T. Gedeon, A. Parker, and A. Dimitrov.
The mathematical structure of Information Bottleneck methods. Entropy
(in review).
J. L. Faulwetter, M. D. Burr, A. E. Parker, O. R. Stein, A. K.
Camper. The influence of sulfate reducing bacteria and ammonia oxidizing
bacteria on nutrient cycling in constructed wetland microcosms.
Microbial Ecology. (in review)
A. Parker and C. Fox. Sampling Gaussian Distributions in Krylov
Spaces with Conjugate Directions.
SIAM
Journal on Scientific Computing (in review).
J. M. Bardsley, A. Solonen, A. Parker, H. Haario, and M.
Howard. An ensemble Kalman filter using the conjugate gradient sampler.
International Journal of Uncertainty Quantification (to appear):
pdf
A. Agostinho, A. Hartman, C. Lipp, A. Parker, P. Stewart, G. James. An in vitro model for the growth and analysis of chronic
wound MRSA biofilms. Journal
of Applied Microbiology, 111,
1275-1282, 2011: pdf
Sabrina Behnke, Albert Parker, Dawn Woodall, and Anne Camper.
Comparing the chlorine disinfection of detached biofilm clusters with
sessile biofilms and planktonic cells in single and dual species cultures.
Applied and Environmental Microbiology, 77(20): 7176-7184, 2011.
A. Corbin, B. Pitts, A. Parker and P. Stewart. Antimicrobial
Penetration and Effcacy in an In-Vitro
Oral Biofilm Model. Antimicrobial Agents and Chemotherapy, 55: 3338 - 3344,
July 2011. July 2011.
A. E. Parker and M. A. Hamilton.
Assessing Resemblance, Repeatability and Reproducibility for quantitative
methods. Center
for Biofilm Engineering, KSA-SM-10,
2011.
D. L. Williams, K. L. Woodbury, A. E. Parker, R. D. Bloebaum. A
Modified CDC Biofilm Reactor to Produce Mature Biofilms on the Surface of
PEEK Membranes for an In Vivo Animal Model Application. Current Microbiology, 62(6): 1657-1663, 2011.
M. A. Hamilton and A. E. Parker.
Enumerating viable cells by pooling counts for several dilutions. Center
for Biofilm Engineering, KSA-SM-06, October 2010.
J. P. Folsom, L. Richards, B. Pitts, F. Roe, G. D.
Ehrlich, A. Mazurie, A. Parker, and P. S. Stewart. Physiology
of Pseudomonas aeruginosa in Biofilms as Revealed by
Transcriptional
Profiling. BMC
Microbiology, 10:294, 2010.
T. Gedeon, A. Parker, C. Campion, and Z. Aldworth. "Annealing and
the normalized N-cut."
Pattern Recognition, 41(2):592-606. February 2008:
pdf.
C. Vogel, D. Arathorn, A. Roorda, and A. Parker. "Retinal motion
estimation and image
dewarping in adaptive optics scanning
laser ophthalmoscopy." Optics
Express, vol 14,
pp. 487-497.
January, 2006:
pdf
C. Vogel, D. Arathorn, A. Parker, and A. Roorda, "Retinal Motion
Tracking
in Adaptive Optics Scanning Laser Ophthalmoscopy," in Adaptive Optics:
Analysis and Methods/Computational Optical Sensing and Imaging/Information
Photonics/Signal Recovery and Synthesis Topical Meetings on CD-ROM,
Technical Digest (Optical Society of America, 2005), paper JTuC2.
A. Dimitrov, T. Gedeon, B. Mumey, R. Snider, A. E. Parker, and J.
P. Miller. Derivation of natural
stimulus feature set using a data-driven model. In P. M. A. Sloot, D.
Abramson, A. V. Bogdanov,
J. Dongarra, A. Y. Zomaya, and Y. E. Gorbachev, editors,
International
Conference on Computational
Science, volume 2660 of Lecture Notes in Computer
Science,
pages 337.345.
Springer, August 2003:
pdf
Albert E. Parker. "Symmetry Breaking Bifurcations of the
Information Distortion." Ph.D. Thesis. Montana State
University-Bozeman. May 2003.
(double spaced for one sided printing):
pdf (1.6MB);
(singlespaced for two sided
printing): pdf (1.6MB).
Tomas Gedeon, Albert E. Parker and Alexander G. Dimitrov.
"Information Distortion and Neural Coding". Canadian
Applied
Mathematics Quarterly, volume 10, number 1, pp 33-70. Spring,
2003:
pdf or ps
A. G. Dimitrov, J.P. Miller, Z. Aldsworth, T. Gedeon and
A. E. Parker. "Analysis of neural coding through quantization with an
information-based distortion measure."
Network: Computation in Neural Systems, vol 14,
pp 151-176, February 2003: pdf
A. G. Dimitrov, J.P. Miller, Z. Aldsworth, and A. Parker. "Spike
pattern-based coding schemes in the cricket cercal sensory system."
Neurocomputing,
44-46, 373–379, 2002: ps
S. Kubiak, H. Lehr, R. Levy, T. Moeller, A. Parker, and E. Swim.
"Modeling Control of HIV Infection through Structured Treatment
Interruptions with Recommendations for Experimental Protocol."
Report 5 in Pierre A. Gremaud, Zhilin Li, Ralph C. Smith, and Hien T.
Tran,
editors, Center for
Research in Scientific Computing at North
Carolina State University Technical Report, CRSC-TR01-27.
November
2001: pdf or ps
"Polynomial Accelerated Iterative Sampling of Normal Distributions"
SIAM's 7th International Congress
on Industrial and Applied Mathematics, Statistics, Computations,
and Inverse Problems Symposium. Vancouver, BC, Canada, July 19,
2011.
"Using equivalence testing in microbiology
at the Biofilm Science & Technology Meeting,
MSU-Bozeman, July, 2011: ppt
"Differences in Bacterial Transfer and Fluid Path Colonization
through Needle-free Connector-Catheter
Systems In Vitro." Ryder, M., James, G., Pulcini, E. Bickle, L., Pesch,
M., Parker, A. The Society
for Healthcare and Epidemiology of America, Poster Session at the Annual
Scienti¯c Meeting.
Dallas. April 1-4, 2011.
"Drawing samples from high dimensional Gaussians using
polynomials" at the American Statistical Association Montana Chapter
meeting, Bozeman, MT. September 14, 2010.
"A Modified CDC Biofilm Reactor to Produce Mature Biofilms on the
Surface of PEEK Membranes for
an In Vivo Animal Model Application. Williams, D.L., Woodbury, K.L.,
Parker, A.E., and
Bloebaum, R.D. Poster Session at the Montana Biofilm Meeting, MSU-Bozeman,
July 2010.
"Statistically assessing
limits of detection and performance standards"
at the Biofilm Science & Technology Meeting,
MSU-Bozeman, July, 2010: ppt
"Importance of Statistical Design and Analysis" at
the Biofilm Science & Technology Meeting Workshop, MSU-Bozeman, July,
2010: ppt.
"A Modified CDC Biofilm Reactor to Produce Mature Biofilms on the
Surface of PEEK Membranes for
an In Vivo Animal Model Application. Williams, D.L., Woodbury, K.L.,
Parker, A.E., and
Bloebaum, R.D. Poster Session at the 110th Am. Soc. Microbiol. Gen. Meet.
2820. May, 2010.
"Accelerating Gibbs sampling using matrix decompositions."
Workshop on Statistical Inference and Partial Differential Equations
(SIPE). New Zealand Institute of Mathematics.
University of Otago, Dunedin, New Zealand. January 18, 2010
"Ruggedness assessment and experimental design in
the biofilm laboratory." Biological and Economic
Analysis Division (BEAD) and Antimicrobials Division (AD) of the EPA, Fort
Meade, Maryland, December 2-3, 2009.
"Ruggedness Assessment and Experimental Design in the Biofilm
Laboratory." 5th American Society for Microbiology Conference on
Biofilms. Standardized Biofilm Methods Workshop. Cancun, Mexico.
November 15, 2009.
"Using linear solvers to sample large Gaussians" at the Applied
Math
Seminar, MSU-Bozeman, October 29, 2009: pptx
"Accelerated Gibbs sampling from multivariate normal distributions"
at the
Department of
Mathematical Sciences Colloquim at the University
of Montana, Missoula. October 19, 2009.
"Some Statistical considerations in molecular methods" at the
Biofilm
Science & Technology Meeting, MSU-Bozeman, July 9, 2009: ppt.
"Ruggedness Assessment and Experimental Design in the Biofilm
Laboratory" at the Biofilm Science & Technology Meeting Workshop,
MSU-Bozeman, July 6, 2009: ppt
"Statistical thinking in antibiofilm research" with
Cord and Marty at the Medical
Biofilm Lab and then the
Standardized Biofilm Methods Lab, Montana State University. October 22, 2008: ppt
"CG optimizers, Lanczos Eigensolvers, and sampling"
Electronics
Lab Meeting. University
of Otago, Dunedin. March 13, 2008.
"Exact versus Lanczos Eigensolvers"
Electronics
Lab Meeting. University
of Otago, Dunedin. February 28, 2008.
"Gaussian Processes" Electronics
Lab Meeting. University
of Otago, Dunedin. October 5, 2007.
"Eye Motion Estimation and
Image Dewarping using a
Map Seeking Circuit"
Center for Adaptive Optics Spring Retreat, Image Processing
Workshop. UC Santa Cruz. March 30, 2006: pdf
"Symmetry Breaking when deciphering the neural code," Department of
Mathematical Sciences Colloquim at the University
of Montana, Missoula. September 12, 2005: ppt
"Dewarping Images from a Scanning Laser Ophthalmoscope"
Center for Adaptive Optics, SLO image processing meeting. UC
Berkeley, April 19, 2005: ppt
"Tracking Eye Motion from Retinal Scan Data with a Map Seeking
Circuit" Center for Adaptive Optics Fall Retreat, Controlling Eye
Movements Session. UCLA Conference Center, Lake Arrowhead, CA.
November 13, 2004: pdf
"Your Brain, Crickets, and Math" Longfellow Elementary School.
Bozeman, MT. May, 2004.
"Phase Transitions in the Information Distortion" Neural Information
Processing Systems 2003 workshop on
Information Theory and Learning:
The Bottleneck and Distortion Approach. Whistler, BC, Canada. December 13,
2003: ppt.
"Modelling and Control Issues Arising in the Quest for a
Neural Decoder"
Computation, Control, and
Biological Systems Conference VIII.
MSU-Bozeman. July 30, 2003: ppt
"A Bifurcation Theoretical Approach to Solving the Neural Coding
Problem" IGERT Symposium. Carnegie Mellon University, Pittsburgh,
PA. June 28, 2003: ppt
"Symmetry Breaking Bifurcations of the Information Distortion"
Dissertation Defense, Bozeman, MT. April 8, 2003: ppt
"Annealing and the Rate Distortion Problem" NIPS, Poster
Session. Vancouver, Canada. December 11, 2002: ppt
"Symmetry Breaking Bifurcation of the Distortion Problem"
American Mathematical Society Sectional Meeting. University of
Wisonsin, Madison, WI.
October 13, 2002: ppt
"Coninuation and Bifurcation of the Distortion Problem"
American Mathematical Society Sectional Meeting, Poster Session.
University of Wisonsin, Madison, WI.
October 13, 2002: ppt
"Continuation and Symmetry Breaking Bifurcation of the Information
Distortion Function" Applied Mathematics Seminar, MSU-Bozeman.
September 19, 2002: ppt
"Gottfried Leibniz, Carl Gauss and Neural Coding" Bozeman High School.
Bozeman, MT. May 9, 2002:ppt
"Information Distortion and Neural Coding" First SIAM
Conference on the Life Sciences, Poster Session. Boston, MA. March
7, 2002: ppt
"Recognition" Journal Club, Center for Computational Biology, MSU-Bozeman.
February 26, 2002: ppt
"Functional Magnetic Resonance". Journal Club, Center for
Computational Biology, MSU-Bozeman. February 20, 2002:ppt
"Neural Coding Through the Ages". Complex Biological Systems
Seminar, MSU-Bozeman. February 1, 2002: ppt
"Approaches to Discovering Neural Coding Schemes" Applied
Mathematics Seminar, MSU-Bozeman. January 31, 2002: ppt
"PhD Oral Examination: Information Theory and Neural Coding"
Applied Mathematics Seminar, MSU-Bozeman. November 29, 2001:
ppt
"A Probability Model for
Neural Coding" Meeting of the Montana
Chapter of the American Statistical
Association. Montana Tech, Butte, MT. October 23, 2001. ppt
"Devising an Experimental Protocol for Controlling HIV Infection
through Structured Treatment Interruptions." S. Kubiak, H. Lehr, R.
Levy, T. Moeller, A. Parker, and E. Swim.
Applied Mathematics
Seminar, MSU-Bozeman. October 11,2001: pdf
and ps
"My Research: Neural Coding and Decoding" Complex Biological
Systems Retreat. Bridger Ski Resort. September, 2001: ppt
"Modeling Control of HIV Infection through Structured
Treatment Interruptions"
Industrial Mathematical Modeling Workshop. North
Carolina State University, Raleigh, NC. August, 2001: three seperate
files, all in ps: slides, more
slides and more slides.
"Computational Issues when Modelling Neural Coding Schemes"
Meeting of Montana NSF EPSCoR
Project Participants. Northern Rockies Center for Applied
Computational Science. MSU-Bozeman. July 9, 2001: ppt
"Probability Theory and Neural Coding" Final
Project for Probability Theory: MATH586. MSU-Bozeman. May 4, 2001: pdf or ps
"Functionalism" Journal Club, Center for Computational Biology,
MSU-Bozeman. May 3, 2001: ppt
"The Fundamentals of Neural Coding and Decoding" Montana Academy
of the Sciences.
MSU-Bozeman. April, 2001: ppt
"Large Scale Optimization Techniques for Alex's Neural Coding and
Decoding Model" Center for Computational Biology. MSU-Bozeman.
February 27, 2001: pdf or ps
