Stella inattivaStella inattivaStella inattivaStella inattivaStella inattiva
 

Pubblicazioni

 

Multidisciplinari

(Multidisciplinary)

 

Science United ° TACC ° WCG ° YoYo

 

 

SU/UP

 

Science United

 

Anderson D.P. - "Globally Scheduling Volunteer Computing." Future Internet 13(229), 2021. Link

 

Anderson D.P. - "Coordinated volunteer computing". 2018 Link

 


SU/UP

TACC

 

Redondo C., Ritu A. - "Greyfish: An Out-of-the-Box, Reusable, Portable Cloud Storage Service". PEARC 2019. Link

Ritu A., Gerald J. - "Scalable Software Infrastructure for Integrating Supercomputing with Volunteer Computing and Cloud Computing". SCEC 2018. Link

Wilson L.A., Anderson D.P. - "VAST: Integrating Volunteer Computing into ExistingCyberinfrastructure". 2017. Link

 


SU/UP

wcg

WCG

 

Smash Childhood Cancer +HelpStopTb + OpenZika + Mapping Cancer Markers + Go Fight Against Malaria (completed) + Computing For Clean Water + Discovery Degnue Drugs (completed) + Drug Search for Leishmaniasis (completed) + FightAIDS (completed) + Genome Comparison (completed) + Help Conquer Cancer (completed) + Help Cure Muscolar Dystrophy (completed) + Help Defeat Cancer (completed) + Help Fight Childhood Cancer (completed) + Human Proteome Folding (completed) + Nutritious Rice for the World (completed) + Clean Energy Project

 

 

Progetto "Smash Childhood Cancer"

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

 

Progetto "Help Stop TB"

--2016--

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"

--2020--

Silva S., Shimizu J.F. et al. - "A diarylamine derived from anthranilic acid inhibits ZIKV replication". Nature Scientic Reports 9(17703), 2019. Link

--2019--

Hernandez H.W., Soeung M., Mottin M. et al. - "High Throughput and Computational Repurposing for Neglected Diseases". Pharmaceutical Research 36(27), 2019. Link

--2018--

Mottin M., Andrade C.H. et al. - "Computational Drug Discovery for the Zika Virus". Brazilian Jour of Pharm Science 54(1), 2018. Link

Mottin M. - "Discovery of new antiviral candidates against zika virus". ACS National Meeting, 2018. Link

Mottin M., Andrade C.H. et al. - "The A–Z of Zika drug discovery". Drug Discovery Today, 2018. Link

--2017--

Mottin M. - "OpenZika: Opening the Discovery of New Antiviral candidates against Zika Virus and Insights into Dynamic behavior of NS3 Helicase". 46th World Chemist Congress, 2017. Link

Motin M., Braga R.C., Silva J.H. et al - "Molecular Dynamics simulations of Zika Virus NS3 helicase: Insights into RNA binding site activity". Biochem and Biophys Research Commun 492(4), 2017. Link

--2016--

Motim M., Perryman A.L. et al. - "OpenZika: an open science collaboration project to discover drug candidates against Zika virus". 8th Brazilian Symposium on Medicinal Chem, 2016. Link

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"

 

Hauschild A.C., Jurisica I. et al. - "Visualization of Biomedical Networks".Encyclopedia of Bioinf and Comput Biology 81, 2018. Link

Paulitti A, Jurisica I, et al. - "The ablation of the matricellular protein EMILIN2 causes defective vascularization due to impaired EGFR-dependent IL-8 production affecting tumor growth". Oncogene, Feb 27. 2018. Link

Wong S., Jurisica I. et al. - "SDREGION: Fast spotting of changing communities in biological networks". BMC Cancer 18(1):408, 2018. Link

Rahmati S., Jurisica I. et al - "Two Decades of Biological Pathway Databases: Results and Challenges". Encyclopedia of Bioinf and Comput Biology 81, 2018. Link

Haushid A-C., Jurisica I. et al. - "Network motif families for lung cancer diagnostics - A World Community Grid approach". GLBio 2017. Link

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"

--2018--

Cao W., Wang J. et al. - "Carbon nanostructure based mechano-nanofluidics". J of Micromod and Microeng 28(3), 2018. Link

--2015--

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

--2011--

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"

--2014--

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

--2009--

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"

--2016--

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

--2012--

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"

--2020--

Craveur P., Gres A.T et al. - "Novel Intersubunit Interaction Critical for HIV-1 Core AssemblyDefines a Potentially Targetable Inhibitor Binding Pocket". Americ Society for Microb, 2020. Link

--2019--

Xia J., Flynn W., Gallicchio E. et al. - "Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network". J of Chemic Inform and Modelling 59(4), 2019. Link

--2015--

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

--2014--

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

--2010--

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

--2009--

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

--2007--

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"

--2012--

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

--2010--

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"

--2012--

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

--2010--

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

--2008--

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"

--2019--

Dequeker C., Carbone A. et al. - "Decrypting protein surfaces by combining evolution, geometry, and molecular docking". Proteins 87(11), 2019. Link

--2018--

Lagarde N., Carbone A. et al. - "Hidden partners: Using cross-docking calculations to predict binding sites for proteins with multiple interactions". Proteins 86(7), 2018. Link

--2017--

Laine E., Carbone A. - "Protein social behavior makes a stronger signal for partner identification than surface geometry". Proteins 85(1), 2017.Link

--2016--

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

--2013--

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

--2012--

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

--2009--

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

--2008--

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"

--2011--

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

--2010--

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

--2009--

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

--2008--

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"

--2016--

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

--2014--

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"

--2012--

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

--2011--

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

--2008--

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

--2007--

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

--2006--

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"

--2017--

Hung L.H., Samudrala R. - "Rice protein models from the Nutritious Rice for the World Project" (In Press). Link

--2014--

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

--2012--

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

--2011--

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"

--2017--

Lopez S.A., Sanchez-Lengeling B. et al. - "Design Principles and Top Non-Fullerene Acceptor Candidates for Organic Photovoltaics". Joule 1(4), 2017. Link

Lopez S.A. - "Identification of next-generation materials for organic solar cells via a collaborative theory-experimental approach". ICNM Seminars, 2017. Link

--2015--

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

--2013--

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

--2011--

Hachmann J., Olivares-Amaya R. et al. - "Design principles and top non-fullerene acceptor candidates for organic photovoltaics using the Harvard clean energy project". J of Phys Chem 2(17), 2011. 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

 


SU/UP

yoyo

Yoyo@Home

Evolution + ORG + Muon + Harmonious Trees

 

Progetto "Evolution"

--2010-- 

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

--2008--

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. 

--2007--

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

--2006--

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

--2005--

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

--2002--

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"

--2010--

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

--2006--

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

 

Progetto "Harmonious Tree"

Fang W., Beckert U. - "Parallel Tree Search in Volunteer Computing: a Case Study". J of Grid Computing 15, 2017. Link


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