Cook DL, Galdzicki M, Neal ML, Mejino JLV, and Gennari JH. (in press) HeartCyc, a cardiac cycle process ontology based in the Ontology of Physics for Biology. Proceedings of the 2011 International Conference on Biomedical Ontology.
An ontological approach to representing the processes of the heart cycle.
Gennari JH, Neal ML, Galdzicki M, Cook DL. Multiple ontologies in action: composite annotations for biosimulation models. Journal of Biomedical Informatics. 2011. 44(1):146-154.
A description of a composite approach to model annotation that leverages multiple, orthogonal ontologies.
Neal ML, Kerckhoffs RC. Current progress in patient-specific modeling. Briefings in Bioinformatics. 2010;11(1):111-26.
A review of patient-specific modeling papers published between 1/2008 and 5/2009
Neal ML. Modular, semantics-based composition of biosimulation models. Ph.D. Dissertation. University of Washington. 2010.
My doctoral dissertation on semantics-based model integration
Cook DL, Mejino JLV, Neal ML, Gennari JH. Composite Annotations: Requirements for Mapping Multiscale Data and Models to Biomedical Ontologies. The Engineering in Medicine and Biology Conference. 2009.
A schema for creating composite, machine-readable annotations for biosimulation codewords
Gennari JH, Neal ML, Mejino JVL, Cook DL. Using multiple ontologies: Managing composite annotations. International Conference on Biomedical Ontology. 2009.
A discussion on how to use multiple reference ontologies to create composite annotations for biosimulation codewords
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 2009.
The pitfalls of merging biosimulation models coded in different languages
Cook DL, Mejino Jr. JLV, Neal ML, Gennari JH. Bridging Ontologies and Biosimulation: The Ontology of Physics for Biology. AMIA Annual Symposium Proceedings. 2008.
Introducing the Ontology of Physics for Biology, a reference source essential for annotating biosimulation variables
Neal ML, Bassingthwaighte JB. Subject-specific models for the estimation of cardiac output and blood volume during hemorrhage. Cardiovasc Eng. 2007 Sep;7(3):97-120.
Using individualized models to estimate cardiac output from blood pressure and heart rate
Gennari JH, Neal ML, Carlson BR, Cook DL. Integration of multi-scale biosimulation models via light-weight semantics. Pacific Symposium on Biocomputing, 2008: 414-25.
A new, ontology-based, scalable biosimulation model description format
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. Ann Biomed Eng. 2007 Jan;35(1):1-18.
A closed-loop, multi-scale model of the canine circulatory system
Rubin DL, Grossman D, Neal M, Cook DL, Bassingthwaighte JB, Musen MA. Ontology-based representation of simulation models of physiology. AMIA Annu Symp Proc. 2006;664-8.
A first stab at ontological representation of physiological models - won a distinguished paper award
Lamanna JC, Neal M, Xu K, Haxhiu MA. Differential expression of intracellular acidosis in rat brainstem regions in response to hypercapnic ventilation. Adv Exp Med Biol. 2003;536:407-13.
Locating the regions of the brain that respond to high carbon dioxide inhalation
Neal ML, Hannibal JT. Paleoecologic and taxonomic implications of Sphenothallus and Sphenothallus-like specimes from Ohio and areas adjacent to Ohio. Journal of Paleontology. May 2000; v. 74; no. 3; p. 369-380.
Fossil tube worms from 350 million years ago!
