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| website              = {{URL|https://www.worldcommunitygrid.org/}}
| website              = {{URL|https://www.worldcommunitygrid.org/}}
}}


[https://www.worldcommunitygrid.org/ '''''World Community Grid'''''] uses [[BOINC]] to accelerate science by creating a supercomputer empowered by a global community of volunteers.
[https://www.worldcommunitygrid.org/ '''''World Community Grid'''''] uses [[BOINC]] to accelerate science by creating a supercomputer empowered by a global community of volunteers.
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== Scientific Publications ==
== Publications ==
=== Papers using BOINC-computed data ===


World Community Grid research teams have produced over 50 peer-reviewed scientific publications in journals including ''PLOS Neglected Tropical Diseases'', ''Cancer Medicine'', and others.<ref name="wcg-submit">{{cite web |url=https://www.worldcommunitygrid.org/research/viewSubmitAProposal.do |title=Submit a Proposal |publisher=World Community Grid |access-date=2026-05-25}}</ref> A curated list of papers arising from BOINC-based computing — including World Community Grid — is maintained by BOINC at Berkeley.<ref name="boinc-pubs">{{cite web |url=https://boinc.berkeley.edu/pubs.php |title=Publications by BOINC Projects |publisher=BOINC / UC Berkeley |access-date=2026-05-25}}</ref>
==== Computing for Clean Water ====
# {{Cite journal
|authors=Cao, Wei, Jin Wang and Ming Ma
|title=Carbon nanostructure based mechano-nanofluidics
|url=https://iopscience.iop.org/article/10.1088/1361-6439/aaa782
|journal=Journal of Micromechanics and Microengineering
|date=2018
|doi=10.1088/1361-6439/aaa782
}}
# {{Cite journal
|authors=Ma, Ming, François Grey, Luming Shen, Michael Urbakh, Shuai Wu, Jefferson Zhe Liu, Yilun Liu and Quanshui Zheng
|title=Water transport inside carbon nanotubes mediated by phonon-induced oscillating friction
|url=https://www.nature.com/articles/nnano.2015.134
|journal=Nature Nanotechnology
|date=2015
|doi=10.1038/nnano.2015.134
}}
# {{Cite journal
|authors=Ma, Ming D., Luming Shen, John Sheridan, Jefferson Zhe Liu, Chao Chen and Quanshui Zheng
|title=Friction of water slipping in carbon nanotubes
|url=https://link.aps.org/doi/10.1103/PhysRevE.83.036316
|journal=Physical Review E
|date=2011
|doi=10.1103/PhysRevE.83.036316
}}


Selected publications directly arising from World Community Grid research include:
==== Discovering Dengue Drugs ====
# {{Cite journal
|authors=Viswanathan, Usha, Suzanne M. Tomlinson, John M. Fonner, Stephen A. Mock and Stanley J. Watowich
|title=Identification of a novel inhibitor of dengue virus protease through use of a virtual screening drug discovery Web portal
|url=https://pubmed.ncbi.nlm.nih.gov/25263519/
|journal=Journal of Chemical Information and Modeling
|date=2014
|doi=10.1021/ci500531r
}}
# {{Cite journal
|authors=Tomlinson, S. M., R. D. Malmstrom and S. J. Watowich
|title=New Approaches to Structure-Based Discovery of Dengue Protease Inhibitors
|url=https://www.eurekaselect.com/article/29502
|journal=Infectious Disorders - Drug Targets
|date=2009
|doi=10.2174/1871526510909030327
}}


* Ekins S, Perryman AL, Andrade CH. '''OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery.''' ''PLOS Neglected Tropical Diseases.'' 2016;10(10):e0005023. DOI: [https://doi.org/10.1371/journal.pntd.0005023 10.1371/journal.pntd.0005023]<ref name="openzika"/>
==== Drug Search for Leishmaniasis ====
# {{Cite journal
|authors=Ochoa, Rodrigo, Stanley J. Watowich, Andrés Flórez, Carol V. Mesa, Sara M. Robledo and Carlos Muskus
|title=Drug search for leishmaniasis: a virtual screening approach by grid computing
|url=https://doi.org/10.1007/s10822-016-9921-4
|journal=Journal of Computer-Aided Molecular Design
|date=2016
|doi=10.1007/s10822-016-9921-4
}}
# {{Cite web
|authors=Flórez, Andrés F., Stanley Watowich, Carlos Muskus, Andrés F. Flórez, Stanley Watowich and Carlos Muskus
|title=Current Advances in Computational Strategies for Drug Discovery in Leishmaniasis
|url=https://www.intechopen.com/state.item.id
|date=2012
}}


* Surpeta B ''et al.'' '''FightAIDS@Home — Phase 2: Discovery of New HIV-1 Capsid Vulnerabilities.''' (Peer-reviewed; referenced in Wikipedia citations 10-13.)<ref name="wcg-wp"/>
==== FightAIDS@Home ====
# {{Cite journal
|authors=Sun, Q., A. Biswas, R. S. K. Vijayan et al.
|title=Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid
|url=https://doi.org/10.1007/s10822-022-00446-5
|journal=Journal of Computer-Aided Molecular Design
|date=2022
|doi=10.1007/s10822-022-00446-5
}}
# {{Cite journal
|authors=Goodsell, David S., Michel F. Sanner, Arthur J. Olson and Stefano Forli
|title=The AutoDock suite at 30
|url=https://onlinelibrary.wiley.com/doi/10.1002/pro.3934
|journal=Protein Science
|date=2021
|doi=10.1002/pro.3934
}}
# {{Cite journal
|authors=Craveur, Pierrick, Anna T. Gres, Karen A. Kirby et al
|title=Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket
|url=https://journals.asm.org/doi/10.1128/mBio.02858-18
|journal=mBio
|date=2019
|doi=10.1128/mBio.02858-18
}}
# {{Cite journal
|authors=Xia, Junchao, William Flynn, Emilio Gallicchio, Keith Uplinger, Jonathan D. Armstrong, Stefano Forli, Arthur J. Olson and Ronald M. Levy
|title=Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network
|url=https://doi.org/10.1021/acs.jcim.8b00817
|journal=Journal of Chemical Information and Modeling
|date=2019
|doi=10.1021/acs.jcim.8b00817
}}
# {{Cite web
|authors=Forli, Stefano and Arthur J. Olson
|title=Computational Challenges of Structure-Based Approaches Applied to HIV
|url=https://link.springer.com/10.1007/82_2015_432
|website=The Future of HIV-1 Therapeutics
|date=2015
}}
# {{Cite journal
|authors=Xia, Junchao, William F. Flynn, Emilio Gallicchio, Bin W. Zhang, Peng He, Zhiqiang Tan and Ronald M. Levy
|title=Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis
|url=https://onlinelibrary.wiley.com/doi/abs/10.1002/jcc.23996
|journal=Journal of Computational Chemistry
|date=2015
|doi=10.1002/jcc.23996
}}
# {{Cite journal
|authors=Gallicchio, Emilio, Junchao Xia, William F. Flynn, Baofeng Zhang, Sade Samlalsingh, Ahmet Mentes and Ronald M. Levy
|title=Asynchronous replica exchange software for grid and heterogeneous computing
|url=https://www.sciencedirect.com/science/article/pii/S0010465515002556
|journal=Computer Physics Communications
|date=2015
|doi=10.1016/j.cpc.2015.06.010
}}
# {{Cite journal
|authors=Perryman, Alexander L., Daniel N. Santiago, Stefano Forli, Diogo Santos-Martins and Arthur J. Olson
|title=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
|url=http://link.springer.com/10.1007/s10822-014-9709-3
|journal=Journal of Computer-Aided Molecular Design
|date=2014
|doi=10.1007/s10822-014-9709-3
}}
# {{Cite journal
|authors=Perryman, Alexander L., Qing Zhang, Holly H. Soutter, Robin Rosenfeld, Duncan E. McRee, Arthur J. Olson, John E. Elder and C. David Stout
|title=Fragment-Based Screen against HIV Protease
|url=https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1747-0285.2009.00943.x
|journal=Chemical Biology & Drug Design
|date=2010
|doi=10.1111/j.1747-0285.2009.00943.x
}}
# {{Cite journal
|authors=Perryman, Alex L., Stefano Forli, Garrett M. Morris et al
|title=A Dynamic Model of HIV Integrase Inhibition and Drug Resistance
|url=https://linkinghub.elsevier.com/retrieve/pii/S0022283610000793
|journal=Journal of Molecular Biology
|date=2010
|doi=10.1016/j.jmb.2010.01.033
}}
# {{Cite journal
|authors=Cosconati, Sandro, Stefano Forli, Alex L Perryman, Rodney Harris, David S Goodsell and Arthur J Olson
|title=Virtual Screening with AutoDock: Theory and Practice
|url=http://www.tandfonline.com/doi/full/10.1517/17460441.2010.484460
|journal=Expert Opinion on Drug Discovery
|date=2010
|doi=10.1517/17460441.2010.484460
}}
# {{Cite journal
|authors=Morris, Garrett M., Ruth Huey, William Lindstrom, Michel F. Sanner, Richard K. Belew, David S. Goodsell and Arthur J. Olson
|title=AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
|url=https://onlinelibrary.wiley.com/doi/10.1002/jcc.21256
|journal=Journal of Computational Chemistry
|date=2009
|doi=10.1002/jcc.21256
}}
# {{Cite journal
|authors=Chang, Max W., William Lindstrom, Arthur J. Olson and Richard K. Belew
|title=Analysis of HIV Wild-Type and Mutant Structures via in Silico Docking against Diverse Ligand Libraries
|url=https://doi.org/10.1021/ci700044s
|journal=Journal of Chemical Information and Modeling
|date=2007
|doi=10.1021/ci700044s
}}


* Hachmann AB ''et al.'' (Clean Energy Project). '''Large-scale computational screening of organic photovoltaic materials'''; database of 2.3+ million characterized organic molecules published 2013.<ref name="wcg-wp"/>
==== GO Fight Against Malaria ====
# {{Cite journal
|authors=Perryman, Alexander L., Weixuan Yu, Xin Wang et al
|title=A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of Mycobacterium tuberculosis InhA
|url=https://doi.org/10.1021/ci500672v
|journal=Journal of Chemical Information and Modeling
|date=2015
|doi=10.1021/ci500672v
}}


For the complete and current list of World Community Grid-related papers, see: [https://boinc.berkeley.edu/pubs.php#World BOINC Publications — World Community Grid].
==== Genome Comparison ====
# {{Cite web
|authors=Lifschitz, Sérgio, Carlos Juliano M. Viana, Cristian Tristão, Marcos Catanho, Wim M. Degrave, Antonio Basílio de Miranda, Márcia Bezerra and Thomas D. Otto
|title=Design and Implementation of ProteinWorldDB
|url=http://link.springer.com/10.1007/978-3-642-31927-3_13
|website=Advances in Bioinformatics and Computational Biology
|date=2012
}}
# {{Cite journal
|authors=Otto, Thomas Dan, Marcos Catanho, Cristian Tristão et al
|title=ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes
|url=https://doi.org/10.1093/bioinformatics/btq011
|journal=Bioinformatics
|date=2010
|doi=10.1093/bioinformatics/btq011
}}
 
==== Help Conquer Cancer ====
# {{Cite journal
|authors=Kotseruba, Yulia, Christian A. Cumbaa and Igor Jurisica
|title=High-throughput protein crystallization on the World Community Grid and the GPU
|url=https://dx.doi.org/10.1088/1742-6596/341/1/012027
|journal=Journal of Physics: Conference Series
|date=2012
|doi=10.1088/1742-6596/341/1/012027
}}
# {{Cite journal
|authors=Cumbaa, Christian A. and Igor Jurisica
|title=Protein crystallization analysis on the World Community Grid
|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2857471/
|journal=Journal of Structural and Functional Genomics
|date=2010
|doi=10.1007/s10969-009-9076-9
}}
# {{Cite journal
|authors=Snell, Edward H., Angela M. Lauricella, Stephen A. Potter et al
|title=Establishing a training set through the visual analysis of crystallization trials. Part II: crystal examples
|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631118/
|journal=Acta Crystallographica Section D: Biological Crystallography
|date=2008
|doi=10.1107/S0907444908028059
}}
# {{Cite journal
|authors=Snell, Edward H., Joseph R. Luft, Stephen A. Potter et al
|title=Establishing a training set through the visual analysis of crystallization trials. Part I: ~150 000 images
|url=https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2631114/
|journal=Acta Crystallographica Section D: Biological Crystallography
|date=2008
|doi=10.1107/S0907444908028047
}}
 
==== Help Cure Muscular Dystrophy ====
# {{Cite journal
|authors=Dequeker, Chloé, Elodie Laine and Alessandra Carbone
|title=Decrypting protein surfaces by combining evolution, geometry, and molecular docking
|url=https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.25757
|journal=Proteins: Structure, Function, and Bioinformatics
|date=2019
|doi=10.1002/prot.25757
}}
# {{Cite journal
|authors=Lagarde, Nathalie, Alessandra Carbone and Sophie Sacquin-Mora
|title=Hidden partners: Using cross-docking calculations to predict binding sites for proteins with multiple interactions
|url=https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.25506
|journal=Proteins: Structure, Function, and Bioinformatics
|date=2018
|doi=10.1002/prot.25506
}}
# {{Cite journal
|authors=Laine, Elodie and Alessandra Carbone
|title=Protein social behavior makes a stronger signal for partner identification than surface geometry
|url=https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.25206
|journal=Proteins: Structure, Function, and Bioinformatics
|date=2017
|doi=10.1002/prot.25206
}}
# {{Cite journal
|authors=Vamparys, Lydie, Benoist Laurent, Alessandra Carbone and Sophie Sacquin-Mora
|title=Great interactions: How binding incorrect partners can teach us about protein recognition and function
|url=https://onlinelibrary.wiley.com/doi/abs/10.1002/prot.25086
|journal=Proteins: Structure, Function, and Bioinformatics
|date=2016
|doi=10.1002/prot.25086
}}
# {{Cite journal
|authors=Lopes, Anne, Sophie Sacquin-Mora, Viktoriya Dimitrova, Elodie Laine, Yann Ponty and Alessandra Carbone
|title=Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information
|url=https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003369
|journal=PLOS Computational Biology
|date=2013
|doi=10.1371/journal.pcbi.1003369
}}
# {{Cite journal
|authors=Bertis, Viktors, Raphaël Bolze, Frédéric Desprez and Kevin Reed
|title=From Dedicated Grid to Volunteer Grid: Large Scale Execution of a Bioinformatics Application
|url=https://doi.org/10.1007/s10723-009-9130-7
|journal=Journal of Grid Computing
|date=2009
|doi=10.1007/s10723-009-9130-7
}}
# {{Cite journal
|authors=Engelen, Stefan, Ladislas A. Trojan, Sophie Sacquin-Mora, Richard Lavery and Alessandra Carbone
|title=Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling
|url=https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000267
|journal=PLOS Computational Biology
|date=2009
|doi=10.1371/journal.pcbi.1000267
}}
# {{Cite journal
|authors=Sacquin-Mora, Sophie, Alessandra Carbone and Richard Lavery
|title=Identification of Protein Interaction Partners and Protein–Protein Interaction Sites
|url=https://www.sciencedirect.com/science/article/pii/S002228360800973X
|journal=Journal of Molecular Biology
|date=2008
|doi=10.1016/j.jmb.2008.08.002
}}
 
==== Help Defeat Cancer ====
# {{Cite journal
|authors=Foran, David J, Lin Yang, Wenjin Chen et al
|title=ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology
|url=https://academic.oup.com/jamia/article-lookup/doi/10.1136/amiajnl-2011-000170
|journal=Journal of the American Medical Informatics Association
|date=2011
|doi=10.1136/amiajnl-2011-000170
}}
# {{Cite web
|authors=Wang, Fusheng
|title=Grid-Enabled, High-performance Microscopy Image Analysis
|url=https://www.academia.edu/en/50457695/Grid_Enabled_High_performance_Microscopy_Image_Analysis
|date=2010
}}
# {{Cite journal
|authors=Lin Yang, Wenjin Chen, P. Meer, G. Salaru, L.A. Goodell, V. Berstis and D.J. Foran
|title=Virtual Microscopy and Grid-Enabled Decision Support for Large-Scale Analysis of Imaged Pathology Specimens
|url=http://ieeexplore.ieee.org/document/4814676/
|journal=IEEE Transactions on Information Technology in Biomedicine
|date=2009
|doi=10.1109/TITB.2009.2020159
}}
# {{Cite journal
|authors=Lin Yang, O. Tuzel, Wenjin Chen, P. Meer, G. Salaru, L.A. Goodell and D.J. Foran
|title=PathMiner: A Web-Based Tool for Computer-Assisted Diagnostics in Pathology
|url=http://ieeexplore.ieee.org/document/4757270/
|journal=IEEE Transactions on Information Technology in Biomedicine
|date=2009
|doi=10.1109/TITB.2008.2008801
}}
# {{Cite journal
|authors=DiPaola, Robert S., Dmitri Dvorzhinski, Anu Thalasila et al
|title=Therapeutic starvation and autophagy in prostate cancer: A new paradigm for targeting metabolism in cancer therapy
|url=https://onlinelibrary.wiley.com/doi/abs/10.1002/pros.20837
|journal=The Prostate
|date=2008
|doi=10.1002/pros.20837
}}
 
==== Help Fight Childhood Cancer ====
# {{Cite journal
|authors=Fukuda, Mayu, Atsushi Takatori, Yohko Nakamura, Akiko Suganami, Tyuji Hoshino, Yutaka Tamura and Akira Nakagawara
|title=Effects of novel small compounds targeting TrkB on neuronal cell survival and depression-like behavior
|url=https://www.sciencedirect.com/science/article/pii/S0197018616300869
|journal=Neurochemistry International
|date=2016
|doi=10.1016/j.neuint.2016.04.017
}}
# {{Cite journal
|authors=Nakamura, Yohko, Akiko Suganami, Mayu Fukuda et al
|title=Identification of novel candidate compounds targeting TrkB to induce apoptosis in neuroblastoma
|url=https://onlinelibrary.wiley.com/doi/abs/10.1002/cam4.175
|journal=Cancer Medicine
|date=2014
|doi=10.1002/cam4.175
}}
 
==== Help Stop TB ====
# {{Cite journal
|authors=Groenewald, Wilma, Ricardo A. Parra-Cruz, Christof M. Jäger and Anna K. Croft
|title=Revealing solvent-dependent folding behavior of mycolic acids from Mycobacterium tuberculosis by advanced simulation analysis
|url=http://link.springer.com/10.1007/s00894-019-3943-5
|journal=Journal of Molecular Modeling
|date=2019
|doi=10.1007/s00894-019-3943-5
}}
 
==== Human Proteome Folding ====
# {{Cite journal
|authors=Baltz, Alexander G., Mathias Munschauer, Björn Schwanhäusser et al
|title=The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts
|url=https://linkinghub.elsevier.com/retrieve/pii/S1097276512004376
|journal=Molecular Cell
|date=2012
|doi=10.1016/j.molcel.2012.05.021
}}
# {{Cite journal
|authors=Pentony, M. M., P. Winters, D. Penfold-Brown, K. Drew, A. Narechania, R. DeSalle, R. Bonneau and M. D. Purugganan
|title=The Plant Proteome Folding Project: Structure and Positive Selection in Plant Protein Families
|url=https://doi.org/10.1093/gbe/evs015
|journal=Genome Biology and Evolution
|date=2012
|doi=10.1093/gbe/evs015
}}
# {{Cite journal
|authors=Drew, Kevin, Patrick Winters, Glenn L. Butterfoss et al
|title=The Proteome Folding Project: Proteome-scale prediction of structure and function
|url=http://genome.cshlp.org/lookup/doi/10.1101/gr.121475.111
|journal=Genome Research
|date=2011
|doi=10.1101/gr.121475.111
}}
# {{Cite journal
|authors=Boxem, Mike, Zoltan Maliga, Niels Klitgord et al
|title=A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis
|url=https://www.sciencedirect.com/science/article/pii/S0092867408008866
|journal=Cell
|date=2008
|doi=10.1016/j.cell.2008.07.009
}}
# {{Cite journal
|authors=Bonneau, Richard, Marc T. Facciotti, David J. Reiss et al
|title=A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell
|url=https://www.cell.com/cell/abstract/S0092-8674(07)01416-X
|journal=Cell
|date=2007
|doi=10.1016/j.cell.2007.10.053
}}
# {{Cite journal
|authors=Malmström, Lars, Michael Riffle, Charlie E. M. Strauss, Dylan Chivian, Trisha N. Davis, Richard Bonneau and David Baker
|title=Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology
|url=https://pubmed.ncbi.nlm.nih.gov/17373854/
|journal=PLoS biology
|date=2007
|doi=10.1371/journal.pbio.0050076
}}
# {{Cite journal
|authors=Andersen-Nissen, Erica, Kelly D. Smith, Richard Bonneau, Roland K. Strong and Alan Aderem
|title=A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin
|url=https://doi.org/10.1084/jem.20061400
|journal=Journal of Experimental Medicine
|date=2007
|doi=10.1084/jem.20061400
}}
# {{Cite journal
|authors=Avila-Campillo, Iliana, Kevin Drew, John Lin, David J. Reiss and Richard Bonneau
|title=BioNetBuilder: automatic integration of biological networks
|url=https://doi.org/10.1093/bioinformatics/btl604
|journal=Bioinformatics
|date=2007
|doi=10.1093/bioinformatics/btl604
}}
# {{Cite web
|authors=Malmström, Lars
|title=Genome-wide structural and functional protein characterization by ab initio protein structure prediction
|url=http://lars.malmstroem.net/lars.malmstroem.thesis.no_articles.pdf
|website=Report / Department of Electrical Measurements. Lund Institute of Technology
|date=2005
}}
 
==== Mapping Cancer Markers ====
# {{Cite journal
|authors=Kotlyar, M., C. Pastrello, M. Abovsky, A. Mizeranschi, A. Keating, L. C. Cameron, V. Chandran and I. Jurisica
|title=IID 2025: Physical protein interaction data with detection types, co-purified protein sets, molecular docking, and immune cell networks
|url=https://doi.org/10.1093/nar/gkaf1259
|journal=Nucleic Acids Research
|date=2026
}}
# {{Cite journal
|authors=Kotlyar, M., C. Pastrello, Z. Ahmed, J. Chee, Z. Varyova and I. Jurisica
|title=IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis
|url=https://doi.org/10.1093/nar/gkab1034
|journal=Nucleic Acids Research
|date=2022
|doi=10.1093/nar/gkab1034
}}
# {{Cite journal
|authors=Kotlyar, M., C. Pastrello, Z. Malik and I. Jurisica
|title=IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species
|url=https://doi.org/10.1093/nar/gky1037
|journal=Nucleic Acids Research
|date=2019
}}
# {{Cite journal
|authors=Kotlyar, M., C. Pastrello, N. Sheahan and I. Jurisica
|title=Integrated Interactions Database: tissue-specific view of the human and model organism interactomes
|url=https://doi.org/10.1093/nar/gkv1115
|journal=Nucleic Acids Research
|date=2016
}}
# {{Cite web
|authors=Pastrello, C., M. Kotlyar and I. Jurisica
|title=Informed Use of Protein-Protein Interaction Data: A Focus on the Integrated Interactions Database (IID)
|url=https://doi.org/10.1007/978-1-4939-9873-9_10
|website=Methods in Molecular Biology
|date=2020
}}
# {{Cite journal
|authors=Wong, S. W. H., C. Pastrello, M. Kotlyar, C. Faloutsos and I. Jurisica
|title=USNAP: fast unique dense region detection and its application to lung cancer
|url=https://doi.org/10.1093/bioinformatics/btad477
|journal=Bioinformatics
|date=2023
|doi=10.1093/bioinformatics/btad477
}}
# {{Cite journal
|authors=Wong, S. W. H., N. Cercone and I. Jurisica
|title=Comparative network analysis via differential graphlet communities
|url=https://doi.org/10.1002/pmic.201400233
|journal=Proteomics
|date=2015
|doi=10.1002/pmic.201400233
}}
# {{Cite web
|authors=Hauschild, Anne-Christin, Chiara Pastrello, Andrea E.M. Rossos and Igor Jurisica
|title=Visualization of Biomedical Networks
|url=https://linkinghub.elsevier.com/retrieve/pii/B9780128096338204305
|website=Encyclopedia of Bioinformatics and Computational Biology
|date=2019
}}
# {{Cite journal
|authors=Paulitti, Alice, Eva Andreuzzi, Dario Bizzotto et al
|title=The ablation of the matricellular protein EMILIN2 causes defective vascularization due to impaired EGFR-dependent IL-8 production affecting tumor growth
|url=https://www.nature.com/articles/s41388-017-0107-x
|journal=Oncogene
|date=2018
|doi=10.1038/s41388-017-0107-x
}}
# {{Cite journal
|authors=Wong, Serene W.H., Chiara Pastrello, Max Kotlyar, Christos Faloutsos and Igor Jurisica
|title=SDREGION: Fast Spotting of Changing Communities in Biological Networks
|url=https://dl.acm.org/doi/10.1145/3219819.3219854
|journal=KDD '18: The 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining
|date=2018
|doi=10.1145/3219819.3219854
}}
# {{Cite journal
|authors=Anne-Christin Hauschild, Christian A Cumbaa, Mike Tsay and Igor Jurisica
|title=Network Motif Families for Lung Cancer Diagnostics: A World Community Grid Approach
|url=http://rgdoi.net/10.13140/RG.2.2.34687.51363
|date=2017
|doi=10.13140/RG.2.2.34687.51363
}}
# {{Cite journal
|authors=Fortney, Kristen, Joshua Griesman, Max Kotlyar, Chiara Pastrello, Marc Angeli, Ming Sound-Tsao and Igor Jurisica
|title=Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data
|url=https://dx.plos.org/10.1371/journal.pcbi.1004068
|journal=PLOS Computational Biology
|date=2015
|doi=10.1371/journal.pcbi.1004068
}}
# {{Cite journal
|authors=Kotlyar, Max, Chiara Pastrello, Flavia Pivetta et al
|title=In silico prediction of physical protein interactions and characterization of interactome orphans
|url=https://www.nature.com/articles/nmeth.3178
|journal=Nature Methods
|date=2015
|doi=10.1038/nmeth.3178
}}
 
==== Microbiome Immunity Project ====
# {{Cite journal
|authors=Koehler Leman, Julia, Pawel Szczerbiak, P. Douglas Renfrew et al
|title=Sequence-structure-function relationships in the microbial protein universe
|url=https://www.nature.com/articles/s41467-023-37896-w
|journal=Nature Communications
|date=2023
|doi=10.1038/s41467-023-37896-w
}}
 
==== Nutritious Rice for the World ====
# {{Cite journal
|authors=Hung, Ling-Hong and Ram Samudrala
|title=Rice protein models from the Nutritious Rice for the World Project
|url=https://www.biorxiv.org/content/10.1101/091975v1
|date=2016
|doi=10.1101/091975
}}
# {{Cite journal
|authors=Hung, Ling-Hong and Ram Samudrala
|title=fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data
|url=https://doi.org/10.1093/bioinformatics/btu098
|journal=Bioinformatics
|date=2014
|doi=10.1093/bioinformatics/btu098
}}
# {{Cite journal
|authors=Hung, Ling-Hong and Ram Samudrala
|title=Accelerated protein structure comparison using TM-score-GPU
|url=https://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/bts345
|journal=Bioinformatics
|date=2012
|doi=10.1093/bioinformatics/bts345
}}
# {{Cite journal
|authors=Hung, Ling-Hong, Michal Guerquin and Ram Samudrala
|title=GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition
|url=https://bmcresnotes.biomedcentral.com/articles/10.1186/1756-0500-4-97
|journal=BMC Research Notes
|date=2011
|doi=10.1186/1756-0500-4-97
}}
 
==== OpenZika ====
# {{Cite journal
|authors=Mottin, Melina, Bruna Katiele de Paula Sousa, Nathalya Cristina de Moraes Roso Mesquita et al
|title=Discovery of New Zika Protease and Polymerase Inhibitors through the Open Science Collaboration Project OpenZika
|url=https://pubs.acs.org/doi/10.1021/acs.jcim.2c00596
|journal=Journal of Chemical Information and Modeling
|date=2022
|doi=10.1021/acs.jcim.2c00596
}}
# {{Cite journal
|authors=Silva, Suely, Jacqueline Farinha Shimizu, Débora Moraes de Oliveira et al
|title=A diarylamine derived from anthranilic acid inhibits ZIKV replication
|url=https://www.nature.com/articles/s41598-019-54169-z
|journal=Scientific Reports
|date=2019
|doi=10.1038/s41598-019-54169-z
}}
# {{Cite journal
|authors=Hernandez, Helen W., Melinda Soeung, Kimberley M. Zorn et al
|title=High Throughput and Computational Repurposing for Neglected Diseases
|url=http://link.springer.com/10.1007/s11095-018-2558-3
|journal=Pharmaceutical Research
|date=2019
|doi=10.1007/s11095-018-2558-3
}}
# {{Cite journal
|authors=Mottin, Melina, Joyce Villa Verde Bastos Borba, Cleber Camilo Melo-Filho et al
|title=Computational drug discovery for the Zika virus
|url=http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1984-82502018000700401&lng=en&tlng=en
|journal=Brazilian Journal of Pharmaceutical Sciences
|date=2018
|doi=10.1590/s2175-97902018000001002
}}
# {{Cite journal
|authors=Mottin, Melina, Joyce V.V.B. Borba, Rodolpho C. Braga et al
|title=The A–Z of Zika drug discovery
|url=https://linkinghub.elsevier.com/retrieve/pii/S1359644618300412
|journal=Drug Discovery Today
|date=2018
|doi=10.1016/j.drudis.2018.06.014
}}
# {{Cite journal
|authors=Mottin, Melina, Rodolpho C. Braga, Roosevelt A. da Silva, Joao H. Martins da Silva, Alexander L. Perryman, Sean Ekins and Carolina Horta Andrade
|title=Molecular dynamics simulations of Zika virus NS3 helicase: Insights into RNA binding site activity
|url=https://linkinghub.elsevier.com/retrieve/pii/S0006291X1730534X
|journal=Biochemical and Biophysical Research Communications
|date=2017
|doi=10.1016/j.bbrc.2017.03.070
}}
# {{Cite journal
|authors=Ekins, Sean, Alexander L. Perryman and Carolina Horta Andrade
|title=OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery
|url=https://dx.plos.org/10.1371/journal.pntd.0005023
|journal=PLOS Neglected Tropical Diseases
|date=2016
|doi=10.1371/journal.pntd.0005023
}}
# {{Cite journal
|authors=Ekins, Sean, John Liebler, Bruno J. Neves, Warren G. Lewis, Megan Coffee, Rachelle Bienstock, Christopher Southan and Carolina H. Andrade
|title=Illustrating and homology modeling the proteins of the Zika virus
|url=https://f1000research.com/articles/5-275/v2
|journal=F1000Research
|date=2016
|doi=10.12688/f1000research.8213.2
}}
 
==== The Clean Energy Project ====
# {{Cite journal
|authors=Lopez, Steven A., Benjamin Sanchez-Lengeling, Julio De Goes Soares and Alán Aspuru-Guzik
|title=Design Principles and Top Non-Fullerene Acceptor Candidates for Organic Photovoltaics
|url=https://linkinghub.elsevier.com/retrieve/pii/S2542435117301307
|journal=Joule
|date=2017
|doi=10.1016/j.joule.2017.10.006
}}
# {{Cite journal
|authors=Pyzer-Knapp, Edward O., Changwon Suh, Rafael Gómez-Bombarelli, Jorge Aguilera-Iparraguirre and Alán Aspuru-Guzik
|title=What Is High-Throughput Virtual Screening? A Perspective from Organic Materials Discovery
|url=https://doi.org/10.1146/annurev-matsci-070214-020823
|journal=Annual Review of Materials Research
|date=2015
|doi=10.1146/annurev-matsci-070214-020823
}}
# {{Cite journal
|authors=Pyzer-Knapp, Edward O., Kewei Li and Alan Aspuru-Guzik
|title=Learning from the Harvard Clean Energy Project: The Use of Neural Networks to Accelerate Materials Discovery
|url=https://onlinelibrary.wiley.com/doi/abs/10.1002/adfm.201501919
|journal=Advanced Functional Materials
|date=2015
|doi=10.1002/adfm.201501919
}}
# {{Cite journal
|authors=Hachmann, Johannes, Roberto Olivares-Amaya, Adrian Jinich et al
|title=Lead candidates for high-performance organic photovoltaics from high-throughput quantum chemistry – the Harvard Clean Energy Project
|url=http://xlink.rsc.org/?DOI=C3EE42756K
|journal=Energy Environ. Sci.
|date=2014
|doi=10.1039/C3EE42756K
}}
# {{Cite journal
|authors=Olivares-Amaya, Roberto, Carlos Amador-Bedolla, Johannes Hachmann, Sule Atahan-Evrenk, Roel S. Sánchez-Carrera, Leslie Vogt and Alán Aspuru-Guzik
|title=Accelerated computational discovery of high-performance materials for organic photovoltaics by means of cheminformatics
|url=http://xlink.rsc.org/?DOI=c1ee02056k
|journal=Energy & Environmental Science
|date=2011
|doi=10.1039/c1ee02056k
}}
# {{Cite journal
|authors=Hachmann, Johannes, Roberto Olivares-Amaya, Sule Atahan-Evrenk et al
|title=The Harvard Clean Energy Project: Large-Scale Computational Screening and Design of Organic Photovoltaics on the World Community Grid
|url=https://doi.org/10.1021/jz200866s
|journal=The Journal of Physical Chemistry Letters
|date=2011
|doi=10.1021/jz200866s
}}
# {{Cite journal
|authors=Sokolov, Anatoliy N., Sule Atahan-Evrenk, Rajib Mondal et al
|title=From computational discovery to experimental characterization of a high hole mobility organic crystal
|url=https://www.nature.com/articles/ncomms1451
|journal=Nature Communications
|date=2011
|doi=10.1038/ncomms1451
}}
 
=== Other project-related publications ===
<!-- The papers below are additional Jurisica Lab / Mapping Cancer Markers output found on https://www.cs.toronto.edu/~juris/jlab/wcg.html that could not be confirmed as using WCG/BOINC-computed data for this specific paper (general cancer genomics/clinical studies, database papers like pathDIP/mirDIP/MatrixDB, and review/book chapters). 28 of the 116 entries below have a DOI link constructed directly from the DOI given in the source list; the remaining ~88 (mostly pre-2017 papers) had no DOI listed on the source page and would need individual lookups to add a link. Review before publishing. -->
 
==== Mapping Cancer Markers (general lab output) ====
# {{Cite journal
|authors=Khan S, Chakraborty M, Wu F, Chen N, Wang T, Chan YT, Sayad A, Kotlyar M, Alibhai FJ, Woo M, Li RK, Husain M, Jurisica I, Gehring AJ, Ohashi PS, Furman D, Tsai S, Winer S, Winer DA
|title=B cells drive CD4 T cell immunosenescence and age-associated health decline
|url=https://doi.org/10.1177/24755303251344134
|journal=Sci Immunol
|date=2026
|doi=10.1177/24755303251344134
}}
# {{Cite journal
|authors=Ganatra D, Kotlyar M, Dohey A, Codner D, Li Q, Abji F, Rasti M, Eder L, Gladman D, Rahman P, Jurisica I, Chandran V
|title=Combining Clinical, Genetic and Protein Markers Using Machine Learning Models Discriminates Psoriatic Arthritis Patients From Those With Psoriasis
|url=https://doi.org/10.1177/24755303251344134
|journal=J Psoriasis Psoriatic Arthritis. doi
|date=2025
|doi=10.1177/24755303251344134
}}
# {{Cite journal
|authors=Yuan Z, Ostrowska-Podhorodecka Z, Cox T, Norouzi M, Wang Y, Robaszkiewicz K, Siatkowska M, Xia K, Ali A, Abovsky M, Jurisica I, Smith P, McCulloch CA
|title=Annexin A2 Contributes to Release of Extracellular Vimentin in Response to Inflammation
|journal=FASEB J
|date=2025
}}
# {{Cite journal
|authors=Samarasinghe KW, Kotlyar M, Vallet SD, Hayes C, Naba A, Jurisica I, Lisacek F, Ricard-Blum S
|title=MatrixDB 2024: an increased coverage of extracellular matrix interactions, a new Network Explorer and a new web interface
|journal=Nucleic Acids Res
|date=2025
}}
# {{Cite journal
|authors=Sigalotti L, Frezza AM, Sbaraglia M, Del Savio E, Baldazzi D, Valenti B, Bellan E, De Benedictis I, Doni M, Gambarotti M, Vincenzi B, Brunello A, Baldi GG, Palmerini E, Pasquali S, Ciuffetti ME, Varano V, Cappello F, Appolloni V, Pastrello C, Jurisica I, Gronchi A, Stacchiotti S, Casali PG, Dei Tos AP, Maestro R
|title=Proximal and classic epithelioid sarcomas are distinct molecular entities defined by MYC/GATA3 and SOX17/endothelial markers, respectively
|journal=Mod Pathol
|date=2024
}}
# {{Cite journal
|authors=Maier A, Hartung M, Abovsky M, Adamowicz K, Bader GD, Baier S, Blumenthal DB, Chen J, Elkjaer ML, Garcia-Hernandez C, Helmy M, Hoffmann M, Jurisica I, Kotlyar M, Lazareva O, Levi H, List M, Lobentanzer S, Loscalzo J, Malod-Dognin N, Manz Q, Matschinske J, Mee M, Oubounyt M, Pastrello C, Pico AR, Pillich RT, Poschenrieder JM, Pratt D, Przulj N, Sadegh S, Saez-Rodriguez J, Sarkar S, Shaked G, Shamir R, Trummer N, Turhan U, Wang RS, Zolotareva O, Baumbach J
|title=Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing
|journal=Nucleic Acids Res
|date=2024
}}
# {{Cite journal
|authors=Pastrello C, Kotlyar M, Abovsky M, Lu R, Jurisica I
|title=PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful
|journal=Nucleic Acids Res
|date=2024
}}
# {{Cite journal
|authors=van Gogh M, Glaus Garzon JF, Sahin D, Knopfova L, Benes P, Boyman O, Jurisica I, Borsig L
|title=Tumor cell-intrinsic c-Myb upregulation stimulates antitumor immunity in a murine colorectal cancer model
|url=https://doi.org/10.1158/2326-6066.CIR-22-0912
|journal=Cancer Immunol Res
|date=2023
|doi=10.1158/2326-6066.CIR-22-0912
}}
# {{Cite journal
|authors=D'Angelo E, Pastrello C, Biccari A, Marangio A, Sensi F, Crotti S, Fassan M, Jurisica I, Pucciarelli S, Agostini M
|title=An integrated multiomics analysis of rectal cancer patients identified POU2F3 as a putative druggable target and entinostat as a cytotoxic enhancer of 5-fluorouracil
|journal=Int J Cancer
|date=2023
}}
# {{Cite journal
|authors=Hauschild AC, Pastrello C, Ekaputeri GKA, Bethune-Waddell D, Abovsky M, Ahmed Z, Kotlyar M, Lu R, Jurisica I
|title=MirDIP 5.2: tissue context annotation and novel microRNA curation
|journal=Nucl Acids Res
|date=2023
}}
# {{Cite journal
|authors=Pathmanathan S, Yao Z, Coelho P, Valla R, Drecun L, Benz C, Snider J, Saraon P, Grozavu I, Kotlyar M, Jurisica I, Park M, Stagljar I
|title=B cell linker protein (BLNK) is a regulator of Met receptor signaling and trafficking in non-small cell lung cancer
|journal=iScience
|date=2022
}}
# {{Cite journal
|authors=Agapito G, Niu Y, Pastrello C, Jurisica I
|title=Pathway integration and annotation: building a puzzle with non-matching pieces and no picture to follow
|journal=Briefings in Bioinformatics
|date=2022
}}
# {{Cite journal
|authors=Pastrello C, Abovsky M, Lu R, Ahmed Z, Kotlyar M, Veillette C, Jurisica I
|title=Osteoarthritis Data Integration Portal (OsteoDIP): A web-based gene and non-coding RNA expression database
|journal=Osteoarthritis and Cartilage Open
|date=2022
}}
# {{Cite journal
|authors=Tokar T, Pastrello C, Abovsky M, Rahmati S, Jurisica I
|title=miRAnno-network-based functional microRNA annotation
|url=https://doi.org/10.3389/fonc.2021.777834
|journal=Bioinformatics
|date=2022
|doi=10.3389/fonc.2021.777834
}}
# {{Cite journal
|authors=Bhat M, Pasini E, Pastrello C, Angeli M, Baciu C, Abovsky M, Coffee A, Adeyi O, Kotlyar M, Jurisica I
|title=Estrogen Receptor 1 Inhibition of Wnt/Beta-catenin Signaling Contributes to Sex Differences in Hepatocarcinogenesis
|url=https://doi.org/10.3389/fonc.2021.777834
|journal=Frontiers in Oncology
|date=2021
|doi=10.3389/fonc.2021.777834
}}
# {{Cite journal
|authors=Cohn DE, Barros-Filho MC, Minatel BC, Pewarchuk ME, Marshall EA, Vucic EA, Sage AP, Telkar N, Stewart GL, Jurisica I, Reis PP, Robinson WP, Lam WL
|title=Reactivation of Multiple Fetal miRNAs in Lung Adenocarcinoma
|journal=Cancers
|date=2021
}}
# {{Cite journal
|authors=Bhat M, Pasini E, Pastrello C, Rahmati S, Angeli M, Kotlyar M, Ghanekar A, Jurisica I
|title=Integrative Analysis of Layers of Data in Hepatocellular Carcinoma Reveals Pathway Dependencies
|journal=World J Hepatology
|date=2021
}}
# {{Cite journal
|authors=Porras P, Barrera E, Bridge A, Del-Toro N, Cesareni G, Duesbury M, Hermjakob H, Iannuccelli M, Jurisica I, Kotlyar M, Licata L, Lovering RC, Lynn DJ, Meldal B, Nanduri B, Paneerselvam K, Panni S, Pastrello C, Pellegrini M, Perfetto L, Rahimzadeh N, Ratan P, Ricard-Blum S, Salwinski L, Shirodkar G, Shrivastava A, Orchard S
|title=Towards a unified open access dataset of molecular interactions
|journal=Nat Commun
|date=2020
}}
# {{Cite journal
|authors=Glaus Garzon JF, Pastrello C, Jurisica I, Hottiger MO, Wenger RH, Borsig L
|title=Tumor cell endogenous HIF-1a activity induces aberrant angiogenesis and interacts with TRAF6 pathway required for colorectal cancer development
|journal=Neoplasia
|date=2020
}}
# {{Cite journal
|authors=Yao Z, Aboualizadeh F, Akula I, Snider J, Tang P, Kotlyar M, Jurisica I, Stagljar I
|title=Split Intein-Mediated Protein Ligation, a Novel Method for Detecting Protein-Protein Interactions and Their Inhibition
|journal=Nat Commun
|date=2020
}}
# {{Cite journal
|authors=Pinheiro M, Lupinacci FCS, Santiago KM, Drigo SA, Marchi FA, Fonseca-Alves CE, Andrade SCDS, Aagaard MM, Basso TR, Dos Reis MB, Villacis RAR, Roffa M, Hajj GNM, Jurisica I, Kowalski LP, Achatz MI, Rogatto SR
|title=Constitutional and Somatic Rare Variant Analysis of Individuals with Rare Genetic Syndromes and Second Primary Tumours
|url=https://doi.org/10.3390/cancers12051289
|journal=Cancers
|date=2020
|doi=10.3390/cancers12051289
}}
# {{Cite journal
|authors=Reis PP, Tokar T, Goswami RS, Xuan Y, Sukhai M, Seneda AL, Moz LES, Perez-Ordonez B, Simpson C, Goldstein D, Brown D, Gilbert R, Gullane P, Irish J, Jurisica I, Kamel-Reid S
|title=A 4-gene signature from histologically normal surgical margins predicts local recurrence in patients with oral carcinoma: clinical validation
|url=https://doi.org/10.1038/s41598-020-58688-y
|journal=Scientific Reports
|date=2020
|doi=10.1038/s41598-020-58688-y
}}
# {{Cite journal
|authors=Tokar T, Pastrello C, Jurisica I
|title=GSOAP: A tool for visualization of gene set over-representation analysis
|url=https://doi.org/10.1093/bioinformatics/btaa001
|journal=Bioinformatics
|date=2020
|doi=10.1093/bioinformatics/btaa001
}}
# {{Cite journal
|authors=Rahmati R, Abovsky M, Pastrello C, Kotlyar M, Lu R, Cumbaa CA, Rahman P, Chandran V, Jurisica I
|title=pathDIP 4: an extended pathway annotations and enrichment analysis resource for human, model organisms and domesticated species
|url=https://doi.org/10.1093/nar/gkz989
|journal=Nucl Acids Res
|date=2020
|doi=10.1093/nar/gkz989
}}
# {{Cite journal
|authors=Kennedy S, Jarboui MA, Srihari S, Raso C, Bryan K, Dernayka L, Charitou T, Bernal-Llinares M, Herrera-Montavez C, Krstic A, Matallanas D, Kotlyar M, Jurisica I, Curak J, Wong V, Stagljar I, LeBihan T, Imrie L, Pillai P, Lynn M, Fasterius E, Szigyarto CAK, Breen J, Kiel C, Serrano L, Rauch N, Rukhlenko O, Kholodenko B, Iglesias-Martinez L, Ryan C, Pilkington R, Cammareri P, Sansom O, Shave S, Auer M, Horn N, Klose F, Ueffing M, Boldt K, Lynn D, Kolch W
|title=Extensive Rewiring of the EGFR Network in Colorectal Cancer Cells Expressing Transforming Levels of KRASG13D
|url=https://doi.org/10.1038/s41467-019-14224-9
|journal=Nat Commun
|date=2020
|doi=10.1038/s41467-019-14224-9
}}
# {{Cite journal
|authors=Enfield KSS, Marshall EA, Anderson C, Ng KW, Rahmati S, Xu Z, Fuller M, Milne K, Lu D, Shi R, Rowbotham DA, Becker-Santos DD, Johnson FD, English JC, MacAulay CE, Lam S, Lockwood WW, Chari R, Karsan A, Jurisica I, Lam WL
|title=Epithelial tumor suppressor ELF3 is a lineage-specific amplified oncogene in lung adenocarcinoma
|url=https://doi.org/10.1038/s41467-019-13295-y
|journal=Nat Commun
|date=2019
|doi=10.1038/s41467-019-13295-y
}}
# {{Cite journal
|authors=Monette A, Bergeron D, Ben Amor A, Meunier L, Caron C, Mes-Masson AM, Kchir N, Hamzaoui K, Jurisica I, Lapointe R
|title=Immune-enrichment of non-small cell lung cancer baseline biopsies for multiplex profiling define prognostic immune checkpoint combinations for patient stratification
|url=https://doi.org/10.1186/s40425-019-0544-x
|journal=J Immunother Cancer
|date=2019
|doi=10.1186/s40425-019-0544-x
}}
# {{Cite journal
|authors=Monette A, Morou A, Al-Banna NA, Rousseau L, Lattouf JB, Rahmati S, Tokar T, Routy JP, Cailhier JF, Kaufmann DE, Jurisica I, Lapointe R
|title=Failed immune responses across multiple pathologies share pan-tumor and circulating lymphocytic targets
|url=https://doi.org/10.1172/JCI125301
|journal=J Clin Invest
|date=2019
|doi=10.1172/JCI125301
}}
# {{Cite journal
|authors=Kaufmann KB, Garcia-Prat L, Liu Q, Ng SWK, Takayanagi SI, Mitchell A, Wienholds E, van Galen P, Cumbaa CA, Tsay MJ, Pastrello C, Wagenblast E, Krivdova G, Minden MD, Lechman ER, Zandi S, Jurisica I, Wang JCY, Xie SZ, Dick JE
|title=A stemness screen reveals C3orf54/INKA1 as a promoter of human leukemia stem cell latency
|url=https://doi.org/10.1182/blood-2018-10-881441
|journal=Blood
|date=2019
|doi=10.1182/blood-2018-10-881441
}}
# {{Cite journal
|authors=Mandilaras V, Garg S, Cabanero M, Tan Q, Pastrello C, Burnier J, Karakasis K, Wang L, Dhani NC, Butler MO, Bedard PL, Siu LL, Clarke B, Shaw PA, Stockley T, Jurisica I, Oza AM
|title=TP53 mutations in high grade serous ovarian cancer and impact on clinical outcomes: a comparison of next generation sequencing and bioinformatics analyses
|url=https://doi.org/10.1136/ijgc-2018-000087
|journal=Int J Gyn Cancer
|date=2019
|doi=10.1136/ijgc-2018-000087
}}
# {{Cite journal
|authors=del Toro N, Duesbury M, Koch M, Perfetto L, Shrivastava A, Ochoa D, Wagih O, Pinero J, Kotlyar M, Pastrello C, Beltrao P, Furlong LI, Jurisica I, Hermjakob H, Orchard S, Porras P
|title=Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set
|journal=Nat Commun
|date=2019
}}
# {{Cite journal
|authors=Li L, Guturi KKN, Gautreau B, Patel PS, Saad A, Morii M, Mateo F, Palomero L, Barbour H, Gomez A, Ng D, Kotlyar M, Pastrello C, Jackson HW, Khokha R, Jurisica I, Affar EB, Raught B, Sanchez O, Alaoui-Jamali M, Pujana MA, Hakem A, Hakem R
|title=Ubiquitin ligase RNF8 suppresses Notch signaling to regulate mammary development and tumorigenesis
|url=https://doi.org/10.1172/JCI120401
|journal=J Clin Invest
|date=2018
|doi=10.1172/JCI120401
}}
# {{Cite journal
|authors=Singh M, Venugopal C, Tokar T, McFarlane N, Subapanditha MK, Qazi M, Bakhshinyan D, Vora P, Murty N, Jurisica I, Singh SK
|title=Therapeutic targeting of the pre-metastatic stage in human brain metastasis
|url=https://doi.org/10.1158/0008-5472.CAN-18-1022
|journal=Cancer Res
|date=2018
|doi=10.1158/0008-5472.CAN-18-1022
}}
# {{Cite journal
|authors=Tokar T, Pastrello C, Ramnarine VR, Zhu CQ, Craddock KJ, Pikor L, Vucic EA, Vary S, Shepherd FA, Tsao MS, Lam WL, Jurisica I
|title=Differentially expressed microRNAs in lung adenocarcinoma invert effects of copy number aberrations of prognostic genes
|journal=Oncotarget
|date=2018
}}
# {{Cite journal
|authors=Paulitti A, Corallo D, Andreuzzi E, Bizzotto D, Marastoni S, Pellicani R, Tarticchio G, Pastrello C, Jurisica I, Ligresti G, Bucciotti F, Doliana R, Colladel R, Braghetta P, Di Silvestre A, Bressan G, Colombatti A, Bonaldo P, Mongiat M
|title=The ablation of the matricellular protein EMILIN2 causes defective vascularization due to impaired EGFR-dependent IL-8 production affecting tumor growth
|journal=Oncogene
|date=2018
}}
# {{Cite journal
|authors=Tokar T, Pastrello C, Rossos A, Abovsky M, Hauschild AC, Tsay M, Lu R, Jurisica I
|title=mirDIP 4.1 - Integrative database of human microRNA target predictions
|journal=Nucl Acids Res
|date=2018
}}
# {{Cite journal
|authors=Kotlyar M, Pastrello C, Rossos A, Jurisica I
|title=Prediction of protein-protein interactions
|journal=Current Protocols in Bioinf
|date=2017
}}
# {{Cite journal
|authors=Singh M, Venugopal C, Tokar T, Brown KB, McFarlane N, Bakhshinyan D, Vijayakumar T, Manoranjan B, Mahendram S, Vora P, Qazi M, Dhillon M, Tong A, Durrer K, Murty N, Hallet R, Hassell JA, Kaplan D, Jurisica I, Cutz JC, Moffat J, Singh DK
|title=RNAi screen identifies essential regulators of human brain metastasis initiating cells
|journal=Acta Neuropathologica
|date=2017
}}
# {{Cite journal
|authors=Wong SWH, Pastrello C, Kotlyar M, Faloutsos C, Jurisica I
|title=Modeling tumor progression via the comparison of stage-specific graphs
|journal=Methods
|date=2018
}}
# {{Cite journal
|authors=Pastrello C, Tsay M, McQuaid R, Abovsky M, Pasini E, Shirdel E, Angeli M, Tokar T, Jamnik J, Kotlyar M, Jurisicova A, Kotsopoulos J, El-Sohemy A, Jurisica I
|title=Retraction: Circulating plant miRNAs can regulate human gene expression in vitro
|journal=Sci Rep
|date=2017
}}
# {{Cite journal
|authors=Wang D, Pham NA, Tong JF, Sakashita S, Allo G, Kim L, Yanagawa N, Raghavan V, Wei YH, To C, Trinh QM, Starmans MHW, Chan-Seng-Ye MA, Chadwick D, Li L, Zhu CQ, Liu N, Li M, Lee S, Ignatchenko V, Strumpf D, Taylor P, Moghal N, Liu G, Boutros PC, Kislinger T, Pintilie M, Jurisica I, Shepherd FA, McPherson J, Muthuswami L, Moran MF, Tsao MS
|title=Molecular heterogeneity of non-small cell lung carcinoma patient-derived xenografts closely reflect their primary tumors
|journal=Int J Cancer
|date=2017
}}
# {{Cite journal
|authors=Pinheiro M, Drigo SA, Tonhosolo R, Andrade SCS, Marchi FA, Jurisica I, Kowalski LP, Achatz MI, Rogatto SR
|title=HABP2 p.G534E variant in patients with family history of thyroid and breast cancer
|journal=Oncotarget
|date=2017
}}
# {{Cite journal
|authors=Citron F, Armenia J, Barzan L, Franchin G, Polesel J, Talamini R, Sulfaro S, Croce CM, Klement W, Pastrello C, Jurisica I, Vecchione A, Belletti B, Baldassarre G
|title=A microRNA signature identifies SP1 and TGFbeta pathways as potential mediators of local recurrences in head and neck squamous carcinomas
|journal=Clin Cancer Res
|date=2017
}}
# {{Cite journal
|authors=Sokolina K, Kittanakom S, Snider J, Kotlyar M, Maurice P, Gandia J, Benleulmi-Chaachoua A, Tadagaki K, Wong V, Malty RH, Deineko V, Aoki H, Amin S, Riley L, Yao Z, Morato X, Otasek D, Kobayashi H, Menendez J, Auerbach D, Angers S, Przulj N, Bouvier M, Babu M, Ciruela F, Jockers R, Jurisica I, Stagljar I
|title=Systematic protein-protein interaction mapping for clinically-relevant human GPCRs
|journal=Mol Sys Biol
|date=2017
}}
# {{Cite journal
|authors=Yao Z, Darowski K, St-Denis N, Wong V, Offensperger F, Villedieu A, Amin S, Malty R, Aoki H, Guo H, Xu Y, Iorio C, Kotlyar M, Emili A, Jurisica I, Babu M, Neel B, Gingras AC, Stagljar I
|title=A global analysis of the protein phosphatase interactome
|journal=Mol Cell
|date=2017
}}
# {{Cite journal
|authors=Petschnigg J, Kotlyar M, Blair L, Jurisica I, Stagljar I, Ketteler R
|title=Systematic identification of oncogenic EGFR interaction partners
|journal=J Mol Biol
|date=2017
}}
# {{Cite journal
|authors=Rahmati S, Abovsky M, Pastrello C, Jurisica I
|title=pathDIP: An annotated resource for known and predicted human gene-pathway associations and pathway enrichment analysis
|journal=Nucl Acids Res
|date=2017
}}
# {{Cite journal
|authors=Chehade R, Pettapiece-Phillips R, Salmena L, Kotlyar M, Jurisica I, Narod SA, Akbari MR, Kotsopoulos J
|title=Reduced BRCA1 transcript levels in freshly isolated blood leukocytes from BRCA1 mutation carriers is mutation specific
|journal=Breast Cancer Res
|date=2016
}}
# {{Cite journal
|authors=Cierna Z, Mego M, Jurisica I, Machalekova K, Chovanec M, Miskovska V, Svetlovska D, Hainova K, Kajo K, Mardiak J, Babal P
|title=Fibrillin-1 (FBN-1) a new marker of germ cell neoplasia in situ
|journal=BMC Cancer
|date=2016
}}
# {{Cite journal
|authors=Becker-Santos DD, Thu KL, English JC, Pikor LA, Chari R, Lonergan KM, Martinez VD, Zhang M, Vucic EA, Luk MTY, Carraro A, Korbelik J, Piga D, Lhomme NM, Tsay MJ, Yee J, MacAulay CE, Lockwood WW, Robinson WP, Jurisica I, Lam WL
|title=Developmental transcription factor NFIB is a putative target of oncofetal miRNAs and is associated with tumour aggressiveness in lung adenocarcinoma
|journal=J Pathology
|date=2016
}}
# {{Cite journal
|authors=Stojanova A, Tu WB, Ponzielli R, Kotlyar M, Chan PK, Boutros PC, Khosravi F, Jurisica I, Raught B, Penn LZ
|title=MYC interaction with the tumor suppressive SWI/SNF complex member INI1 regulates transcription and cellular transformation
|journal=Cell Cycle
|date=2016
}}
# {{Cite journal
|authors=Li YH, Tavallaee G, Tokar T, Nakamura A, Sundararajan K, Weston A, Sharma A, Mahomed NN, Gandhi R, Jurisica I, Kapoor M
|title=Identification of synovial fluid microRNA signature in knee osteoarthritis: Differentiating early- and late-stage knee Osteoarthritis
|journal=Osteoarthritis and Cartilage
|date=2016
}}
# {{Cite journal
|authors=Cinegaglia NC, Andrade SCS, Tokar T, Pinheiro M, Severino FE, Oliveira RA, Hasimoto EN, Cataneo DC, Cataneo AJM, Defaveri J, Souza CP, Marques MMC, Carvalho RF, Coutinho LL, Gross JL, Rogatto SR, Lam WL, Jurisica I, Reis PP
|title=Integrative transcriptome analysis identifies deregulated microRNA-transcription factor networks in lung adenocarcinoma
|journal=Oncotarget
|date=2016
}}
# {{Cite journal
|authors=Vargas A, Angeli M, Pastrello C, McQuaid R, Li H, Jurisicova A, Jurisica I
|title=Robust quantitative scratch assay
|journal=Bioinformatics
|date=2016
}}
# {{Cite journal
|authors=Snider J, Kotlyar M, Saraon P, Yao Z, Jurisica I, Stagljar I
|title=Fundamentals of protein interaction network mapping
|journal=Mol Sys Biol
|date=2015
}}
# {{Cite journal
|authors=Pettapiece-Phillips R, Kotlyar M, Chehade R, Salmena L, Narod SA, Akbari M, Jurisica I, Kotsopoulos J
|title=Uninterrupted sedentary behavior downregulates BRCA1 gene expression
|journal=Cancer Prevention Res
|date=2016
}}
# {{Cite journal
|authors=Navab R, Strumpf D, To C, Pasko E, Kim KS, Park CJ, Hai J, Liu J, Jonkman J, Barczyk M, Bandarchi B, Wang YH, Venkat K, Ibrahimov E, Pham NA, Ng C, Radulovich N, Zhu CQ, Pintilie M, Wang D, Lu A, Jurisica I, Walker GC, Gullberg D, Tsao MS
|title=Integrin a11b1 regulates cancer stromal stiffness and promotes tumorigenecity in non-small cell lung cancer
|journal=Oncogene
|date=2016
}}
# {{Cite journal
|authors=Agostini M, Janssen KP, Kim LJ, D'Angelo E, Pizzini S, Zangrando A, Zanon C, Pastrello C, Maretto I, Digito M, Bedin C, Jurisica I, Rizzolio F, Giordano A, Bortoluzzi S, Nitti D, Pucciarelli S
|title=An integrative approach for the identification of prognostic and predictive biomarkers in rectal cancer
|journal=Oncotarget
|date=2015
}}
# {{Cite journal
|authors=Singh M, Garg N, Venugopal C, Hallett RM, Tokar T, McFarlane N, Arpin C, Page B, Haftchenary S, Todic A, Rosa DA, Lai P, Gomez-Biagi R, Ali AM, Lewis A, Geletu M, Mahendram S, Bakhshinyan D, Manoranjan B, Vora P, Qazi M, Murty NK, Hassell JA, Jurisica I, Gunning P, Singh SK
|title=STAT3 pathway regulates lung-derived brain metastasis initiating cell capacity through miR-21 activation
|journal=Oncotarget
|date=2015
}}
# {{Cite journal
|authors=Agostini M, Zangrando A, Pastrello C, D'Angelo E, Romano G, Giovannoni R, Giordan M, Maretto I, Bedin C, Zanon C, Digito M, Esposito G, Mescoli C, Lavitrano M, Rizzolio F, Jurisica I, Giordano A, Pucciarelli S, Nitti D
|title=A functional biological network centered on XRCC3: a new possible marker of chemoradiotherapy resistance in rectal cancer patients
|journal=Cancer Biol Ther
|date=2015
}}
# {{Cite journal
|authors=Stewart EL, Mascaux C, Pham NA, Sakashita S, Sykes J, Kim L, Yanagawa N, Allo G, Ishizawa K, Wang D, Zhu CQ, Li M, Ng C, Liu N, Pintilie M, Martin P, John T, Jurisica I, Leighl NB, Neel BG, Waddell TK, Shepherd FA, Liu G, Tsao MS
|title=Clinical Utility of Patient Derived Xenografts to Determine Biomarkers of Prognosis and Map Resistance Pathways in EGFR-Mutant Lung Adenocarcinoma
|journal=J Clin Oncol
|date=2015
}}
# {{Cite journal
|authors=Camargo JF, Resende M, Zamel R, Klement W, Bhimji A, Huibner S, Kumar D, Humar A, Jurisica I, Keshavjee S, Kaul R, Husain S
|title=Potential role of CC chemokine receptor 6 (CCR6) in prediction of late-onset CMV infection following solid organ transplant
|journal=Clin Transplant
|date=2015
}}
# {{Cite journal
|authors=Fortney K, Griesman G, Kotlyar M, Pastrello C, Angeli M, Tsao MS, Jurisica I
|title=Prioritizing therapeutics for lung cancer: An integrative meta-analysis of cancer gene signatures and chemogenomic data
|journal=PLoS Comp Biol
|date=2015
}}
# {{Cite journal
|authors=Starmans MH, Pintilie M, Chan-Seng-Yue M, Moon NC, Haider S, Nguyen F, Lau SK, Liu N, Kasprzyk A, Wouters BG, Der SD, Shepherd FA, Jurisica I, Penn LZ, Tsao MS, Lambin P, Boutros PC
|title=Integrating RAS status into prognostic signatures for adenocarcinomas of the lung
|journal=Clin Cancer Res
|date=2015
}}
# {{Cite journal
|authors=Tu WB, Helander S, Pilstal R, Hickman KA, Lourenco C, Jurisica I, Raught B, Wallner B, Sunnerhagen M, Penn LZ
|title=Myc and its interactors take shape
|journal=Biochim Biophys Acta
|date=2015
}}
# {{Cite journal
|authors=Dingar D, Kalkat M, Chan MPK, Bailey SD, Srikumar T, Tu WB, Ponzielli R, Kotlyar M, Jurisica I, Huang A, Lupien M, Penn LZ, Raught B
|title=BioID identifies novel c-MYC interacting partners in cultured cells and xenograft tumors
|journal=J Proteomics
|date=2015
}}
# {{Cite journal
|authors=Wong SWH, Cercone N, Jurisica I
|title=Comparative network analysis via differential graphlet communities
|journal=Special Issue of Proteomics
|date=2015
}}
# {{Cite journal
|authors=Vucic EA, Thu KT, Pikor LA, Enfield KSS, Yee J, English JC, MacAulay CE, Lam S, Jurisica I, Lam WL
|title=Smoking status impacts microRNA mediated prognosis and lung adenocarcinoma biology
|journal=BMC Cancer
|date=2014
}}
# {{Cite journal
|authors=Lalonde E, Ishkanian AS, Sykes J, Fraser M, Ross-Adam H, Erho N, Dunning M, Lamb AD, Moon NC, Zafarana G, Warren AY, Meng A, Thoms J, Grzadkowski MR, Berlin A, Halim S, Have CL, Ramnarine VR, Yao CQ, Malloff CA, Lam LL, Xie H, Harding NJ, Mak DYF, Chu KC, Chong LC, Sendorek DH, P'ng C, Collins CC, Squire JA, Jurisica I, Cooper C, Eeles R, Pintilie M, Pra AD, Davicioni E, Lam WL, Milosevic M, Neal DE, van der Kwast T, Boutros PC, Bristow RG
|title=Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study
|journal=Lancet Oncology
|date=2014
}}
# {{Cite journal
|authors=Berlin A, Lalonde E, Sykes J, Zafarana G, Chu KC, Ramnarine VR, Ishkanian A, Sendorek DHS, Pasic I, Lam WL, Jurisica I, van der Kwast T, Milosevic M, Boutros PC, Bristow RG
|title=NBN Gain Is Predictive for Adverse Outcome Following Image-Guided Radiotherapy for Localized Prostate Cancer
|url=https://doi.org/10.1038/oncsis.2014.45
|journal=Oncotarget
|date=2014
|doi=10.1038/oncsis.2014.45
}}
# {{Cite journal
|authors=Lapin V, Shirdel E, Wei X, Mason J, Jurisica I, Mak TW
|title=Kinome-wide screening of HER2+ breast cancer cells for molecules that mediate cell proliferation or sensitize cells to trastuzumab therapy
|url=https://doi.org/10.1038/oncsis.2014.45
|journal=Oncogenesis
|date=2014
|doi=10.1038/oncsis.2014.45
}}
# {{Cite journal
|authors=Cancer Genome Atlas Research Network
|title=Comprehensive molecular profiling of lung adenocarcinoma
|url=https://doi.org/10.1038/nature13385
|journal=Nature
|date=2014
|doi=10.1038/nature13385
}}
# {{Cite journal
|authors=Kotlyar M, Pastrello C, Pivetta F, Lo Sardo A, Cumbaa C, Li H, Naranian T, Niu Y, Ding Z, Vafaee F, Broackes-Carter F, Petschnigg J, Mills GB, Jurisicova A, Stagljar I, Maestro R, Jurisica I
|title=In silico prediction of physical protein interactions and characterization of interactome orphans
|url=https://doi.org/10.1016/j.bbrc.2014.01.151
|journal=Nat Methods
|date=2015
|doi=10.1016/j.bbrc.2014.01.151
}}
# {{Cite journal
|authors=Pastrello C, Pasini E, Kotlyar M, Otasek D, Wong S, Sangrar W, Rahmati S, Jurisica I
|title=Integration, visualization and analysis of human interactome
|url=https://doi.org/10.1016/j.bbrc.2014.01.151
|journal=J Biochemical & Biophysical Research Communications
|date=2014
|doi=10.1016/j.bbrc.2014.01.151
}}
# {{Cite journal
|authors=Cervigne, N.K., J. Machado, R.S. Goswami, B. Sadikovic, G. Bradley, B. Perez-Ordonez, N.N. Galloni, R. Gilbert, P. Gullane, J.C. Irish, I. Jurisica, P.P. Reis and S. Kamel-Reid
|title=Recurrent genomic alterations in sequential progressive leukoplakia and oral cancer: drivers of oral tumorigenesis?
|url=https://doi.org/10.1093/hmg/ddt657
|journal=Human Molecular Genetics
|date=2014
|doi=10.1093/hmg/ddt657
}}
# {{Cite journal
|authors=Petschnigg J, Groisman B, Kotlyar M, Taipale M, Zheng Y, Kurat C, Sayad A, Sierra J, Mattiazzi Usaj M, Snider J, Nachman A, Krykbaeva I, Tsao MS, Moffat J, Pawson T, Lindquist S, Jurisica I, Stagljar I
|title=Mammalian Membrane Two-Hybrid assay (MaMTH): a novel split-ubiquitin two-hybrid tool for functional investigation of signaling pathways in human cells
|url=https://doi.org/10.1038/nmeth.2895
|journal=Nat Methods
|date=2014
|doi=10.1038/nmeth.2895
}}
# {{Cite journal
|authors=Der SD, Sykes J, Pintilie M, Zhu CQ, Strumpf D, Liu N, Jurisica I, Shepherd FA, Tsao MS
|title=Validation of a histology-independent prognostic gene signature for early-stage, non-small-cell lung cancer including stage IA patients
|url=https://doi.org/10.1097/JTO.0000000000000042
|journal=J Thorac Oncol
|date=2014
|doi=10.1097/JTO.0000000000000042
}}
# {{Cite journal
|authors=Cirilo PDR, Marchi FA, Filho MCB, Rocha RM, Domingues MAC, Jurisica I, Pontes A, Rogatto SR
|title=An integrative genomic and transcriptomic analysis reveals potential targets associated with cell proliferation in uterine leiomyomas
|journal=PLoS One
|date=2013
}}
# {{Cite journal
|authors=Vafaee F, Rosu D, Broackes-Carter F, Jurisica I
|title=Novel semantic similarity measure improves an integrative approach to predicting gene functional associations
|journal=BMC Sys Biol
|date=2013
}}
# {{Cite journal
|authors=Goswami RS, Atenafu EG, Xuan Y, Waldron L, Pintor dos Reis P, Sun T, Datti A, Xu W, Kuruvilla J, Good DJ, Lai R, Church AJ, Lam W, Baetz T, LeBrun DP, Sehn LH, Farinha P, Jurisica I, Bailey DJ, Gascoyne RD, Crump M, Kamel-Reid S
|title=A microRNA signature obtained from the comparison of aggressive to indolent non-Hodgkin lymphomas can be used in the prognosis of mantle cell lymphoma
|journal=J Clin Oncol
|date=2013
}}
# {{Cite journal
|authors=Berger T, Ueda T, Arpaia E, Chio II, Shirdel EA, Jurisica I, Hamada K, You-Ten A, Haight J, Wakeham A, Cheung CC, Mak TW
|title=Flotillin-2 deficiency leads to reduced lung metastases in a mouse breast cancer model
|journal=Oncogene
|date=2013
}}
# {{Cite journal
|authors=Pastrello C, Otasek D, Fortney K, Agapito G, Cannataro M, Shirdel EA, Jurisica I
|title=Visual data mining of biological networks: one size does not fit all
|journal=PLoS Comp Biol
|date=2013
}}
# {{Cite journal
|authors=Fortney K, Xie W, Kotlyar M, Griesman J, Kotseruba J, Jurisica I
|title=NetwoRx: Connecting drugs to networks and phenotypes in S
|journal=Cerevisiae. Nucl Acids Res
|date=2013
}}
# {{Cite journal
|authors=Hammerman PS et al (Cancer Genome Atlas Research Network)
|title=Comprehensive genomic characterization of squamous cell lung cancers
|journal=Nature
|date=2012
}}
# {{Cite journal
|authors=McKee CM, Xu D, Cao Y, Kabraji S, Allen D, Kearsmans V, Beech J, Smart S, Hamdy F, Ishkanian A, Sykes J, Pintile M, Milosevic M, Kwast T van der, Zafarana G, Ramnarine R, Jurisica I, Mallof C, Lam W, Bristow RG, Muschel RJ
|title=Protease Nexin 1 modulates prostate adenocarcinoma by regulating the Hedgehog pathway
|journal=J Clin Invest
|date=2012
}}
# {{Cite journal
|authors=Kotlyar M, Fortney F, Jurisica I
|title=Network-based characterization of drug-regulated genes, drug targets, and toxicity
|journal=Methods
|date=2012
}}
# {{Cite journal
|authors=Hai J, Zhu CQ, Bandarchi-Chamkhaleh B, Wang YH, Navab R, Shepherd FA, Jurisica I, Tsao MS
|title=L1 Cell Adhesion Molecule promotes tumorigenicity and metastatic potential in non-small-cell lung cancer
|journal=Clin Cancer Res
|date=2012
}}
# {{Cite journal
|authors=Arneson N, Moreno, Iakovlev JV, Ghazani A, Warren K, McCready D, Jurisica I, Done SJ
|title=Comparison of whole genome amplification methods for analysis of DNA extracted from microdissected early breast lesions in formalin-fixed paraffin-embedded tissue
|journal=ISRN Oncology
|date=2012
}}
# {{Cite journal
|authors=Locke JA, Zafarana G, Malloff CA, Lam WL, Sykes J, Pintilie M, Ramnarine VR, Jurisica I, Guns ET, van der Kwast T, Milosevic M, Bristow RG
|title=Allelic loss of the loci containing StAR is prognostic for relapse in intermediate-risk prostate cancer
|journal=Prostate
|date=2012
}}
# {{Cite journal
|authors=Zafarana G, Ishkanian AS, Malloff CA, Locke JA, Sykes J, Thoms J, Lam WL, Squire JA, Yoshimoto M, Ramnarine VR, Jurisica I, Milosevic M, Pintilie M, van der Kwast T, Bristow RG
|title=Copy number alterations of c-MYC and PTEN are prognostic factors for relapse following prostate cancer radiotherapy
|journal=Cancer
|date=2012
}}
# {{Cite journal
|authors=Locke JA, Zafarana G, Ishkanian AS, Milosevic M, Thoms J, Have CL, Malloff CA, Lam WL, Squire JA, Pintilie M, Sykes J, Ramnarine VR, Meng A, Ahmed O, Jurisica I, van der Kwast T, Bristow RG
|title=NKX3.1 haploinsufficiency is prognostic for prostate cancer relapse following image-guided radiotherapy
|journal=Clinical Cancer Research
|date=2012
}}
# {{Cite journal
|authors=Waldron L, Pintilie M, Tsao MS, Shepherd FA, Huttenhower C, Jurisica I
|title=Optimized application of penalized regression methods to diverse genomic data
|journal=Bioinformatics
|date=2011
}}
# {{Cite journal
|authors=Hakem A, Bohgaki M, Lemmers B, Tai E, Salmena L, Matysiak-Zablocki E, Lopez-Bahr WI, Karaskova J, Boutros P, Sheng Y, Arrowsmith C, Chesi M, Bergsagel L, Perez-Ordonez B, Squire J, Jurisica I, Penn L, Sanchez O, Benchimol S, Hakem R
|title=Role of Pirh2 in mediating the regulation of p53 and c-Myc
|journal=PLoS Genetics
|date=2011
}}
# {{Cite journal
|authors=Reis PP, Waldron L, Perez-Ordonez B, Pintilie M, Galloni N, Xuan Y, Cervigne NK, Warner GC, Makitie AA, Simpson C, Goldstein D, Brown D, Gilbert R, Gullane P, Irish J, Jurisica I, Kamel-Reid S
|title=A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence
|journal=BMC Cancer
|date=2011
}}
# {{Cite journal
|authors=Djebbari A, Ali M, Otasek D, Kotlyar M, Fortney K, Wong S, Hrvojic A, Jurisica I
|title=NAViGaTOR: Scalable and Interactive Navigation and Analysis of Large Graphs
|journal=Internet Mathematics
|date=2011
}}
# {{Cite journal
|authors=Eppert K, Takenaka K, Lechman ER, Waldron L, Nilsson B, van Galen P, Metzeler K, Poeppl A, Ling V, Beyene J, Canty AJ, Danska JS, Bohlander SK, Buske C, Minden MD, Golub TR, Jurisica I, Ebert BL, Dick JE
|title=Stem cell gene expression programs influence clinical outcome in human leukemia
|journal=Nat Medicine
|date=2011
}}
# {{Cite journal
|authors=Notta F, Doulatov S, Laurenti E, Poeppl A, Jurisica I, Dick JE
|title=Isolation of single human hematopoietic stem cells capable of long-term multilineage engraftment
|journal=Science
|date=2011
}}
# {{Cite journal
|authors=Reis PP, Waldron L, Goswami RS, Xu W, Xuan Y, Ordonez BP, Gullane P, Irish J, Jurisica I, Kamel-Reid S
|title=mRNA transcript quantification in archival samples using multiplexed, color-coded probes
|journal=BMC Biotechnology
|date=2011
}}
# {{Cite journal
|authors=Navab R, Strumpf D, Bandarchi B, Zhu CQ, Pintilie M, Ramnarine VR, Ibrahimov E, Radulovich N, Leung L, Barczyk M, Panchal D, To C, Yun JJ, Der S, Shepherd FA, Jurisica I, Tsao MS
|title=Prognostic gene-expression signature of carcinoma-associated fibroblasts in non-small cell lung cancer
|journal=PNAS
|date=2011
}}
# {{Cite journal
|authors=Elschenbroich S, Ignatchenko V, Clarke B, Kalloger SE, Boutros PC, Gramolini AO, Shaw P, Jurisica I, Kislinger T
|title=In-depth proteomics of ovarian cancer ascites: combining shotgun proteomics and selected reaction monitoring mass spectrometry
|journal=J Proteome Res
|date=2011
}}
# {{Cite journal
|authors=Fortney K, Jurisica I
|title=Integrative computational biology for cancer research
|journal=Human Genetics
|date=2011
}}
# {{Cite journal
|authors=Chang Q, Jurisica I, Do T, Hedley DW
|title=Hypoxia predicts for aggressive growth and spontaneous metastasis formation from orthotopically-grown primary xenografts of human pancreatic cancer
|journal=Cancer Res
|date=2011
}}
# {{Cite journal
|authors=Shirdel EA, Xie W, Mak TW, Jurisica I
|title=NAViGaTing the micronome: Using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs
|journal=PLoS ONE
|date=2011
}}
# {{Cite journal
|authors=Wei Y, Tong J, Taylor P, Strumpf D, Ignatchenko V, Pham NA, Yanagawa N, Liu G, Jurisica I, Shepherd FA, Tsao MS, Kislinger T, Moran MF
|title=Primary Tumor Xenografts of Human Lung Adeno and Squamous Cell Carcinoma Express Distinct Proteomic Signatures
|journal=J Proteome Res
|date=2011
}}
# {{Cite journal
|authors=Jurisica I
|title=Integrative Computational Biology, AI, and Radiomics: Building Explainable Models by Integration of Imaging, Omics, and Clinical Data
|url=https://doi.org/10.1007/978-1-0716-1839-4_5
|journal=In
|date=2022
|doi=10.1007/978-1-0716-1839-4_5
}}
# {{Cite journal
|authors=Kotlyar M, Wong SWH, Pastrello C, Jurisica I
|title=Improving Analysis and Annotation of Microarray Data with Protein Interactions
|url=https://doi.org/10.1007/978-1-0716-1839-4_5
|journal=Methods Mol Biol
|date=2022
|doi=10.1007/978-1-0716-1839-4_5
}}
# {{Cite journal
|authors=Pastrello C, Niu Y, Jurisica I
|title=Pathway Enrichment Analysis of Microarray Data
|url=https://doi.org/10.1007/978-1-0716-1839-4_10
|journal=Methods Mol Biol
|date=2022
|doi=10.1007/978-1-0716-1839-4_10
}}
# {{Cite journal
|authors=Hauschild AC, Pastrello C, Kotlyar M, Jurisica I
|title=Protein-protein interaction data, their quality, and major public databases
|journal=In
|date=2019
}}
# {{Cite journal
|authors=Wong S, Pastrello C, Kotlyar M, Faloutsos C, Jurisica I
|title=SDREGION: Fast spotting of changing communities in biological networks (conference version)
|journal=Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery and Data Mining
|date=2018
}}
# {{Cite journal
|authors=Kotlyar M, Pastrello C, Rossos A, Jurisica I
|title=Protein-protein interaction databases
|journal=In
|date=2018
}}
# {{Cite journal
|authors=Rahmati S, Pastrello C, Rossos A, Jurisica I
|title=Two Decades of Biological Pathway Databases: Results and Challenges
|journal=In
|date=2018
}}
# {{Cite journal
|authors=Hauschild AC, Pastrello C, Rossos A, Jurisica I
|title=Visualization of Biomedical Networks (book chapter)
|journal=In
|date=2018
}}
# {{Cite journal
|authors=Jeanquartier F, Jean-Quartier C, Kotlyar M, Tokar T, Hauschild AC, Jurisica I, Holzinger A
|title=Machine Learning for In Silico Modeling of Tumor Growth
|journal=In
|date=2016
}}
# {{Cite journal
|authors=Larsen SJ, Alkaersig FG, Ditzel LJ, Jurisica I, Alcaraz N, Baumbach J
|title=A Simulated Annealing Algorithm for Maximum Common Edge Subgraph Detection in Biological Networks
|journal=GECCO
|date=2016
}}
# {{Cite journal
|authors=Veillette CJH, Jurisica I
|title=Precision Medicine for Osteoarthritis
|journal=In
|date=2015
}}
# {{Cite journal
|authors=Otasek D, Pastrello C, Holzinger A, Jurisica I
|title=Visual data mining: Effective exploration of the biological universe
|journal=In
|date=2014
}}


== See Also ==
== See Also ==

Latest revision as of 18:40, 8 July 2026



World Community Grid
Project
StatusActive
CategoryBiomedical / Humanitarian science
ComputeCPU
RequiresNone
Development
DeveloperUnited Devices (2004); IBM (2004–2022); Krembil Research Institute / UHN (2022–present)
AuthorIBM Corporate Social Responsibility
SponsorUniversity Health Network
MaintainerDr. Igor Jurisica, Krembil Research Institute
Initial releaseNovember 16, 2004  (22 years ago)
Software
Operating systemWindows, Linux, macOS, Android, Raspberry Pi OS
BOINC statistics
Stats as ofJanuary 1, 2023  (3 years ago)
Performance402 TFLOPS
Active users23,248
Total users79,354
Active hosts57,672
Total hosts5,517,865
Metadata
Websitehttps://www.worldcommunitygrid.org/

World Community Grid uses BOINC to accelerate science by creating a supercomputer empowered by a global community of volunteers.

Open Pandemics BOINC Screensaver
Open Pandemics - COVID-19 BOINC Screensaver

World Community Grid (WCG) is a volunteer computing platform dedicated to humanitarian and biomedical scientific research. It harnesses the idle processing power of everyday devices (personal computers, laptops, Android smartphones, and Raspberry Pi systems) to perform large-scale scientific calculations that would otherwise require decades of supercomputing time. Since its founding in 2004, the project has expanded to cover diseases including HIV/AIDS, cancer, tuberculosis, dengue fever, Ebola, Zika virus, and COVID-19, as well as research into clean energy, water purification, food security, and climate science.[1]

Why World Community Grid?

World Community Grid began on November 16, 2004, as a philanthropic initiative of IBM Corporate Social Responsibility, the corporate social responsibility and philanthropy division of IBM.[2] The project was inspired by a successful predecessor: in 2003, IBM and other partners sponsored the United Devices Smallpox Research Grid Project, which used a distributed computing grid to screen 35 million potential drug molecules against several smallpox proteins. In the first 72 hours alone, 100,000 results were returned, and by the project's end, 44 strong treatment candidates had been identified.[3] Encouraged by those results, IBM launched World Community Grid with the goal of creating a permanent technical environment where humanitarian research of this kind could be run continuously.

Through Corporate Social Responsibility, IBM donated its technology and talent to address some of the world's most pressing social and environmental issues. The platform was initially Windows-only and used the proprietary Grid MP client software from United Devices.[4] Demand for broader platform support led to the addition of the open-source BOINC (Berkeley Open Infrastructure for Network Computing) framework in November 2005, bringing Mac OS X and Linux support to the project.[4] By 2007, the Grid MP client had been fully retired and the project consolidated entirely on BOINC.[4]

In September 2021, IBM announced that it had transferred ownership of World Community Grid to the Krembil Research Institute, part of the University Health Network (UHN) in Toronto, Ontario, Canada.[5] Operational management formally transferred to Krembil in February 2022.

Goal

The overarching goal of World Community Grid is to help scientists identify the most important results to study in the laboratory, bringing them one step closer to discoveries that save lives and address global problems. Rather than replacing lab research, WCG acts as a filter: by computationally screening millions — sometimes billions — of candidate molecules or parameter sets, researchers can focus their scarce lab resources on only the most promising leads.

"WCG continues to support open-source and open-data research and helps reduce computational time to allow scientists to address the world's most pressing questions at no cost to the researchers."[5]

All data generated by World Community Grid volunteers must be released into the public domain and made freely available to the scientific community — a foundational requirement for any project accepted onto the platform.[1]

How It Works

World Community Grid runs on top of BOINC, an open-source middleware system developed at the University of California, Berkeley, originally under a National Science Foundation grant.[6] After downloading the WCG client (a pre-configured BOINC installer) from the official website, the software runs quietly in the background. It monitors available system resources and, when the device is idle, downloads a work unit from the WCG servers, performs the required calculations, and sends the results back.

To ensure accuracy, the servers distribute multiple copies of each work unit to different volunteers. When results are returned, they are validated against each other, and statistical outliers are discarded before final data is accepted.[7]

Credits and Points

Volunteer contributions are tracked using the BOINC Credit System. Upon completing a work unit, the BOINC client reports a point value based on software benchmarks (measured in cobblestones, where 1cobblestone=1200GigaFLOP-day). The WCG servers compare claims from each machine that processed the same work unit, discard outliers, and award the averaged value to each contributor.[7] Points allow users to track their personal contribution and compete on leaderboards.

Teams and Partners

Users may join teams created by organizations or individuals, fostering community identity and friendly competition. As of April 2021, World Community Grid had 452 recognized partner organizations promoting the grid within their communities.[7]

CPU Throttling

The BOINC client is designed not to slow down the host computer. World Community Grid sets conservative defaults: the CPU throttle is 60% by default, meaning the client runs at full load for roughly 3 seconds, then pauses for 2 seconds, cycling continuously. This pattern avoids sustained heat buildup. Windows users can additionally install TThrottle, a third-party add-on that reads CPU and GPU temperatures in real time and adjusts computation accordingly.[7]

Methods

Screensaver HUMAN PROTEOME FOLDING Phase2. World Community Grid solving the Human Proteome Folding Project.

Dr. Igor Jurisica's research drives World Community Grid's current scientific direction. Dr. Jurisica is a Senior Scientist at the Krembil Research Institute and a Professor at the University of Toronto, with appointments at Toronto Western Hospital. His work focuses on integrative computational biology — combining large-scale data analysis, machine learning, and network biology to understand complex diseases.

Research within Krembil is focused on the development of diagnostics, treatments and management strategies across three programmatic areas:

  1. Chronic neurological and neurosurgical disorders — including Parkinson's disease, stroke, epilepsy, spinal cord injuries, dementia, concussion, pain, and depression.
  2. Ophthalmologic disorders — including glaucoma, macular degeneration, and retinopathy.
  3. Musculoskeletal system disorders — including osteoarthritis, rheumatoid arthritis, systemic lupus erythematosus, and ankylosing spondylitis.

The primary computational technique used across WCG's biomedical projects is molecular docking, in which candidate drug molecules are algorithmically fitted to target protein structures to predict binding affinity. A typical project may dock tens of millions of compounds against one or more proteins — a task that would require tens of thousands of years of computing time on a single machine, but can be completed in months across the volunteer grid.[8]

Project Team / Sponsors

World Community Grid is currently managed by Dr. Igor Jurisica and his team at the Krembil Research Institute, part of the University Health Network (UHN) in Toronto, Ontario, Canada.[5]

UHN has Canada's largest hospital-based research program, comprising four major teaching hospitals: Toronto Western Hospital, Toronto General Hospital, Princess Margaret Cancer Centre, and Toronto Rehabilitation Institute, as well as The Michener Institute of Education.[9]

Previously, the project was funded and operated by IBM from its launch in November 2004 through February 2022. IBM provided all server infrastructure, administrative overhead, and technical support during that nearly two-decade period. The project is grateful for IBM's extensive financial and operational support.[5]

Research Overview

World Community Grid operates as an umbrella platform hosting multiple research projects simultaneously. Users are enrolled in all active projects by default but may opt out of any they choose.[7] Over the life of the project, WCG volunteers have collectively donated the equivalent of more than 2 million years of computing time and completed more than 6 billion work units.[7]

Active Research

  1. OpenPandemics - COVID-19 — Launched to enable a rapid-response platform for global disease outbreaks, the project uses molecular docking to screen drug candidates against SARS-CoV-2 proteins in partnership with scientists at Scripps Research. The goal is to identify compounds that could block viral replication, potentially forming the basis of antiviral drugs for COVID-19 and future pandemic pathogens.
  1. Mapping Cancer Markers — One of WCG's longest-running and most ambitious projects, this research aims to identify robust molecular biomarkers associated with various cancer types. By decoding cancer-rewired biological networks, researchers hope to enable earlier detection and more personalized treatment strategies.

Intermittent Research

  1. Africa Rainfall Project — Uses regional climate modelling to improve weather forecasts and agricultural planning across sub-Saharan Africa, where rain-fed agriculture supports the food supply for hundreds of millions of people.
  1. Smash Childhood Cancer — An expansion of earlier WCG work on neuroblastoma, this project searches for the best drug candidates targeting key molecular proteins across a broader range of childhood cancers.
  1. Help Stop TB — Focuses on finding new drug leads for tuberculosis (TB), which remains one of the world's leading infectious disease killers. The project performs virtual screening of millions of compounds against TB target proteins.

Completed Research (28)

Over the course of the project's history, 28 research projects have been completed.[10] These include:

Project Focus Area Notable Outcome
Human Proteome Folding (Phase 1 & 2) Protein structure prediction Produced a database of ~120,000 protein domain structures; computation that would have taken 100 years conventionally was done in one year.[11]
FightAIDS@Home (Phase 1 & 2) HIV/AIDS drug discovery Discovered two compounds representing a potentially new class of AIDS-fighting drugs; identified new vulnerabilities on the HIV-1 capsid protein as a possible new drug target.[7]
Help Fight Childhood Cancer Neuroblastoma Screened over 3 million drug candidates; identified 7 compounds that destroy neuroblastoma cells without apparent side effects.[12]
The Clean Energy Project (Phase 1 & 2) Solar cell materials Published a database of over 2.3 million organic molecules; identified 35,000 compounds with potential to double the efficiency of carbon-based organic solar cells.[7]
OpenZika Zika virus drug discovery Identified compound FAM 3, which inhibits the NS3 Helicase protein of the Zika virus, reducing viral replication by up to 86%.[13]
GO Fight Against Malaria Malaria and drug-resistant TB First WCG project to complete a billion docking calculations; discovered several molecules effective against malaria and drug-resistant tuberculosis including TDR-TB.[7]
Discovering Dengue Drugs Together (Phase 1 & 2) Dengue fever and Flaviviridae Identified several new dengue protease inhibitors, many of which also inhibit the West Nile virus protease.[7]
Help Conquer Cancer Protein crystallography for cancer Analysis that would have taken 162 years on conventional computers was completed in under 2 years.[14]
Nutritious Rice for the World Food security / crop genetics Predicted protein structures for major rice strains to help breed higher-yield, more disease-resistant varieties.[10]
Computing for Clean Water Nanotechnology / water filtration Studied molecular-scale water flow through novel filter materials to guide development of low-cost water filters.[10]
Drug Search for Leishmaniasis Neglected tropical disease Tested top 10 compounds in vivo; one compound induced near-complete curing of lesions in hamsters.[7]
AfricanClimate@Home Climate modelling Developed more accurate regional climate models for Africa.[10]
Outsmart Ebola Together Ebola drug discovery Screened millions of compounds against Ebola viral proteins to identify drug leads.[10]
Microbiome Immunity Project Human microbiome Comprehensive study of the role of gut bacteria in human disease.[10]
Uncovering Genome Mysteries Genomics Examined close to 200 million genes from diverse organisms.[10]
Help Cure Muscular Dystrophy (Phase 1 & 2) Neuromuscular diseases Investigated protein interactions for more than 2,200 structurally known proteins linked to muscular dystrophy and related diseases.[10]
Influenza Antiviral Drug Search Influenza Searched for drugs effective against drug-resistant and novel influenza strains.[10]
Smash Childhood Cancer Pediatric cancers (broader) Expanded neuroblastoma drug discovery to additional childhood cancer types.[10]
Help Defeat Cancer Tissue microarray analysis Examined cancer tissue microarrays to improve precision medicine diagnosis and treatment.[10]
Genome Comparison Comparative genomics Compared genomic information to improve biological data quality and host-pathogen understanding; led by Fiocruz (Oswaldo Cruz Institute), Brazil.[10]
Say No to Schistosoma Schistosomiasis Identified potential drug candidates for schistosomiasis, a neglected tropical disease affecting hundreds of millions.[10]
Computing for Sustainable Water Watershed ecology Modelled nutrient flows and ecological responses across 64,000 km2 of the Chesapeake Bay watershed.[10]

Publications

Papers using BOINC-computed data

Computing for Clean Water

  1. (2018).Carbon nanostructure based mechano-nanofluidics. Journal of Micromechanics and Microengineering. DOI: 10.1088/1361-6439/aaa782.
  2. (2015).Water transport inside carbon nanotubes mediated by phonon-induced oscillating friction. Nature Nanotechnology. DOI: 10.1038/nnano.2015.134.
  3. (2011).Friction of water slipping in carbon nanotubes. Physical Review E. DOI: 10.1103/PhysRevE.83.036316.

Discovering Dengue Drugs

  1. (2014).Identification of a novel inhibitor of dengue virus protease through use of a virtual screening drug discovery Web portal. Journal of Chemical Information and Modeling. DOI: 10.1021/ci500531r.
  2. (2009).New Approaches to Structure-Based Discovery of Dengue Protease Inhibitors. Infectious Disorders - Drug Targets. DOI: 10.2174/1871526510909030327.

Drug Search for Leishmaniasis

  1. (2016).Drug search for leishmaniasis: a virtual screening approach by grid computing. Journal of Computer-Aided Molecular Design. DOI: 10.1007/s10822-016-9921-4.
  2. (2012).Current Advances in Computational Strategies for Drug Discovery in Leishmaniasis.

FightAIDS@Home

  1. (2022).Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid. Journal of Computer-Aided Molecular Design. DOI: 10.1007/s10822-022-00446-5.
  2. (2021).The AutoDock suite at 30. Protein Science. DOI: 10.1002/pro.3934.
  3. (2019).Novel Intersubunit Interaction Critical for HIV-1 Core Assembly Defines a Potentially Targetable Inhibitor Binding Pocket. mBio. DOI: 10.1128/mBio.02858-18.
  4. (2019).Massive-Scale Binding Free Energy Simulations of HIV Integrase Complexes Using Asynchronous Replica Exchange Framework Implemented on the IBM WCG Distributed Network. Journal of Chemical Information and Modeling. DOI: 10.1021/acs.jcim.8b00817.
  5. (2015).Computational Challenges of Structure-Based Approaches Applied to HIV. The Future of HIV-1 Therapeutics.
  6. (2015).Large-scale asynchronous and distributed multidimensional replica exchange molecular simulations and efficiency analysis. Journal of Computational Chemistry. DOI: 10.1002/jcc.23996.
  7. (2015).Asynchronous replica exchange software for grid and heterogeneous computing. Computer Physics Communications. DOI: 10.1016/j.cpc.2015.06.010.
  8. (2014).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. Journal of Computer-Aided Molecular Design. DOI: 10.1007/s10822-014-9709-3.
  9. (2010).Fragment-Based Screen against HIV Protease. Chemical Biology & Drug Design. DOI: 10.1111/j.1747-0285.2009.00943.x.
  10. (2010).A Dynamic Model of HIV Integrase Inhibition and Drug Resistance. Journal of Molecular Biology. DOI: 10.1016/j.jmb.2010.01.033.
  11. (2010).Virtual Screening with AutoDock: Theory and Practice. Expert Opinion on Drug Discovery. DOI: 10.1517/17460441.2010.484460.
  12. (2009).AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry. DOI: 10.1002/jcc.21256.
  13. (2007).Analysis of HIV Wild-Type and Mutant Structures via in Silico Docking against Diverse Ligand Libraries. Journal of Chemical Information and Modeling. DOI: 10.1021/ci700044s.

GO Fight Against Malaria

  1. (2015).A Virtual Screen Discovers Novel, Fragment-Sized Inhibitors of Mycobacterium tuberculosis InhA. Journal of Chemical Information and Modeling. DOI: 10.1021/ci500672v.

Genome Comparison

  1. (2012).Design and Implementation of ProteinWorldDB. Advances in Bioinformatics and Computational Biology.
  2. (2010).ProteinWorldDB: querying radical pairwise alignments among protein sets from complete genomes. Bioinformatics. DOI: 10.1093/bioinformatics/btq011.

Help Conquer Cancer

  1. (2012).High-throughput protein crystallization on the World Community Grid and the GPU. Journal of Physics: Conference Series. DOI: 10.1088/1742-6596/341/1/012027.
  2. (2010).Protein crystallization analysis on the World Community Grid. Journal of Structural and Functional Genomics. DOI: 10.1007/s10969-009-9076-9.
  3. (2008).Establishing a training set through the visual analysis of crystallization trials. Part II: crystal examples. Acta Crystallographica Section D: Biological Crystallography. DOI: 10.1107/S0907444908028059.
  4. (2008).Establishing a training set through the visual analysis of crystallization trials. Part I: ~150 000 images. Acta Crystallographica Section D: Biological Crystallography. DOI: 10.1107/S0907444908028047.

Help Cure Muscular Dystrophy

  1. (2019).Decrypting protein surfaces by combining evolution, geometry, and molecular docking. Proteins: Structure, Function, and Bioinformatics. DOI: 10.1002/prot.25757.
  2. (2018).Hidden partners: Using cross-docking calculations to predict binding sites for proteins with multiple interactions. Proteins: Structure, Function, and Bioinformatics. DOI: 10.1002/prot.25506.
  3. (2017).Protein social behavior makes a stronger signal for partner identification than surface geometry. Proteins: Structure, Function, and Bioinformatics. DOI: 10.1002/prot.25206.
  4. (2016).Great interactions: How binding incorrect partners can teach us about protein recognition and function. Proteins: Structure, Function, and Bioinformatics. DOI: 10.1002/prot.25086.
  5. (2013).Protein-Protein Interactions in a Crowded Environment: An Analysis via Cross-Docking Simulations and Evolutionary Information. PLOS Computational Biology. DOI: 10.1371/journal.pcbi.1003369.
  6. (2009).From Dedicated Grid to Volunteer Grid: Large Scale Execution of a Bioinformatics Application. Journal of Grid Computing. DOI: 10.1007/s10723-009-9130-7.
  7. (2009).Joint Evolutionary Trees: A Large-Scale Method To Predict Protein Interfaces Based on Sequence Sampling. PLOS Computational Biology. DOI: 10.1371/journal.pcbi.1000267.
  8. (2008).Identification of Protein Interaction Partners and Protein–Protein Interaction Sites. Journal of Molecular Biology. DOI: 10.1016/j.jmb.2008.08.002.

Help Defeat Cancer

  1. (2011).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. DOI: 10.1136/amiajnl-2011-000170.
  2. (2010).Grid-Enabled, High-performance Microscopy Image Analysis.
  3. (2009).Virtual Microscopy and Grid-Enabled Decision Support for Large-Scale Analysis of Imaged Pathology Specimens. IEEE Transactions on Information Technology in Biomedicine. DOI: 10.1109/TITB.2009.2020159.
  4. (2009).PathMiner: A Web-Based Tool for Computer-Assisted Diagnostics in Pathology. IEEE Transactions on Information Technology in Biomedicine. DOI: 10.1109/TITB.2008.2008801.
  5. (2008).Therapeutic starvation and autophagy in prostate cancer: A new paradigm for targeting metabolism in cancer therapy. The Prostate. DOI: 10.1002/pros.20837.

Help Fight Childhood Cancer

  1. (2016).Effects of novel small compounds targeting TrkB on neuronal cell survival and depression-like behavior. Neurochemistry International. DOI: 10.1016/j.neuint.2016.04.017.
  2. (2014).Identification of novel candidate compounds targeting TrkB to induce apoptosis in neuroblastoma. Cancer Medicine. DOI: 10.1002/cam4.175.

Help Stop TB

  1. (2019).Revealing solvent-dependent folding behavior of mycolic acids from Mycobacterium tuberculosis by advanced simulation analysis. Journal of Molecular Modeling. DOI: 10.1007/s00894-019-3943-5.

Human Proteome Folding

  1. (2012).The mRNA-Bound Proteome and Its Global Occupancy Profile on Protein-Coding Transcripts. Molecular Cell. DOI: 10.1016/j.molcel.2012.05.021.
  2. (2012).The Plant Proteome Folding Project: Structure and Positive Selection in Plant Protein Families. Genome Biology and Evolution. DOI: 10.1093/gbe/evs015.
  3. (2011).The Proteome Folding Project: Proteome-scale prediction of structure and function. Genome Research. DOI: 10.1101/gr.121475.111.
  4. (2008).A Protein Domain-Based Interactome Network for C. elegans Early Embryogenesis. Cell. DOI: 10.1016/j.cell.2008.07.009.
  5. (2007).A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell. Cell. DOI: 10.1016/j.cell.2007.10.053.
  6. (2007).Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS biology. DOI: 10.1371/journal.pbio.0050076.
  7. (2007).A conserved surface on Toll-like receptor 5 recognizes bacterial flagellin. Journal of Experimental Medicine. DOI: 10.1084/jem.20061400.
  8. (2007).BioNetBuilder: automatic integration of biological networks. Bioinformatics. DOI: 10.1093/bioinformatics/btl604.
  9. (2005).Genome-wide structural and functional protein characterization by ab initio protein structure prediction. Report / Department of Electrical Measurements. Lund Institute of Technology.

Mapping Cancer Markers

  1. (2026).IID 2025: Physical protein interaction data with detection types, co-purified protein sets, molecular docking, and immune cell networks. Nucleic Acids Research.
  2. (2022).IID 2021: towards context-specific protein interaction analyses by increased coverage, enhanced annotation and enrichment analysis. Nucleic Acids Research. DOI: 10.1093/nar/gkab1034.
  3. (2019).IID 2018 update: context-specific physical protein-protein interactions in human, model organisms and domesticated species. Nucleic Acids Research.
  4. (2016).Integrated Interactions Database: tissue-specific view of the human and model organism interactomes. Nucleic Acids Research.
  5. (2020).Informed Use of Protein-Protein Interaction Data: A Focus on the Integrated Interactions Database (IID). Methods in Molecular Biology.
  6. (2023).USNAP: fast unique dense region detection and its application to lung cancer. Bioinformatics. DOI: 10.1093/bioinformatics/btad477.
  7. (2015).Comparative network analysis via differential graphlet communities. Proteomics. DOI: 10.1002/pmic.201400233.
  8. (2019).Visualization of Biomedical Networks. Encyclopedia of Bioinformatics and Computational Biology.
  9. (2018).The ablation of the matricellular protein EMILIN2 causes defective vascularization due to impaired EGFR-dependent IL-8 production affecting tumor growth. Oncogene. DOI: 10.1038/s41388-017-0107-x.
  10. (2018).SDREGION: Fast Spotting of Changing Communities in Biological Networks. KDD '18: The 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. DOI: 10.1145/3219819.3219854.
  11. (2017).Network Motif Families for Lung Cancer Diagnostics: A World Community Grid Approach. DOI: 10.13140/RG.2.2.34687.51363.
  12. (2015).Prioritizing Therapeutics for Lung Cancer: An Integrative Meta-analysis of Cancer Gene Signatures and Chemogenomic Data. PLOS Computational Biology. DOI: 10.1371/journal.pcbi.1004068.
  13. (2015).In silico prediction of physical protein interactions and characterization of interactome orphans. Nature Methods. DOI: 10.1038/nmeth.3178.

Microbiome Immunity Project

  1. (2023).Sequence-structure-function relationships in the microbial protein universe. Nature Communications. DOI: 10.1038/s41467-023-37896-w.

Nutritious Rice for the World

  1. (2016).Rice protein models from the Nutritious Rice for the World Project. DOI: 10.1101/091975.
  2. (2014).fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data. Bioinformatics. DOI: 10.1093/bioinformatics/btu098.
  3. (2012).Accelerated protein structure comparison using TM-score-GPU. Bioinformatics. DOI: 10.1093/bioinformatics/bts345.
  4. (2011).GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition. BMC Research Notes. DOI: 10.1186/1756-0500-4-97.

OpenZika

  1. (2022).Discovery of New Zika Protease and Polymerase Inhibitors through the Open Science Collaboration Project OpenZika. Journal of Chemical Information and Modeling. DOI: 10.1021/acs.jcim.2c00596.
  2. (2019).A diarylamine derived from anthranilic acid inhibits ZIKV replication. Scientific Reports. DOI: 10.1038/s41598-019-54169-z.
  3. (2019).High Throughput and Computational Repurposing for Neglected Diseases. Pharmaceutical Research. DOI: 10.1007/s11095-018-2558-3.
  4. (2018).Computational drug discovery for the Zika virus. Brazilian Journal of Pharmaceutical Sciences. DOI: 10.1590/s2175-97902018000001002.
  5. (2018).The A–Z of Zika drug discovery. Drug Discovery Today. DOI: 10.1016/j.drudis.2018.06.014.
  6. (2017).Molecular dynamics simulations of Zika virus NS3 helicase: Insights into RNA binding site activity. Biochemical and Biophysical Research Communications. DOI: 10.1016/j.bbrc.2017.03.070.
  7. (2016).OpenZika: An IBM World Community Grid Project to Accelerate Zika Virus Drug Discovery. PLOS Neglected Tropical Diseases. DOI: 10.1371/journal.pntd.0005023.
  8. (2016).Illustrating and homology modeling the proteins of the Zika virus. F1000Research. DOI: 10.12688/f1000research.8213.2.

The Clean Energy Project

  1. (2017).Design Principles and Top Non-Fullerene Acceptor Candidates for Organic Photovoltaics. Joule. DOI: 10.1016/j.joule.2017.10.006.
  2. (2015).What Is High-Throughput Virtual Screening? A Perspective from Organic Materials Discovery. Annual Review of Materials Research. DOI: 10.1146/annurev-matsci-070214-020823.
  3. (2015).Learning from the Harvard Clean Energy Project: The Use of Neural Networks to Accelerate Materials Discovery. Advanced Functional Materials. DOI: 10.1002/adfm.201501919.
  4. (2014).Lead candidates for high-performance organic photovoltaics from high-throughput quantum chemistry – the Harvard Clean Energy Project. Energy Environ. Sci.. DOI: 10.1039/C3EE42756K.
  5. (2011).Accelerated computational discovery of high-performance materials for organic photovoltaics by means of cheminformatics. Energy & Environmental Science. DOI: 10.1039/c1ee02056k.
  6. (2011).The Harvard Clean Energy Project: Large-Scale Computational Screening and Design of Organic Photovoltaics on the World Community Grid. The Journal of Physical Chemistry Letters. DOI: 10.1021/jz200866s.
  7. (2011).From computational discovery to experimental characterization of a high hole mobility organic crystal. Nature Communications. DOI: 10.1038/ncomms1451.

Other project-related publications

Mapping Cancer Markers (general lab output)

  1. (2026).B cells drive CD4 T cell immunosenescence and age-associated health decline. Sci Immunol. DOI: 10.1177/24755303251344134.
  2. (2025).Combining Clinical, Genetic and Protein Markers Using Machine Learning Models Discriminates Psoriatic Arthritis Patients From Those With Psoriasis. J Psoriasis Psoriatic Arthritis. doi. DOI: 10.1177/24755303251344134.
  3. (2025).Annexin A2 Contributes to Release of Extracellular Vimentin in Response to Inflammation. FASEB J.
  4. (2025).MatrixDB 2024: an increased coverage of extracellular matrix interactions, a new Network Explorer and a new web interface. Nucleic Acids Res.
  5. (2024).Proximal and classic epithelioid sarcomas are distinct molecular entities defined by MYC/GATA3 and SOX17/endothelial markers, respectively. Mod Pathol.
  6. (2024).Drugst.One - a plug-and-play solution for online systems medicine and network-based drug repurposing. Nucleic Acids Res.
  7. (2024).PathDIP 5: improving coverage and making enrichment analysis more biologically meaningful. Nucleic Acids Res.
  8. (2023).Tumor cell-intrinsic c-Myb upregulation stimulates antitumor immunity in a murine colorectal cancer model. Cancer Immunol Res. DOI: 10.1158/2326-6066.CIR-22-0912.
  9. (2023).An integrated multiomics analysis of rectal cancer patients identified POU2F3 as a putative druggable target and entinostat as a cytotoxic enhancer of 5-fluorouracil. Int J Cancer.
  10. (2023).MirDIP 5.2: tissue context annotation and novel microRNA curation. Nucl Acids Res.
  11. (2022).B cell linker protein (BLNK) is a regulator of Met receptor signaling and trafficking in non-small cell lung cancer. iScience.
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See Also

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