List of Publications:

Books:

Winters-Hilt S. Machine-Learning based sequence analysis, bioinformatics & nanopore transduction detection. ISBN: 978-1-257-64525-1.

Refereed/Invited Publications:

Winters-Hilt S. Event transduction analysis of individual DNA interactions with transcription-factor and HIV integrase. Book Chapter in AIDS / Book 4, 2011. ISBN 978-953-307-686-7.

Winters-Hilt, S. Single nucleotide polymorphism detection via cheminformatics analysis of nanopore-blockades engineered for event transduction. Proceedings of the 3rd International Conference on Bioinformatics and Computational Biology (BICoB), March 23 - 25, 2011.

Winters-Hilt, S. Classification and Clustering using Generalized Support Vector Machines and Tuning Metaheuristics. Submitted to Advances in Artificial Intelligence, 2011.

Winters-Hilt, S. , J. Morrison, and J. Chao. Ad Hoc Signal Acquisition and Stochastic Carrier-Wave Signal Processing via FSAs, generalized HMMs, and generalized SVMs. Submitted to BMC Bioinformatics, 2011.

Winters-Hilt, S. , E. Morales, and E. Horton-Chao. The NTD Nanoscope Kit. Submitted to BMC Bioinformatics, 2011.

Winters-Hilt, S. , E. Horton-Chao, and E. Morales. The NTD Nanoscope. Submitted to BMC Bioinformatics, 2011.

Winters-Hilt, S. , J. Chao, and J. Morrison. Web Access Portals to the Stochastic Sequential Analysis Protocol and Methods. Submitted to BMC Bioinformatics, 2011.

Winters-Hilt, S. and C. Baribault. A Meta-state HMM with application to gene structure identification in eukaryotes. EURASIP Journal of Advances in Signal Processing, Special Issue on Genomic Signal Processing, 2010.

Winters-Hilt, S., Jiang, Z., and C. Baribault. Hidden Markov model with duration side-information for novel HMMD derivation, with application to eukaryotic gene finding. EURASIP Journal of Advances in Signal Processing, Special Issue on Genomic Signal Processing, 2010.

Eren AM, Amin I, Alba A, Morales E, Stoyanov A, and Winters-Hilt S. Pattern Recognition Informed Feedback for Nanopore Detector Cheminformatics. Accepted paper in book “Advances in Computational Biology”, to be published by Springer in Advances in Experimental Medicine and Biology, AEMB 2010 book series.

Winters-Hilt S and Jiang Z. A hidden Markov model with binned duration algorithm. IEEE Trans. on Sig. Proc., Vol. 58 (2), Feb. 2010.

Winters-Hilt S. Nanopore Cheminformatics based Studies of Individual Molecular Interactions. Ch. 19 in Yanqing Zhang and Jagath C. Rajapakse, editors, Machine Learning in Bioinformatics, John Wiley & Sons, 2009.

Alexander Churbanov, Stephen Winters-Hilt, Eugene V Koonin and Igor B Rogozin. Accumulation of GC donor splice signals in mammals. Biology Direct 2008, 3:30.

Churbanov, Alexander and S. Winters-Hilt. Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory. BMC Bioinformatics 2008, 9:228.

Churbanov A and Winters-Hilt S. Clustering ionic flow blockade toggles with a Mixture of HMMs. BMC Bioinf. 9 S9, S13 (2008).

Roux B and Winters-Hilt S. Hybrid SVM/MM Structural Sensors for Stochastic Sequential Data. BMC Bioinf. 9 S9, S12 (2008).

Winters-Hilt S. The alpha-Hemolysin Nanopore Transduction Detector -- single-molecule binding studies and immunological screening of antibodies and aptamers. BMC Bioinf. 8 S7, S9 (2007).

Thomson K, Amin I, Morales E, and Winters-Hilt S. Preliminary Nanopore Cheminformatics Analysis of Aptamer-Target Binding Strength. BMC Bioinf. 8 S7, S11 (2007).

Winters-Hilt S., Davis, A, Amin, I, and Morales E. Nanopore current transduction analysis of protein binding to non-terminal and terminal DNA regions: analysis of transcription factor binding, retroviral DNA terminus dynamics, and retroviral integrase-DNA binding. BMC Bioinf. 8 S7, S10 (2007).

Winters-Hilt S, Morales E, Amin, I., and Stoyanov, A. Nanopore-based kinetics analysis of individual antibody-channel and antibody-antigen interactions. BMC Bioinf. 8 S7, S20 (2007).

Winters-Hilt S and Merat S. SVM Clustering. BMC Bioinf. 8 S7, S18 (2007).

Churbanov A, Baribault C, Winters-Hilt S. Duration learning for nanopore ionic flow blockade analysis. BMC Bioinf. 8 S7, S14 (2007).

Landry M, Winters-Hilt S. Analysis of nanopore detector measurements using machine learning methods, with application to single-molecule kinetic analysis. BMC Bioinf. 8 S7, S12 (2007).

Winters-Hilt, S and C Baribault. A novel, fast, HMM-with-Duration implementation - for application with a new, pattern recognition informed, nanopore detector. BMC Bioinf. 8 S7, S19 (2007).

Winters-Hilt, S., Landry M, Akeson M, Tanase M, Amin I, Coombs A, Morales E, Millet J, Baribault C, and Sendamangalam S. Cheminformatics Methods for Novel Nanopore analysis of HIV DNA termini. BMC Bioinformatics 2006, Sept. 26, 7 S2: S22.

Winters-Hilt, S: Nanopore Detector based analysis of single-molecule conformational kinetics and binding interactions. BMC Bioinformatics 2006, Sept. 26, 7 S2: S21.

Winters-Hilt S, Yelundur A, McChesney C, Landry M: Support Vector Machine Implementations for Classification & Clustering. BMC Bioinformatics 2006, Sept. 26, 7 S2: S4.

Iqbal R, Landry M, Winters-Hilt S: DNA Molecule Classification Using Feature Primitives. BMC Bioinformatics 2006, Sept. 26, 7 S2: S15.

Winters-Hilt S: Hidden Markov Model Variants and their Application. BMC Bioinformatics 2006, 7 S2: S14.

Deamer, David W. and S. Winters-Hilt, Nanopore analysis of DNA.” Encyclopedia of Nanoscience and Nanotechnology, Ed. H. S. Nalwa. 2005. Vol. 7, pgs 229-235.

Winters-Hilt, S., Single-molecule Biochemical Analysis Using Channel Current Cheminformatics, Fourth International Conference on Unsolved Problems of Noise and Fluctuations, June 6–10, 2005.

Winters-Hilt, S. and M. Akeson, "Nanopore cheminformatics," DNA and Cell Biology, Vol. 23 (10), Oct. 2004.

Winters-Hilt, S., "Nanopore detection using channel current cheminformatics," SPIE Second International Symposium on Fluctuations and Noise, 25-28 May, 2004.

Winters-Hilt S, "Highly Accurate Real-Time Classification of Channel-Captured DNA Termini," Third International Conference on Unsolved Problems of Noise and Fluctuations, 2003.

S. Winters-Hilt, W. Vercoutere, V. S. DeGuzman, D. Deamer, M. Akeson, and D. Haussler, "Highly Accurate Classification of Watson-Crick Base-Pairs on Termini of Single DNA Molecules," Biophys. J. Vol. 84, pg 967, 2003.

W. Vercoutere, S. Winters-Hilt, V. S. DeGuzman, D. Deamer, S. Ridino, J. T. Rogers, H. E. Olsen, A. Marziali, and M. Akeson, "Discrimination Among Individual Watson-Crick Base-Pairs at the Termini of Single DNA Hairpin Molecules," Nucl. Acids Res. Vol.31, 1311-1318, 2003.

W. Vercoutere, S. Winters-Hilt, H. Olsen, D. Deamer, D. Haussler, and M. Akeson, "Rapid Discrimination Among Individual DNA Molecules at Single Nucleotide Resolution Using an Ion Channel," Nature Biotechnology, Vol. 19, pg 248, 2001.

Winters-Hilt S, I. H. Redmount, and L. Parker, "Physical distinction among alternative vacuum states in flat spacetime geometries," Phys. Rev. D 60, 124017 (1999).

Friedman J. L., J. Louko, and S. Winters-Hilt, "Reduced Phase space formalism for spherically symmetric geometry with a massive dust shell," Phys. Rev. D 56, 7674-7691 (1997).

Louko J, J. Z. Simon, and S. Winters-Hilt, "Hamiltonian thermodynamics of a Lovelock black hole," Phys. Rev. D 55, 3525-3535 (1997).

Louko J and S. Winters-Hilt, "Hamiltonian thermodynamics of the Reissner-Nordstrom-anti de Sitter black hole," Phys. Rev. D 54, 2647-2663 (1996).

Manuscripts in-process:

Books:

Winters-Hilt, S. Thermal Quantum Gravity.

Papers:

Winters-Hilt, S et al. Nanopore Cheminformatics Analysis of Single Antibody-Antigen Binding. Work in progress.

Winters-Hilt, S et al. Analysis of HIV integrase binding to viral DNA using Nanopore-based Channel Current. Work in progress.

Winters-Hilt, S et al. Nanopore cheminformatics analysis of DNA aptamer interactions. Work in progress.

Winters-Hilt, S et al. Boot-strap prokaryotic gene structure identification. Paper in preparation for submission to BMC Bioinf.

Winters-Hilt S et al. Alternative-Splice Gene Prediction by use of Generalized Hidden Markov Models and Support Vector Machines. Work in progress.

Winters-Hilt S et al. SVM Kernel selection and tuning using genetic algorithms. Work in progress.

Winters-Hilt S et al. Hidden Markov models for stochastic sequential analysis and stochastic carrier-wave signal processing.