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Publications &
Presentations
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- Srivatsan
Pallavaram, Pierre-François D’Haese, Chris Kao, Hong
Yu, Michael Remple, Joseph S. Neimat, Peter E. Konrad, Benoit
M. Dawant, A new method for creating electrophysiological maps
for DBS surgery and their application to surgical guidance, Medical
Image Computing and Computer Assisted Intervention (MICCAI), New
York, 2008, Lecture Notes in Computer Science, Springer-Verlag
(Accepted).
- Joseph S.
Neimat, Srivatsan Pallavaram, Pierre-François D’Haese,
Chris Kao, Hong Yu, Michael Remple, Peter E. Konrad, Benoit M.
Dawant, Computerized brain atlas provides anatomic prediction
of stimulation efficacy in patients undergoing deep brain stimulation(DBS)
of the subthalamic nucleus(STN), Poster at American Society of
Sterotactic and Functional Neurosurgery (ASSFN) Biennial meeting,
Vancouver, BC, Canada, June 1-4, 2008.
- Michael S.
Remple, Srivatsan Pallavaram, Pierre F. D’Haese, Benoit
M. Dawant, Joseph S. Neimat, Organization of sensorimotor responses
in the human subthalamic nucleus (STN), American Society of Neurophysiological
Monitoring (ASNM), May 2-4, Chicago, IL
- Benjamin
P. Rosenbaum, Pierre-François D’Haese, Hong Yu, Srivatsan
Pallavaram, Benoit M. Dawant, Joseph S. Neimat, Peter E. Konrad,
Brain Shift during Deep Brain Stimulation Surgery Correlates Directly
to Pneumocephalus and Inversely to Age, Poster at American Society
of Sterotactic and Functional Neurosurgery (ASSFN) Biennial meeting,
Vancouver, BC, Canada, June 1-4, 2008.
- Hong Yu,
Pierre-François D’Haese, Tatsuki Koyama, Srivatsan Pallavaram,
Benoit M. Dawant, Joseph Niemat, Peter E. Konrad, Automated Algorithm
Selects Anterior and Posterior Commissure Points Better than Experienced
Neurosurgeons, Poster at American Society of Sterotactic and Functional
Neurosurgery (ASSFN) Biennial meeting, Vancouver, BC, Canada,
June 1-4, 2008.
- Hong Yu,
Benjamin P. Rosenbaum, Pierre-François D’Haese, Srivatsan
Pallavaram, Prashanth Dumpuri, Benoit M. Dawant, Joseph S.
Neimat, Peter E. Konrad, Predicting Brain Shift in Deep Brain
Stimulation Surgery, Poster at American Society of Sterotactic
and Functional Neurosurgery (ASSFN) Biennial meeting, Vancouver,
BC, Canada, June 1-4, 2008.
- Srivatsan
Pallavaram, Hong Yu, John Spooner, Pierre-François
D’Haese, Bobby Bodenheimer, Peter E. Konrad, Benoit M. Dawant,
"Inter-surgeon variability in the selection of anterior and
posterior commissures and its potential effects on target localization",
Journal of Stereotact Funct Neurosurg 2008;86:113-119 (DOI: 10.1159/000116215).
- Anusha Sathyanarayanan,
Srivatsan Pallavaram, Robert Bodenheimer, Kevin Robinson,
Benoit Dawant, Thomas L. Davis, "Quantification of Movement
Using a Nintendo Wii Remote", American Neurological Association
(132nd meeting), 2007.
- Hong Yu,
Pierre-Francois D'Haese, Srivatsan Pallavaram, Benoit M.
Dawant, Peter E. Konrad, "The use of a functional atlas for
automated targeting in deep brain stimulation surgery", Southern
Neurosurgical Society Annual Meeting, Sea Island, Georgia, March
14 - 17, 2007.
- Andrew B.
Conrad, Thomas L. Davis, Peter E. Konrad, Benoit Dawant, Srivatsan
Pallavaram, Michael Gensheimer, "Ventricular Volume Associations
With Transient Encephalopathy Following Deep Brain Stimulation
Surgery", American Academy of Neurology (AAN) conference,
Boston: April 28-May 5, 2007.
- Benoit Dawant,
Pierre-François D’Haese, Srivatsan Pallavaram, Hong
Yu, John Spooner, Thomas Davis, Chris Kao, Peter E. Konrad, "The
VU-DBS project: integrated and computer-assisted planning, intra-operative
placement, and post-operative programming of deep brain stimulators",
SPIE Medical Imaging Symposium, Visualization and Image-Guided
Procedures conference, San Diego, February 2007.
- Srivatsan
Pallavaram, Hong Yu, John Spooner, Pierre-François
D’Haese, Tatsuki Koyama, Bobby Bodenheimer, Peter E. Konrad, Benoit
M. Dawant, "Automated selection of anterior and posterior
commissures based on a deformable atlas and its evaluation based
on manual selections by neurosurgeons", Proc. of SPIE Medical
Imaging, Vol. 6509, pp: 65091C-1:9, 2007.
- Pierre-François
D’Haese, Srivatsan Pallavaram, Hong Yu, John Spooner, Peter
E. Konrad, Benoit M. Dawant, "Internet portal for computer
aided deep brain stimulation therapy: from target planning to
programming", Movement Disorders - 10th International Congress
of Parkinson's Disease and Movement Disorders, Oct' 28-Nov' 2,
2006, Kyoto, Japan.
- Pierre-François
D’Haese, Srivatsan Pallavaram, Hong Yu, John Spooner, Peter
E. Konrad, Benoit M. Dawant, "Automated selection of programming
parameters for Deep Brain Stimulators based on a probabilistic
atlas", Movement Disorders - 10th International Congress
of Parkinson's Disease and Movement Disorders, Oct' 28-Nov' 2,
2006, Kyoto, Japan.
- Srivatsan
Pallavaram, Pierre-François D’Haese, Bobby Bodenheimer,
John Spooner, Hong Yu, Peter E. Konrad, Benoit M. Dawant, "Automated
selection of anterior and posterior commissures based on a deformable
atlas can remove variability in the current frame of reference
used for stereotactic neurosurgical procedures", Poster at
American Society of Sterotactic and Functional Neurosurgery (ASSFN)
Biennial meeting, Boston, MA, USA, June 1-4, 2006.
- Pierre-François
D’Haese, Srivatsan Pallavaram, Hong Yu, John Spooner, Peter
E. Konrad, Benoit M. Dawant, "Deformable Physiological Atlas-Based
Programming of Deep Brain Stimulators: A Feasibility Study",
WBIR (Workshop on Biomedical Image Registration), 2006.
- John Spooner,
Hong Yu, Pierre-Francois D'Haese, Srivatsan Pallavaram,
Benoit M. Dawant, Peter E. Konrad, "Fully automated deep
brain stimulation target selection better than traditional methods",
ASSFN (American Society of Stereotactic and Functional Neurosurgery),
2006.
- Pierre-Francois
D'Haese, Srivatsan Pallavaram, Ken Niermann, John Spooner,
Chris Kao, Peter E. Konrad, Benoit M. Dawant, "Electrophysiological
atlas based fully automatic selection of DBS target points: a
multiple atlases approach", MICCAI (Medical Image Computing
and Computer Assisted Intervention), Palm Springs, California,
USA, Oct' 26-29, 2005.
- Pierre-Francois
D'Haese, Srivatsan Pallavaram, Chris Kao, Peter E. Konrad,
Benoit M. Dawant, "Computer-aided placement of deep brain
stimulators: from planning to intra-operative guidance",
SPIE, Medical Imaging, San Diego, California, USA, Feb' 12-17,
2005.
- S. Pallavaram,
M. Carli, J. Berger, A. Neri, S.K. Mitra, "Spot identification
in microarray images using Gauss-Laguerre wavelets", Proc. IEEE
Workshop on Genomic Signal Processing and Statistics (GENSIPS),
The Johns Hopkins University, Baltimore, Maryland, USA, May 26-28,
2004. (pdf)
- M. Rice,
R. Golledge, D. Jacobson, D. Jones, S. Pallavaram, “Axis
Scalling and Symbolization Issues for Haptic Maps", the 100th
AAG Annual Meeting, Philadelphia, PA, USA, 14-19 March 2004 [abstract
(pdf)].
- M. Rice,
R. Golledge, D. Jacobson, D. Jones, S. Pallavaram, “Evaluating
Shapes Via a Non-Visual Computer Interface”, the 100th AAG Annual
Meeting, Philadelphia, PA, USA, 14-19 March 2004[abstract
(pdf)].
- M. Rice,
D. Jacobson, R.G. Golledge, D. Jones, S. Pallavaram , "Object
Size Discrimination and Non-visual Cartographic Symbolization",
in Web Proceedings, American Congress of Surveying and Mapping
2003 Annual Conference, Phoenix, Arizona, USA, Mar 30–Apr 02,
2003, http://www.acsm.net [full
paper (pdf)]
- D. Jacobson,
M. Rice, R.G. Golledge, D. Jones, P. Hayward, S. Pallavaram,
"Cartographic Symbolization Issues for Haptic and Auditory Map
Interfaces", Association of American Geographers (AAG) 99th Annual
Conference, New Orleans, Louisiana, USA, March 5-8, 2003
- Srivatsan
PS, Anusha SR, “A novel technique for dynamically stopping
iterations in turbo decoding”, National Level Symposium (APOGEE
02), Birla Institute of Technology & Science, Pilani, India,
2002
- Senthilnathan
T, Srivatsan PS, Anusha SR, Bhaskaran A, Rajan RD, “Analysis
of ambient air pollutants in Chennai during the year 2000”, Proc
National Conf Pollution Prevn. & Control, Nagpur, India, 2002
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| Good Bibilography |
DNA Sequence
Analysis
- D. Anastassiou,
“Genomic Signal Processing”, IEEE Signal Processing Magazine,
pp 8-20, July 2001.
- P. Bernaola-Galvan,
I. Grosse, P. Carpena, J.L. Oliver, R. Roman-Roland, H.E. Stanley,
“Finding borders between coding and noncoding DNA regions by an
entropic segmentation method”, Physical Review E, vol. 85(6),
pp 1342-1345, 2000.
- Daniel Nicorici,
John A. Berger, Jakko Astola, Sanjit K Mitra, “Finding borders
between coding and noncoding DNA regions using recursive segmentation
and statistics of stop codons”, Finnish Signal Processing Symposium
(FINSIG'03), Tampere, Finland, pp. 231-235, May 19, 2003.
- Gene bank:
http://www.ncbi.nih.gov/
- Bayesian
network toolbox: http://www.ai.mit.edu/~murphyk/Software/BNT/bnt.html#features
I.T. Jolliffe. Principal Component Analysis. Springer-Verlag,
1986.
- Qicheng Ma,
Jason T. L. Wang and Cathy H. Wu ,"Application of Bayesian Neural
Networks to Biological Data Mining: A Case Study in DNA Sequence
Classification," Proceedings of the Twelfth International Conference
on Software
- Y. Wang,
C-T Zhang and P. Dong. “Recognizing Shorter Coding Regions of
Human Genes Based on the Statistics of Stop Codons”, Biopolymers,
Vol. 63, 207-216, 2002
- M. Yan, Z-S.
Lin and C-T. Zhang. “A new Fourier transform approach for protein
coding measure based on the format of the Z curve”, Bioinformatics,
Vol. 14, no. 8, 685-690, 1998
C-T. Zhang, J. Wang. Nucleic Acids Res 2000, 28, 2804-2814
- Distribution
of base pair repeats in coding and noncoding DNA sequences, N.V.
Dakholyan et al, Physical Review Letters, Vol. 79, no. 25, Dec
’97
- Computing
Linear Transforms of Symbolic Signals, Wang and Johnson
cDNA Microarray
Image Processing
- Microarray
image processing based on clustering and morphological analysis,
Wu & Yan
- Quality control
in Microarray image analysis, Kuklin et al
- Robust Microarray
image analysis, Katzer et al
- Image metrics
in the statistical analysis of DNA Microarray data, Brown et al
- A markov
random field model of Microarray gridding. Katzer et al
- A novel method
using edge detection for signal extraction from cDNA Microarray
image analysis, Kim et al
- Fully automatic
quantification of Microarray image data, Jain et al
- Dapple: Improved
techniques for finding spots on DNA microarrays UW CSE Technical
Report
- Microarray
Image Processing based on clustering and morphological analysis,
Wu & Yan
- Robust adaptive
spot segmentation of DNA microarray images, Liew, yan & Yang
- An adaptive
logical method for binarization of degraded document images, Yang
& Yan
- Ratio based
decisions and the quantitative analysis of cDNA microarray images,
Chen et al
Good
Image Processing Lectures
Good
Video Processing and Compression Lectures
WAVELAB
A good image processing bibiliography
Good image processing projects
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