioli R.A., Foldit players et al. - "WeFold community . Application of Replica Exchange Molecular Dynamics with Implicit Solvation for Refinement of Collaboratively Generated and Ranked Models". CASP 10 Meeting, 2012. Link

Cooper S., Khatib F., Makedon I., Barbero J., Baker D., Foldit players et al. - "Analysis of social gameplay macros in the Foldit cookbook".  6th International Conference on the Foundations of Digital Games, 2011. Link

Gilski M., Kazmierczyk M., Krzywda S., Zábranská H., Cooper S."High-resolution structure of a retroviral protease folded as a monomer". Acta Crystallographica D67, 2011. Link

Khatib F., Cooper S., Tyka M.D., Xu K., Makedon I., Popovic Z., Baker D., Foldit players - "Algorithm discovery by protein folding game players". National Academy of Sciences of USA 108(47), 2011. Link

Khatib F., DiMaio F., Cooper S., Kazmierczyk M., Foldit players et al. - "Crystal structure of a monomeric retroviral protease solved by protein folding game players". Nature Structural and Molecular Biology 18, 2011. Link

Cooper S., Khatib F., Treuille A., Baker D., Foldit players et al. - "Predicting protein structures with a multiplayer online game". Nature 466, 2010. Link

Cooper S., Treuille A., Barbero J., Leaver-Fay A., Baker D., Foldit players et al. - "The challenge of designing scientific discovery games". 5th International Conference on the Foundations of Digital Games, 2010. Link

 

Su Fold.IT (About Fold.IT)

Curtis V. - "Motivation to Participate in an Online Citizen Science Game A Study of Foldit". Science Commun 37(6), 2015. Link

Parslow G.R. - "Commentary: crowdsourcing, Foldit, and scientific discovery games".  Biochem Mol. Biol. Educ 41(2), 2013. Link

Farley P.C. - "Using the computer game "FoldIt" to entice students to explore external representations of protein structure in a biochemistry course for nonmajors". Biochem Mol. Biol. Educ 41(1), 2013. Link

Good B.M., Al S. - "Games with a scientific purpose". Genome Biol. 12(12), 2011. Link

 

 


gimps

Gimps

 

Childers G. - "Factorization of a 1061-bit number by the Special Number Field Sieve". 2012. Link

Wanko J.J, Venable C.H. - "Investigating Prime Numbers and The Great Internet Mersenne Prime Search". Mathematics teaching in the Middle School 8(2), 2002. Link

Woltman G. - "On the discovery of the 38th known Mersenne Prime". 1999. Link

Gage J.S. - "The great Internet Mersenne prime search". MD Comput. 15(4), 1998. Link

 


 

HashClash

 

Stevens M. - "Attacks on Hash Functions and Applications". Phd Thesis, 2012. Link

Stevens M. - "Single-block collision attack on MD5". Cryptology ePrint Archive 40, 2012. Link

Stevens M., Lenstra A. and De Weger B. - "Chosen-prefix Collisions for MD5 and Applications". Journal of Cryptology 2(4), 2012. Link

Stevens M., Lenstra A., De Weger B. et al - "Short Chosen-Prefix Collisions for MD5 and the Creation of a Rogue CA Certificate". Crypto 2009. Link

Stevens M. - "On Collisions for MD5". Master Thesis 2007. Link

Stevens M., Lenstra A., and De Weger B. - "Chosen-prefix Collisions for MD5 and Colliding X.509 Certificates for Different Identities". Lecture Notes in Computer Science 4515, 2007. Link

Stevens M. - "Fast Collision Attack on MD5". Cryptology ePrint Archive 104, 2006. Link

Stevens M., Lenstra A., De Weger B. - "Target Collisions for MD5 and Colliding X.509 Certificates for Different Identities". Cryptology ePrint Archive 360, 2006. Link

 


 

LifeMapper

 

Cavner J.A., Stewart A.M. et al. - "An innovative Web Processing Services based GIS architecture for global biogeographic analyses of species distributions". OSGeo Journal 10, 2012. Link

Stewart A. - "LifeMapper: Open Source Geospatial Tools for the Biological Community". GIS Day at Kansas University, 2008. Link

Stockwell D.R.B., Beach J.H., Stewart A., et al. - "The use of the GARP genetic algorithm and internet grid computing in the Lifemapper world atlas of species biodiversity". Ecological Modeling, 2006. Link

Beach J.H., Stewart A.M., Vorontsov G.Y., et al. - "The Future of Biodiversity: Mapping and Predicting the Distribution of Life with Distributed Computation".  ESRI User Conference, 2002. Link

 


Muon1

 

Brooks S. - "Muon capture schemes for the Neutrino Factory". Phd Thesis, 2010. Link

 


 

phylo

Phylo

 

William S. - "Biology: A Game for a Crowd". Biomed Comput. Review, 2014. Link

Kwak D., Kam A., Becerra D., Zhou Q. et al. - "Open-Phylo: a customizable crowd-computing platform for multiple sequence alignment". Genome Biol. 14(10), 2013. Link

Kawrykow A., Roumanis G., Kam A., Kwak D. et al. - "Phylo: a citizen science approach for improving multiple sequence alignment". PloS One 7(3), 2012. Link

 


SetiLive

 

Nikitin I. - "Statistical analysis of narrow-band signals at setilive.org". In Press. Link

 


 

Seventeen Or Bust

 

Helm L. - "Colbert Number". MathWorld Wolfram Web Resource, 2009. Link

Helm L., Moore P., Samidoost P., Woltman G. - "Resolution of the Mixed Sierpinski Problem." Integers: Elec. J. Combin. Numb. Th. 8(A61), 2008. Link

Helm L., Norris D. - "Seventeen or Bust: a distribuited attack on Sierpinski Problem". NSDL Scout Report for Math 1(17), 2002. Link

 

 


stardust

Stardust@Home

 

 

Westphal A.J., Bechtel H.A., Brenker F.E. et al. - "Final reports of the Stardust Interstellar Preliminary Examination". Meteoritics & Planetary Science 49 (9), 2014. Link

Stroud R.M., Allen C., Ansari A. et al. - "Stardust Interstellar Preliminary Examination XI: Identification and elemental analysis of impact craters on Al foils from the Stardust Interstellar Dust Collector". Meteoritics & Planetary Science 49 (9), 2014. Link

Sterken V.J., Westphal A.J., Altobelli N. - "Stardust Interstellar Preliminary Examination X: Impact speeds and directions of interstellar grains on the Stardust dust collector". Meteoritics & Planetary Science 49 (9), 2014. Link

Postberg F., Hillier J.K., Armes S.P. et al. - "Stardust Interstellar Preliminary Examination IX: High-speed interstellar dust analog capture in Stardust flight-spare aerogel". Meteoritics & Planetary Science 49 (9), 2014. Link

Gainsforth Z., Brenker F.E., Simionovici A.S. et al. - "Stardust Interstellar Preliminary Examination VIII: Identification of crystalline material in two interstellar candidates". Meteoritics & Planetary Science 49 (9), 2014. Link

Flynn G.J., Sutton S.R. et al. - "Stardust Interstellar Preliminary Examination VII: Synchrotron X-ray fluorescence analysis of six Stardust interstellar candidates measured with the Advanced Photon Source 2-ID-D microprobe". Meteoritics & Planetary Science 49 (9), 2014. Link

Simionovici A.S., Lamelle L. et al. - "Stardust Interstellar Preliminary Examination VI: Quantitative elemental analysis by synchrotron X-ray fluorescence nanoimaging of eight impact features in aerogel". Meteoritics & Planetary Science 49 (9), 2014. Link

Brenker F.E., Westphal A.J., Vincze L. et al. - "Stardust Interstellar Preliminary Examination V: XRF analyses of interstellar dust candidates at ESRF ID13". Meteoritics & Planetary Science 49 (9), 2014. Link

Buttherworth A., Westphal A.J., Tyliszczak T. et al. - "Stardust Interstellar Preliminary Examination IV: Scanning transmission X-ray microscopy analyses of impact features in the Stardust Interstellar Dust Collector". Meteoritics & Planetary Science 49 (9), 2014. Link

Bechtel H.A., Flynn G.J., Allen C. et al. - "Stardust Interstellar Preliminary Examination III: Infrared spectroscopic analysis of interstellar dust candidates". Meteoritics & Planetary Science 49 (9), 2014. Link

Frank D.R., Westphal A.J., Zolensky M.E. et al. - "Stardust Interstellar Preliminary Examination II: Curating the interstellar dust collector, picokeystones, and sources of impact tracks".Meteoritics & Planetary Science 49 (9), 2014. Link

 Westphal A.J., Anderson D.A., Buttherworth A. et al. - "Stardust Interstellar Preliminary Examination I: Identification of tracks in aerogel". Meteoritics & Planetary Science 49 (9), 2014. Link

 Westphal A.J., Stroud R.M, Bechtel H.A. et al. - "Evidence for interstellar origin of seven dust particles collected by the Stardust spacecraft". Science 345(6198), 2014. Link

 Westphal A.J., De Gregorio B., Lettieri R. et al. - "Community Supported Stardust Compendia". NASA Technical Report 20130004203, 2013. Link

Westphal A.J., Allen C., Bajt S. et al. - "Constraints on the Interstellar Dust Flux Based on Stardust@Home Search Results". 42th NASA Lunar and Planetary Science Conference, 2011. Link

Westphal A.J., Buttherworth A., Frank D. et al. - "Discovery of Interstellar Dust Candidates in Stardust aerogel collectors through Stardust@home". Fall Meeting of American Geophysical Union, 2010. Link

Westphal A.J., Allen C. et al. - "Two interstellar dust candidates from the stardust aerogel interstellar dust collector". Meteoritics and Planetary Science Supplement 73(5302), 2010. Link

Westphal A.J., Allen C., Bajt S. et al. - "Stardust Interstellar Preliminary Examination (ISPE)". 40th NASA Lunar and Planetary Science Conference, 2009. Link

Westphal A.J., Bastien R.K. et al. - "Search for Conteporary Interstellar Dust in the Stardust Collector". 38th NASA Lunar and Planetary Science Conference, 2007. Link

Westphal A.J., Buttherworth A., Snead C.J. et al. - "Stardust@home: A Massively Distributed Public Search for Interstellar Dust in the Stardust Interstellar Dust Collector". 36th NASA Lunar and Planetary Science Conference, 2005. Link

 

 


 

The Cure

 

Good B.M., Loguercio S., Griffith O.L., Nanis M. et al. - "The Cure: Design and Evaluation of a Crowdsourcing Game for Gene Selection for Breast Cancer Survival Prediction". JMIR Serious Games 2(2), 2014. Link

 


 zooniverse

ZooUniverse

 

Progetti "GalaxyZoo/GalaxyZoo 2/GalaxyZoo Supernova/GalaxyZoo Hubble/RadioGalaxy Zoo/MoonZoo"

 

Kunchner M.J., Silverberg S.M. et al. - "Disk Detective:  Discovery of New Circumstellar Disk Candidates through Citizen Science". Astrophy Jour 830(2), 2016. Link

Holincheck A.J., "Galaxy Zoo: Mergers - Dynamical Models of Interacting Galaxies". Monthly Not. of the Royal Astron. Soc. 2016.
Link

Master K., Younh Ho e., Cox J. et al. -  "Science Learning via Participation in Online Citizen Science". J of Science Commun, 2016.
Link

Cox J., Younh Ho e. et al. - "How is success defined and measured in online citizen science?  A case study of Zooniverse projects". Comput in Science and Engineering 17(4), 2016. Link

Bugiolacchi R., Bamfort S., Tar P. et al - "The Moon Zoo citizen science project: Preliminary results for the Apollo 17 landing site". Icarus 01.021, 2016. Link

More A., Verma A., Marshall P.J. et al. - "Space Warps: II. New Gravitational Lens Candidates from the CFHTLS Discovered through Citizen Science". Monthly Not. of the Royal Astron. Soc. 455(2), 2015. Link

Banfield J.K., Wong O.I.. Willett K.W. et al. - "Radio Galaxy Zoo: host galaxies and radio morphologies derived from visual inspection". Monthly Not. of the Royal Astron. Soc. 453(3), 2015. Link

Dieleman S., Willett K.W., Dambre J. - "Rotation-invariant convolutional neural networks for galaxy morphology prediction". Monthly Not. of the Royal Astron. Soc. 450(2), 2015. Link

Willett K.W., Schawinski K., Simmons B.D. et al. - "Galaxy Zoo: the dependence of the star formation-stellar mass relation on spiral disk morphology". Monthly Not. of the Royal Astron. Soc. 499(1), 2015. Link

Smethurst R.J., Lintott C.J., Simmons B.D. et al. - "Galaxy Zoo: Evidence for Diverse Star Formation Histories through the Green Valley". Monthly Not. of the Royal Astron. Soc. 450(1), 2015. Link

Galloway M.A., Willet K.W., Fortson L.F. et al. - "Galaxy Zoo: the effect of bar-driven fueling on the presence of an active galactic nucleus in disc galaxies". Monthly Not. of the Royal Astron. Soc. 448(4), 2015. Link

Clifton Johnson L., Seth A.C., Dalcanton J.J. et al. - "Phat stellar cluster survey II. Andromeda project cluster catalog". The Astrophys Jour 802(2), 2015. Link

Kung R., Saha P., More A. et al. - "Gravitational Lens Modelling in a Citizen Science Context". Monthly Not. of the Royal Astron. Soc. 447(3), 2015. Link

Keel W.C., Manning A.M., Holwerda B.W. et al. - "Galaxy Zoo: The Ultraviolet Attenuation Law in Backlit Spiral Galaxies". The Astronomical Jour. 147(2), 2014. Link

Simmons B.D., Melvin T., Lintott C. et al. - "Galaxy Zoo: CANDELS Barred Disks and Bar Fractions". Monthly Not. of the Royal Astron. Soc. 445(4), 2014. Link

Cheung E., Trump J.R., Athanassoula E. et al. - "Galaxy Zoo: Are Bars Responsible for the Feeding of Active Galactic Nuclei at 0.2< z <1.0?". Monthly Not. of the Royal Astron. Soc. 447(1), 2014. Link

Cox J., Younh Ho e. et al. - "Playing with science: Gamised aspects of gamification found on the online citizen science project – Zooniverse". GameON Conference, 2014. Link

Ponciano L., Brasileiro F. - "Finding Volunteers’ Engagement Profiles in Human Computation for Citizen Science Projects". Human Computation 1(2), 2014. Link

Schawinski K., Urry C.M., Simmons B., Fortson L. et al. - "The Green Valley is a Red Herring: Galaxy Zoo reveals two evolutionary pathways towards quenching of star formation in early- and late-type galaxies". Monthly Not. of the Royal Astron. Soc., 2014. Link

Melvin T., Masters K.L., Lintott C. et al. - "Galaxy Zoo: An independent look at the evolution of the bar fraction over the last eight billion years from HST-COSMOS".  Monthly Not. of the Royal Astron. Soc. 438(4), 2014. Link

Kuminski E., George J. et al. - "Combining human and machine learning for morphological analysis of galaxy images". Astronomical Society of the Pacific 126(944), 2014. Link

Madison M.J. - "Commons at the Intersection of Peer Production, Citizen Science, and Big Data: Galaxy Zoo". Governing Knowledge Commons Oxford University Press, 2014. Link

Cheung E., Athanassoula E., Masters K.L. et al. - "Galaxy Zoo: Observing Secular Evolution Through Bars". Astrophys Jour. 779(2), 2013. Link

Willett K.W., Lintott C.J., Bamford S.P. et al. - "Galaxy Zoo 2: detailed morphological classifications for 304,122 galaxies from the Sloan Digital Sky Survey". Monthly Not. of the Royal Astron. Soc. 435(4), 2013. Link

Rodriguez S., Padilla N.D. - "The Intrinsic Shape of Galaxies in SDSS/Galaxy Zoo". Monthly Not. of the Royal Astron. Soc. 434(3), 2013. Link

Tojero R., Masters K.L., Richards J., Percival W.J et al. - "The different star-formation histories of blue and red spiral and elliptical galaxies". Monthly Not. of the Royal Astron. Soc. 432(1), 2013. Link

Lintott C.J., Masters K.L., Brooke S. et al. - "Morphology in the Era of Large Surveys". Astronomy&Geophysics 54(5), 2013. Link

Masters K.L. - "A Zoo of Galaxies". Highlights of Astronomy 16, 2013. Link

Raddick M.J., Bracey G., Gay P.L., Lintott C.J. et al. - "Galaxy Zoo: Motivations of Citizen Scientists". Astronomy Education Review 12, 2013. Link

Keel W.C., Manning A., Holwerda B.W. et al. - "Galaxy Zoo: A Catalog of Overlapping Galaxy Pairs for Dust Studies". Publ. Astron. Soc. Pac. 125, 2013. Link

Levitan D., Kupfer T., Groot P.J. et al. - "Five new outbursting AM CVn systems discovered by the Palomar Transient Factory". Monthly Not. of the Royal Astron. Soc. 430(2), 2012. Link

Casteels K.R.V, Bamford S.P., Skibba R.A et al. - "Galaxy Zoo: quantifying morphological indicators of galaxy interaction". Monthly Not. of the Royal Astron. Soc. 429(2), 2012. Link

Maguire K., Sullivan M. et al. - "Hubble Space Telescope studies of low-redshift Type Ia supernovae: evolution with redshift and ultraviolet spectral trends". Monthly Not. of the Royal Astron. Soc. 426(3), 2012. Link

Masters K.L., Nichol R.C., Haynes M.P et al. - "Galaxy Zoo and ALFALFA: atomic gas and the regulation of star formation in barred disc galaxies". Monthly Not. of the Royal Astron. Soc. 424(3), 2012. Link

Skibba R.A., Masters K.L., Nichol R.C., et al. - "Galaxy Zoo: the environmental dependence of bars and bulges in disc galaxies". Monthly Not. of the Royal Astron. Soc. 423(49), 2012. Link

Kaviraj S., Ting Y-S., Bureau M. et al. - "Galaxy Zoo: Dust and molecular gas in early-type galaxies with prominent dust lanes", Monthly Not. of the Royal Astron Soc 423(49), 2012. Link

Shabala S.S., Ting Y-S., Kaviraj S. et al. - "Galaxy Zoo: Dust lane early-type galaxies are tracers of recent, gas-rich minor mergers", Monthly Not. of the Royal Astron. Soc. 423(49), 2012. Link

Hoyle B., Masters K.L., Nichol R.C et al. - "The fraction of early-type galaxies in low-redshift groups and clusters of galaxies". Monthly Not. of the Royal Astron. Soc. 423(4), 2012. Link

Finkelman I., Funes J.G., Brosch N. - "Polar ring galaxies in the Galaxy Zoo". Monthly Not. of the Royal Astron. Soc. 422(3), 2012. Link

Carpineti A., Kaviraj S., Darg D., Lintott C.J. et al. - "Spheroidal post-mergers in the local Universe". Monthly Not. of the Royal Astron. Soc. 420(3), 2012. Link

Wong O.I., Schawinski K., Kaviraj S. et al. - "Galaxy Zoo: building the low-mass end of the red sequence with local post-starburst galaxies". Monthly Not. of the Royal Astron. Soc. 420(2), 2012. Link

Keel W.C., Chojnowski S.D., Bennert - "The Galaxy Zoo survey for giant AGN-ionized clouds: past and present black hole accretion events". Monthly Not. of the Royal Astron. Soc. 420(1), 2012. Link

Simpson E., Roberts S., Psorakis I. et al. - "Dynamic Bayesian Combination of Multiple Imperfect Classifiers". Decision Making and Imperfection Book, 2012. Link

Teng S.H., Schawinski K., Urry C.M., Darg D.W. et al. - "Chandra Observations of Galaxy Zoo Mergers: Frequency of Binary Active Nuclei in Massive Mergers". Astrophys Jour. 753(2), 2012. Link

Clery D. - "Galaxy Zoo Volunteers Share Pain and Glory of Research". Science 333(6039), 2011. Link

Kaviraj S., Darg D., Lintott C., et al. - "Tidal dwarf galaxies in the nearby Universe". Monthly Not. of the Royal Astron. Soc. 419(1), 2011. Link

Maguire K., Sullivan M. et al. - "PTF10ops - a subluminous, normal-width light curve Type Ia supernova in the middle of nowhere". Monthly Not. of the Royal Astron. Soc. 418(2), 2011. Link

Way M.J. - "Galaxy Zoo Morphology and Photometric Redshifts in the Sloan Digital Sky Survey". The Astrophys. Jour. Lett. 734(1), 2011. Link

Hoyle B., Masters K.L., Nichol R.C et al., - "Galaxy Zoo : Bar Lengths in Nearby Disk Galaxies", Monthly Not. of the Royal Astron. Soc. 415, 2011. Link

Robbins S.J., Chapman C.R., Gay P.L. - "Moon Zoo: Lessons learned from the first year of citizen scientists identifying Lunar Craters". 2nd Planetary Crater Consortium, 2011. Link

Gay P.L., Brown S., Huang D. et al. - "Moon Zoo: Making the public part of a crater survey algorithm". EPSC-DPS Joint Meeting, 2011. Link

Joy K., Cramford I., Grindod P. et al. - "Moon Zoo: A Citizen Science in Lunar Exploration." Astronomy & Geophysics 52(2), 2011.
Link

Smith A. M, Linn S., Sullivan M. et al., 2011, "Galaxy Zoo Supernovae", Monthly Not. of the Royal Astron. Soc., 412(1309), 2011. Link

Darg D. W., Kaviraj S., Lintott C.J. et al., "Galaxy Zoo: Multi-Mergers and the Millennium Simulation", Monthly Not. of the Royal Astron. Soc. 416(1745), 2010. Link

Masters K.L., Nichol R.C, Hoyle B. et al. - "Galaxy Zoo: bars in disk galaxies". Monthly Not. of the Royal Astron. Soc. 411(3), 2011. Link

Lintott C., Schawinski K., Bamford S. et al. - "Galaxy Zoo 1 : Data Release of Morphological Classifications for nearly 900,000 galaxies", Monthly Not. of the Royal Astron. Soc. 410(1), 2011. Link

Banerji M., Lahav O., Lintott C.J. et al. - "Galaxy Zoo: Reproducing galaxy morphologies via machine learning". Monthly Not. of the Royal Astron. Soc. 406(1), 2010. Link

Masters K.L., Mosleh M., Romer A.K. et al. - "Galaxy Zoo: passive red spirals", Monthly Not. of the Royal Astron. Soc. 405(2), 2010. Link

Masters K.L., Nichol R., Bamford S. et al. - "Galaxy Zoo: dust in spiral galaxies", Monthly Not. of the Royal Astron. Soc. 404(2), 2010. Link

Schawinski K., Evans D.A., Virani S. et al. - "The Sudden Death of the Nearest Quasar", The Astrophys. Jour. Lett. 724(1), 2010. Link

Schawinski K., Urry C.M., Virani S. et al. - "Galaxy Zoo: The Fundamentally Different Co-Evolution of Supermassive Black Holes and Their Early- and Late-Type Host Galaxies". The Astrophys. Jour. Lett. 711(1), 2010. Link

Jimenez R., Slosar A., Verde L. et al. - "Galaxy Zoo: a correlation between the coherence of galaxy spin chirality and star formation efficiency". Monthly Not. of the Royal Astron. Soc. 404(2), 2010. Link

Raddick J.M., Bracey G., Gay P.L. et al. - "Galaxy Zoo: Exploring the Motivations of Citizen Science Volunteers". Astronomy Education Review 9(1), 2010. Link

Darg D. W., Kaviraj S., Lintott C.J. et al. - "Galaxy Zoo: The properties of merging galaxies in the nearby Universe - local environments, colours, masses, star-formation rates and AGN activity". Monthly Not. of the Royal Astron. Soc. 401(3), 2010. Link

Darg D., Kaviraj S., Lintott C.J. et al. - "Galaxy Zoo: the fraction of merging galaxies in the SDSS and their morphologies". Monthly Not. of the Royal Astron. Soc. 401(2), 2009. Link

Cardamone C., Schawinski K., Sarzi M. et al. - "Galaxy Zoo Green Peas: Discovery of A Class of Compact Extremely Star-Forming Galaxies". Monthly Not. of the Royal Astron. Soc., 399(2), 2009. Link

Skibba R.A., et al. - "Galaxy Zoo: disentangling the environmental dependence of morphology and colour". Monthly Not. of the Royal Astron. Soc., 399(2), 2009. Link

Lintott C.J., Schawinski K., Keel W. et al. - "Galaxy Zoo: 'Hanny's Voorwerp', a quasar light echo?". Monthly Not. of the Royal Astron. Soc. 399(1), 2009. Link

Schawinski K., Lintott C., Thomas D. et al. - "Galaxy Zoo : A sample of blue early-type galaxies at low redshift". Monthly Not. of the Royal Astron. Soc. 396(2), 2009.
Link

Bamford S.P., Nichol R.C., Baldry I.K. et al. - "Galaxy Zoo: the dependence of morphology and colour on environment". Monthly Not. of the Royal Astron. Soc. 393(4), 2009. Link

Slosar A., Land K., Bamfort S. et al. - "Galaxy Zoo: Chiral correlation function of galaxy spins". Monthly Not. of the Royal Astron. Soc. 392(3), 2009. Link

Lintott C.J., Schawinski K., Slosar A. et al. - "Galaxy Zoo: Morphologies derived from visual inspection of galaxies from the Sloan Digital Sky Survey". Monthly Not. of the Royal Astron. Soc. 389(3), 2008. Link

Land K., Slosar A., Lintott C.J. et al. - "Galaxy Zoo: The large-scale spin statistics of spiral galaxies in the Sloan Digital Sky Survey". Monthly Not. of the Royal Astron. Soc. 388(4), 2008. Link

 

Progetto "Cell Slider"

Pharoah P. - "Contributing to Cancer research with Cell Slider". American Association for the Advancement of Science, 2014. Link


Progetto "SolarStorm Watch"

Bernard L., Scott C. et al. - "Differences between the CME fronts tracked by an expert, an automated algorithm, and the Solar Stormwatch project". Space Wheater 13(10), 2015. Link

Tucker-Hood K., Scott C. et al. - "Validation of a priori CME arrival predictions made using real-time heliospheric imager observations". Space Wheater 13(1), 2015. Link

Bernard L., Scott C. et al. - "The Solar Stormwatch CME catalogue: Results from the first space weather citizen science project". Space Wheater 12(12), 2014. Link 

Davis C.J., Davies J.A. et al. - "The distribution of interplanetary dust between 0.96 and 1.04 AU as inferred from impacts on the STEREO spacecraft observed by the Heliospheric Imagers". Monthly Not. of the Royal Astron. Soc. 420(2), 2012. Link

Savani N.P., Davies J.A., Davis C.J. et al. - "Observational Tracking of the 2D Structure of Coronal Mass Ejections Between the Sun and 1 AU". Solar Physics 279(2), 2012. Link

 


Progetto "Milky Way"

 

Kendrew S., Beuther H. et al. - "The Milky Way Project and ATLASGAL: The distribution and physical properties of cold clumps near infrared bubbles". Astrophys J, 2016. Link

Kerton C.R., Wolf-Chase G., Lintott C.J. et al. - "The Milky Way Project: What are Yellowballs?". Astrophys Jour. 799(153), 2015. Link

Beaumont C., Goodman A. et al. - "The Milky Way Project: Leveraging Citizen Science and Machine Learning to Detect Interstellar Bubbles". Astrophys J, 2014. Link

Kendrew S., Simpson R.J., Bressert E. et al. - "The Milky Way Project: A Statistical Study of Massive Star Formation Associated with Infrared Bubbles". Astrophys J. 775(1), 2012. Link

Simpson R.J., Povich M.S., Kendrew S. et al. - "The Milky Way Project First Data Release: a bubblier Galactic disc". Monthly Not. of the Royal Astron. Soc. 424(4), 2012. Link

 


Progetto "Old Weather"


Jennette C. - "I want to be a Captain! I want to be a Captain!": Gamification in the Old Weather citizen science project". Gamification, 2013. Link

Jennette C. et al. - "Creativity in citizen cyberscience: All for one and one for all". ACM WebSci, 2013. Link

Loetzer L., Schneider D., Jettett C. et al. - "Learning by volunteer computing, thinking and gaming: What and how are volunteers learning by participating in Virtual Citizen Science". 7th ESREA European Conference, 2013. Link

 


Progetto "Planet Hunter"


Wang J., Fischer D.A., Barclay T. et al. - "Planet Hunters V. A Confirmed Jupiter-Size Planet in the Habitable Zone and 42 Planet Candidates from the Kepler Archive". Astrophys J. 776(10), 2013. Link

Gies D.R., Guo Z., Howell S.B. et al. - "Planet Hunters: KIC 9406652: An Unusual Cataclysmic Variable in the Kepler Field of View". Astrophys J. 775(1), 2013. Link

Lintott C.J., Schwamb M.E. et al. - "Planet Hunters: New Kepler planet candidates from analysis of quarter 2". The Astronomical J. 145(6), 2013. Link

Schwamb M.E., Orosz J.A. et al. - "Planet Hunters: A Transiting Circumbinary Planet in a Quadruple Star System". Astrophys J. 768(2), 2013. Link

Fischer D.A., Schwamb M.E. et al. - "Planet Hunters: the first two planet candidates identified by the public using the Kepler public archive data". Monthly Not. of the Royal Astron. Soc. 419(4), 2012. Link

Schwamb M.E., Lintott C.J. et al. - "Planet Hunters: Assessing the Kepler Inventory of Short-period Planet". Astrophys J. 754(2), 2012. Link

 


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Progetti Chiusi

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Abc ° Aqua ° BraTS ° Climate ° Constellation ° Correlizer ° Docking ° DrugDiscovery ° Edges ° EoN2 ° Etremadura ° Feynman ° Genome ° Hep ° Hydrogen ° Magnetism ° NanoHive ° NetMax ° Neurona ° Nrg ° Oproject ° Optima ° Physiome ° Predictor ° Proteins ° RenderFarm ° RiojaScience ° ScreensaverLifeSaver ° Simap ° Spinhenge ° SuperLink ° Tampaku ° Ufluids ° Van Der Waerden Numbers ° Virtual Prairie ° VRS

 

 

 

abc

ABC@Home

 

Martin G., Miao W. - "ABC Triples". Arxiv, 2014. Link

Palenstijn W.J. - "Enumerating ABC Triples". DIAMANT/EIDMA Symposium, 2010. Link

 


 

aqua

Aqua@Home


Karimi K., Dickson N., Hamze F. - "High-Performance Physics Simulations Using Multi-Core CPUs and GPGPUs in a Volunteer Computing Context". J of High Perform Comp Applic 24(1), 2011. Link

Dickson N., Karimi K. et al. - "Importance of Explicit Vectorization for CPU and GPU Software Performance". Journal of Computational Physics 230(13), 2011. Link

Karimi K. et al. - "Investigating the Performance of an Adiabatic Quantum Optimization Processor". Quantum Information Processing, 2011. Link

Hamze F., Dickson N., Karimi K. - "Robust Parameter Selection for Parallel Tempering". International Journal of Modern Physics C 21(5), 2010. Link

 


 

BraTS@Home

 

Coss R., Flores R. - "Gravitational Lensing Shear Simulations Using Fast Fourier Transform". NASA Missouri Space Grant Consortium, 2009. Link

Coss R., Flores R. - "BRaTS@Home and BOINC Distributed Computing for Parallel Computation". American Astronomical Society 40, 2008. Link

 


climatehome

Climate@Home


Li J., Li Z. et al. - "Cloud-Enabled Climate@Home". Spatial Cloud Computing: A practical Approach Book, 2013. Link

Yang C., Bambacus M., Freeman S. et al. - "A Computing Infrastructure for Supporting Climate Studies". American Geophysical Union Meeting, 2011. Link

Xu C., Yang C., Bambacus M. et al. - "Climate@Home: Crowdsourcing Climate Change Research". American Geophysical Union Meeting, 2011. Link

Freeman S., Boller R.A., Yang C. et al. - "Using an Open-Source Grid Framework and Virtualization for Embarrassingly Parallel Computations". American Geophysical Union Meeting, 2010. Link

Sun M., Li J., Huang Q. - "Be a Citizen Scientist for Climate Change". GIS Days, 2010. Link


constellation

Constellation@Home

 

Hornig A., Birkeland R. et al. - "Opportunities of an open-source global senso network monitoring the radio spectrum for the (new) space community". 66th Internat. Astronautical Congress, 2015. Link

Hornig A., Homeister M. - "TYCHO: Demonstrator and operational satellite mission to Earth–Moon-Libration point EML-4 for communication relay provision as a service". Acta Astronautica 108, 2015. Link

Hornig A., Eversmeyer T., Beyermann U. - "Distributed Ground Station Network - a global system for tracking and communication with small satellites as an open service". 64th International Astronautical Congress, 2013. Link

Hornig A. - "Building a Distributed Satellite Ground Station Network - A Call To Arms". 28th Chaos Communication Congress, 2011. Link

Hornig A. - "Constellation Platform - A distributed super-computer for aerospace science". Poster at 6th OpenFOAM Workshop, 2011. Link

 


 

correlizer

Correlizer


Abuseiris A., Emmen A., Knoch T.A. - "Porting and Use of “Correlizer” to Investigate DNA Sequence Correlations". 3rd Almeregrid Desktop Experience, 2010. Link

Knoch T.A., Göker M. et al. - "Fine-structured multi-scaling long-range correlations in completely sequenced genomes—features, origin, and classification". Eur. Biophys. J., 2009. Link

Knoch T.A., Baumgartner V. et al. - "Large-Scale Resource Sharing at Public Funded Organizations". 4th International Conference on e-Social Science, 2008. Link


docking

Docking@Home

 

Zhang B., Estrada T., Cicotti P., Taufer M. - "On efficiently capturing scientific properties in distributed Big Data without moving the data - A Case Study in Distributed Structural Biology using MapReduce". 16th IEEE International Conferences on Computational Science and Engineering, 2013. Link

Estrada T., Pusecker M., Torres M., Cohoon J., Taufer M. - "Benchmarking Gender Differences in Volunteer Computing Projects". 3rd Workshop on Analyzing and Improving Collaborative eScience with Social Networks (eSoN), 2013. Link

Matheny M, Schlachter S., Crouse L., Kimmel E., Estrada T., Taufer M. et al. - "ExSciTecH: Expanding Volunteer Computing to Explore Science, Technology, and Health". 2nd workshop on Analyzing and Improving Collaborative eScience with Social Networks, 2012. Link

Estrada T.,Zhang B., Ciccotti P., Armen R., Taufer M. - "A scalable and accurate method for classifying protein-ligand binding geometries using a MapReduce approach". Computers in Biology and Medicine 42(7), 2012. Link

Estrada T.,Zhang B., Ciccotti P., Armen R., Taufer M. - "Reengineering high-throughput molecular datasets for scalable clustering using MapReduce". 14th IEEE International Conference on High Performance Computing and Communications, 2012. Link

Rahaman O., Estrada T., Doren D., Taufer M., Brooks C.L., Armen R.S. - "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". J. Chem. Information and Modeling 51(9), 2011. Link

Estrada T. and Taufer M. - "Providing Application-Level Quality of Science in Volunteer Computing". 13th IEEE International Conference on High Performance Computing and Communications (HPCC-2011). Link

Estrada T., R. Armen, Taufer M. - "Automatic Selection of Near-Native Protein-Ligand Conformations using a Hierarchical Clustering and Volunteer Computing". International Conference On Bioinformatics and Computational Biology (ACM-BCB),2010. Link

Estrada T., Taufer M., Anderson D. - "Performance Prediction and Analysis of BOINC Projects: An Empirical Study with EmBOINC". Journal of Grid Computing 7(4), 2009. Link

Taufer M., Armen R.S., Chen J., Teller P.J., Brooks C.L. - "Computational Multi-Scale Modeling in Protein-Ligand Docking". IEEE Engineering in Medicine and Biology Magazine 28(2), 2009. Link

Atlas J., Estrada T., Decker K., Taufer M. - "Balancing Scientist Needs and Volunteer Preferences in Volunteer Computing using Constraint Optimization". International Conference on Computational Science (ICCS), 2009. Link

Estrada T., Reed K., Anderson D., Taufer M. - "EmBOINC: An Emulator for Performance Analysis of BOINC Projects". PCGrid Conferenze, 2009. Link

Estrada T., Reed K., Taufer M. - "Modeling Job Lifespan Delays in Volunteer Computing Projects". 9th IEEE International Symposium on Cluster Computing and Grid (CCGrid), 2009. Link

Estrada T., Fuentes O., Taufer M. - "A Distributed Evolutionary Method to Design Scheduling Policies for Volunteer Computing". ACM Computing Frontiers, 2008. Link

Lopez G., Taufer M., Teller P.J. - "Evaluation of IEEE 754 Floating-Point Arithmetic Compliance Across a Wide Range of Heterogeneous Computers". Richard Tapia Celebration of Diversity in Computing Conference, 2007. Link

Taufer M., Kerstens A., Estrada T., Flores D.A., Teller P.J. - "SimBA: a Discrete Event Simulator for Performance Prediction of Volunteer Computing Projects". International Workshop on Principles of Advanced and Distributed Simulation 2007 (PADS'07). Link

Taufer M., Kerstens A., Estrada T., Flores D.A., Zamudio R., et al. - "Moving Volunteer Computing towards Knowledge-Constructed, Dynamically-Adaptive Modeling and Scheduling". First Workshop on Large-Scale, Volatile Desktop Grids (PCGrid'07), 2007. Link

Estrada T., Flores D.A., Taufer M., Teller P., Kerstens A., Anderson D. - "The Effectiveness of Threshold-based Scheduling Policies in BOINC Projects". 2st IEEE International Conference on e-Science and Grid Technologies,2006. Link

Taufer M., Crowley M., Price D., Chien A.A., Brooks C.L. - "Study of an Accurate and Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics". Concurrency and Computation: Practice and Experience. Volume 17, 2005. Link

Taufer M., Teller P.J, Anderson D., Brooks C.L. - "Metrics for Effective Resource Management in Global Computing Environments". 1st IEEE International Conference on e-Science and Grid Technologies, 2005. Link

Taufer M., Anderson D., Ciccotti P., Brooks C.L. - "Homogeneous Technique to Ensure Integrity of Molecular Simulation Results Using Public Resources". 14th Heterogeneous Computing Workshop, 2005. Link

Taufer M., Crowley M., Price D., Chien A.A., Brooks C.L. - "Study of an Fast Protein-Ligand Docking Algorithm based on Molecular Dynamics". IEEE International Workshop on High Performance Computational Biology, 2004. Link

 


 

drugdiscovery

DrugDiscovery@Home

 

Voronkov A., Shultz J. - "Drugdiscovery@home - distributed volunteer computing project in the fields of cancer, aging and stem cells". SENS Research Conference 4, 2009. Link


 edges

Edges@Home

 

Riguardanti l'infrastruttura Edges-Edgi (Concerning the Edges-Edgi infrastructure).

 

Kacsuk P., Farkas Z., Marosi A. et al. - "Desktop grid in the era of Cloud Computing". Grid Computing: Techniques and Future Prospects, 2015. Link

Sjaugi M.F., Tan S. et al. - "g-FLUA2H: a web-based application to study the dynamics of animal-to-human mutation transmission for influenza viruses". BMC Medical Genomics 8, 2015. Link

Fedak G. - "Contributions to Desktop Grid". Phd Thesis, 2015. Link

Visegradi A., Kovacs J., Kasuk P. - " Efficient extension of gLite VOs with BOINC based desktop grids". Future Gen. Comp. Syst. 32, 2014. Link

Marosi A., Kovacs J., Kacsuk P. - "Towards a volunteer cloud system". Future Generation Computer Systems 29(6), 2013. Link

Ponciano L., Brasileiro F. - "Assessing Green Strategies in Peer-to-Peer Opportunistic Grids". J. of Grid Computing 11(1), 2013. Link

Hanappe P. - "Latest developments on energy measurements". 9th Boinc Workshop, 2013. Link

Visegradi A. - "Random Linear Coding in Distributed Storage Systems". 9th Boinc Workshop, 2013. Link

Delamare S., Fedak G., Kondo D. et al. - "Advanced QoS Prototype for the EDGI Infrastructure". EDGI JRA2, 2013. Link

Delamare S., Fedak G., Kondo D. et al. - "Intermediate QoS Prototype for the EDGI Infrastructure". EDGI JRA2, 2013. Link

Delamare S., Fedak G., Kondo D. et al. - "SpeQuloS: a QoS service for hybrid and elastic computing infrastructures". Cluster Computing, 2013. Link

Grunzke R., Birkenheuer G, Blunk D., Breuers S., Brinkmann A. et al. - "A Data Driven Science Gateway for Computational Workflows", UNICORE Summit 15, 2012. Link

Terstyanszky G., Kiss T., Kukla T., Lichtenberger Z., Winter S., Greenwell P. et al. - "Application Repository and Science Gateway for Running Molecular Docking and Dynamics Simulations". Stud. Health. Tech. Inform. 175, 2012. Link

Acs S., Kovacs J., Terstyanszky G. - "Application Repository based evaluation of the EDGI infrastructure", MIPRO Conference 2012. Link

Boychenko S., Araujo F. - "Benchmarking the EDGI Infrastructure", INForum 2012. Link

Kacsuk P., Marosi A. - "Supporting Web 2.0 communities by volunteer desktop grids". Desktop Grid Computing Book, 2012. Link

Kacsuk P., Marosi A. - "Towards Hybrid Desktop Grid and Cloud Infrastructures".Desktop Grid Computing Book, 2012. Link

Sottrup C.U., Kovacs J. - "Transparent execution of ARC jobs on Desktop Grid resources". MIPRO, 2012. Link

Kovacs J., Keller M., Araujo F. et al. - "Monitoring UNICORE jobs executed on Desktop Grid resources". MIPRO, 2012. Link

Terstyanszky G., Kiss T., Kukla T., Lichtenberger Z. et al. - "Application Repository and Science Gateway for Molecular Docking and Diynamic Simulations". Stud.Health Technol. Inform 175, 2012. Link

Terstyanszky G., Kiss T., Kukla T., Winter S. et al.- "Combining Desktop and Service Grids to support e-Scientists to run Simulations".  5th International Conference on Distributed Computing and Grid-technologies in Science and Education, 2012. Link

Lodygensky O., Urbah E., Dadoun S., Simonet A. et al. - "FlyingGrid : from Volunteer Computing to Volunteer Cloud". Computing in High Energy and Nuclear Physics, 2012. Link

Mohammadmersad G. - "Investigating Volunteer Computing for Simul8, a Feasibility Study". Operational Research Society Simulation Workshop 2012. Link

Kecskemeti G., Kertesz A., Marosi A. et al. - "Interoperable Resource Management for Establishing Federated Clouds". 2012. Link

Delamare S., Fedak G., Kondo D., Lodygensky O. - "SpeQuloS: A QoS Service for BoT Applications Using Best Effort Distributed Computing Infrastructures". High Performance and Distribuited Computing Conference, 2012. Link

Taylor S.J.R, Ghorbani M.,Mustafee N. et al. - "Distributed Computing and Modelling and Simulation: Speeding up Simulations and Creating Large Models". Winter Simulation Conference, 2011. Link

Kovacs J., Marosi A.C., Kacsuk P. - "GBAC: Virtualization based execution environment for Desktop Grids". Cracov Grid Workshop, 2011. Link

Kacsuk P. - "How to make Boinc-Based desktop grids even more popular?". IEEE International Symposium on Parallel and Distribuited Processing, 2011. Link

Delamare S. - "Hybrid Distributed Computing Infrastructure Experiments in Grid5000: Supporting QoS in Desktop Grids with Cloud Resources". Grid5000 Spring School, 2011. Link

Keller M., Kovacs J., Brinkmann A. - "Desktop Grids Opening up to UNICORE". Unicore summit 2011. Link

Kacsuk P. - "Enable the use of BOINC for new communities - the IDGF experience". 7th Boinc Workshop, 2011. Link

Kelley I. - "Attic Data Distribution Framework". 7th Boinc Workshop, 2011. Link

Schott B., Emmen A. - "Green Desktop-Grids: Scientific Impact, Carbon Footprint, Power Usage Efficency". Scalable Computing:Practice and Experience 12(2), 2011. Link

Elwaer A., Harrison A., Kelley I., Taylor I. - "Attic: A Case Study for Distributing Data in BOINC Projects". IEEE International Symposium on Parallel and Distribuited Processing, 2011. Link

Reynolds C.J., Winter S., Kiss T. et al. - "Scientific Workflow Makespan Reduction Through Cloud Augmented Desktop Grids". IEEE Conference on Cloud Computing Tech and Science, 2011. Link

Kertesz A., Farkas Z., Kacsuk P. - "Multi-level Brokering Solution for Interoperating Service and Desktop Grids". Lectures in Computer Science 6586, 2011. Link

Lovas R. - "The first year of DEGISCO: hybrid infrastructure and new applications based on BOINC". 7th Boinc Workshop, 2011. Link

Marosi A, Kecskemeti G., Kertesz A., Kacsuk P. - "FCM: an Architecture for Integrating IaaS Cloud Systems". 2nd International Conference on Cloud Computing, Grids and Virtualization, 2011. Link

Kiss T., Kelley I., Kacsuk P. - "Porting Computation and Data Intensive Applications to Distributed Computing Infrastructures Incorporating Desktop Grids". International Symposium on Grids and Clouds, 2011. Link

Elwaer A., Taylor I., Rana O. - "Preference Driven Server Selection in Peer-2-Peer Data Sharing Systems". 4th International Workshop on Data-Intensive distribuited Computing, 2011. Link

Marosi A., Kacsuk P. - "Workers in the Clouds". 19th Euromicro International Conference on Parallel, Distribuited and Network-Base Processing, 2011. Link

Kacsuk P., Kovaks J. - "Towards a Powerful European DCI Based on Desktop Grids". J. of Grid Computing 9(2), 2011. Link

Marosi A.C., Kacsuk P. - "Sandboxing for Desktop Grids Using Virtualization". Parallel, Distributed and Network-Based Processing Conference, 2010. Link

Delamare S., Fedak G., Kondd D, Lodygensky O. - "SpeQuloS: A QoS Service for Hybrid Distributed Computing Infrastructures". Cluster Computing, 2010. Link

Schott B., Emmen A. - "Green Methodologies in Desktop-Grid. An invitation for discussion by the DEGISCO Project". Intern. Multiconference on Computer Science, 2010. Link

Emmen A. - "Desktop Grids take their place in the e-Science distributed computing infrastructure". Proc. Cracow Grid Workshop, 2010. Link

Marosi A., Kovas A. et al. - "The BinSys application on the EDGeS infrastructure". 3rd Almeregrid Workshop, 2010. Link

Farkas Z. - "Improved 3G Bridge scalability to support desktop grid executions". 6th Boinc Workshop, 2010. Link

Marosi A. - "Remote validation of BOINC results – The Web2Grid project". 6th Boinc Workshop, 2010. Link

Marosi A. - "Virtualization for Desktop Grid Clients". 5th Boinc Workshop, 2009. Link

Balaton Z. - "3G-Bridge: Bridging the Gap between BOINC and Other Systems". 5th Boinc Workshop, 2009. Link

Terstyanszky G., Kiss T. - "Porting applications to the Grid using the EDGeS Application Development". 25th Open Grid Forum Meeting, 2009. Link

Urbah E., Kacsuk P., Farkas Z. et al. - "EDGeS: Bridging EGEE to BOINC and XtremWeb". J of Grid Computing, 2009. Link

Ivaki N.R., Ferreira D., Araujo F - "Benckmarking the 3G-Bridge in the EDGeS Infrastructure". Proc. Cracow Grid Workshop, 2009. Link

Kovaks J. - "Programming Applications for Desktop Grids". EDGes Summer School, 2009. Link

Urbah E. - "Why does EDGeS need OGF PGI?". EDGes FP7 Inititive, 2008. Link

 

Progetto "Mopac"

Brandmaier S., Srivstava V., Tetko I. et al. - "MOPAC@home - A Structural Database for small chemical compounds". 3th Almeregrid Desktop Conference, 2010. Link

 

Progetto "ISDEP"

Riverol A., Bustos A. et al. - "ISDEP, a fusion application deployed in the EDGeS project". 3rd AlmereGrid Desktop Experience Workshop, 2010. Link

 

Progetto "Slinca"

Gatsenko O., Baskova O., Fedak G., Lodygensky O., Gordienko Y. - "From Quantity To Quality: Massive Molecular Dynamics Simulation of Nanostructures under Plastic Deformation".  Desktop and Service Grid Distributed Computing Infrastructure, Computer Science, 14, 2013. Link

Gatsenko O., Baskova O., Fedak G., Lodygensky O., Gordienko Y. - "Application of Desktop Grid Technology in Material Science". 5th Distributed Computing and Grid-technologies in Science and Education, 2012. Link

Gatsenko O., Baskova O., Fedak G., Lodygensky O., Gordienko Y. - "Statistical Properties of Deformed Single-Crystal Surface under Real-Time Video". Monitoring and Processing in the Desktop Grid Distributed Computing Environment, Key Engineering Materials 465, 2011. Link

Gatsenko O., Baskova O., Fedak G., Lodygensky O., Gordienko Y. - "Porting Multiparametric MATLAB Application for Image and Video Processing to Desktop Grid for High-Performance Distributed Computing". International Conference of Supercomputer, 2010. Link

Gatsenko O., Baskova O., Fedak G., Lodygensky O., Gordienko Y. - "Kinetics of Defect Aggregation in Materials Science Simulated in Desktop Grid Computing Environment Installed in Ordinary Material Science Lab". 3rd Grid Experience Workshop - Desktop Grid Applications for eScience, 2010. Link

Gatsenko O., Gordienko Y. - "Desktop Grid Computing in Materials Science Lab - Example of Development and Execution of Application for Defect Aggregation Simulations". Proc. Cracow Grid Conf, 2009. Link

 


Progetto "Autodock"

Kiss T., Szmetanko G. et al. - "Molecular Docking Simulations on a Combined Desktop and Service Grid Infrastructure". 3rd AlmereGrid Desktop Experience Workshop, 2010. Link

 


eon2

EoN2

 

Xu L., Mei D., Henkelman G., - "Adaptive kinetic Monte Carlo simulation of methanol decomposition on Cu(100)". Journal Chemical Phys. 131, 2009. Link

Pedersen N A., Henkelman G., Schiøtz J., Jónsson H. - "Long time scale simulation of a grain boundary in copper". Journal Phys. 11, 2009. Link

Mei D., Xu L., Henkelman G. - "Potential energy surface of methanol decomposition on Cu(110)". Journal Chemical Phys. C 113, 2009. Link

Xu L., Henkelman G. - "Adaptive kinetic Monte Carlo for first-principles accelerated dynamics". Journal Chemical Phys. 129(11), 2008. Link

Henkelman G., Jónsson H. - "Multiple time scale simulations of metal crystal growth reveal importance of multi-atom surface processes". Phys. Rev. Lett. 90(11), 2003. Link

 


 

Extremadura@Home

 

Laredo J.L.J., Bouvry P., Fernandez De Vega F. et al. - "Designing robust volunteer-based evolutionary algorithms". Genetic Programming and Evolvable Machines 15(1), 2014. Link

Lombrana Gonzales D., Fernandez De Vega F. et al. - "Characterizing fault tolerance in genetic programming". Future Generation Comp Syst. 26(6), 2010. Link

Gonzalez D.L., De Vega F.F. et al. - "Increasing GP Computing Power for Free via Desktop GRID Computing and Virtualization". 17th Euromicro Inter. Confer. on Parallel, Distribuited and Network-base Processing, 2009. Link

Lombrana Gonzales D., Fernandez De Vega F. et al. - "Interpreted Applications within BOINC Infrastructure". 2nd Ibergrid Conference, 2008. Link

Cardenas Montes M., Vega-Rodriguez M.A. et al. - "Volunteer Computing, an Interesting Option for Grid Computing: Extremadura as Case Study". Lecture Notes in Computer Science 4805, 2007. Link

Chavez de la O F.; Rubio del Solar M. et al. - "A Genetic Programming infrastructure profiting from public computation resources". Spanish Conference on e-Science Grid Computing, 2007. Link

 


 

Feynman@Home

 

Perret-Gallix D. - "Simulate with Grace!". ASCFA Meeting, 2007. Link

 


 

genome

Genome@Home

 

Larson S.M., Desjarlais J.R., Pande V. - "Sequence optimization for native state stability determines the evolution and folding kinetics of a small protein". J of Molec Biol 332(1), 2003. Link

Larson S.M., Garg A., Desjarlais J.R., Pande V. - "Increased detection of structural templates using alignments of designed sequences". Proteins: Structure, Function, and Genetics 51(3), 2003. Link

Larson S.M., Snow C.D., Shirts M.R., Pande V. - "Folding@Home and Genome@Home: Using distributed computing to tackle previously intractable problems in computational biology." Computational Genomics, 2003. Link

Larson S.M., England J.L., Desjarlais J.R., Pande V. - "Thoroughly sampling sequence space: large-scale protein design of structural ensembles". Protein Science 11(12), 2002. Link

Larson S.M. - "Identifying structural templates using alignments of designed sequences." SAC-CASP, 2002. Link

Larson S.M. - "Folding@home and Genome@home: Protein folding and design with distributed computing." Carleton University Biochemistry & Chemistry Society, 2001. Link

 


 

Hep@Home

 

Amorin A., Villate J., Andrade P. - "HEP@Home - A distributed computing system based on BOINC". CHEP2004 on CERN Publications, 2004. Link

 


hydrogen

Hydrogen@Home

 

Shultz J. - "Modeling Biological Hydrogen Production". 4th Boinc Workshop, 2008. Link

 


magnetism

Magnetism@Home


Metlov K.L. - "Magnetization patterns in ferromagnetic nano-elements as functions of complex variable". Physic Rev. Lett. 105, 2010. Link


 

nanohive

NanoHive@Home

 

Allis D.G., Helfrich B., Freitas R.A. et al. - "Analysis of Diamondoid Mechanosynthesis Tooltip Pathologies Generated via a Distributed Computing Approach". Journal of Computational and Theoretical Nanoscience 8, 2011. Link

Helfrich B. - "NanoHive@Home - NanoSystems Simulation". Distributed & Grid Computing - Science Made Transparent for Everyone Book, 2008. Link

 


NetMax

 

Kurochkin I. - "Adaptation of a conveyor processing method for the distributed computing on the BOINC platform". Proceeding of Boinc:Fast, 2015. Link

Kurochkin I. - "NetMax@Home. The project of the voluntary distribuited computing". 6th Int. Conf. of Distribuited Computing and Grid Tech in Science and Educ, 2014. Link

 


 

Neurona@Home

 

Acedo L., Lamprianidou E. et al. - "Firing patterns in a random network cellular automata model of the brain". Physica A: Statistical Mechanics and it's Applications 435, 2015. Link

Acedo L., Villanueva-Oller J., Morano J.A. - "The Neurona@Home project: Simulating a large-scale cellular automata brain in a distributed computing environment". AIP Conference 1510(1), 2013. Link

 


 nrg

NRG@Home

 

Samish I., Bourne P.E., Najmanovich R. - "Achievements and challenges in structural bioinformatics and computational biophysics". Bioinformatics 31(1), 2015. Link

Gaudreault F, Najmanovich R. - "FlexAID: Revisiting docking on non native-complex structures". J Chem Inf Model 55(7), 2015. Link

Duchene D., Colombo E, Najmanovich R. et al. - "Analysis of Subpocket Selectivity and Identification of Potent Selective Inhibitors for Matriptase and Matriptase-2". Jour of Chem Medicine 57, 2014. Link

Naimanovich R.J., Samish I., Bourne P. - "Achievements and challenges in structural bioinformatics and computational biophysics". Bioinformatics Btu769, 2014. Link

 

 


 Oproject

 

Swierczewski L. - "The Distributed Computing Model Based on The Capabilities of The Internet". Arxiv, 2012. Link

 


Optima@Home

 

Andrey Fomin, Yuri Orlov, Mikhail Posypkin,  "Using Simulation to Study Performance of Parallel Tree Search Scheduler". Proceedings of Optimization and Applications (OPTIMA-2015), 2015. Link

Afanasiev, A. P., Bychkov, I. V., Manzyuk, M. O., "Technology for Integrating Idle Computing Cluster Resources into Volunteer Computing Projects". 5th Int Workshop on Computer Science and Engineering:WCSE 2015-IPCE. Link

Afanasiev A., Putilina E. - "The signal recovery by multiple integrals and desktop-grid computing". 5th Inter Conf on Optimization Methods and Applications, 2014. Link

Tian B., Posypkin M.A. - "Efficient implementation of branch-and-bound method on desktop grids". Computer Science 15(3), 2014. Link

Tian B., Posypkin M.A. - "BnBTest@HOME - A Distributed implementation of branch and bound method". 4th Int. Conf on Optimization Methods and Algorithms, 2013. Link

Kholodkov K.I., Alshin I.M., Koryagin V.N. et al. - "Experience on Deploying a Grid Infrastructure for the Support of Computational Web Services". Scientific and Technical Information Processing 39(2), 2011. Link

Afanasiev A., Oferkin I. et al. - "A Comparative Study of Different Optimization Algorithms for Molecular Docking". 3rd Intern. Workshop on Science Gateways for Life Science (IWSG), 2011. Link

Crochemore M., Kubica M., et al. - "Extracting Powers and Periods in a String from its Runs Structure". Lecture Notes in Computer Science 6393, 2010. Link

Sukhoroslov O.V. - "Running Bag-of-Tasks Applications in EGEE with MaWo". 5th EGEE User Forum, 2010. Link

Voloshinov V.V., Smirnov S. - "Error-Free Inversion of Ill-Conditioned Matrices in Distributed Computing System of RESTful-Services of Computer Algebra". 4th Intern. Conf. Distributed Computing and Grid-Technologies in Science and Education, 2010. Link

Neverov V.S., Voloshinov V.V., Afanisev A.P. et al. - "Distributed computing and optimization algorithms for interpretation of x-ray scattering by carbon nanostructures in the deposited films from TOKAMAK ?-10". 4th Intern. Conf. Distributed Computing and Grid-Technologies in Science and Education, 2010. Link

Sukhoroslov O.V. - "On Development of Grid-enabled Applications and Service-Oriented Scientific Environments." 4th Intern. Conf. Distributed Computing and Grid-Technologies in Science and Education, 2010. Link

Kolpakov R., Kucherov G. - "Periodic Structures in Words". Encyclopedia of Mathematics and its Applications vol. 104, 2005. Link


 

Physiome

 

Tomas Kulhanek - "Utilization of GRID technology in processing of medical information". Phd Thesis, 2015. Link

 


 

Predictor@Home

 

Taufer M., An C., Kerstens A., Brooks C. - "Predictor@Home: A "Protein Structure Prediction Supercomputer' Based on Global Computing". IEEE Transact on Parallel and Distribuited Systems 17(8), 2006. Link

 


 

Proteins@Home

 

Busch M.S., Sedano A., Simonson T. - "Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition". PloS One 5(5), 2010. Link

Busch M.S., Mignon D, Simonson T. - "Computational protein design as a tool for fold recognition". Proteins 77(1), 2009. Link

Busch M.S., Lopes A., Mignon D, Simonson T. - "Computational protein design: Software implementation, parameter optimization, and performance of a simple model". J. Comput. Chem. 29(7), 2008. Link

Busch M.S., Lopes A., Amara N. et al. - "Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design". Bioinformatics 9, 2008. Link

 

 


RenderFarm


Kaukonen J. - "Renderfarm.fi: Making movies with a screensaver". 7th Boinc Workshop, 2011. Link

 


 

Riojascience

 

Martinez R., Enriquez P.A. et al. - "Dynamics of the O(3P) + CH4 ? OH + CH3 Reaction Is Similar To That of a Triatomic Reaction". J. Phys. Chem. A 116(21), 2012. Link

 


 Screensaver Lifesaver

 

Richards W.G. - "Virtual screening using grid computing: the screensaver project". Nature Reviews Drug Discovery 1(7), 2002. Link

Richards W.G., Davies E.K. et al. - "Pattern recognition and massively distributed computing". J of Computational Chemistry 23(16), 2002. Link


 

Simap@Home

 

Arnold R., Goldenberg F., Mewes H.W., Rattei T. - "SIMAP The database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage". Nucleic Acids Res. 42, 2014. Link

Rattei T., Tischler P., Götz S., Jehl M.A., Hoser J., et al. - "SIMAP A comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters". Nucleic Acids Res. 38, 2010. Link

Rattei T., Tischler P., Arnold R., Hamberger F., Krebs J., et al. - "SIMAP Structuring the network of protein similarities". Nucleic Acids Res. 36, 2008. Link

Arnold R., Rattei T., Tischler P., Truong M.D., Stümpflen V., Mewes W. - "SIMAP The similarity matrix of proteins". Nucleic Acids Res. 34, 2006. Link

 


spinhenge

Spinhenge@Home

 

Powell G., Engelhardt L., Schroder C., Hilbig T. - "How to use 100,000 PCs for studying magnetism". 76th Meeting of American Physical Society 54(16), 2009. Link

Rainey C., Engelhardt L., Schroder C., Hilbig T. - "QMC Goes BOINC: Using Public Resource Computing to Perform Quantum Monte Carlo Calculations". 75th Meeting of American Physical Society 53(13), 2008. Link

Schröder C., Prozorov R., Kögerler P., Vannette M.D. et al. - "Multiple nearest-neighbor exchange model for the frustrated Keplerate magnetic molecules Mo72Fe30 and Mo72Cr30". Phys. Rev. B, 2008. Link

Schröder C. - "The world is not enough! Spin dynamics simulations for magnetic nanostructures on a global scale". PhD Phys Presentation Univ of Osbabruck, 2007. Link

 


superlink

Superlink@technion

 

Silberstein M., Sharov A., Schuster A. et al. - "Superlink-Online. A distribuited System for Genetic Linkage Analysis using EGEE and Boinc". EGEE Forum, 2008. Link

Silberstein M., Geiger D., Schuster A. - "A Distributed System for Genetic Linkage Analysis". Lecture Notes in Computer Science 4360, 2007. Link

 


tanpaku

Tampaku@Home

 

Ando T., Yamato I. - "Brownian Dynamics Approach to Protein Folding". Fronteers of Comput. Science, 2007. Link

Ando T., Yamato I. - "Free Energy Landscapes of Two Model Peptides: Beta-Helical and Beta-Hairpin Peptides Explored with Brownian Dynamics Simulation". Molecular Simulation 31(10), 2005. Link

Ando T., Meguro T., Yamato I. - "A New Implicit Solvent Model for Brownian Dynamics Simulation: Solvent-Accessible Surface Area Dependent Effective Charge Model". Journal of Computational Chemestry Japan 3(4), 2004. Link

Ando T., Meguro T., Yamato I. - "Multiple Time Step Brownian Dynamics for Long Time Simulation of Biomolecules". Molecular Simulation 29(8), 2003. Link

Meguro T., Ando T., Yamato I. - "Development of Multifunctional Object-Oriented Program Library for Molecular Simulation and Structure Analysis". Journal of Computational Chemestry Japan 2(1), 2003. Link

 


 

ufluids

UFluids@Home

 


Manning R.E., Collicott S.H. - "Liquid plugs in rectangular channels under a transverse gravity field". 49th AIAA Conference, 2010. Link

Braun J.P. - "Zero Gravity Two-Phase Stability Solutions of Droplets in a bent circular cylinder". Master Thesis, 2008. Link

Manning R.E. - "Gas Bubble Stability in a Sphere Layer". Master Thesis, 2006. Link

Manning R.E., Collicott S.H. - "Bubble Penetration Through a Single Layer Sphere Bed". 44rd AIAA Conference, 2006. Link

 

 


 

Van Der Waerden Numbers

 

Monroe D. - "New Lower Bounds for van der Waerden Numbers Using Distributed Computing". Arxiv, 2016. Link

 


 

 

virtualpraire

Virtual Prairie

 

Bittebière, A.-K. & Mony, C., 2014. "Plant trait responses to fine-scale competitive landscape: evidence of spatio-temporal disintegration". Annals of botany 115(1), 2014. Link

Smaoui M., Garbey M. - "Improving volunteer computing scheduling for evolutionary algorithms". Future Generation Comp Syst 29(1), 2013. Link

Oborny B., Mony C., Herben T. - "From virtual plants to real communities: a review of modeling clonal growth". Ecological Modelling 234, 2012. Link

Garbey M., Smaoui M., et al. - "The Vitual Prairie Project". 2nd International Conference on Parallel, Distributed, Gris and Cloud Computing for Engineering, 2011. Link

Mony C., Garbey M., Smaoui M., Benot M.L. - "Large Scale Parameter Study of an Individual Based Model of Clonal Plant with Volunteer Computing". Ecological Modelling 222, 2011. Link

Mony C., & Garbey M. - "Updates on the Virtual Prairie Project". The 5th Pan-Galactic BOINC Workshop, 2009. Link

Smaoui M. & Garbey M. - "Parallel Genetic Algorithm Implementation for BOINC". Parallel Computing: From Multicores and GPU's to Petascale 19, ICPC 2009. Link

Smaoui M., Garbey M., & Mony C. - "Virtual Prairie: Going green with volunteer computing". IEEE Asia-Pacific Services Computing Conference, 2008. Link

Garbey M. - "Virtual Prairies with Boinc". The 4th Pan-Galactic BOINC Workshop, 2008. Link

Mony C., Garbey M., & Smaoui M. - "Using modelling to understand clonal strategies in optimal growing conditions". 51st Annual Symposium of the International Association for Vegetation Science, 2008. Link

Garbey M., Mony C. & Smaoui M. - "Fluid flow - agent based hybrid model for the simulation of virtual prairies". Lecture Notes in Computational Science and Engineering 74,(PCFD Conference 2008). Link

 


 

VRS@Home

 

Acedo L., Morano J.A., Villanueva-Oller J., Villanueva R.J. - "Using random networks to study the dynamics of respiratory syncytial virus (RSV) in the Spanish region of Valencia". Mathem Models of Addictive Behav, Med&Engin 54(7-8), 2011. Link

 


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Progetti Italiani

(Italian's projects)

 

 

tngrid

Gene@Home

 

Asnicar F., Masera L., Coller E., Cavecchia V. et al. - "NES2RA: Network expansion by stratified variable subsetting and ranking aggregation". Inter J of High Perform Comput, 2016. Link

Asnicar F., Sella N., Morettin P., Cavecchia V. et al. - "TN-Grid and Gene@home project: Volunteer Computing for Bioinformatics". BOINC:FAST 2015. Link

Erculiani L., Asnicar F., Sella N., Cavecchia V. et al. - "Discovering Candidates for Gene Network Expansion by Variable Subsetting and Ranking Aggregation". Network Biology in SIG Poster, 2015. Link

Cavecchia V. - "Gene@Home - Computational Biology project for GEne Networks Expansion on a Distibuited Platform". 10th Boinc Workshop, 2014. Link

Blanzieri E., Moser C., Cavecchia V, SCC11 Team - "Gene@Home - GEne Network Expansion". ICT Days, 2014. Link

 


simone

Simone@Home

 

Pieraccini S., Conti S., Chaurasia S., Sironi M. - "Modelling the effect of osmolytes on peptide mechanical unfolding". Chem Physics Letters 578, 2013. Link

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Multidisciplinari

 

Cas ° CSG ° Ibercivis ° Sztaki ° WCG ° YoYo

 

 

cas

Cas@home

 

Protein Structure

Bu D. - "TreeThreader - Predicting protein structure by using cloud computing". Conference Open Science at the Global Scale: Sharing e-Infrastructures, Sharing Knowledge, Sharing Progress, 2015. Link

Legrand A. - "Replication and redundancy in Boinc - Cas@Home case". 10th Boinc Workshop, 2014. Link

Wenjing W., Chen G. - "Harness public computing resources for protein structure prediction computing". Inter Sympos on Grid and Clouds, 2013. Link

Wenjing W. - "Cas@Home Status". The 9th BOINC Workshop, 2013. Link

Shao M., Wang S., Wang C., Yuan X. et al. - "Research Incorporating Ab Initio energy into threading approaches for protein structure prediction". BMC Bioinformatics 12(1), 2011. Link

 

High Energy Physic

Wenjing W. - "Port Boss on CAS". CERN OpenLab 2011. Link

Wu J. - "BOSS and LHC computing using CernVM and BOINC". CERN OpenLab 2010. Link

 

Nanotechnologies

Wan Y. - "Make full use of free computing resources: An introduction of how to run a LAMMPS job on CAS@home". Group Meeting Scheduled Tsinghua University, 2012. Link

 

 


CSG

 

Progetto DNA

 

Zarns K, Desell T., Nechaev S., Dhasarathy A. - "Searching the Human Genome for Snail and Slug With DNA@Home". EScience Conference, 2015. Link

Desell T., Newberg L.A., Szymanski B.K. et al. - "DNA@Home: Using Volunteered Computers for Finding Transcription Factor Binding Sites". 2nd Intern Congr on Comput Applic and Comput Science vol. 144, 2012. Link

Desell T., Newberg L.A., Szymanski B.K. et al. - "Finding Protein Binding Sites Using Volunteer Computing Grids". 2nd International Congress on Computer Appl and Comput Science (CACS 2011). Link

 

Progetto Wildlife

 

Barnas A., Mattingly M., Desell T. et al. - "Developing a Citizen Science Web Portal for Manual and Automated Ecological Image Detection". 12th IEEE EScience, 2016. Link

Bowley C., Andes A., Desell T. et al. - "Detecting Wildlife in Uncontrolled Outdoor Video using Convolutional Neural Networks". 12th IEEE EScience, 2016. Link

Goehner K., Desell T., Eckroad R. et al. - "A Comparison of Background Subtraction Algorithms for Detecting Avian Nesting Events in Uncontrolled Outdoor Video". EScience Conference, 2015. Link

Desell T., Goehner K., Andes A. et al. - "On the Effectiveness of Crowd Sourcing Avian Nesting Video Analysis at Wildlife@Home". Procedia Comput Science 51, 2015. Link

Palarski J., Conrad N. - "Predation and Parental Care at Blue-Winged Teal (Anas discors) Nests in North Dakota". The Wildlife Society's 22nd Conference, 2015. Link

Saul A., Eckroad R.A., Goehner K. et al. - "Effectiveness of Citizen Science vs Expert Observation in Classification of Nesting Bird Behaviors Captured on Camera". The Wildlife Society's 22nd Conference, 2015. Link

Desell T., Ellis-Felege S.N. et al. - "A Bird’s Eye View of ... Birds. Combining Technology and Citizen Science for Conservation." The Wildlife Professional, 2014. Link

Goehner K, Desell T. - "Computer Vision to Aid in WIldlife Surveillance". The 2014 EPSCoR/IDeA Conference, 2014. Link

Desell T., Ellis-Felege S.N. et al. - "Wildlife@Home: Conservation Outreach Using Nest Cameras, Citizen Science and Computer vision". The North Dakota Chapter of the Wildlife Society Conference, 2014. Link

Desell T., Marsh R., Goehner K. et al. - "Wildlife@Home: Combining Crowd Sourcing and Volunteer Computing to Analyze Avian Nesting Video". 9th IEEE International Conf on E-Science, 2013. Link

 

Progetto SubnetSum

 

O'Neil T., Desell T. - "Empirical Support for the High-Density Subset Sum Decision Threshold". 14th IEEE Canadian Workshop on Information Theory (CWIT'15). Link

 

 


 ibercivis

Ibercivis

 

Riguardanti l'infrastruttura Ibercivis

 

Guerrero Hernandez G.D., Imbernon B. et al. - "A performance/cost evaluation for a GPU-based drug discovery application on volunteer computing". Biomed Research International, 2014. Link

Ferred D. - "Boinc Balanced Multi Server Enviroment". 7th Boinc Workshop, 2011. Link

Benito D., Castejon F., Castelo V. et al. - "Ibercivis: infrastructure, applications anddevelopment workflow". 3rd Ibergrid Conference, 2009. Link

Rivero A. - "Ibercivis: status, configuration, and expectations". 4th Boinc Workshop, 2008. Link

Antoli B., Castejon F., Giner A., Losilla G. et al. - "ZIVIS: A City Computing Platform Based on Volunteer Computing". 1st Ibergrid Conference, 2007. Link

 

Progetto "SOCIENTIZE"


Silva C., Monteiro A.J., Manahl C. et al. - "Cell Spotting: Educational and Motivational Outcomes of Cell Biology Citizen Science Project in the Classroom". Journ of Science Communic, 2016. Link

Serrano F. - "Green Paper on Citizen Science. Citizen Science for Europe: Towards a better society of empowered citizens and enhanced research". EU Conference, 2015. Link

Lostal E., Monteiro A.J. et al. -  "Citizen Science in Education: Students Becoming Cell Biology Researchers". Citizen Science Conference, 2015. Link

Monteiro A.J., Silva G.C., Villar J.C. - "Cell Spotting - let's figth cancer together". Science in School Journal 31, 2015. Link

Sagarra O., Gutierrez-Roig M. et al. - "Citizen Science practices for Computational Social Sciences research: The conceptualization of Pop-Up Experiments". Front. Phys. 3(93), 2015. Link

Serrano F. - "White paper on citizen science for Europe". Socientize Conference, 2014. Link

Silva C.G., Brito R.M.M, Monteiro A. et al. - "SOCIENTIZE participatory experiments, dissemination and networking activities in perspective". Human Computation  1(2), 2014. Link

Ponciano L., Brasileiro F. - "Finding Volunteers’ Engagement Profiles in Human Computation for Citizen Science Projects". Human Comput 1(2), 2014. Link

Serrano F., Brasileiro F. - "Semantics map application report". 2013. Link

Lostal E., Almonacid S. - "Cell Images Application Report". 2013.Link

 

Progetto "AMILOIDE"

 

Simoes C.J.V., Murkherjee T., Brito R.M. M., Jackson R.M. - "Toward the Discovery of Functional Transthyretin Amyloid Inhibitors: Application of Virtual Screening Methods",  J. Chem. Inf. Model. 50(10), 2010. Link

Simoes C.J.V., Riviero A., Brito R.M. M. - "Searching for Anti-Amyloid Drugs with the Help of Citizens: the ‘AMILOIDE’ Project on the IBERCIVIS Platform". ERCIM News 82, 2010. Link

Simoes C.J.V., Riviero A., Taracon A., Serrano S., et al. - "Running faster and further together: the AMILOIDE project, the onset of the Portuguese participation on the Ibercivis volunteer computing network". IBERGRID’10, 2010. Link

 

Progetto "BINDSURF"

Guerrero G.D., Imbernon B., Sanz F. et al. - "A Performance/Cost Evaluation for a GPU-Based Drug Discovery Application on Volunteer Computing". BioMed Research International vol.2014, 2014. Link


Progetto "CELLS"

Lostal Lanza E., Serrano Sanz F., Carrodeguas Villar J.A., Martinez Alonso P. et al. - "Cell Images Analysis as a Case of Citizen Science for Advanced Education: Laboratory and School, Back and Forth". 7th International Technology, Education and Development Conference (INTED13), 2013. Link

Lostal Lanza E., Serrano Sanz F., Carrodeguas Villar J.A. et al. - "A case of Citizen Science for Cell Biology Images Analysis". 33th Congresso da Sociedade Brasileira de Computação (CSBC 2013), 2013. Link

 
Progetto "CRITICALIDAD"

Martinez-Mendoza A.J., Mendez-Bermudez J.A., Varga I. - "Conductance statistics for the power-law banded random matrix model", IV Mexican Meeting on Experimental and Theoretical Physics, AIP Conf. Proc. 1319, 2010. Link

 
Progetto "CUANTICABLES"

Camjayi A., Arrachea L. - "Conductance of a quantum dot in the Kondo regime connected to dirty wires". Physical Review B 86, 235143 (2013). Link



Progetto "FUSION"

Bustos A., Castejon F., Fernandez L.A. , Garcia J. et al. - "Impact of 3D features on ion collisional transport in ITER". Nuclear Fusion 50(12), 2010. Link

Velasco J.L., Castejon F., Tarancon A. - "Finite orbit width effect in ion collisional transport in TJ-II". Phys. Plasma 16, 2009. Link

Castejon F., Serrano F. et al. - "Fusion Plasma Simulation in the Interactive Grid". Computing and Informatics 27, 2008. Link

 

Progetto "MATERIALES"

Fernandez L.A., Gordillo-Guerrero A., Martin-Mayor V., Ruiz Lorenzo J.J. - "Numerical test of the Cardy-Jacobsen conjecture in the site-diluted Potts model in three dimensions". Physical Review B 86, 2012. Link


Progetto "NEUROSIM"

Cruz V.L., Ramos J., Martinez-Salazar J. - "Assessment of the Intrinsic Conformational Preferences of Dipeptide Amino Acids in Aqueous Solution by Combined Umbrella Sampling/MBAR Statistics. A Comparison with Experimental Results". J. Phys. Chem. B 116(1), 2012. Link

Cruz V.L., Ramos J., Martinez-Salazar J. - "Water-Mediated Conformations of the Alanine Dipeptide as Revealed by Distributed Umbrella Sampling Simulations, Quantum Mechanics Based Calculations, and Experimental Data". J. Phys. Chem. B 115(16), 2011. Link

 
Progetto "PRISIONER DILEMMA"

Gracia Lazaroa C., Ferrer A., Ruiz G. et al. - "Heterogeneous networks do not promote cooperation when humans play a Prisoner’s Dilemma",  PNAS 109(32), 2012. Link

 
Progetto "SANIDAD"

Ramos Garcia L.I., Almansa J.F. - "Technical Note: An algorithm to calculate the tissue phantom ratio from depth dose in radiosurgery", Medical Phisics 38(5), 2011. Link

 

 


 staky

Sztaki@Home

 

Marosi A., Kacsuk P. - "Volunteer Clouds: From Volunteer Computing to Interconnected Infrastructures". Develop Interop and Feder Cloud Archit Book, 2016. Link

Kacsuk P., Farkas Z., Kovacs J. et al. - "Desktop grid in era of Cloud Computing". Grid Computing: Techniques and Future Prospects, 2015. Link

Marosi A., Lovas R. - "Defining volunteer computing: a formal approach". Computer Research and Modeling 7(3), 2015. Link

Marosi A., Kacsuk P. et al. - "Brokering Solution for Science Gateways using Multiple Distributed Computing Infrastructures". 7th Int Workshop on Science Gateways, 2015. Link

Marosi A. - "SZTAKI Desktop Grid". IGDF Technical Meeting, 2014. Link

Gordienko Y., Bekenov L. et al. - "Complex Workflow Management and Integration of Distributed Computing Resources by Science Gateway Portal for Molecular Dynamics Simulations in Materials Science". 3th Intern Confer "HPC-UA", 2013. Link

Micsik A., Pallinger P. et al. - "Using the BonFIRE Testbed for Testing Scalability of the KOPI Service". ERCIM News 95, 2013. Link

Kiss A.K. - "Loopholes of Plagiarism Detection Software". Procedia-Social and Behavioral Science 106, 2013. Link

Pataki M,, Marosi A. - "Searching for translated plagiarism whit the help of desktop grids". J of Grid Comp 11(1), 2013. Link

Kovacs A., Tihanyi N. - "Efficient computing of n-dimensional simultaneous Diophantine approximation problems". Acta Univ. Sapientiae Informatica 5, 2013. Link

Tihanyi N. - "10305 peak values of the Riemann-Siegel Z function where Z(t) >500". Acta Univ. Sapientiae Informatica 5, 2013. Link

Gordienko Y.G. - "Change of Scaling and Appearance of Scale-Free Size Distribution in Aggregation Kinetics by Additive Rules". Physica A: Statistical Mechanics and Applications, 2011. Link

Kovacs A., Kacsuk P. - "Using a private desktop grid system for accelerating drug discovery". Future Generation Computer System 27(6), 2011. Link

Odor G., "Surface pattern formation and scaling described by conserved lattice gases". Physical Review E 81, 2010. Link

Marosi A., Odor G. - "Exploring University Classes in Nonequilibrium Systems on SZTAKI Desktop Grid". 3rd Almeregrid Workshop, 2010. Link

Kacsuk P., Kovacs J. et al. - "SZTAKI Desktop Grid (SZDG): A Flexible and Scalable Desktop Grid System". J. of Grid Computing 7(4), 2009. Link

Odor G., Liedke B. et al. - "Mapping of 2+1 dimensional KPZ growth onto driven lattice fas model of dimers". Physical Review E 79, 2009. Link

Burksi P, Kovacs A. - "Exhaustive search methods for CNS polynomials". Monatshfte fur Mathematik 155(3-4), 2008. Link

Kovaks J. - "KOPI Protection instead of Copy Protection". 2nd International Conference on Automated Production of Cross Media Content (Axmedis), 2006. Link

 

 


 

wcg

WCG

 

 

Progetto "Help Stop TB"


Meletiou A., Shannon G. et al. - "Utilising IBM’s World Community Grid (WCG) virtual supercomputer to model mycolic acids from Mycobacterium tuberculosis". Big Data in Biomolec Syst Confer, 2016. Link

 

Progetto "OpenZika"


Ekins S., Perryman A.L., Andrade C.H. - "OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery". PLOS Neglected Tropical Disease, 2016. Link

Ekins S., Andrade C.H. et al. - "Illustrating and homology modeling the proteins of the Zika virus". F1000 Research 5(275), 2016. Link

 

Progetto "Mapping Cancer Markers"

Fortney K, Griesman J, Jurisica I. et al. - "Prioritizing therapeutics for lung cancer: An integrative meta-analysis of cancer gene signatures and chemogenomic data". Plos One 11(3), 2015. Link

Kotlyar M., Pastrello C., Jurisica I. et al. - "In silico prediction of physical protein interactions and characterization of interactome orphans". Nature Methods 12 (79-84), 2015. Link

Wong S., Cercone N. and Jurisica I. - "Comparative network analysis via differential graphlet communities". Proteomics 15 (2-3), 2015. Link

 

Progetto "Go Fight against Malaria"

Perryman A.L., Yu W., Wang X. et al - "A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of Mycobacterium tuberculosis InhA". J Chem Inform Model, 2015. Link

 

Progetto "Computing for Clean Water"

Ma M., Grey F., Shen L. et al. - "Water transport inside carbon nanotubes mediated by phonon-induced oscillating friction". Nature Nanotech 10, 2015. Link

Ming D. Ma, Shen L., Sheridan J., Liu Z.J. et al. - "Friction of water slipping in carbon nanotubes". Physical Review E 83, 2011. Link

 

Progetto "Discovery Dengue Drugs"

Viswanathan U., Tomlinson S.M., Fonner J.M. et al. - "Identification of a Novel Inhibitor of Dengue Virus Protease through Use of a Virtual Screening Drug Discovery Web Portal". J. Chem. Inform. Model 54(10), 2014. Link

Tomlinson S.M., Malmstrom R.D., Watowich S.J. – "New approaches to structure-based discovery of dengue protease inhibitors". Infect Disor. Drug Target 9(3), 2009. Link

 

Progetto "Drug Search for Leishmaniasis"

Ochoa, R, et al. "Drug search for leishmaniasis: a virtual screening approach by grid computing." Journal of Computer-Aided Molecular Design30(7), 2016. Link

Flórez A.F., Watowich S., Muskus C. - "Current Advances in Computational Strategies for Drug Discovery in Leishmaniasis". Current Topics in Tropical Medicine  cap.16, 2012. Link
 

 

Progetto "FightAIDS@Home"

Gallicchio E., Xia J. et al. - "Asynchronous replica exchange software for grid and heterogeneous computing". Comp Phys Comunic 196, 2015. Link

Xia J., Flynn W., Gallicchio E. et al. - "Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis". J of Comput Chemis 2015. Link

Forli S., Olson A.J.- "Computational Challenges of Structure-Based Approaches Applied to HIV". Current Topics in Microbiol. and Immunol. 389, 2015. Link

Perryman A.L., Santiago D.N., Forli S., Santos-Martins D., Olson A.J. - "Virtual screening with AutoDock Vina and the common pharmacophore engine of a low diversity library of fragments and hits against the three allosteric sites of HIV integrase: participation in the SAMPL4 protein–ligand binding challenge". J. of Computer Aided Molecular Desing 28(4), 2014. Link

Perryman A.L., Forli S., Morris G.M., Burt C., Cheng Y., Palmer M.J. et al. – "A dynamic model of HIV integrase inhibition and drug resistance". J. of Molecular Biology 397(2),  2010. Link

Cosconati S., Forli S., Perryman A.L., Harris R. et al. - "Virtual Screening with AutoDock: Theory and Practice". Expert Opin. Drug Discovery 5(6), 2010. Link

Perryman A.L., Zhang Q., Soutter H.H., Rosenfeld R., McRee D.E. et al. – "Fragment-Based Screen against HIV Protease". Chem. Biol. Drug Des. 75(3), 2010. Link

Morris G.M., Huey R., Lindstrom W., Sanner M.F., Belew R.K. – "AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility". J. of Computer Chem. 30(16), 2009.  Link

Chang M.W., Lindstrom W., Olson A.J., Belew R.K – "Analysis of HIV Wild-Type and Mutant Structures via in Silico Docking against Diverse Ligand Libraries". J. of Chemical Information and Modeling 47(3), 2007. Link

 


Progetto "Genome Comparison"
Lifschitz S., Viana C.J.M., Tristão C., Marcos Catanho M. et al. - "Design and Implementation of ProteinWorldDB". Lecture Notes in Computer Science 7409, 2012. Link

Otto T.D., Catanho M., Tristao C.,  – "ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes". Oxford Journal of Bioinformatics 25(5), 2010.  Link

 

Progetto "Help Conquer Cancer"
Kotseruba Y., Cumbaa C.A., Jurisica I. - "High-throughput protein crystallization on the World Community Grid and the GPU". J.Phys.Conf.Ser. 341, 2012. Link

Cumbba C.A., Jurisica I. – "Protein crystallization analysis on the World Community Grid". J. Struct. Funct. Genomics 11(1), 2010. Link

Snell E.H., Luft J.R., Potter S.A. et al. – "Establishing a training set through the visual analysis of crystallization trials. Part I: 150 000 images". Acta Crystal D Biol. 64(11), 2008.  Link

Snell E.H., Luft J.R., Potter S.A. et al. – "Establishing a training set through the visual analysis of crystallization trials. Part II: crystal examples".  Acta Crystal D Biol. 64(11), 2008. Link

 

 

Progetto "Help Cure Muscolar Dystrophy"

Vamparys L., Benoist L. et al. - "Great interactions: How binding incorrect partners can teach us about protein recognition and function". Proteins:Structure, Function and Bioinfor, 2016. Link

Lopes A., Sacquin-Mora S., Dimitrova V., Laine E. et al. - "Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information". PLOS Computational Biology 9(12), 2013. Link

Bard N., Bertis V, Bolze R, Despez F. - "A Volunteer Computing Platform Experience for Neuromuscular Disease Problems". Desktop Grid Computing Book, 2012. Link

Bertis V., Bolze R., Desprez F., Reed K. – "From Dedicated Grid to Volunteer Grid: Large Scale Execution of a Bioinformatics Application". J. of Grid Computing 7(4), 2009. Link

Engelen S., Trojan L.A., Mora S.S., Lavery R., Carbone A. – "Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling". PLOS Comput. Biol. 5(1), 2009. Link

Mora S.S., Carbone A., Lavery R. – "Identification of Protein Interaction Partners and Protein–Protein Interaction Sites". J of Molec Biology 382(5), 2008. Link

 

 

Progetto "Help Defeat Cancer"
Foran D.J., Yang L., Chen W., Hu J., Goodell L.A., Reiss M. et al. - "ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology". Journal of the American Medical Informatics Association 18(4), 2011. Link

Widener P., Chen W., Wang F., Yang L. et al. - "Grid-Enabled, High-performance Microscopy Image Analysis". 2010. Link

Yang L., Chen W., Meer P., Salaru G. et al. – "Virtual Microscopy and Grid-enabled Decision Support for Large Scale Analysis of Imaged Pathology Specimens". IEEE Trans Inf. Technol. Biomed. 13(4), 2009. Link

Yang L., Chen W., Meer P., Salaru G. et al. – "PathMiner: A Web-Based Tool for Computer-Assisted Diagnostics in Pathology". IEEE Trans Inf. Technol. Biomed. 13(3),  2009. Link

DiPaola R., Dvorzhinski D., Thalasila A. et al. – "Therapeutic starvation and autophagy in prostate cancer: A new paradigm for targeting metabolism in cancer therapy". Prostate 68(16), 2008.  Link

 

 

Progetto "Help Fight Childhood Cancer"

Fukuda M., Takatori A. et al. - "Effects of novel small compounds targeting TrkB on neuronal cell survival and depression-like behavior". Neurochem Internat 97, 2016. Link

Yohko Nakamura Y., Suganami A., Fukuda M., Hasan K. et al. - "Identification of novel candidate compounds targeting TrkB to induce apoptosis in neuroblastoma". Cancer Medicine 3(1), 2014. Link

 

 

Progetto "Human Proteome Folding"

Baltz A.G., Munschauer M., Schwanhäusser B., Vasile A., Murakawa Y. et al. - "The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts". Molecular Cell 46(5), 2012.  Link

Pentony M.M., Winters P., Penfold-Brown D., Drew K, Narechania A. - "The Plant Proteome Folding Project: Structure and Positive Selection in Plant Protein Families". Genome Biology and Evolution 4(3), 2012.  Link

Drew K., Winters P., Butterfoss G.L. et al. - "The proteome folding project: Proteome-scale prediction of structure and function". Genome Research 21(11), 2011. Link

Boxem M., Maliga Z., Klitgord N. et al – "A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis".  Cell 134(3), 2008. Link

Bonneau R., Facciotti M.T., Reiss D.J. et al – "A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell". Cell 131(7), 2007.  Link

Malmstrom L., Riffle M., Strauss C.E., Chivian D., Baker D. et al. – "Superfamily Assignments for the Yeast Proteome through Integration of Structure Prediction with the Gene Ontology", PLOS Comput. Biol 5(4), 2007. Link

Nissen E.A., Smith K.D., Bonneau R., Strong R.K., Aderem A. – "A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin". J. of Experimental Medicine 204(2), 2007. Link

Avila-Campillo I., Drew K., Lin J., Reiss D.J., Bonneau R.  – "BioNetBuilder: automatic integration of biological networks". Bioinformatics 23(3), 2006. Link

Malmstrom L. – "Genome-wide structural and functional protein characterization by ab initio protein structure prediction". Lund University Press 4(5), 2006. Link

 

 

Progetto "Nutritious Rice for the World"
Hung L.H., Samudrala R. - "Fast protein cluster: parallel and optimized clustering of large-scale protein modeling data". Bioinformatics, 2014. Link

Hung LH., Samudrala R. - "Accelerated protein structure comparison using TM-score-GPU". Bioinformatics 28(16), 2012. Link

Hung L.H., Guerquin M., Samudrala R. - "GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition". BioMed Central Research Notes 4(97), 2011.Link

 


Progetto "Clean Energy Project"

Pyzer-Knapp E.O., Suh C. et al. - "What Is High-Throughput Virtual Screening? A Perspective from Organic Materials Discovery". Annual Rev of Materials Research 45, 2015. Link

Pyzer-Knapp E., Li K., Aspuru-Guzik A. - "Learning from the Harvard Clean Energy Project: The Use of Neural Networks to Accelerate Materials Discovery". Advanced Functional Materials 25(36),  2015. Link

Hachmann J., Olivares-Amaya R., Jinich A., Appleton A.L., Blood-Forsythe M. et al. - "Lead candidates for high-performance organic photovoltaics from high-throughput quantum chemistry - Harvard Clean Energy Project". Energy & Environmental Science 7, 2013. Link

Hachmann J., Olivares-Amaya R. et al. - "Accelerated computational discovery of high-performance materials for organic photovoltaics by means of cheminformatics". Energy & Environmental Science 12, 2011. Link

Hachmann J., Olivares-Amaya R. et al. - "The Harvard Clean Energy Project: Large-Scale Computational Screening and Design of Organic Photovoltaics on the World Community Grid". Physical Chemistry Letters 2(17), 2011. Link


Sokolov A.N., Atahan-Evrenk S., Mondal R., Akkerman HB et al. - "From computational discovery to experimental characterization of a high hole mobility organic crystal". Nature Communications 2, 2011. Link

 


yoyo

Yoyo@Home

 

Progetto "Evolution"

 

Waxman D., Loewe L. - “A stochastic model for a single click of Muller’s ratchet”.  Journal of theoretical Biology, 2010.Link

Loewe L., Charlesworth B. - "Quantifying the threat from Muller's ratchet in the Amazon molly (Poecilia Formosa)". BMC Evolutionary Biology 8(88), 2008. Link

Loewe L., Cutter A. - "On the potential for extinction by Muller’s Ratchet in Caenorhabditis Elegans", BMC Evolutionary Biology 8(125), 2008. Link

Loewe L. - "Evolution@home: The first global computing system for evolutionary biology". Distributed & Grid Computing Book, 2008. 

Loewe L. - "Evolution@home: observations on participant choice, work unit variation and low-effort global computing". Software Practice & Experience 37, 2007. Link

Loewe L. - "Quantifying the genomic decay paradox due to Muller's ratchet in human mitochondrial DNA". Genetics Research 87, 2006. Link

Loewe L. - "Evolution@home: Global computing quantifies evolution due to Muller's ratchet", BMC Bioinformatics 6(3), 2005. Link

Loewe L. - "Evolution@home: Experiences with Work Units That Span More than 7 Orders of Magnitude in Computational Complexity". 2nd IEEE/ACM Internat Sympos on Cluster Computing and Grid, 2002. Link

Loewe L. - "Global computing for bioinformatics". Briefings in Bioinformatics 3(4), 2002. Link

 

Progetto "ORG"

Gerbicz R. - "All solutions of the Diophantine equation a^6+b^6=c^6+d^6+e^6+f^6+g^6 for a,b,c,d,e,f,g < 250000 found with a distributed Boinc project". Arvix, 2011. Link

 

Progetto "Muon"

Brooks S. -"Muon Capture Schemes for the Neutrino Factory". Degree Thesis, 2010. Link

Brooks S. - "Secondary particle production and capture for muon accelerator applications". 10th Europ Particle Acceler Conf, 2006.
Link

Brooks S. - "Muon1 Distributed Particle Accelerator Design". 2006. Link

 


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