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IMO Publications

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2010

1) Rejniak KA, McCawley LJ, (2010) Current trends in mathematical modeling of tumor-microenvironment interactions: a survey of tools and applications, Experimental biology and Medicine, 235:411-423

2) Strand D., Franco O. E., Basanta D., Anderson A. R. A.,Hayward S. W. (2010). Perspectives on tissue interactions in development and disease. Current Mol. Med., in press.

3) McDougall S.R.,  Chaplain M.A.J., St´ephanou A., Anderson A.R.A. (2010). Modelling the Impact of Pericyte Migration and Coverage of Vessels on the Efficacy of Vascular Disrupting Agents. Math. Model. Nat. Phenom. 5: 163-202.

4) Gerlee P. and Anderson, A. R. A. (2010). Diffusion Limited Tumour Growth: Simulations and Analysis. Math Biosci Eng, 7(2): 387-402.

5) Silva, A.S., Gatenby, R.A., Gillies, R.J., Yunes, J.A. (2010).  A quantitative theoretical model for the development of malignancy in ductal carcinoma in situ. J Theor Biol. 262 (4): 601-613.

 

2009

1) Anderson ARA, Rejniak KA, Gerlee P, Quaranta V, Microenvironment driven invasion: a multiscale multimodel investigation, Journal of Mathematical biology, 58:579-624

2) Robey IF, Baggett BK, Kirkpatrick ND, Roe DJ, Dosescu J, Sloane BF, Hashim AI, Morse DL, Raghunand N, Gatenby RA, Gillies RJ. Bicarbonate Increases Tumor pH and Inhibits Spontaneous Metastases. Cancer Res. 2009 Mar;. Pubmed ID: 19276390.   Pubmed ID: 19276390.

3) Silva AS, Yunes JA, Gillies RJ, Gatenby RA. The Potential Role of Systemic Buffers in Reducing Intratumoral Extracellular pH and Acid-Mediated Invasion. Cancer Res. 2009 Mar;. Pubmedid: 19276380.   Pubmed ID: 19276380

4) Poplawski NJ, Agero U, Gens JS, Swat M, Glazier JA, Anderson AR. Front Instabilities and Invasiveness of Simulated Avascular Tumors. Bull Math Biol. 2009 Feb;. Pubmed ID: 19234746.   Pubmed ID: 19234746

5) Ramis-Conde I, Chaplain MA, Anderson AR, Drasdo D. Multi-scale modelling of cancer cell intravasation: the role of cadherins in metastasis. Phys Biol. 2009 Mar 25; 6(1):16008. PMID: 19321920

6) Gerlee P, Lundh T, Zhang and Anderson AR. Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms. Royal Society Interface.  2009 Mar 18. PMID: 19324678

7) Gerlee P and Anderson AR. Evolution of cell motility in an individual-based model of tumour growth. J Theor Biol. 2009 Mar 12. PMID: 19285513

8) Gatenby R., Silva A., Gillies R. amd Frieden B. Adaptative Therapy. Cancer Research, June 2009.

9) P. Gerlee & Anderson, A. R. A. Modelling evolutionary cell behaviour using neural networks: Application to tumour growth, BioSystems, 95,166174. 2009.

10) R. Gatenby. A change of strategy in the war on cancer. Nature, Vol. 459, pp. 508-9. 28 May 2009.

11) Y. Kam & V. Quaranta. Cadherin-bound beta-catenin feeds into the Wnt pathway upon adherens junctions dissociation: evidence for an intersection between beta-catenin pools. PLoS One. 2009;4(2):e4580. Epub 2009 Feb 24.

12) Kam Y, Karperien A, Weidow B, Estrada L, Anderson AR, Quaranta V. Nest expansion assay: a cancer systems biology approach to in vitro invasion measurements. BMC Res Notes. 2009 Jul 13;2:130.

13) Hinow, P, Gerlee, P, McCawley, LJ, Quaranta, V, Ciobanu, M, Wang, S, Graham, JM, Ayati, BP, Claridge, J, Swanson, KR, Loveless, M, Anderson, AR. (2009). A spatial model of tumor-host interaction: Application of chemotherapy. Math Biosci Eng, 6(3): 521-46.

14) David Basanta, Douglas W. Strand, Ralf B. Lukner, Omar E. Franco, David E. Cliffel, Gustavo E. Ayala, Simon W. Hayward, and Alexander R.A. Anderson. Cancer Res 2009 69: 7111-7120. doi: 10.1158/0008-5472.CAN-08-3957

15) Enderling, H., Anderson  A. R. A. , Chaplain M. A. J., Beheshti A., Hlatky L. R., Hahnfeldt P. J. (2009) Paradoxical dependencies of tumor dormancy and progression on  basic cell kinetics. Cancer Res. 698797-8806

16) Anderson A. R. A., Hassanein M, Branch K. M., Li J., Lobdell N. A., Maier J., Basanta D., Weidow B.,Narasanna A., Arteaga C. L., Reynolds A. B., Quaranta V., Estrada L., Weaver A. M. (2009). Microenvironmental independence associated with tumor progression. Cancer Res. 69, 8814-8821.

17) Gatenby RA, Brown J.,  Vincent T. (2009). Lessons from Applied Ecology: Cancer Control Using an Evolutionary Double Bind. Cancer Res. 69(19): 7499-7502.

 

2008

1) Anderson, A. R. A. & Quaranta, V. Integrative Mathematical Oncology, Nature Rev. Cancer, (2008) 8, 227-234

2) Anderson, A. R. A., Rejniak, K. A., Gerlee, P. & Quaranta, V.  Microenviroment Driven Invasion: A Multiscale Multimodel Investigation, J. Math. Biol., (2008) DOI: 10.1007/s00285-008-0210-2.

3) Balagurunathan Y, Morse DL, Hostetter G, Shanmugam V, Stafford P, Shack S, Pearson J, Trissal M, Demeure MJ, Von Hoff DD, Hruby VJ, Gillies RJ, Han H., Gene expression profiling-based identification of cell-surface targets for developing multimeric ligands in pancreatic cancer. Mol Cancer Ther. (2008) 7(9): 3071-80.

4) Basanta D and Deutsch A., A game theoretical perspective on the somatic evolution of cancer. Chapter in In Selected topics on cancer modelling: genesis, evolution, inmune competition, therapy (N. Bellomo, M. Chaplain and E. De Angelis Eds.). Birkhauser, Boston. (2008)

5) D. Basanta, H. Hatzikirou and A. Deutsch., A game theoretical study of evolution of invasion in tumours. Eur. Phys. Journal B. (2008)

6) Basanta D, Miodownik M, Baum B, Robust homeostasis and wound healing in evolved artificial multicellular organisms.  The Evolution of Robust Development and Homeostasis in Artificial Organisms. PLoS Comput Biol (2008) 4(3)

7) D. Basanta, M. Simon, H. Hatzikirou and A. Deutsch., Evolutionary game theory elucidates the role of glycolysis in glioma progression and invasion.  Cell Proliferation 2008.

8) Black K, Kirkpatrick N, Troutman T, Xu L, Vagner J, Gillies R, Barton J, Utzinger U, Romanowski M. Gold nanorods targeted to delta opioid receptor: plasmon-resonant contrast and photothermal agents. Mol Imaging. 2008 Jan;7(1):50-57.   Pubmed ID: 18384724

9) Borden M, Zhang H, Gillies R, Dayton P, Ferrara K. A stimulus-responsive contrast agent for ultrasound molecular imaging. Biomaterials. 2008 Feb;29(5):597-606.   Pubmed ID: 17977595

10) Conde-Ramis, I., Drasdo, D. Anderson, A. R. A. & Chaplain, M. A. J.,  Modelling the influence of the E-Cadherin - β -Catenin pathway in cancer cell invasion: A multi-scale approach, Biophys J. , (2008) 95, 155-165.

11) Enderling, H., Alexander, N., Clark, E., Estrada, L., Crooke, C., Jourquin, J., Lobdell, N., Zaman, M., Anderson, A. R. A. & Weaver, A., A cellular automaton model of invadopodia-ECM interactions, Biophys J., (2008) doi:10.1529/biophysj.108.133199.

12) Fang J, Gillies R, Gatenby R. Adaptation to hypoxia and acidosis in carcinogenesis and tumor progression. Semin Cancer Biol. 2008 Mar 26; (3): . In Press.   Pubmed ID: 18455429

13) Frieden BR, Gatenby RA.  Equations of Biological Population Growth from Hartree Scattering.  Accepted Physical Review E.

14) Gatenby R, Gillies R. A microenvironmental model of carcinogenesis. Nat Rev Cancer. 2008 Jan;8(1):56-61.   Pubmed ID: 18059462

15) Gatenby RA, Frieden BR.  Inducing catastrophe in malignant growth. Mathematical Medicine & Biology. 2008.

16) Gillies R, Robey I, Gatenby R. Causes and consequences of increased glucose metabolism of cancers. J Nucl Med. 2008 Jun;49: 24S-42S.   Pubmed ID: 18523064

17) Han H, Gillies RJ, Morse DL, Hruby VJ. Patent: Method of Identifying Pancreatic Cancer Cells. 2008.

18) Huang L, Lai Y-C, Gatenby RA Alternating synchronizability of complex clustered networks with regular local structure. Phys Rev E Stat Nonlin Soft Matter Phys. 77:016103, 2008.

19) Huang L, Lai Y, Park K, Gatenby RA. Optimization of synchronization in complex modular networks. Chaos. 18(1):013101, 2008.

20) Jagannathan NR, Kumar V, Kumar R, Thulkar S. Role of magnetic resonance (MR) methods in the evaluation of prostate cancer: An Indian perspective. MAGMA 2008 Epub PMID:18633658.

21) Jennings D, Raghunand N, Gillies R. Imaging hemodynamics. Cancer Metastasis Rev. 2008 May 28; : . In Press.   Pubmed ID: 18506397

22) Kam Y, Guess C, Estrada L, Weidow B, Quaranta V. A novel circular invasion assay mimics in vivo invasive behavior of cancer cell lines and distinguishes single-cell motility in vitro. BMC Cancer. 2008 Jul 14;8:198.

23) Kumar V, Jagannathan NR, Kumar R, Thulkar S, Gupta SD, Hemal AK, Gupta NP. Evaluation of the role of magnetization transfer imaging in prostate: A preliminary study. Magnetic Resonance Imaging 2008; 26(5): 644-649.

24) Kumar R, Nayyar R, Kumar V, Gupta NP, Hemal AK, Jagannathan NR, Gupta SD, Thulkar S. The potential of magnetic resonance spectroscopic imaging in predicting absence of prostate cancer in men with serum prostate specific antigen between 4-10 ng/mL: a follow up study. Urology 2008 Epub PMID 18329078.

25) Lope-Piedrafita S, Garcia-Martin M, Galons J, Gillies R, Trouard T. Longitudinal diffusion tensor imaging in a rat brain glioma model. NMR Biomed. 2008 May 12; (5): . In Press.   Pubmed ID: 18470959

26) Macklin, P., McDougall, S., Anderson, A. R. A., Chaplain, M. A. J., Cristini, V., Lowengrub, J. (2008) “Multiscale Modelling and Nonlinear Simulation of Vascular Tumour Growth” , J. Math. Biol., doi:10.1007/s00285-008-0216-9.

27) Moellering R, Black K, Krishnamurty C, Baggett B, Stafford P, Rain M, Gatenby R, Gillies R. Acid treatment of melanoma cells selects for invasive phenotypes. Clin Exp Metastasis. 2008;25(4):411-425.   Pubmed ID: 18301995

28) Morse DL, Carroll D, Day S, Gray H, Sadarangani P, Murthi S, Job C, Baggett B, Raghunand N, Gillies RJ. Characterization of breast cancers and therapy response by MRS and quantitative gene expression profiling in the choline pathway. NMR Biomed. 2008 (in press).

29) Quaranta, V., Rejniak, K. A., Gerlee, P. & Anderson, A. R. A. (2008)“Cancer invasion emerges from microenvironment selection: Quantitative predictions from multiscale mathematical models”, Seminars. Cancer. Biol.,18, 338-48.

30) Rejniak, K.A., Anderson, A.R.A, A computational study of the development of epithelial acini. I. Sufficient conditions for the formation of a hollow structure, Bulletin of Mathematical Biology, 70(3):677–712, 2008

31) Rejniak, K.A., Anderson, A.R.A., A computational study of the development of epithelial acini. II. Necessary conditions for structure and lumen stability, Bulletin of Mathematical Biology, 70(5):1450–1479, 2008

32) Robey IF, Stephen RM, Brown KS, Baggett BK, Gatenby RA, Gillies RJ.  Regulation of the Warburg effect in early-passage breast cancer cells.  Neoplasia.  10(8):745-56, 2008.

33) Sinha S, Kumar V, Jagannathan NR, Pandey RM. Proton magnetic resonance spectroscopy of brain to study the cerebral abnormalities in COPD patients: A case control study in North India. Indian Journal of Chest Diseases and Allied Sciences 2008 (In Press).

34) Sinha S, Misra A, Rathi M, Kumar V, Pandey RM, Luthra K, Jagannathan NR. Proton magnetic resonance spectroscopy and biochemical investigation of type 2 diabetes mellitus in Asian Indians: observation of high muscle lipids and C-reactive protein levels. Magnetic resonance Imaging 2008 Epub PMID 18687549.

35) Smallbone K, Gatenby RA, Maini PK.  Mathematical modeling of tumor acidity.  Accepted to Journal of Theoretical Biology. 2008.

36)Vagner J, Xu L, Handl HL, Josan JS, Morse DL, Mash EA, Gillies RJ, Hruby VJ. Heterobivalent Ligands Crosslink Multiple Cell-Surface Receptors: The Human Melanocortin-4 and delta-Opioid Receptors. Angew Chem Int Ed Engl. 2008; 47(9): 1685-8.

37) Vincent TL, Gatenby RA   An evolutionary model for initiation, promotion, and progression in carcinogenesis.  International Journal of Oncology. 32:729-737, 2008.

38) Vincent, TL, Gatenby, RA, Somatic evolution of cancer.  International Game Theory Review. 10(1): 101-118, 2008.

39) Enderling, H., Anderson, A. R. A., Chaplain, M. A. A model of breast carcinogenesis and recurrence after radiotherapy. PAMM, 7, 1121701-2. 2008

40)  Macklin, P., McDougall, S., Anderson, A. R. A., Chaplain, M. A. J., Cristini, V., Lowengrub, J. Multiscale Modelling and Nonlinear Simulation of Vascular Tumour Growth, J. Math. Biol., 58, 765-798. 2008

41) Conde-Ramis, I., Drasdo, D. Anderson, A. R. A. & Chaplain, M. A. J. Modelling the influence of the E-Cadherin - Beta -Catenin pathway in cancer cell invasion: A multi-scale approach, Biophys J. , (2008) 95, 155-165.

 

2007

1) Ackerstaff E, Artemov D, Gillies R, Bhujwalla Z. Hypoxia and the presence of human vascular endothelial cells affect prostate cancer cell invasion and metabolism. Neoplasia. 2007 Dec;9(12):1138-1151.   Pubmed ID: 18084621

2) Anderson, A.R.A, Rejniak, K.A., Gerlee, P., Quaranta, V., Modelling of cancer growth, evolution and invasion: bridging scales and models, Mathematical Modelling of Natural Phenomena, 2(3):1-29, 2007 

3) Borden M, Caskey C, Little E, Gillies R, Ferrara K. DNA and polylysine adsorption and multilayer construction onto cationic lipid-coated microbubbles. Langmuir. 2007 Aug 28;23(18):9401-9408.   Pubmed ID: 17665937

4) Bowen M, Monguchi Y, Sankaranarayanan R, Vagner J, Begay L, Xu L, Jagadish B, Hruby V, Gillies R, Mash E. Design, synthesis, and validation of a branched flexible linker for bioactive peptides. J Org Chem. 2007 Mar 2;72(5):1675-1680.   Pubmed ID: 17279799

5) Enderling, H., Chaplain, M. A. J., Anderson, A. R. A., Vaidya, J. S. (2007) “Mathematical model of breast cancer development, local treatment and recurrence” J. Theor. Biol., 264, 245-259.

6) Gatenby RA, Frieden BR.  Information Theory in Living Systems, Methods, Applications, and Challenges.  Bulletin of Mathematical Biology. 69(2):635-57, 2007.

7) Gatenby R, Gillies R. Glycolysis in cancer: a potential target for therapy. Int J Biochem Cell Biol. 2007;39(7-8):1358-1366.   Pubmed ID: 17499003

8) Gatenby R, Smallbone K, Maini P, Rose F, Averill J, Nagle R, Worrall L, Gillies R. Cellular adaptations to hypoxia and acidosis during somatic evolution of breast cancer. Br J Cancer. 2007 Sep 3;97(5):646-653.   Pubmed ID: 17687336

9) Gerlee, P. & Anderson, A. R. A. (2007) “An Evolutionary Hybrid Cellular Automaton Model of Solid Tumour Growth” J. Theor. Biol., 247, 583-603.

10) Gerlee, P. & Anderson, A. R. A. (2007) “Stability Analysis of a Hybrid Cellular Automaton Model of Cell Colony Growth”, Phys Rev. E, 75, 051911.

11) Gerlee, P. & Anderson, A. R. A. (2007) “A Hybrid Cellular Automaton Model of Clonal Evolution in Cancer: The Emergence of the Glycolytic Phenotype” J. Theor. Biol., 250, 705-722.

12) Gillies R, Gatenby R. Adaptive landscapes and emergent phenotypes: why do cancers have high glycolysis. J Bioenerg Biomembr. 2007 Jun;39(3):251-257.   Pubmed ID: 17624581

13) Gillies R, Gatenby R. Hypoxia and adaptive landscapes in the evolution of carcinogenesis. Cancer Metastasis Rev. 2007 Jun;26(2):311-317.   Pubmed ID: 17404691

14) Handl H, Sankaranarayanan R, Josan J, Vagner J, Mash E, Gillies R, Hruby VJ. Synthesis and evaluation of bivalent NDP-alpha-MSH(7) peptide ligands for binding to the human melanocortin receptor 4 (hMC4R). Bioconjug Chem. 2007 Jul;18(4):1101-1109.   Pubmed ID: 17591746

15) Jagadish B, Sankaranarayanan R, Xu L, Richards R, Vagner J, Hruby V, Gillies RJ, Mash E. Squalene-derived flexible linkers for bioactive peptides. Bioorg Med Chem Lett. 2007 Jun 15;17(12):3310-3313.   Pubmed ID: 17448660

16) Kumar V, Jagannathan NR, Kumar R, Thulkar S, Gupta SD, Hemal AK, Gupta NP. Transrectal ultrasound-guided biopsy of prostate voxels identified as suspicious of malignancy on three-dimensional 1H MR spectroscopic imaging in patients with abnormal digital rectal examination or raised prostate specific antigen level of 4 -10 ng/ml. NMR in Biomedicine 2007; 20:11-20.

17) Kumar V, Jagannathan NR, Kumar R, Thulkar S, Gupta SD, Dwivedi SN, Hemal AK, Gupta NP. Apparent diffusion coefficient of prostate in men prior to biopsy: Determination of a cut-off value to predict malignancy of the peripheral zone. NMR in Biomedicine 2007; 20: 505-511.

18) Morse D, Galons J, Payne C, Jennings D, Day S, Xia G, Gillies R. MRI-measured water mobility increases in response to chemotherapy via multiple cell-death mechanisms. NMR Biomed. 2007 Oct;20(6):602-614.   Pubmed ID: 17265424

19) Morse D, Raghunand N, Sadarangani P, Murthi S, Job C, Day S, Howison C, Gillies R. Response of choline metabolites to docetaxel therapy is quantified in vivo by localized (31)P MRS of human breast cancer xenografts and in vitro by high-resolution (31)P NMR spectroscopy of cell extracts. Magn Reson Med. 2007 Aug;58(2):270-280.   Pubmed ID: 17654590

20) Pearce, I. G., Chaplain, M. A. J., Schofield, P. G., Anderson, A. R.A., Hubbard, S. F. (2007)  “Chemotaxis-induced spatio-temporal hetereogeneity in multi-species host-parasitoid systems” J. Theor. Biol., 55, 365-388.

21) Rejniak, K.A., An immersed boundary framework for model ling the growth of  individual cells: an application to the early tumour development, Journal of Theoretical Biology, 247:186–204, 2007 

22) Rejniak, K.A., Modelling the Development of Complex Tissues using Individual Viscoelastic Cells, chapter in "Single-Cell-Based Models in Biology and Medicine" edited by A.R.A. Anderson, M.A.J. Chaplain, K.A. Rejniak, 2007, Birkhauser-Verlag in the Mathematics and Biosciences in Interaction (MBI) series

23) Rejniak, K.A., Dillon, R.H., A single cell based model of the ductal tumour microarchitecture, Computational and Mathematical Methods in Medicine, 8(1):51–69, 2007

24) Rosca E, Stukel J, Gillies R, Vagner J, Caplan M. Specificity and mobility of biomacromolecular, multivalent constructs for cellular targeting. Biomacromolecules. 2007 Dec;8(12):3830-3835.   Pubmed ID: 18039007

25) Sharma U, Kumar V, Wadhwa S, Jagannathan NR. In vivo 31P MRS study of skeletal muscle metabolism in patients with postpolio residual paralysis. Magnetic Resonance Imaging 2007; 25:244-249.

26) Smallbone K, Gatenby R, Gillies R, Maini P, Gavaghan D. Metabolic changes during carcinogenesis: potential impact on invasiveness. J Theor Biol. 2007 Feb 21;244(4):703-713.   Pubmed ID: 17055536

27) Stephen R, Gillies R. Promise and progress for functional and molecular imaging of response to targeted therapies. Pharm Res. 2007 Jun;24(6):1172-1185.   Pubmed ID: 17385018

28) Walter G., Jourquin J., Estrada, L., Anderson, A. R. A., Quaranta, V. and Wikswo, J.P. (2007) “Model-controlled hydrodynamic focusing to generate multiple overlapping gradients of surface-immobilized proteins in microfluidic devices” Lab on a chip, 8, 238-244.

 
 
 
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