Computational Bioengineering Laboratory Publications

Here are some of the more recent publications from the members of the Computational Bioengineering Laboratory.

Books

  • Alberto Corrias, Peng Du, and Martin Buist. New Advances in Gastrointestinal Motility Research, chapter Modelling Tissue Electrophysiology in the GI Tract: Past, Present and Future, pages 167–195. Springer, 2013.
  • Andrew Pullan, Martin Buist, and Leo Cheng. Mathematically modelling the electrical activity of the heart: From cell to body surface and back again. World Scientific, Singapore, 2005.

Articles

  • Yohsuke Imai, Ikuma Kobayashi, Shunichi Ishida, Takuji Ishikawa, Martin Buist, and Takami Yamaguchi. Antral recirculation in the stomach during gastric mixing. Am J Physiol Gastrointest Liver Physiol, 304(5):G536–G542, Mar 2013. (doi:10.1152/ajpgi.00350.2012)
  • Gary R Mirams, Christopher J Arthurs, Miguel O Bernabeu, Rafel Bordas, Jonathan Cooper, Alberto Corrias, Yohan Davit, Sara-Jane Dunn, Alexander G Fletcher, Daniel G Harvey, Megan E Marsh, James M Osborne, Pras Pathmanathan, Joe Pitt-Francis, James Southern, Nejib Zemzemi, and David J Gavaghan. Chaste: an open source c++ library for computational physiology and biology. PLoS Comput Biol, 9(3):e1002970, 2013. (doi:10.1371/journal.pcbi.1002970)
  • Cheuk Wang Chung and Martin L. Buist. A novel nonlinear viscoelastic solid model. Nonlinear Analysis: Real World Applications, 13:1480–1488, 2012. (doi:10.1016/j.nonrwa.2011.11.011)
  • Alberto Corrias, Pras Pathmanathan, David J Gavaghan, and Martin L Buist. Modelling tissue electrophysiology with multiple cell types: applications of the extended bidomain framework. Integr Biol (Camb), 4(2):192–201, Feb 2012. (doi:10.1039/c2ib00100d)
  • Yong Cheng Poh, Arthur Beyder, Peter R Strege, Gianrico Farrugia, and Martin L. Buist. Quantification of gastrointestinal sodium channelopathy. Journal of Theoretical Biology, 293:41–8, Jan 2012. (doi:10.1016/j.jtbi.2011.09.014)
  • Yong Cheng Poh, Alberto Corrias, Nicholas Cheng, and Martin L. Buist. A quantitative model of human jejunal smooth muscle cell electrophysiology. PLoS ONE, 7(8):e42385, Aug 2012. (doi:10.1371/journal.pone.0042385)
  • Carlos Sanchez, Alberto Corrias, Alfonso Bueno-Orovio, Mark Davies, Jonathan Swinton, Ingemar Jacobson, Pablo Laguna, Esther Pueyo, and Blanca Rodriguez. The na+/k+ pump is an important modulator of refractoriness and rotor dynamics in human atrial tissue. Am J Physiol Heart Circ Physiol, 302(5):H1146–H1159, Mar 2012. (doi:10.1152/ajpheart.00668.2011)
  • Alberto Corrias, Wayne Giles, and Blanca Rodriguez. Ionic mechanisms of electrophysiological properties and repolarization abnormalities in rabbit purkinje fibers. Am J Physiol Heart Circ Physiol, 300(5):H1806–H1813, May 2011. (doi:10.1152/ajpheart.01170.2010)
  • Viveka Gajendiran and Martin L. Buist. A quantitative description of active force generation in gastrointestinal smooth muscle. International Journal for Numerical Methods in Biomedical Engineering, 27(3):450?460, March 2011. (doi:10.1002/cnm.1419)
  • Du Peng, Yong Cheng Poh, Jee Lean Lim, Viveka Gajendiran, Greg O?Grady, Martin L. Buist, Andrew J. Pullan, and Leo K. Cheng. A preliminary model of gastrointestinal electromechanical coupling. IEEE Trans Biomed Eng, 58(12):3491–5, Dec 2011. (doi:10.1109/TBME.2011.2166155)
  • Yong Cheng Poh and Martin L. Buist. A computational approach to understanding gastrointestinal motility in health and disease. Conf Proc IEEE Eng Med Biol Soc, 2011:429–32, 2011. (doi:10.1109/IEMBS.2011.6090057)
  • Esther Pueyo, Alberto Corrias, Laszlo Virag, Norbert Jost, Tamas Szel, Andras Varro, Norbert Szentandrassy, Peter P Nanasi, Kevin Burrage, and Blanca Rodriguez. A multiscale investigation of repolarization variability and its role in cardiac arrhythmogenesis. Biophys J, 101(12):2892–2902, Dec 2011. (doi:10.1016/j.bpj.2011.09.060)
  • David Abramson, Miguel O Bernabeu, Blair Bethwaite, Kevin Burrage, Alberto Corrias, Colin Enticott, Slavisa Garic, David Gavaghan, Tom Peachey, J. Pitt-Francis, E. Pueyo, Blanca Rodriguez, Anna Sher, and Jefferson Tan. High-throughput cardiac science on the grid. Philos Transact A Math Phys Eng Sci, 368(1925):3907–3923, Aug 2010. (doi:10.1098/rsta.2010.0170)
  • Martin L. Buist and Yong Cheng Poh. An extended bidomain framework incorporating multiple cell types. Biophysical journal, 99 (1):13–8, July 7 2010. (doi:10.1016/j.bpj.2010.03.054)
  • Martin L. Buist, Corrias Alberto, and Yong Cheng Poh. A model of slow wave propagation and entrainment along the stomach. Ann Biomed Eng, 38(9):3022–3030, 2010. (doi:10.1007/s10439-010-0051-1)
  • A. Corrias, X. Jie, L. Romero, M. J. Bishop, M. Bernabeu, E. Pueyo, and B. Rodriguez. Arrhythmic risk biomarkers for the assessment of drug cardiotoxicity: from experiments to computer simulations. Philos Transact A Math Phys Eng Sci, 368(1921):3001–3025, Jun 2010. (doi:10.1098/rsta.2010.0083)
  • Alberto Corrias and Martin L Buist. Quantitative cellular description of gastric slow wave activity. Am J Physiol Gastrointest Liver Physiol, 294(4):G989–G995, Apr 2008. (doi:10.1152/ajpgi.00528.2007)
  • David P Nickerson, Alberto Corrias, and Martin L Buist. Reference descriptions of cellular electrophysiology models. Bioinformatics, 24(8):1112–1114, Apr 2008. (doi:10.1093/bioinformatics/btn080)
  • Leo K Cheng, Rie Komuro, Travis M Austin, Martin L Buist, and Andrew J Pullan. Anatomically realistic multiscale models of normal and abnormal gastrointestinal electrical activity. World J Gastroenterol, 13(9):1378–1383, Mar 2007.
  • A. Corrias and M. L. Buist. A Quantitative Model of Gastric Smooth Muscle Cellular Activation. Ann Biomed Eng, 35(9):1595–1607, September 2007. (doi:10.1007/s10439-007-9324-8)
  • Travis M Austin, Darren A Hooks, Peter J Hunter, David P Nickerson, Andrew J Pullan, Gregory B Sands, Bruce H Smaill, and Mark L Trew. Modeling cardiac electrical activity at the cell and tissue levels. Ann N Y Acad Sci, 1080:334–347, Oct 2006. (doi:10.1196/annals.1380.025)
  • M. L. Buist, L. K. Cheng, K. M. Sanders, and A. J. Pullan. Multiscale modelling of human gastric electric activity: can the electrogastrogram detect functional electrical uncoupling? Exp Physiol, 91(2):383–390, Mar 2006. (doi:ol.2005.031021)
  • L K Cheng, M Gallucci, A J Pullan, and M L Buist. Relationship between standard EGG electrode configurations and the stomach location. Neurogastroenterol Motil, 18(6):486–486, 2006. (doi:10.1111/j.1365-2982.2006.00789_21.x)
  • Andrei Irimia, Leo K Cheng, Martin L Buist, Andrew J Pullan, and L. Alan Bradshaw. An integrative software package for gastrointestinal biomagnetic data acquisition and analysis using squid magnetometers. Comput Methods Programs Biomed, 83(2):83–94, Aug 2006. (doi:10.1016/j.cmpb.2006.03.006)
  • A. S. Lin, M. L. Buist, L. K. Cheng, N. P. Smith, and A. J. Pullan. Computational simulations of the human magneto- and electroenterogram. Ann Biomed Eng, 34(8):1322–1331, Aug 2006. (doi:10.1007/s10439-006-9142-4)
  • Anita Shu-Han Lin, Martin L Buist, Nicolas P Smith, and Andrew J Pullan. Modelling slow wave activity in the small intestine. J Theor Biol, 242(2):356–362, Sep 2006. (doi:10.1016/j.jtbi.2006.03.004)
  • D. P. Nickerson and P. J. Hunter. The noble cardiac ventricular electrophysiology models in cellml. Prog Biophys Mol Biol, 90(1-3):346–359, 2006. (doi:10.1016/j.pbiomolbio.2005.05.007)
  • D P Nickerson, M P Nash, P F Nielsen, N P Smith, and P J Hunter. Computational multiscale modeling in the IUPS Physiome Project: modeling cardiac electromechanics. IBM J. Res. & Dev., 50(6):617–630, 2006. (doi:10.1147/rd.506.0617)
  • M. Buist, N. P. Smith, and A. J. Pullan. Cardiac electromechanics and the forward/inverse problems of electrocardiology. Conf Proc IEEE Eng Med Biol Soc, 7:7198–7200, 2005.
  • L K Cheng, M L Buist, W O Richards, L A Bradshaw, and A J Pullan. Noninvasive localization of gastric electrical activity. International Journal of Bioelectromagnetism, 7(1):1–4, 2005.
  • J. W. Fernandez, M. L. Buist, D. P. Nickerson, and P. J. Hunter. Modelling the passive and nerve activated response of the rectus femoris muscle to a flexion loading: a finite element framework. Med Eng Phys, 27(10):862–870, Dec 2005. (doi:10.1016/j.medengphy.2005.03.009)
  • David Nickerson, Nicolas Smith, and Peter Hunter. New developments in a strongly coupled cardiac electromechanical model. Europace, 7 Suppl 2:118–127, Sep 2005. (doi:10.1016/j.eupc.2005.04.009)
  • M. L. Buist, L. K. Cheng, R. Yassi, L. A. Bradshaw, W. O. Richards, and A. J. Pullan. An anatomical model of the gastric system for producing bioelectric and biomagnetic fields. Physiol Meas, 25(4):849–861, Aug 2004.
  • M L Buist, L K Cheng, R Yassi, L A Bradshaw, W O Richards, and A J Pullan. An anatomical model of the gastric system for producing bioelectric and biomagnetic fields. Physiol Meas, 25(4):849–861, 2004. (doi:10.1088/0967-3334/25/4/006)
  • A. S H Lin, N. P. Smith, A. J. Pullan, and M. L. Buist. An anatomically based model of small intestine excitation. Conf Proc IEEE Eng Med Biol Soc, 2:887–889, 2004. (doi:10.1109/IEMBS.2004.1403301)
  • S. Niederer, M. Buist, A. Pullan, and N. Smith. Computing work in the ischemic heart. Conf Proc IEEE Eng Med Biol Soc, 5:3646–3649, 2004. (doi:10.1109/IEMBS.2004.1404025)
  • Andrew Pullan, Leo Cheng, Rita Yassi, and Martin Buist. Modelling gastrointestinal bioelectric activity. Prog Biophys Mol Biol, 85(2-3):523–550, 2004. (doi:10.1016/j.pbiomolbio.2004.02.003)
  • Martin L Buist and Andrew J Pullan. The effect of torso impedance on epicardial and body surface potentials: a modeling study. IEEE Trans Biomed Eng, 50(7):816–824, Jul 2003.
  • Martin Buist, Gregory Sands, Peter Hunter, and Andrew Pullan. A deformable finite element derived finite difference method for cardiac activation problems. Ann Biomed Eng, 31(5):577–588, May 2003. (doi:10.1114/1.1567283)
  • Andrew J Pullan, Martin L Buist, Greg B Sands, Leo K Cheng, and Nicolas P Smith. Cardiac electrical activity–from heart to body surface and back again. J Electrocardiol, 36 Suppl:63–67, 2003.
  • Nicolas P Smith, Martin L Buist, and Andrew J Pullan. Altered t wave dynamics in a contracting cardiac model. J Cardiovasc Electrophysiol, 14(10 Suppl):S203–S209, Oct 2003.
  • Martin Buist and Andrew Pullan. Torso coupling techniques for the forward problem of electrocardiography. Ann Biomed Eng, 30(10):1299–1312, 2002. (doi:10.1114/1.1527045)
  • G T Lines, M L Buist, P Grottum, A J Pullan, J Sundnes, and A Tveito. Mathematical models and numerical methods for the forward problem in cardiac electrophysiology. Computing and Visualization in Science, 5(4):215–239, 2002. (doi:10.1007/s00791-003-0101-4)
  • M. L. Buist and A. J. Pullan. From cell to body surface: a fully coupled approach. J Electrocardiol, 34 Suppl:191–195, 2001.

Book Chapters

  • Alberto Corrias, Peng Du, and Martin Buist. New Advances in Gastrointestinal Motility Research, chapter Modelling Tissue Electrophysiology in the GI Tract: Past, Present and Future, pages 167–195. Springer, 2013.
  • D P Nickerson. Cardiac electromechanical coupling. In Metin Akay, editor, Wiley Encyclopedia of Biomedical Engineering. John Wiley and Sons, Inc., Hoboken, 2006. (doi:10.1002/9780471740360.ebs1487)

Conferences

  • Yong Cheng Poh, Alberto Corrias, and M.L. Buist. A computational investigation of gastrointestinal channelopathy in a novel cellular model. In 4th NUS Graduate School of Integrative Sciences and Engineering Symposium, National University of Singapore, Singapore, January 2012.
  • M. L. Buist, C. W. Chung, and V. Gajendiran. Quantifying gastrointestinal smooth muscle cell mechanics. In International Symposium on Mechanobiology (5TH Shanghai International Conference on Biophysics and Molecular Biology), Shanghai (China), November 2011.
  • M. L. Buist, V. Gajendiran, and C. W. Chung. Gastrointestinal smooth muscle cell motility models. In New Advances in Gastrointestinal Motility Meeting, Auckland (New Zealand), October 2011.
  • C. W. Chung, C. T. Lim, and M. L. Buist. Quantification of soft tissue biomechanics using a novel nonlinear viscoelastic model. In Engineering Mechanics Institute Conference (EMI2011), Boston, MA (USA), June 2011.
  • RL Green, Beyder Arthur, Farrugia Gianrico, GregoryO'Grady, Yong Cheng Poh, Martin Buist, and Andrew J. Pullan. Computational modeling of the human sodium channel: Mechanical stretch effects on the electrical function of interstitial cells of cajal and smooth muscle cells. In Oral presentation at the Digestive Disease Week 2011, Chicago, Illinois, U.S.A., May 2011.
  • Yong Cheng Poh and M.L. Buist. A computational approach to understanding gastrointestinal motility in health and disease. In 33rd IEEE Engineering in Medicine and Biology Conference, Boston Marriott Copley Place Hotel, Boston, Massachusetts, August 2011.
  • Yong Cheng Poh and M.L. Buist. Computational electro-mechanics to investigate pathogenic factors for gastrointestinal dysmotility. In 5th Mechanobiology Conference, Shaw Alumni House, NUS, Singapore, November 2011.
  • Yong Cheng Poh and M.L. Buist. Computational investigation of cellular electrophysiology for gastrointestinal dysmotility. In 3rd DUNES Scientific Symposium, DUKE-NUS Graduate Medical School, Singapore, October 2011.
  • Yong Cheng Poh and M.L. Buist. Electrophysiological consequences of genetic perturbations in gastrointestinal diseases - a computational investigation. In 3rd NUS Graduate School (NGS) Symposium, Singapore, February 2011.
  • Yong Cheng Poh and M.L. Buist. A model of intestinal smooth muscle activity. In 5th East Asian Pacific Student Workshop on Nano-Biomedical Engineering, National University of Singapore, Singapore, December 2011.
  • Yong Cheng Poh and M.L. Buist. Multi-scale framework to understand gastrointestinal motility disorder. In WACBE 5th World Congress of Biomedical Engineering, Tainan, Taiwan, August 2011.
  • Yong Cheng Poh and M.L. Buist. Quantitative study of gastrointestinal motility channelopathy. In Biomedical Engineering Society of Singapore 5th Scientific Meeting, Nanyang Technological University, Singapore, May 2011.
  • Yong Cheng Poh, Alberto Corrias, and M.L. Buist. A channelopathy for irritable bowel syndrome? In 5th East Asian Pacific Student Workshop on Nano-Biomedical Engineering, National University of Singapore, Singapore, December 2011.
  • C. W. Chung and M. L. Buist. Quantification of mammalian gastrointestinal tissue viscoelasticity. In Graduate Students' seminars, Singapore, October 2010.
  • C. W. Chung, M. Lin, and M. L. Buist. Quantification of mammalian gastrointestinal tissue viscoelasticity. In 6th World Congress of Biomechanics, Singapore, August 2010.
  • Aishwariya Kannan and M.L Buist. A computational investigation of gastric electrical stimulation. In 4th East Asian Pacific Student Workshop on Nano-Biomedical Engineering, NUS, Singapore, December 2010.
  • Yong Cheng Poh and M.L. Buist. Cellular consequences of a genetic defect in the gastrointestinal tract. In 4th East Asian Pacific Student Workshop on Nano-Biomedical Engineering, NUS, Singapore, December 2010.
  • Yong Cheng Poh and M.L.. Buist. Computational investigation of a sodium channelopathy. In 6th World Congress of Biomechanics (in conjunction with 14th ICBME, 5th APBiomech), 2010, Singapore, August 2010.
  • Yong Cheng Poh and M.L. Buist. Linking genotype to phenotype in the gastrointestinal tract. In Invited poster presentation at the 2nd NUS Graduate School (NGS) Symposium, NUS, Singapore, February 2010.
  • Yong Cheng Poh and M.L. Buist. Quantifying a sodium channelopathy in the gastrointestinal tract. In 2010 Joint International Neurogastroenterology and Motility Meeting, Westin Copley Place Boston, Massachusetts, August 2010.
  • M.L. Buist and Yong Cheng Poh. From cell to organ: A multi-scale challenge in gi electrophysiology. In Neurogastroenterology and Motility Conference 2009, Chicago, August 2009.
  • C. W. Chung and M. L. Buist. Quantification of smooth muscle cell viscoelasticity. In Graduate Students' seminars, Singapore, October 2009.
  • C.W. Chung, M. L. Buist, and C. T. Lim. Design of a micro-tensile tester for probing smooth muscle cell viscoelasticity. In 3rd East Asian Pacific Student Workshop on Naono-Biomedical Engineering, Singapore, December 2009.
  • Yong Cheng Poh and M.L. Buist. Computational modeling of the gastrointestinal tract. In Bioengineering Seminar Series, Division of Bioengineering, NUS, Singapore, 23rd October 2009.
  • Yong Cheng Poh and M.L. Buist. Linking genotype to phenotype. In 3rd East Asian Pacific Student Workshop on Nano-Biomedical Engineering, NUS, Singapore, December 2009.
  • M.L. Buist, Alberto Corrias, and Yong Cheng. Poh. Multi-scale models of gastrointestinal electrophysiology. In 13th International Conference of Biomedical Engineering 2008, Singapore, Dec 2008.
  • Viveka Gajendiran and M.L. Buist. A mathematical model to study the regulation of active stress production in gi smooth muscle. In 13th International Conference of Biomedical Engineering 2008, Singapore, Singapore, Dec 2008.
  • David Nickerson and Martin Buist. Describing mathematical models of cellular physiology. In CellML Workshop 2008, Auckland, New Zealand, March 2008.
  • A Corrias and M. L. Buist. Computational Modelling of Gastric Electrophysiology. In The Graduate Students' seminars (invited speaker), Singapore, 14 February 2007.
  • A. Corrias and M. L. Buist. A model of gastric smooth muscle cellular activation. In The 3rd WACBE World Congress on Bioengineering, Bangkok (Thailand), 11 July 2007.
  • A. Corrias and M. L. Buist. A quantitative Cellular Description of gastric pacemaker activity. In The 4th Scientific Meeting of the Biomedical Engineering Society, Singapore, 19 May 2007.
  • A. Corrias and M. L. Buist. A Quantitative Cellular Description of Gastric Pacemaker Activity. In The 21st International Symposium on Neurogastroenterology and Motility, Jeju Island (South Korea), 2 September 2007.
  • David Nickerson and Martin Buist. Modelling with CellML 1.1. In CellML Workshop 2007, Auckland, New Zealand, April 2007.
  • A. Corrias and M. L. Buist. A model of gastric smooth muscle cellular activation. In 1st GPBE-NGS Bioengineering Conference, Singapore, 24 August 2006.
  • A. Corrias and M. L. Buist. A model of gastric smooth muscle cellular activation. In Joint International Neurogastroenterology and Motility Meeting, Boston, MA (USA), 14 September 2006.
  • C.T. Lim, A. Corrias, D. Isakov, and R. Mbagaya. KRIS BioMEMS, the next generation of Biomedical Research. In Association of Pacific Rim Universities (APRU) Conference: Extra Chapter Challenge (Business Plan Competition), Singapore, 17 July 2006.
  • D P Nickerson, S A Niederer, C Stevens, M P Nash, and P J Hunter. A computational model of cardiac electromechanics. In The 28th Annual IEEE Engineering and Medicine in Biology Society Conference, New York City, NY, USA, September 2006.
  • D P Nickerson, C Stevens, M D B Halstead, P J Hunter, and P F Nielsen. Toward a curated cellml model repository. In The 28th Annual IEEE Engineering and Medicine in Biology Society Conference, New York City, NY, USA, September 2006.
  • S A Blackett, D P Bullivant, D P Nickerson, and P J Hunter. Multi-scale and multi-physics visualization. In SIGGRAPH 2005: The 32nd International Conference on Computer Graphics and Interactive Techniques, Los Angeles, Ca, USA, August 2005.
  • A. Corrias and M. L. Buist. Electrophysiological Models and their applications. In The Division of Bioengineering Graduate Students' seminars (invited speaker), Singapore, 7 April 2005.
  • A. Corrias and M. L. Buist. Looking up Cardiac Activation. In The 5th GPBE Students' Conference, Singapore, 7 January 2005.
  • A. Corrias, S. Lu, and T. Soong. Effects of two Sodium channel point mutation found in two different species of pufferfish on the electrophysiological response to Tetrodotoxin (TTX). In 6th GPBE Students Conference, Singapore, 4 August 2005.
  • D P Nickerson and P J Hunter. Modelling cardiac electro-mechanics: a multiscale approach. In The FASEB Journal - Experimental Biology/IUPS World Congress 2005, volume 19, page A1319, San Diego, Ca, USA, April 2005.
  • D P Nickerson and P J Hunter. Modelling cardiac electro-mechanics: a multiscale approach. In Satellite Meeting of the 35th International Congress of Physiological Sciences: In Silico Physiology: From Genome to Physiome, San Diego, Ca, USA, March 2005.
  • D P Nickerson and P J Hunter. Using CellML in computational models of multiscale physiology. In The 27th Annual IEEE Engineering and Medicine in Biology Society Conference, Shanghai, China, September 2005.
  • D P Nickerson, C Stevens, and P J Hunter. The Wellcome Trust heart physiome project. In Medical Sciences Congress 2005, Queenstown, New Zealand, December 2005.

Theses

Miscellaneous

  • David Nickerson and Andrew Miller. CellML graph metadata specification. http://www.cellml.org/specifications/metadata/graphs, 2007.
  • A A Cuellar, P F Nielsen, M D B Halstead, D P Bullivant, D P Nickerson, W H Hedley, M R Nelson, and C M Lloyd. CellML 1.1 Specification. http://www.cellml.org/specifications/cellml_1.1/, February 2006.