publications.bib

@INBOOK{fuentesetal09b,
  author = {D.~Fuentes and J.~T.~Oden and K.~R.~Diller and A.~Elliott and Y.~Feng and J.~D.~Hazle and A.~Shetty and and R.~J.~Stafford},
  chapter = {Computational and {MR}-guided Patient-Specific Laser Induced Thermal Therapy of Cancer},
  title = {Dynamic Data Driven Application Systems},
  publisher = {Springer},
  year = {2009},
  note = {submitted for publication}
}
@ARTICLE{fuentesetal09,
  author = {D.~Fuentes and Y.~Feng and A.~Elliott and A.~Shetty and R.~J.~McNichols and J.~T.~Oden and R.~J.~Stafford},
  title = {Adaptive Real-Time Bioheat Transfer Models for Computer Driven MR-guided Laser Induced Thermal Therapy},
  journal = {IEEE Trans. BME},
  year = {2009},
  note = {submitted for publication},
  url = {publications/calib_feb09.pdf}
}
@ARTICLE{Odenetal08,
  author = {J.~T.~Oden and D.~Fuentes and J.~Bass and Y.~Feng},
  title = {Dynamic-data-driven systems aid patient-specific cancer therapy},
  journal = {spie.org},
  year = {2008},
  doi = {10.1117/2.1200810.1220},
  url = {publications/EWC_Feng.pdf}
}
@MISC{TACC08,
  author = {A.~Dubrow},
  title = {{TACC supercomputer performs laser cancer surgery on canine}},
  year = {2008},
  howpublished = { http://www.tacc.utexas.edu/research/users/features/dynamic.php?m\_b\_c=laser },
  url = {http://www.tacc.utexas.edu/research/users/features/dynamic.php?m_b_c=laser}
}
@ARTICLE{Fuentesetal08,
  author = {D.~Fuentes and J.~T.~Oden and K.~R.~Diller  and J.~Hazle and A.~Elliott and  and A.~Shetty and R.~J.~Stafford },
  title = {Computational Modeling and Real-Time Control of Patient-Specific
           Laser Treatment Cancer},
  journal = {Ann. BME.},
  year = {2009},
  number = {4},
  volume = {37},
  pages = {763},
  doi = {10.1007/s10439-008-9631-8},
  url = {publications/annals_bme_june08.pdf}
}
@INPROCEEDINGS{Fengetal08b,
  title = {{MRTI-Based Optimization and Real-Time Laser Surgical Control for Cancer Treatment Using Fast Inverse Analysis Techniques}},
  author = {Yusheng Feng and Fuentes, D. and Hawkins, A. and Oden, J.T.},
  journal = {BioMedical Engineering and Informatics, 2008. BMEI 2008. International Conference on},
  year = {2008},
  month = {May},
  volume = {2},
  number = {},
  pages = {168-172},
  doi = {10.1109/BMEI.2008.282},
  issn = {},
  url = {http://dddas.ices.utexas.edu/publications/BMEI_08_China.pdf}
}
@ARTICLE{Fengetal08,
  author = {Y.~Feng and D.~Fuentes and A.~Hawkins 
            and J.~Bass and M.~N.~Rylander },
  title = {Model-Based Optimization and Real-Time Control 
           for Laser Treatment of  Heterogeneous Soft Tissues},
  journal = {CMAME},
  year = {2009},
  volume = {198},
  number = {21-26},
  pages = {1742-1750},
  note = {{Advances in Simulation-Based Engineering Sciences  Special Issue Honoring Prof. J. Tinsley Oden}},
  url = {publications/cmame_jto_feb08.pdf}
}
@INBOOK{Dilleretal07,
  editor = {W.~J.~Minkowycz and E.~M.~Sparrow},
  author = {K.~R.~Diller and J.~T.~Oden and C.~Bajaj and J.~C.~Browne and J.~Hazle and I.~Babu\v{s}ka and J.~Bass and L.~Bidaut and L.~Demkowicz and A.~Elliott and Y.~Feng and D.~Fuentes and S.~Goswami and A.~Hawkins and S.~Khoshnevis and B.~Kwon and S.~Prudhomme and R.~J.~Stafford },
  chapter = {9: Computational Infrastructure for the Real-Time
            Patient-Specific Treatment of Cancer},
  volume = {3: Numerical Implementation of Bioheat Models and Equations},
  title = {Advances in Numerical Heat Transfer},
  year = {2008},
  publisher = {Taylor \& Francis Group},
  url = {publications/adv_num_ht_sept07.pdf}
}
@ARTICLE{Fengetal07,
  author = {Y.~Feng and D.~Fuentes and A.~Hawkins and J.~Bass and M.~N.~Rylander and A.~Elliott and A.~Shetty and R.~J.~Stafford and J.~T.~Oden},
  title = {Nanoshell-Mediated Laser Surgery Simulation for Prostate Cancer Treatment},
  journal = {Engineering with Computers},
  doi = {10.1007/s00366-008-0109-y},
  year = {2009},
  volume = {25},
  number = {1},
  pages = {3-13},
  url = {publications/EWC_Feng.pdf}
}
@ARTICLE{Odenetal07,
  author = {J.~T.~Oden and K.~R.~Diller and C.~Bajaj and J.~C.~Browne and J.~Hazle and I.~Babu\v{s}ka and J.~Bass and L.~Demkowicz and Y.~Feng and D.~Fuentes and S.~Prudhomme and M.~N.~Rylander and R.~J.~Stafford and Y.~Zhang },
  title = {Dynamic Data-Driven Finite Element Models for Laser Treatment of prostate cancer},
  journal = { Num. Meth. PDE, },
  year = {2007},
  volume = {23},
  number = {4},
  pages = {904-922},
  url = {publications/maflep_jun06.pdf}
}
@INPROCEEDINGS{Bajaetal07,
  author = {C. Bajaj and J. T. Oden and K. R. Diller and J. C. Browne and J. Hazle and I. Babuska and J. Bass and L. Bidaut and L. Demkowicz and A. Elliott and Y. Feng and D. Fuentes and S. Prudhomme and R. J. Stafford and Y. Zhang},
  title = {Using Cyber-Infrastructure for Dynamic Data Driven Laser Treatment of Cancer},
  booktitle = {PROCEEDINGS LECTURE NOTES IN COMPUTER SCIENCE},
  volume = {4487},
  pages = {972-979},
  year = {2007},
  url = {publications/iccs_may07.pdf}
}
@INPROCEEDINGS{Odenetal06,
  author = {J. T. Oden and K. R. Diller and C. Bajaj and J. C. Browne and J. Hazle and I. Babuska and J. Bass and L. Demkowicz and A. Elliott and Y. Feng and D. Fuentes and S. Prudhomme and M. N. Rylander and R. J. Stafford and Y. Zhang},
  title = {Development of a computational paradigm for laser treatment of cancer},
  booktitle = {PROCEEDINGS LECTURE NOTES IN COMPUTER SCIENCE},
  volume = {3993},
  pages = {530-537},
  year = {2006},
  url = {publications/ICCS_2006.pdf}
}
@MISC{Prudhomme06,
  author = {S.~Prudhomme},
  title = {A Dynamic Data-Driven System for Laser Treatment of Cancer},
  month = {November},
  year = {2006},
  note = {SC06 Conference, Tampa, Florida}
}
@MISC{Demkowicz06,
  author = {L.~Demkowicz},
  title = {A Dynamic Data-Driven System for Laser Treatment of cancer},
  month = {January},
  year = {2006},
  note = {Dynamic Data-Driven Application Systems Workshop.            National Science Foundation, Washington D.C. Conference Presentation.  },
  url = {publications/talk.pdf}
}
@MISC{diller06,
  author = { K. R. Diller},
  title = {A Dynamic Data-Driven System for Laser Treatment of Cancer},
  month = {May},
  year = {2006},
  note = {International Conference on Computational Science Reading, U.K. Conference Presentation.}
}
@MISC{oden06,
  author = { J. T. Oden},
  title = {Dynamic Data-Driven Finite Element Models for Laser Treatment of prostate cancer },
  month = {June},
  year = {2006},
  note = {MAFELAP 2006: The Mathematics of Finite Elements and Applications.  Brunel University, Uxbridge, England, Conference Presentation.},
  url = {publications/MAFELAP_june_2006.pdf}
}
@MISC{fuentes06,
  author = { D. Fuentes},
  title = { Development of a Computational Paradigm for Laser Treatment of cancer},
  month = {July},
  year = {2006},
  note = {World Congress on Computational Mechanics.  Los Angeles, California, Conference Presentation.},
  url = {publications/WCCM_july_2006.pdf}
}
@MISC{bajaj07,
  author = {C. Bajaj},
  title = {Using Cyber-Infrastructure for Dynamic Data Driven Laser Treatment of Cancer},
  month = {May},
  year = {2007},
  note = {ICCS 2007: Advancing Science and Society through Computation,  Beijing, China, Conference Presentation. }
}
@MISC{fuentes07,
  author = {D. Fuentes},
  title = { A Data Driven Application System for Laser Treatment of cancer},
  month = {July},
  year = {2007},
  note = {National Congress on Computational Mechanics.  San Francisco, California, Conference Presentation. },
  url = {publications/pres_nccm_july07.pdf}
}
@MISC{hawkins07,
  author = {A. Hawkins },
  title = {A Sensitivity Study of the Pennes Bioheat Transfer Model to Source Term Parameters},
  month = {July},
  year = {2007},
  note = { National Congress on Computational Mechanics.  San Francisco, California, Conference Presentation. }
}
@ARTICLE{JBME07,
  author = {Y.~Feng and J.~T.~Oden and M.N.~Rylander},
  title = {A Statistical Thermodynamics Based Cell Damage Models and its
Validation in vitro},
  journal = {J. Biomech. Eng.},
  volume = {130},
  number = {041016},
  pages = {1-10},
  year = {2008}
}
@ARTICLE{Rylanderetal07,
  author = {M.~N.~Rylander and Y.~Feng and J.~Bass and K.~Diller},
  title = {Heat Shock Protein Expression and Damage Optimization for Laser Therapy Design},
  journal = {Lasers in Surgery and Medicine},
  volume = {39},
  pages = {731-746},
  year = {2007}
}
@MISC{feng07b,
  author = {Y.~Feng},
  title = {Cell Damage Based Optimization and Real-Time Control of Laser Surgery for Prostate Tumor},
  month = {May},
  year = {2007},
  note = {CAIMS, Banff, Canada. Conference Presentation }
}
@MISC{feng07,
  author = {Y. Feng},
  title = {Modeling Bioheat Transfer and Cell Damage Under Hyperthermia Condition in Human Prostate},
  month = {July},
  year = {2007},
  note = {National Congress on Computational Mechanics.  San Francisco, California, Conference Presentation. }
}
@MISC{feng07c,
  author = {Y.~Feng},
  title = {To Kill or Not to Kill: On Fundamental Issues of Thermal Therapies for Cancer Treatment },
  month = {May},
  year = {2007},
  note = {Joint Annual Meeting of Society for Thermal Medicine and World Conference on Interventional Oncology,  Washington D.C., Conference Presentation }
}
@INPROCEEDINGS{bajajetal08,
  title = {Surface Reconstruction From Non-parallel Curve Networks},
  author = {C.~Bajaj and L.~Liu and J.~O.~Deasy  and D.~A.~Low  and T.~Ju },
  journal = {Computer Graphics Forum (Proceedings of Eurographics) Crete, Greece.},
  booktitle = {NIHMSID: 87567. PMC Journal in Process },
  year = {2008},
  month = {May},
  volume = {27},
  number = {2},
  pages = {155-163}
}
@ARTICLE{zhang2009surface,
  title = {{Surface smoothing and quality improvement of quadrilateral/hexahedral meshes with geometric flow http://cvcweb. ices. utexas. edu/cvc/meshing/quadhexgf/index. html}},
  author = {Zhang, Y. and Bajaj, C. and Xu, G.},
  journal = {Communications in Numerical Methods in Engineering},
  volume = {25},
  number = {1},
  year = {2009},
  publisher = {John Wiley \& Sons, Ltd. Chichester, UK}
}
@ARTICLE{bajaj2008modeling,
  title = {{Modeling Cardiovascular Anatomy from Patient-Specific Imaging}},
  author = {Bajaj, C. and Goswami, S.},
  journal = {Advances in Computational Vision and Medical Image Processing: Methods and Applications},
  pages = {1},
  year = {2008},
  publisher = {Springer}
}
@ARTICLE{zhang2007patient,
  title = {{Patient-specific vascular NURBS modeling for isogeometric analysis of blood flow}},
  author = {Zhang, Y. and Bazilevs, Y. and Goswami, S. and Bajaj, C.L. and Hughes, T.J.R.},
  journal = {Computer Methods in Applied Mechanics and Engineering},
  volume = {196},
  number = {29-30},
  pages = {2943--2959},
  year = {2007},
  publisher = {Elsevier}
}
@CONFERENCE{bajaj2008multi,
  title = {{Multi-component heart reconstruction from volumetric imaging}},
  author = {Bajaj, C. and Goswami, S.},
  booktitle = {Proceedings of the 2008 ACM symposium on Solid and physical modeling},
  pages = {193--202},
  year = {2008},
  organization = {ACM New York, NY, USA}
}
@ARTICLE{bajaj2008physically,
  title = {{Physically-Based Surface Texture Synthesis Using a Coupled Finite Element System}},
  author = {Bajaj, C. and Zhang, Y. and Xu, G.},
  journal = {Lecture Notes in Computer Science},
  volume = {4975},
  pages = {344},
  year = {2008},
  publisher = {Springer}
}
@INPROCEEDINGS{garimella2008proceedings,
  title = {{Quality Meshing of a Forest of Branching Structures}},
  booktitle = {{Proceedings of the 17th International Meshing Roundtable}},
  author = {C.~Bajaj and A.~Gillette},
  editor = {Garimella, R.V.},
  year = {2008},
  pages = {433-449},
  publisher = {Springer}
}
@MISC{demkowicz07,
  author = {L.~Demkowicz},
  title = {hp-Adaptive Finite Elements, Moving Forward. Geometry Reconstruction and Coupled Problems},
  month = {May},
  year = {2007},
  note = {Invited keynote talk, International Workshop on High-Order Finite Element Methods, Herrsching am Ammersee, Germany, Conference Presentation. }
}
@MISC{demkowicz07b,
  author = {L.~Demkowicz},
  title = {hp-Adaptive Finite Elements, Moving Forward. Geometry Reconstruction and Coupled Problems},
  month = {July},
  year = {2007},
  note = {Invited seminar, Stanislaw Staszic University of Science and Technology, Cracow, Poland }
}
@MISC{fuentes08,
  author = {D. Fuentes},
  title = {Remote Laser Cancer Surgery: A Minimally Invasive Alternative 
to the Standard Treatment },
  month = {July},
  year = {2008},
  note = {The Austin Forum.  Austin, Texas, Invited Presentation. },
  url = {aus_forum_presentation/aus_forum_presentation.pdf}
}
@MISC{odenPres09,
  author = {J.~T.~Oden},
  title = {Mixed Finite Element Methods for Predictive Phase-Field Models of Tumor Growth.},
  month = {June},
  year = {2009},
  note = {MAFELAP 2009, Brunel University, Uxbridge, United Kingdom. Conference Presentation.}
}
@MISC{fuentes08b,
  author = {J. T. Oden and D. Fuentes},
  title = {Computational Modeling and Real-Time Control of
Patient-Specific Laser Treatment of Cancer },
  month = {September},
  year = {2008},
  note = {Seventh Interventional MRI Symposium.  Baltimore, Maryland, Conference Presentation.},
  url = {fuentes/imri2008.pdf}
}
@MISC{FengPres06e,
  author = {Y.~Feng},
  title = {Toward Real-Time Optimal Control of Laser Surgery for Cancer Treatment: A Mathematical and Computational Framework.},
  month = {August},
  year = {2006},
  note = {Joint SIAM-SMB Conference on Life Sciences, Raleigh, NC. Conference Presentation.}
}
@MISC{FengPres06d,
  author = {Y.~Feng},
  title = {Prediction of Cancer Treatment Outcome for Laser Surgery of Prostate Cancer.},
  month = {August},
  year = {2006},
  note = {Joint SIAM-SMB Conference on Life Sciences, Raleigh, NC. Conference Presentation.}
}
@MISC{FengPres06c,
  author = {Y.~Feng},
  title = {Optimization of Laser Surgery for Cancer Treatment: Are we barking at the wrong tree?},
  month = {March},
  year = {2006},
  note = {Texas Finite Element Rodeo, College Station, Texas. Conference Presentation.}
}
@MISC{FengPres06b,
  author = {Y.~Feng},
  title = {Prediction of Cancer Treatment Outcome for Nanoshell-Mediated Laser Surgery Using Adaptive Finite Element Method},
  month = {July},
  year = {2006},
  note = {Seventh World Congress on Computational Mechanics, Los Angeles, CA. Conference Presentation.}
}
@MISC{FengPres06,
  author = {Y.~Feng},
  title = {Perfusion effect of vasculature in bio-heat transfer and laser treatment of prostate cancer.},
  year = {2006},
  note = {Annual conference of Society of Thermal Medicine, Washington D.C. Conference Presentation.}
}
@MISC{OdenPres06,
  author = {J.~T.~Oden},
  title = {Dynamic Data-Driven Application Systems Workshop. A Dynamic Data-Driven System for Laser Treatment of cancer.},
  year = {2006},
  note = {National Science Foundation, Washington D.C. Conference Presentation.}
}

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