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Maxwell L. Neal, Ph.D. - Publications

Affiliations: 
2010 University of Washington, Seattle, Seattle, WA 
Area:
biomedical and health informatics
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32 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Munarko Y, Sarwar DM, Rampadarath A, Atalag K, Gennari JH, Neal ML, Nickerson DP. NLIMED: Natural Language Interface for Model Entity Discovery in Biosimulation Model Repositories. Frontiers in Physiology. 13: 820683. PMID 35283794 DOI: 10.3389/fphys.2022.820683  0.685
2021 Gennari JH, König M, Misirli G, Neal ML, Nickerson DP, Waltemath D. OMEX metadata specification (version 1.2). Journal of Integrative Bioinformatics. 18. PMID 34668356 DOI: 10.1515/jib-2021-0020  0.717
2021 Welsh C, Nickerson DP, Rampadarath A, Neal ML, Sauro HM, Gennari JH. libOmexMeta: Enabling semantic annotation of models to support FAIR principles. Bioinformatics (Oxford, England). PMID 34132740 DOI: 10.1093/bioinformatics/btab445  0.713
2020 Neal ML, Gennari JH, Waltemath D, Nickerson DP, König M. Open modeling and exchange (OMEX) metadata specification version 1.0. Journal of Integrative Bioinformatics. PMID 32589606 DOI: 10.1515/Jib-2020-0020  0.736
2019 Sarwar DM, Kalbasi R, Gennari JH, Carlson BE, Neal ML, Bono B, Atalag K, Hunter PJ, Nickerson DP. Model annotation and discovery with the Physiome Model Repository. Bmc Bioinformatics. 20: 457. PMID 31492098 DOI: 10.1186/S12859-019-2987-Y  0.734
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, et al. Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics. PMID 30462164 DOI: 10.1093/Bib/Bby087  0.741
2018 Neal ML, Thompson CT, Kim KG, James RC, Cook DL, Carlson BE, Gennari JH. SemGen: a tool for semantics-based annotation and composition of biosimulation models. Bioinformatics (Oxford, England). PMID 30256901 DOI: 10.1093/Bioinformatics/Bty829  0.752
2016 Neal ML, Gennari JH, Cook DL. Qualitative causal analyses of biosimulation models. Ceur Workshop Proceedings. 1747. PMID 28804276  0.725
2015 Neal ML, Carlson BE, Thompson CT, James RC, Kim KG, Tran K, Crampin EJ, Cook DL, Gennari JH. Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases. Plos One. 10: e0145621. PMID 26716837 DOI: 10.1371/Journal.Pone.0145621  0.721
2015 Rockne RC, Trister AD, Jacobs J, Hawkins-Daarud AJ, Neal ML, Hendrickson K, Mrugala MM, Rockhill JK, Kinahan P, Krohn KA, Swanson KR. A patient-specific computational model of hypoxia-modulated radiation resistance in glioblastoma using 18F-FMISO-PET. Journal of the Royal Society, Interface / the Royal Society. 12. PMID 25540239 DOI: 10.1098/Rsif.2014.1174  0.315
2014 Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL, Gennari JH. A reappraisal of how to build modular, reusable models of biological systems. Plos Computational Biology. 10: e1003849. PMID 25275523 DOI: 10.1371/Journal.Pcbi.1003849  0.56
2014 Neal ML, Galdzicki M, Gallimore JT, Sauro HM. A C library for retrieving specific reactions from the BioModels database. Bioinformatics (Oxford, England). 30: 129-30. PMID 24078714 DOI: 10.1093/Bioinformatics/Btt567  0.727
2014 Bassingthwaighte J, Butterworth E, Jardine B, Raymond G, Neal M. JSim, an open-source modeling system for data analysis and reproducibility in research (733.1) The Faseb Journal. 28. DOI: 10.6084/M9.Figshare.1044285.V1  0.465
2013 Butterworth E, Jardine BE, Raymond GM, Neal ML, Bassingthwaighte JB. JSim, an open-source modeling system for data analysis. F1000research. 2: 288. PMID 24555116 DOI: 10.12688/F1000Research.2-288.V1  0.516
2013 Cook DL, Neal ML, Bookstein FL, Gennari JH. Ontology of physics for biology: representing physical dependencies as a basis for biological processes. Journal of Biomedical Semantics. 4: 41. PMID 24295137 DOI: 10.1186/2041-1480-4-41  0.649
2013 Cook DL, Neal ML, Hoehndorf R, Gkoutos GV, Gennari JH. Representing physiological processes and their participants with PhysioMaps. Journal of Biomedical Semantics. 4: S2. PMID 23735231 DOI: 10.1186/2041-1480-4-S1-S2  0.69
2013 Baldock AL, Rockne RC, Boone AD, Neal ML, Hawkins-Daarud A, Corwin DM, Bridge CA, Guyman LA, Trister AD, Mrugala MM, Rockhill JK, Swanson KR. From patient-specific mathematical neuro-oncology to precision medicine. Frontiers in Oncology. 3: 62. PMID 23565501 DOI: 10.3389/Fonc.2013.00062  0.345
2013 Neal ML, Trister AD, Ahn S, Baldock A, Bridge CA, Guyman L, Lange J, Sodt R, Cloke T, Lai A, Cloughesy TF, Mrugala MM, Rockhill JK, Rockne RC, Swanson KR. Response classification based on a minimal model of glioblastoma growth is prognostic for clinical outcomes and distinguishes progression from pseudoprogression. Cancer Research. 73: 2976-86. PMID 23400596 DOI: 10.1158/0008-5472.Can-12-3588  0.324
2013 Neal ML, Cook DL, Gennari JH. An OWL knowledge base for classifying and querying collections of physiological models: A prototype human physiome Ceur Workshop Proceedings. 1060: 16-21.  0.655
2012 Beard DA, Neal ML, Tabesh-Saleki N, Thompson CT, Bassingthwaighte JB, Shimoyama M, Carlson BE. Multiscale modeling and data integration in the virtual physiological rat project. Annals of Biomedical Engineering. 40: 2365-78. PMID 22805979 DOI: 10.1007/S10439-012-0611-7  0.527
2012 Neal ML, Sauro HM. SBML Reaction Finder: Retrieve and extract specific reactions from the BioModels database Nature Precedings. 7: 1-1. DOI: 10.1038/Npre.2012.7028.1  0.395
2011 Gennari JH, Neal ML, Galdzicki M, Cook DL. Multiple ontologies in action: composite annotations for biosimulation models. Journal of Biomedical Informatics. 44: 146-54. PMID 20601121 DOI: 10.1016/J.Jbi.2010.06.007  0.768
2011 Cook DL, Galdzicki M, Neal ML, Mejino JLV, Gennari JH. HeartCyc, a cardiac cycle process ontology based in the ontology of physics for biology Ceur Workshop Proceedings. 833: 41-46.  0.712
2010 Neal ML, Kerckhoffs R. Current progress in patient-specific modeling. Briefings in Bioinformatics. 11: 111-26. PMID 19955236 DOI: 10.1093/Bib/Bbp049  0.379
2009 Cook DL, Mejino JL, Neal ML, Gennari JH. Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 2791-4. PMID 19964601 DOI: 10.1109/IEMBS.2009.5333830  0.611
2009 Neal ML, Gennari JH, Arts T, Cook DL. Advances in semantic representation for multiscale biosimulation: a case study in merging models. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 304-15. PMID 19209710  0.691
2008 Cook DL, Mejino JL, Neal ML, Gennari JH. Bridging biological ontologies and biosimulation: the ontology of physics for biology. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 136-40. PMID 18999003  0.68
2008 Gennari JH, Neal ML, Carlson BE, Cook DL. Integration of multi-scale biosimulation models via light-weight semantics. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 414-25. PMID 18229704  0.7
2007 Neal ML, Bassingthwaighte JB. Subject-specific model estimation of cardiac output and blood volume during hemorrhage. Cardiovascular Engineering (Dordrecht, Netherlands). 7: 97-120. PMID 17846886 DOI: 10.1007/S10558-007-9035-7  0.337
2007 Kerckhoffs RC, Neal ML, Gu Q, Bassingthwaighte JB, Omens JH, McCulloch AD. Coupling of a 3D finite element model of cardiac ventricular mechanics to lumped systems models of the systemic and pulmonic circulation. Annals of Biomedical Engineering. 35: 1-18. PMID 17111210 DOI: 10.1007/S10439-006-9212-7  0.363
2007 Kerckhoffs R, Neal M, Bassinghtwaighte J, Omens J, McCulloch A. Ventricular interaction quantified with a novel multi-scale cardiovascular model Pamm. 7: 1141201-1141201. DOI: 10.1002/Pamm.200701131  0.323
2006 Rubin DL, Grossman D, Neal M, Cook DL, Bassingthwaighte JB, Musen MA. Ontology-based representation of simulation models of physiology. Amia ... Annual Symposium Proceedings / Amia Symposium. Amia Symposium. 664-8. PMID 17238424  0.387
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