Publications by authors named "Daniel L Cook"

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SemGen: a tool for semantics-based annotation and composition of biosimulation models.
Maxwell L Neal, Christopher T Thompson, Karam G Kim, Ryan C James, Daniel L Cook

Bioinformatics· May 2019

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Harmonizing semantic annotations for computational models in biology.
Maxwell Lewis Neal, Matthias König, David Nickerson, Göksel Mısırlı, Reza Kalbasi, Daniel L Cook

Brief Bioinform· March 2019

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BaroFuse, a novel pressure-driven, adjustable-throughput perfusion system for tissue maintenance and assessment.
Austin Rountree, Amit Karkamkar, Gamal Khalil, Albert Folch, Daniel L Cook

Heliyon· December 2016

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Qualitative causal analyses of biosimulation models.
Maxwell L Neal, John H Gennari, Daniel L Cook

CEUR Workshop Proc· August 2016

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Semantics-Based Composition of Integrated Cardiomyocyte Models Motivated by Real-World Use Cases.
Maxwell L Neal, Brian E Carlson, Christopher T Thompson, Ryan C James, Karam G Kim, Daniel L Cook

PLoS One· June 2016

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Quantification of Low-Level Drug Effects Using Real-Time, in vitro Measurement of Oxygen Consumption Rate.
Adam Neal, Austin M Rountree, Craig W Philips, Terrance J Kavanagh, Dominic P Williams, Daniel L Cook

Toxicol Sci· December 2015

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A reappraisal of how to build modular, reusable models of biological systems.
Maxwell L Neal, Michael T Cooling, Lucian P Smith, Christopher T Thompson, Herbert M Sauro, Daniel L Cook

PLoS Comput Biol· October 2014

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Ontology of physics for biology: representing physical dependencies as a basis for biological processes.
Daniel L Cook, Maxwell L Neal, Fred L Bookstein, John H Gennari

J Biomed Semantics· December 2013

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Representing physiological processes and their participants with PhysioMaps.
Daniel L Cook, Maxwell L Neal, Robert Hoehndorf, Georgios V Gkoutos, John H Gennari

J Biomed Semantics· April 2013

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Physical properties of biological entities: an introduction to the ontology of physics for biology.
Daniel L Cook, Fred L Bookstein, John H Gennari

PLoS One· May 2012

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Integrating systems biology models and biomedical ontologies.
Robert Hoehndorf, Michel Dumontier, John H Gennari, Sarala Wimalaratne, Bernard de Bono, Daniel L Cook

BMC Syst Biol· August 2011

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Multiple ontologies in action: composite annotations for biosimulation models.
John H Gennari, Maxwell L Neal, Michal Galdzicki, Daniel L Cook

J Biomed Inform· February 2011

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Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies.
Daniel L Cook, Jose L V Mejino, Maxwell L Neal, John H Gennari

Annu Int Conf IEEE Eng Med Biol Soc· March 2010

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Advances in semantic representation for multiscale biosimulation: a case study in merging models.
Maxwell Lewis Neal, John H Gennari, Theo Arts, Daniel L Cook

Pac Symp Biocomput· March 2009

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Bridging biological ontologies and biosimulation: the ontology of physics for biology.
Daniel L Cook, Jose L V Mejino, Maxwell L Neal, John H Gennari

AMIA Annu Symp Proc· November 2008

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Integration of multi-scale biosimulation models via light-weight semantics.
John H Gennari, Maxwell L Neal, Brian E Carlson, Daniel L Cook

Pac Symp Biocomput· March 2008

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Chalkboard: ontology-based pathway modeling and qualitative inference of disease mechanisms.
Daniel L Cook, Jesse C Wiley, John H Gennari

Pac Symp Biocomput· December 2007

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Ontology-based representation of simulation models of physiology.
Daniel L Rubin, David Grossman, Maxwell Neal, Daniel L Cook, James B Bassingthwaighte

AMIA Annu Symp Proc· September 2007

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A strategy for improving and integrating biomedical ontologies.
Cornelius Rosse, Anand Kumar, Jose L V Mejino, Daniel L Cook, Landon T Detwiler

AMIA Annu Symp Proc· February 2007

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Evolution of a Foundational Model of Physiology: symbolic representation for functional bioinformatics.
Daniel L Cook, Jose L V Mejino, Cornelius Rosse

Stud Health Technol Inform· June 2005

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Non-invasive imaging of beta cell mass: a quantitative analysis.
Ian R Sweet, Daniel L Cook, Ake Lernmark, Carla J Greenbaum, Kenneth A Krohn

Diabetes Technol Ther· October 2004

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Regulation of ATP/ADP in pancreatic islets.
Ian R Sweet, Daniel L Cook, Eric DeJulio, Angela R Wallen, Gamal Khalil

Diabetes· February 2004

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Systematic screening of potential beta-cell imaging agents.
Ian R Sweet, Daniel L Cook, Ake Lernmark, Carla J Greenbaum, Angela R Wallen

Biochem Biophys Res Commun· February 2004

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Synaptic depression in the localization of sound.
Daniel L Cook, Peter C Schwindt, Lucinda A Grande, William J Spain

Nature· January 2003

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Is there a toxicological advantage for non-hyperbolic kinetics in cytochrome P450 catalysis? Functional allostery from "distributive catalysis".
William M Atkins, Weiya Doug Lu, Daniel L Cook

J Biol Chem· September 2002

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