| Year |
Citation |
Score |
| 2023 |
Birgiolas J, Haynes V, Gleeson P, Gerkin RC, Dietrich SW, Crook S. NeuroML-DB: Sharing and characterizing data-driven neuroscience models described in NeuroML. Plos Computational Biology. 19: e1010941. PMID 36867658 DOI: 10.1371/journal.pcbi.1010941 |
0.417 |
|
| 2022 |
Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, ... ... Gleeson P, et al. BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research. PMID 35524558 DOI: 10.1093/nar/gkac331 |
0.623 |
|
| 2020 |
Waltemath D, Golebiewski M, Blinov ML, Gleeson P, Hermjakob H, Hucka M, Inau ET, Keating SM, König M, Krebs O, Malik-Sheriff RS, Nickerson D, Oberortner E, Sauro HM, Schreiber F, et al. The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). Journal of Integrative Bioinformatics. PMID 32598315 DOI: 10.1515/Jib-2020-0005 |
0.431 |
|
| 2020 |
Dai K, Hernando J, Billeh YN, Gratiy SL, Planas J, Davison AP, Dura-Bernal S, Gleeson P, Devresse A, Dichter BK, Gevaert M, King JG, Van Geit WAH, Povolotsky AV, Muller E, et al. The SONATA data format for efficient description of large-scale network models. Plos Computational Biology. 16: e1007696. PMID 32092054 DOI: 10.1371/Journal.Pcbi.1007696 |
0.497 |
|
| 2019 |
Schreiber F, Sommer B, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, König M, Myers C, Nickerson D, Waltemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. Journal of Integrative Bioinformatics. PMID 31301675 DOI: 10.1515/Jib-2019-0035 |
0.345 |
|
| 2019 |
Gleeson P, Cantarelli M, Marin B, Quintana A, Earnshaw M, Sadeh S, Piasini E, Birgiolas J, Cannon RC, Cayco-Gajic NA, Crook S, Davison AP, Dura-Bernal S, Ecker A, Hines ML, et al. Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. Neuron. PMID 31201122 DOI: 10.1016/J.Neuron.2019.05.019 |
0.785 |
|
| 2019 |
Dura-Bernal S, Suter BA, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GMG, Lytton WW. NetPyNE, a tool for data-driven multiscale modeling of brain circuits. Elife. 8. PMID 31025934 DOI: 10.7554/Elife.44494 |
0.554 |
|
| 2019 |
Dura-Bernal S, Suter BA, Gleeson P, Cantarelli M, Quintana A, Rodriguez F, Kedziora DJ, Chadderdon GL, Kerr CC, Neymotin SA, McDougal RA, Hines M, Shepherd GM, Lytton WW. Author response: NetPyNE, a tool for data-driven multiscale modeling of brain circuits Elife. DOI: 10.7554/Elife.44494.016 |
0.34 |
|
| 2018 |
Neal ML, König M, Nickerson D, Misirli G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, ... Gleeson P, et al. Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics. PMID 30462164 DOI: 10.1093/Bib/Bby087 |
0.46 |
|
| 2018 |
Blundell I, Brette R, Cleland TA, Close TG, Coca D, Davison AP, Diaz-Pier S, Fernandez Musoles C, Gleeson P, Goodman DFM, Hines M, Hopkins MW, Kumbhar P, Lester DR, Marin B, et al. Code Generation in Computational Neuroscience: A Review of Tools and Techniques. Frontiers in Neuroinformatics. 12: 68. PMID 30455637 DOI: 10.3389/Fninf.2018.00068 |
0.453 |
|
| 2018 |
Sarma GP, Lee CW, Portegys T, Ghayoomie V, Jacobs T, Alicea B, Cantarelli M, Currie M, Gerkin RC, Gingell S, Gleeson P, Gordon R, Hasani RM, Idili G, Khayrulin S, et al. OpenWorm: overview and recent advances in integrative biological simulation of . Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 373. PMID 30201845 DOI: 10.1098/Rstb.2017.0382 |
0.407 |
|
| 2018 |
Cantarelli M, Marin B, Quintana A, Earnshaw M, Court R, Gleeson P, Dura-Bernal S, Silver RA, Idili G. Geppetto: a reusable modular open platform for exploring neuroscience data and models. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 373. PMID 30201843 DOI: 10.1098/Rstb.2017.0380 |
0.516 |
|
| 2018 |
Gleeson P, Lung D, Grosu R, Hasani R, Larson SD. c302: a multiscale framework for modelling the nervous system of . Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 373. PMID 30201842 DOI: 10.1098/Rstb.2017.0379 |
0.501 |
|
| 2018 |
Larson SD, Gleeson P, Brown AEX. Connectome to behaviour: modelling at cellular resolution. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 373. PMID 30201832 DOI: 10.1098/Rstb.2017.0366 |
0.384 |
|
| 2018 |
Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, et al. Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Standards in Genomic Sciences. 13: 17. PMID 30117501 DOI: 10.1186/S40793-018-0320-4 |
0.409 |
|
| 2018 |
Schreiber F, Bader GD, Gleeson P, Golebiewski M, Hucka M, Keating SM, Novère NL, Myers C, Nickerson D, Sommer B, Waltemath D. Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. Journal of Integrative Bioinformatics. PMID 29596055 DOI: 10.1515/Jib-2018-0013 |
0.311 |
|
| 2017 |
Gleeson P, Davison AP, Silver RA, Ascoli GA. A Commitment to Open Source in Neuroscience. Neuron. 96: 964-965. PMID 29216458 DOI: 10.1016/j.neuron.2017.10.013 |
0.347 |
|
| 2017 |
Eglen SJ, Marwick B, Halchenko YO, Hanke M, Sufi S, Gleeson P, Silver RA, Davison AP, Lanyon L, Abrams M, Wachtler T, Willshaw DJ, Pouzat C, Poline JB. Toward standard practices for sharing computer code and programs in neuroscience. Nature Neuroscience. 20: 770-773. PMID 28542156 DOI: 10.1038/Nn.4550 |
0.302 |
|
| 2017 |
Newton AJH, Seidenstein AH, McDougal RA, Pérez-Cervera A, Huguet G, M-Seara T, Haimerl C, Angulo-Garcia D, Torcini A, Cossart R, Malvache A, Skiker K, Maouene M, Ragognetti G, Lorusso L, ... ... Gleeson P, et al. 26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 Bmc Neuroscience. 18. DOI: 10.1186/S12868-017-0372-1 |
0.726 |
|
| 2017 |
Denham S, Poirazi P, De Schutter E, Friston K, Chan HK, Nowotny T, Han D, Hong S, Rosay S, Wernle T, Treves A, Goethals S, Brette R, Van Pottelbergh T, Sepulchre R, ... ... Gleeson P, et al. 26th Annual Computational Neuroscience Meeting (CNS*2017): Part 1 Bmc Neuroscience. 18. DOI: 10.1186/S12868-017-0370-3 |
0.661 |
|
| 2016 |
Sharpee TO, Destexhe A, Kawato M, Sekulić V, Skinner FK, Wójcik DK, Chintaluri C, Cserpán D, Somogyvári Z, Kim JK, Kilpatrick ZP, Bennett MR, Josić K, Elices I, Arroyo D, ... ... Gleeson P, et al. 25th Annual Computational Neuroscience Meeting: CNS-2016 Bmc Neuroscience. 17: 54. PMID 27534393 DOI: 10.1186/S12868-016-0283-6 |
0.67 |
|
| 2015 |
Ramaswamy S, Courcol JD, Abdellah M, Adaszewski SR, Antille N, Arsever S, Atenekeng G, Bilgili A, Brukau Y, Chalimourda A, Chindemi G, Delalondre F, Dumusc R, Eilemann S, Gevaert ME, ... Gleeson P, et al. The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex. Frontiers in Neural Circuits. 9: 44. PMID 26500503 DOI: 10.3389/Fncir.2015.00044 |
0.426 |
|
| 2015 |
Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, et al. Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE) Standards in Genomic Sciences. DOI: 10.4056/sigs.5279417 |
0.339 |
|
| 2015 |
Quintana A, Cantarelli M, Marin B, Silver RA, Gleeson P. Visualizing, editing and simulating neuronal models with the Open Source Brain 3D explorer Bmc Neuroscience. 16: P82. DOI: 10.1186/1471-2202-16-S1-P82 |
0.528 |
|
| 2015 |
Gleeson P, Cantarelli M, Currie M, Hokanson J, Idili G, Khayrulin S, Palyanov A, Szigeti B, Larson S. The OpenWorm Project: currently available resources and future plans Bmc Neuroscience. 16. DOI: 10.1186/1471-2202-16-S1-P141 |
0.454 |
|
| 2014 |
Szigeti B, Gleeson P, Vella M, Khayrulin S, Palyanov A, Hokanson J, Currie M, Cantarelli M, Idili G, Larson S. OpenWorm: an open-science approach to modeling Caenorhabditis elegans. Frontiers in Computational Neuroscience. 8: 137. PMID 25404913 DOI: 10.3389/Fncom.2014.00137 |
0.44 |
|
| 2014 |
Cannon RC, Gleeson P, Crook S, Ganapathy G, Marin B, Piasini E, Silver RA. LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Frontiers in Neuroinformatics. 8: 79. PMID 25309419 DOI: 10.3389/Fninf.2014.00079 |
0.802 |
|
| 2014 |
Vella M, Cannon RC, Crook S, Davison AP, Ganapathy G, Robinson HP, Silver RA, Gleeson P. libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience. Frontiers in Neuroinformatics. 8: 38. PMID 24795618 DOI: 10.3389/fninf.2014.00038 |
0.523 |
|
| 2014 |
Farinella M, Ruedt DT, Gleeson P, Lanore F, Silver RA. Glutamate-bound NMDARs arising from in vivo-like network activity extend spatio-temporal integration in a L5 cortical pyramidal cell model. Plos Computational Biology. 10: e1003590. PMID 24763087 DOI: 10.1371/Journal.Pcbi.1003590 |
0.787 |
|
| 2014 |
Marin B, Gleeson P, Cantarelli M, Cannon RC, Silver RA. Automated code generation from LEMS, the general purpose model specification language underpinning NeuroML2 Bmc Neuroscience. 15. DOI: 10.1186/1471-2202-15-S1-P45 |
0.501 |
|
| 2013 |
Gleeson P, Cantarelli M, Piasini E, Silver RA. Advanced 3D visualisation of detailed neuronal models using the Open Source Brain repository and interaction with other neuroinformatics resources Bmc Neuroscience. 14. DOI: 10.1186/1471-2202-14-S1-P363 |
0.813 |
|
| 2013 |
Vella M, Palyanov A, Gleeson P, Khayrulin S. Integration of predictive-corrective incompressible SPH and Hodgkin-Huxley based models in the OpenWorm in silico model of C. elegans Bmc Neuroscience. 14. DOI: 10.1186/1471-2202-14-S1-P209 |
0.414 |
|
| 2012 |
Howarth C, Gleeson P, Attwell D. Updated energy budgets for neural computation in the neocortex and cerebellum. Journal of Cerebral Blood Flow and Metabolism : Official Journal of the International Society of Cerebral Blood Flow and Metabolism. 32: 1222-32. PMID 22434069 DOI: 10.1038/jcbfm.2012.35 |
0.325 |
|
| 2012 |
Cannon R, Gleeson P, Crook S, Silver RA. A declarative model specification system allowing NeuroML to be extended with user-defined component types Bmc Neuroscience. 13. DOI: 10.1186/1471-2202-13-S1-P42 |
0.438 |
|
| 2012 |
Le Franc Y, Davison AP, Gleeson P, Imam FT, Kriener B, Larson SD, Ray S, Schwabe L, Hill S, De Schutter E. Computational Neuroscience Ontology: a new tool to provide semantic meaning to your models Bmc Neuroscience. 13. DOI: 10.1186/1471-2202-13-S1-P149 |
0.46 |
|
| 2012 |
Gleeson P, Piasini E, Crook S, Cannon R, Steuber V, Jaeger D, Solinas S, D’Angelo E, Silver RA. The Open Source Brain Initiative: enabling collaborative modelling in computational neuroscience Bmc Neuroscience. 13. DOI: 10.1186/1471-2202-13-S1-O7 |
0.811 |
|
| 2012 |
Gleeson P, Steuber V, Silver RA, Crook S. NeuroML Computational Systems Neurobiology. 489-517. DOI: 10.1007/978-94-007-3858-4_16 |
0.563 |
|
| 2011 |
Raikov I, Cannon R, Clewley R, Cornelis H, Davison A, De Schutter E, Djurfeldt M, Gleeson P, Gorchetchnikov A, Plesser HE, Hill S, Hines M, Kriener B, Le Franc Y, Lo C, et al. NineML: the network interchange for ne uroscience modeling language Bmc Neuroscience. 12. DOI: 10.1186/1471-2202-12-S1-P330 |
0.546 |
|
| 2011 |
Farinella M, Gleeson P, Ruidt DC, Silver AR. Synaptic integration and NMDA spikes in a layer 5 pyramidal neuron model Bmc Neuroscience. 12. DOI: 10.1186/1471-2202-12-S1-P301 |
0.764 |
|
| 2011 |
Gleeson P, Crook S, Silver A, Cannon R. Development of NeuroML version 2.0: greater extensibility, support for abstract neuronal models and interaction with Systems Biology languages Bmc Neuroscience. 12. DOI: 10.1186/1471-2202-12-S1-P29 |
0.753 |
|
| 2010 |
Vervaeke K, Lorincz A, Gleeson P, Farinella M, Nusser Z, Silver RA. Rapid desynchronization of an electrically coupled interneuron network with sparse excitatory synaptic input. Neuron. 67: 435-51. PMID 20696381 DOI: 10.1016/J.Neuron.2010.06.028 |
0.719 |
|
| 2010 |
Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, Silver RA. NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail. Plos Computational Biology. 6: e1000815. PMID 20585541 DOI: 10.1371/Journal.Pcbi.1000815 |
0.735 |
|
| 2009 |
Crook S, Silver RA, Gleeson P. Describing and exchanging models of neurons and neuronal networks with NeuroML Bmc Neuroscience. 10: 1-2. DOI: 10.1186/1471-2202-10-S1-L1 |
0.555 |
|
| 2008 |
Gleeson P, Steuber V, Silver RA. Using Neuroconstruct to Develop and Modify Biologically Detailed 3d Neuronal Network Models in Health and Disease Computational Neuroscience in Epilepsy. 48-70. DOI: 10.1016/B978-012373649-9.50008-9 |
0.651 |
|
| 2008 |
Günay C, Smolinski TG, Lytton WW, Morse TM, Gleeson P, Crook S, Steuber V, Silver A, Voicu H, Andrews P, Bokil H, Maniar H, Loader C, Mehta S, Kleinfeld D, et al. Computational intelligence in electrophysiology: Trends and open problems Studies in Computational Intelligence. 122: 325-359. DOI: 10.1007/978-3-540-78534-7_14 |
0.734 |
|
| 2007 |
Cannon RC, Gewaltig MO, Gleeson P, Bhalla US, Cornelis H, Hines ML, Howell FW, Muller E, Stiles JR, Wils S, De Schutter E. Interoperability of neuroscience modeling software: current status and future directions. Neuroinformatics. 5: 127-38. PMID 17873374 DOI: 10.1007/S12021-007-0004-5 |
0.48 |
|
| 2007 |
Crook S, Gleeson P, Howell F, Svitak J, Silver RA. MorphML: level 1 of the NeuroML standards for neuronal morphology data and model specification. Neuroinformatics. 5: 96-104. PMID 17873371 DOI: 10.1007/s12021-007-0003-6 |
0.438 |
|
| 2007 |
Gleeson P, Steuber V, Silver RA. neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron. 54: 219-35. PMID 17442244 DOI: 10.1016/j.neuron.2007.03.025 |
0.74 |
|
| 2007 |
Gleeson P, Crook S, Steuber V, Silver RA. Using NeuroML and neuroConstruct to build neuronal network models for multiple simulators Bmc Neuroscience. 8. DOI: 10.1186/1471-2202-8-S2-P1 |
0.756 |
|
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