Relevant Publications
From IMAG_Wiki
2012
- Human seizures self-terminate across spatial scales via a critical transition
- Mark A. Kramer, Wilson Truccolo, Uri T. Eden, Kyle Q. Lepage, Leigh R. Hochberg, Emad N. Eskandar, Joseph R. Madsen, Jong W. Lee, Atul Maheshwari, Eric Halgren, Catherine J. Chu, and Sydney S. Cash
- PNAS 2012; published ahead of print Dec 4, 2012
- Article
- Modelling: Computing cancer
- Neil Savage
- Nature 491, S62-63 (22 November 2012)
- Article
- Review Article Computational Cardiology: The Heart of the Matter
- Natalia A. Trayanova
- ISRN Cardiology, Volume 2012, Article ID 269680
- Article
- Computational Medicine: Translating Models to Clinical Care.
- Winslow RL, Trayanova N, German D, Miller MI
- Sci Transl Med, 2012 Oct 31, 4(158): 158rv11
- Article
- Computational Medicine: Translating Models to Clinical Care
- Raimond L. Winslow, Natalia Trayanova, Donald Geman, Michael I. Miller
- Science Translational Medicine 2012 October 31, Vol 4, Issue 158
- Article
- Multiscale Mechanics of Articular Cartilage: Potentials and Challenges of Coupling Musculoskeletal, Joint, and Microscale Computational Models.
- Halloran JP, Sibole S, van Donkelaar CC, van Turnhout MC, Oomens CW, Weiss JA, Guilak F, Erdemir A.
- Ann Biomed Eng. 2012 May 31. [Epub ahead of print]
- Article
- Meet the Skeptics: Why Some Doubt Biomedical Models - and What it Takes to Win Them Over
- Kristin Sainani
- Biomedical Computation Review, June 5, 2012
- Article
- The case for open computer programs
- Darrel C. Ince,1 Leslie Hatton2 & John Graham-Cumming3
- Nature Volume:482,Pages:485–488 Date published:(23 February 2012)
- Article
- Chondrocyte Deformations as a Function of Tibiofemoral Joint Loading Predicted by a Generalized High-Throughput Pipeline of Multi-Scale Simulations, 2012
- Scott C. Sibole, Ahmet Erdemir
- PLoS One: 7(5): e37538. doi:10.1371/journal.pone.0037538
- Article
2011
- Considerations for reporting finite element analysis studies in biomechanics
- Erdemir A, Guess TM, Halloran J, Tadepalli SC, Morrison TM
- Journal of Biomechanics
- In Press
- Pre-print on IMAG Wiki
- Discussion on IMAG Wiki
- Editorial: What Biomedical Engineers Can Do to Impact Multiscale Modeling (TBME Letters Special Issue on Multiscale Modeling and Analysis in Computational Biology and Medicine: Part-2) -- links to the 2009 IMAG Futures Meeting Report, IFM Announcement
- Peng, G. C.Y.
- IEEE Transactions on Biomedical Engineering
- Volume 58, Issue 12, Part 2
- Page(s): 3440 - 3442
- Article
- Automated refinement and inference of analytical models for metabolic networks
- Michael D Schmidt et al
- 2011 Phys. Biol. 8 055011
- Article
- Robot biologist solves complex problem from scratch
- Phil Trans R Soc A Table of Contents for Theme Issue "Towards the virtual physiological human: mathematical and computational case studies"
- compiled and edited by Bindi Brook, Peter Kohl and John King
- 13 November 2011; Vol. 369, No. 1954
- Article
- Relational Grounding Facilitates Development of Scientifically Useful Multiscale Models
- C. Anthony Hunt, Glen E.P. Ropella, Tai ning Lam and Andrew D. Gewitz
- Theoretical Biology and Medical Modelling
- Article
- Predicting Human Blood Viscosity in Silico
- Karniadakis, et.al.
- Article
- A new computational paradigm in multiscale simulations: Application to brain blood flow
- Karniadakis, et.al.
- Accepted as a finalist of the Gordon Bell award for the Supercomputing Conference 2011
- Article
2010
- Noble, D. 2010. Biophysics and systems biology. Philos Transact A Math Phys Eng Sci. 368:1125-39
- Quantifying the biophysical characteristics of Plasmodium-falciparum-parasitized red blood cells in microcirculation.
- Fedosov DA, Caswell B, Suresh S, Karniadakis GE
- Proc Natl Acad Sci U S A. 2010 Dec 20
- Article
- Theory of Hybrid Dynamical Systems and its Applications to Biological and Medical Systems
- Royal Society
- Article
- Towards Whole-body Systems Physiology
- Kuepfer, Lars
- Molecular Systems Biology 6: 409; published online 7 September 2010; doi:10.1038/msb.2010.70
- Article
- Systems Biology: an approach.
- Kohl P, Crampin EJ, Quinn TA, Noble D
- Clinical Pharmacology & Therapeutics (2010) 88 1, 25–33. doi:10.1038/clpt.2010.92
- The Clinical Pharmacology & Therapeutics TOP TEN, charts all the articles that have been downloaded most often, in HTML format, from the Clinical Pharmacology & Therapeutics website in recent weeks. A VPH article on Systems Biology as an approach (published earlier this year) is now at Number 3 in the listing.
- http://www.nature.com/clpt/topten/index.html
- Computational science: ...Error…why scientific programming does not compute.
- Merali, Zeeya
- 13 October 2010 | Nature 467, 775-777 (2010)
- Article
- Publish your computer code: it is good enough
- Nick Barnes
- 13 October 2010 | Nature 467, 753 (2010)
- Article
- Closing the Scientific Loop: Bridging Correlation and Causality in the Petaflop Age
- Gary An
- Science Translational Medicine 2010 July 21, Vol 2, Issue 41
- Article
- Lung High-Performance CFD & FSI Computing and Modeling
- Lin, C.-L.
- 1. Choi, J., G. Xia, M.H. Tawhai, E.A. Hoffman, and C.-L. Lin, “Numerical study of high frequency oscillatory air flow and convective mixing in a CT-based human airway model,” DOI: 10.1007/s10439-010-0110-7, Annals of Biomedical Engineering, 2010.
- 2. Yin, Y., J. Choi, E.A. Hoffman, M.H. Tawhai, and C.-L. Lin, “Simulation of pulmonary air flow with a subject-specific boundary condition,” doi:10.1016/j.jbiomech.2010.03.048, available online, Journal of Biomechanics, 2010.
- 3. Xia, G., M. H. Tawhai, E. A. Hoffman, and C.-L. Lin, “Airway Wall Stiffness and Peak Wall Shear Stress: A Fluid-Structure Interaction Study in Rigid and Compliant Airways,” Annals of Biomedical Engineering, 38(5), 1836-1853, 2010.
- The Physiome: A Mission Imperative
- Multiscale Modeling in Drug Discovery and Development: Future Opportunities and Present Challenges.
- Vicini P
- Clin Pharmacol Ther. 2010 Jun 2
- http://www.ncbi.nlm.nih.gov/pubmed/20520608
- (January 2010) The epistemology of mathematical and statistical modeling: a quiet methodological revolution.
- Rodgers, JL
- American Psychologist. Vol 65(1), 1-12
- http://psycnet.apa.org/index.cfm?fa=search.displayRecord&uid=2009-24989-001
2008
- (October 2008) European Union and NIH Collaborate, Science
- (August 2008) A Brief History of the Hypothesis.
- Glass D, Hall N
- Cell Volume 134, Issue 3: 378-381 Pubmed link
2007
- (April 2007) Error estimation improves multiscale models
- (March 2007) Beyond standardization: dynamic software infrastructures for systems biology
- Morris A. Swertz and Ritsert C. Jansen
- Nature Reviews Genetics, Volume 8, Number 3, pages 235-243, http://www.nature.com/nrg/journal/v8/n3/index.html
- ABSTRACT - Progress in systems biology is seriously hindered by slow production of suitable software infrastructures. Biologists need infrastructure that easily connects to work that is done in other laboratories, for which standardization is helpful. However, the infrastructure must also accommodate the specifics of their biological system, but appropriate mechanisms to support variation are currently lacking. We argue that a minimal computer language, and a software tool called a generator, can be used to quickly produce customized software infrastructures that 'systems biologists really want to have'.
- (February 2007) Mathematical models add more options for life sciences, cancer researchers
- The use of mathematical modeling to better understand the origin and progression of life systems is the subject of American Scientist cover article Multiscale Modeling in Biology featuring the work in mathematical biology of Santiago Schnell and Philip K Maini. A related paper authored by Schnell is ranked first among the Theoretical Biology & Medical Modelling most viewed articles of all time. This is a list of the most frequently accessed articles in the history of the journal, compiled using online access statistics of the publisher BioMedCentral. The article A multiscale mathematical model of cancer, and its use in analyzing irradiation therapies was coauthored with Benjamin Ribba and Thierry Colin, and appeared in Theoretical Biology and Medical Modelling 3:7 (2006). More...
