2014

• USNCTAM PERSPECTIVES ON MECHANICS IN MEDICINE

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2013

• Ten Simple Rules for Reproducible Computational Research

Geir Kjetil Sandve, Anton Nekrutenko, James Taylor, Eivind Hovig

PLOS Computational Biology. 2014 Oct 24; 9(10)

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• Parameterizing the Logistic Model of Tumor Growth by DW-MRI and DCE-MRI Data to Predict Treatment Response and Changes in ::Breast Cancer Cellularity during Neoadjuvant Chemotherapy

Atuegwu NC, Arlinghaus LR, Li X, Chakravarthy AB, Abramson VG, Sanders ME, Yankeelov TE

Transl Oncol. 2013 Jun 1;6(3):256-64

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• Clinically relevant modeling of tumor growth and treatment response.

Yankeelov TE, Atuegwu N, Hormuth D, Weis JA, Barnes SL, Miga MI, Rericha EC, Quaranta V

Sci Transl Med. 2013 May 29;5(187):187ps9.

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• Characterization of Biaxial Mechanical Behavior of Porcine Aorta under Gradual Elastin Degradation

SHAHROKH ZEINALI-DAVARANI, MING-JAY CHOW, RAPHAEL TURCOTTE, and YANHANG ZHANG

Annals of Biomedical Engineering, 41(7), July 2013

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• Computer models figure out sickle cell crisis

Brown University News Release, June 24, 2013

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• Simulation of platelets suspension flowing through a stenosis model using a dissipative particle dynamics approach

Annals of Biomedical Engineering, 06/11/2013

MdLinx Feature

• Improving breast cancer survival analysis through competition-based multidimensional modeling.

Bilal E, Dutkowski J, Guinney J, Jang IS, Logsdon BA, Pandey G, Sauerwine BA, Shimoni Y, Moen Vollan HK, Mecham BH, Rueda OM, Tost J, Curtis C, Alvarez MJ, Kristensen VN, Aparicio S, Børresen-Dale AL, Caldas C, Califano A, Friend SH, Ideker T, Schadt EE, Stolovitzky GA, Margolin AA.

IBM TJ Watson Research, Yorktown Heights, New York, USA.

PLoS Comput Biol. 2013 May;9(5):e1003047. doi: 10.1371/journal.pcbi.1003047. Epub 2013 May 9.

Article

• Drug discovery: A jump-start for electroceuticals

Kristoffer Famm, et al.

Nature 496, 159–161 (11 April 2013) doi:10.1038/496159a

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• Creating Accurate Models of Life: Merging Biology and Computer Science

Leslie Mertz

IEEE Pulse, March/April 2013

Article

2012

• Incorporation of diffusion-weighted magnetic resonance imaging data into a simple mathematical model of tumor growth

Atuegwu NC, Colvin DC, Loveless ME, Xu L, Gore JC, Yankeelov TE.

Phys Med Biol. 2012 Jan 7;57(1):225-40.

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• Fractional proliferation: a method to deconvolve cell population dynamics from single-cell data.

Tyson DR, Garbett SP, Frick PL, Quaranta V

Nat Methods. 2012 Sep;9(9):923-8.

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• A multi-scale approach to airway hyperresponsiveness: from molecule to organ.

Lauzon, A.M., Bates, J.H.T., Donovan, G., Tawhai, M., Sneyd, J. and Sanderson M.J.

Frontiers Physiol. 3 article 191. 2012

DOI: 10.3389/fphys.2012.00191 PMCID: PMC3371674

• 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

• Dynamic Mechanisms of Cell Rigidity Sensing: Insights from a Computational Model of Actomyosin Networks.

Carlos Borau, Taeyoon Kim, Tamara Bidone, Jose´ Manuel Garcıa-Aznar1, Roger D. Kamm

PLoS ONE 7(11). November 5, 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

• The Computing Platelet: Integrating Enbironmental Cues

Sriram Neelamegham

Blood, 120:3-4, 2012, doi:10.1182/blood-2012-05-426007

• 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

• Influence of cell cycle phase on apparent diffusion coefficient in synchronized cells detected using temporal diffusion spectroscopy

Xu J, Xie J, Jourquin J, Colvin DC, Does MD, Quaranta V, Gore JC

Magn Reson Med. 2011 Apr;65(4):920-6

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• Integration of diffusion-weighted MRI data and a simple mathematical model to predict breast tumor cellularity during neoadjuvant chemotherapy

Atuegwu NC, Arlinghaus LR, Li X, Welch EB, Chakravarthy BA, Gore JC, Yankeelov TE.

Magn Reson Med. 2011 Dec;66(6):1689-96

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• 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

• The integration of quantitative multi-modality imaging data into mathematical models of tumors

Atuegwu NC, Gore JC, Yankeelov TE

Phys Med Biol. 2010 May 7;55(9):2429-49.

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• Noble, D. 2010. Biophysics and systems biology. Philos Transact A Math Phys Eng Sci. 368:1125-39

Article

• 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

• Malaria Stiffens Red Blood Cells--NPR Science Friday Highlight

• NIH Annoucement From Brown University, Providence, R.I., "Malaria-infected cells stiffen, block blood flow."

• Scientists discover how malaria blocks blood flow

• Agent Based Models Blog

• 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.

More... http://www.engineering.uiowa.edu/~ching/Publications_BEPH.pdf

• The Physiome: A Mission Imperative

http://biomedicalcomputationreview.org/6/3/6.pdf

• 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

• VPH Papers

• (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

2009

• Microenvironment driven invasion: a multiscale multimodel investigation.

Anderson AR, Rejniak KA, Gerlee P, Quaranta V.

J Math Biol. 2009 Apr;58(4-5):579-624. .

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2008

• Invasion emerges from cancer cell adaptation to competitive microenvironments: quantitative predictions from multiscale mathematical models

Quaranta V, Rejniak KA, Gerlee P, Anderson AR

Semin Cancer Biol. 2008 Oct;18(5):338-48.

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• Integrative mathematical oncology.

Quaranta V, Anderson AR

Nat Rev Cancer. 2008 Mar;8(3):227-34.

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• (October 2008) European Union and NIH Collaborate, Science

http://www.sciencemag.org/content/322/5904/1048.1.short

• (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

http://ascr-discovery.science.doe.gov/universities/oden1.shtml

• (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...