Mathematical methods for artificial intelligence and autonomous systems. - Edward R. Dougherty; Charles R. Giardina (Prentice Hall, 1988)

Closed-form representation of convolution, dilation, and erosion in the context of image algebra. - Edward R. Dougherty; Charles R. Giardina (CVPR, 1988)

A robust image processing language in the context of image algebra. - Edward R. Dougherty; Paramjit S. Sehdev (CVPR, 1988)

Morphology on umbra Matrices. - Edward R. Dougherty; Charles R. Giardina (Int. J. Pattern Recognit. Artif. Intell., 1988)

The dual representation of gray-scale morphological filters. - Edward R. Dougherty (CVPR, 1989)

Hausdorf-metric interpretation of convergence in the Matheron topology for binary mathematical morphology. - Edward R. Dougherty (ICPR (1), 1990)

Minimal search for the optimal mean-square digital gray-scale morphological filter. - Edward R. Dougherty (VCIP, 1990)

Application of the Hausdorff metric in gray-scale mathematical morphology via truncated umbrae. - Edward R. Dougherty (J. Vis. Commun. Image Represent., 1991)

The use of first-order structuring-element libraries to design morphological filters. - Robert P. Loce; Edward R. Dougherty (ICPR (3), 1992)

Optimal mean-square N-observation digital morphological filters : I. Optimal binary filters. - Edward R. Dougherty (CVGIP Image Underst., 1992)

Optimal mean-square N-observation digital morphological filters : II. Optimal gray-scale filters. - Edward R. Dougherty (CVGIP Image Underst., 1992)

Robust Morphologically Continuous Fourier Descriptors I: Projection-Generated Descriptors. - Edward R. Dougherty; Robert P. Loce (Int. J. Pattern Recognit. Artif. Intell., 1992)

Robust Morphologically Continuous Fourier Descriptors II: Continuity and Occlusion Analysis. - Edward R. Dougherty; Robert P. Loce (Int. J. Pattern Recognit. Artif. Intell., 1992)

Morphological image segmentation by local granulometric size distributions. - Edward R. Dougherty; Jeff B. Pelz; Francis Sand; Arnold Lent (J. Electronic Imaging, 1992)

Euclidean gray-scale granulometries: Representation and umbra inducement. - Edward R. Dougherty (J. Math. Imaging Vis., 1992)

Unification of nonlinear filtering in the context of binary logical calculus, part II: Gray-scale filters. - Edward R. Dougherty (J. Math. Imaging Vis., 1992)

Hole-spectrum representation and model-based optimal morphological restoration of binary images degraded by subtractive noise. - Edward R. Dougherty; Robert M. Haralick (J. Math. Imaging Vis., 1992)

Unification of nonlinear filtering in the context of binary logical calculus, part I: Binary filters. - Edward R. Dougherty; Robert M. Haralick (J. Math. Imaging Vis., 1992)

Statistics of the morphological pattern-spectrum moments for a random-grain model. - Francis Sand; Edward R. Dougherty (J. Math. Imaging Vis., 1992)

Model-based characterization of statistically optimal design for morphological shape recognition algorithms via the hit-or-miss transform. - Edward R. Dougherty; Dongming Zhao 001 (J. Vis. Commun. Image Represent., 1992)

Optimal morphological restoration: The morphological filter mean-absolute-error theorem. - Robert P. Loce; Edward R. Dougherty (J. Vis. Commun. Image Represent., 1992)

Asymptotic normality of the morphological pattern-spectrum moments and orthogonal granulometric generators. - Francis Sand; Edward R. Dougherty (J. Vis. Commun. Image Represent., 1992)

Preface. - Jean Serra; Edward R. Dougherty (J. Vis. Commun. Image Represent., 1992)

Fuzzy mathematical morphology. - Divyendu Sinha; Edward R. Dougherty (J. Vis. Commun. Image Represent., 1992)

Morphological texture-based maximum-likelihood pixel classification based on local granulometric moments. - Edward R. Dougherty; John T. Newell; Jeff B. Pelz (Pattern Recognit., 1992)

Estimation of optimal morphological τ-opening parameters based on independent observation of signal and noise pattern spectra. - Edward R. Dougherty; Robert M. Haralick; Yidong Chen 002; Carsten Agerskov; Ulrik Jacobi; Poul Henrik Sloth (Signal Process., 1992)

Computational morphology and representation of operators between complete lattices. - Clara Cuciurean-Zapan; Edward R. Dougherty (VCIP, 1993)

Model-based algorithm for designing suboptimal morphological filters for restoring subtractive-noise-corrupted images. - Ian R. Joughin; Robert M. Haralick; Edward R. Dougherty (J. Electronic Imaging, 1993)

Linear granulometric moments of noisy binary images. - Bruno Bettoli; Edward R. Dougherty (J. Math. Imaging Vis., 1993)

Gray-scale granulometries compatible with spatial scalings. - Eugene J. Kraus; Henk J. A. M. Heijmans; Edward R. Dougherty (Signal Process., 1993)

Optimal nonlinear fax restoration. - John C. Handley; Edward R. Dougherty (Document Recognition, 1994)

Segmentation-free morphological character recognition. - Eugene J. Kraus; Edward R. Dougherty (Document Recognition, 1994)

Adaptive Parameterized Openings. - Yidong Chen 002; Edward R. Dougherty (ISMM, 1994)

Model-based optimal restoration of fax images in the context of mathematical morphology. - John C. Handley; Edward R. Dougherty (J. Electronic Imaging, 1994)

Optimal mean-absolute-error filtering of gray-scale signals by the morphological hit-or-miss transform. - Edward R. Dougherty (J. Math. Imaging Vis., 1994)

Minimal representation of -openings via pattern bases. - Edward R. Dougherty (Pattern Recognit. Lett., 1994)

Precision of morphological-representation estimators for translation-invariant binary filters: Increasing and nonincreasing. - Edward R. Dougherty; Robert P. Loce (Signal Process., 1994)

Computational mathematical morphology. - Edward R. Dougherty; Divyendu Sinha (Signal Process., 1994)

Design and application of binary differencing filters. - Robert P. Loce; Edward R. Dougherty (Document Recognition, 1995)

Multivariate morphological granulometric texture classification using Walsh and wavelet features. - Sinan Batman; Edward R. Dougherty; Mark C. Rzadca; Joseph O. Chapa (Visual Information Processing, 1995)

Filtering clutter by optimal granulometric bandpass filters. - Edward R. Dougherty (Visual Information Processing, 1995)

Representation of Linear Granulometric Moments for Deterministic and Random Binary Euclidean Images. - Edward R. Dougherty; Francis Sand (J. Vis. Commun. Image Represent., 1995)

Morphological pattern-spectrum classification of noisy shapes: Exterior granulometries. - Edward R. Dougherty; Yingchong Cheng (Pattern Recognit., 1995)

Computational Gray-scale Mathematical Morphology on Lattices (A Comparator-based Image Algebra) Part 1: Architecture. - Edward R. Dougherty; Divyendu Sinha (Real Time Imaging, 1995)

Computational Gray-scale Mathematical Morphology on Lattices (A Comparator-based Image Algebra) Part II: Image Operators. - Edward R. Dougherty; Divyendu Sinha (Real Time Imaging, 1995)

Recursive maximum-likelihood estimation in the one-dimensional discrete Boolean random set model. - Edward R. Dougherty; John C. Handley (Signal Process., 1995)

A general axiomatic theory of intrinsically fuzzy mathematical morphologies. - Divyendu Sinha; Edward R. Dougherty (IEEE Trans. Fuzzy Syst., 1995)

Granulometric estimation of distorted shapes. - Sinan Batman; Edward R. Dougherty (Electronic Imaging: Nonlinear Image Processing, 1996)

Maximum-likelihood estimation for the two-dimensional discrete Boolean model using cross-windowed observations. - John C. Handley; Edward R. Dougherty (Electronic Imaging: Nonlinear Image Processing, 1996)

Optimal and Adaptive Design of Reconstructive Granulometric Filters. - Edward R. Dougherty; Yidong Chen 002 (ISMM, 1996)

Optimal restoration of compressed biomedical images: a discrete lattice theoretic approach. - Vivek Swarnakar; Athimootil V. Mathew; Edward R. Dougherty; Claudio H. Sibata (Image Processing, 1996)

Morphological paradigm for loss-function-based design of digital filters. - Edward R. Dougherty; Junior Barrera (Visual Information Processing, 1996)

Adaptive reconstructive tau-openings: convergence and the steady-state distribution. - Yidong Chen 002; Edward R. Dougherty (J. Electronic Imaging, 1996)

Optimal binary differencing filters: design, logic complexity, precision analysis, and application to digital document processing. - Edward R. Dougherty; Robert P. Loce (J. Electronic Imaging, 1996)

Existence and synthesis of minimal-basis morphological solutions for a restoration-based boundary-value problem. - Edward R. Dougherty (J. Math. Imaging Vis., 1996)

Bayesian morphological peak estimation and its application to chromosome counting via fluorescence In situ hybridization. - Edward R. Dougherty; Yidong Chen 002; Amir Waks (Pattern Recognit., 1996)

Optimal nonlinear filter for signal-union-noise and runlength analysis in the directional one-dimensional discrete Boolean random set model. - John C. Handley; Edward R. Dougherty (Signal Process., 1996)

Document restoration and enhancement using optimal iterative and paired morphological filters. - Yeqing (Juliet) Zhang; Robert P. Loce; Edward R. Dougherty (Document Recognition, 1997)

Maximum-Likelihood Estimation for the Two-Dimensional Discrete Boolean Random Set and Function Models Using Multidimensional Linear Samples. - John C. Handley; Edward R. Dougherty (CVGIP Graph. Model. Image Process., 1997)

Automatic programming of binary morphological machines by design of statistically optimal operators in the context of computational learning theory. - Junior Barrera; Edward R. Dougherty; Nina Sumiko Tomita (J. Electronic Imaging, 1997)

Editorial. - Edward R. Dougherty (J. Electronic Imaging, 1997)

Optimal Binary Morphological Bandpass Filters Induced by Granulometric Spectral Representation. - Edward R. Dougherty (J. Math. Imaging Vis., 1997)

Logically Efficient Spatial Resolution Conversion Using Paired Increasing Operators. - Robert P. Loce; Edward R. Dougherty; Ronald E. Jodoin; Michael S. Cianciosi (Real Time Imaging, 1997)

Optimal and adaptive reconstructive granulometric bandpass filters. - Yidong Chen 002; Edward R. Dougherty (Signal Process., 1997)

Optimal reconstructive τ-openings for disjoint and statistically modeled nondisjoint grains. - Edward R. Dougherty; Clara Cuciurean-Zapan (Signal Process., 1997)

Design and analysis of fuzzy morphological algorithms for image processing. - Divyendu Sinha; Purnendu Sinha; Edward R. Dougherty; Sinan Batman (IEEE Trans. Fuzzy Syst., 1997)

Segmentation of Mammograms into Distinct Morphological Texture Regions. - Sooncheol Baeg; Anthony T. Popov; Vishnu G. Kamat; Sinan Batman; Krishnamoorthy Sivakumar; Nasser Kehtarnavaz; Edward R. Dougherty; Robert B. Shah (CBMS, 1998)

Computation of morphological texture features for medical imaging applications. - Manish J. Patel; Nasser Kehtarnavaz; Edward R. Dougherty; Sinan Batman; Krishnamoorthy Sivakumar; Anthony T. Popov (Image Processing, 1998)

Binary filter estimation for large windows. - Edward R. Dougherty (SIBGRAPI, 1998)

Robustness of optimal binary filters. - Artyom M. Grigoryan; Edward R. Dougherty (J. Electronic Imaging, 1998)

Asymptotic granulometric mixing theorem: Morphological estimation of sizing parameters and mixture proportions. - Francis Sand; Edward R. Dougherty (Pattern Recognit., 1998)

Secondarily constrained Boolean filters. - Octavian V. Sarca; Edward R. Dougherty; Jaakko Astola (Signal Process., 1998)

Random processes for image and signal processing. - Edward R. Dougherty (IEEE, 1999)

Hybrid human-machine binary morphological operator design. - Junior Barrera; Edward R. Dougherty; Marcel Brun (Electronic Imaging: Nonlinear Image Processing, 1999)

Optimal range-domain window filters. - Roberto Hirata; Edward R. Dougherty; Junior Barrera (Electronic Imaging: Nonlinear Image Processing, 1999)

Efficient switching algorithm for designing increasing binary filters. - Nina Sumiko Tomita Hirata; Edward R. Dougherty; Junior Barrera (Electronic Imaging: Nonlinear Image Processing, 1999)

Morphological texture-based classification of abnormalities in mammograms. - Sooncheol Baeg; Nasser Kehtarnavaz; Edward R. Dougherty (Image Processing, 1999)

Nonlinear filters in genomic control. - Edward R. Dougherty; Michael L. Bittner; Yidong Chen 002; Seungchan Kim; Krishnamoorthy Sivakumar; Junior Barrera; Paul S. Meltzer; Jeffrey M. Trent (NSIP, 1999)

The Granulometric Size Density in Filter Optimization. - Edward R. Dougherty (SIBGRAPI, 1999)

Design of Statistically Optimal Stack Filters. - Nina S. T. Hirata; Junior Barrera; Edward R. Dougherty (SIBGRAPI, 1999)

Unsupervised morphological granulometric texture segmentation of digital mammograms. - Sooncheol Baeg; Sinan Batman; Edward R. Dougherty; Vishnu G. Kamat; Nasser Kehtarnavaz; Seungchan Kim; Anthony T. Popov; Krishnamoorthy Sivakumar; Robert B. Shah (J. Electronic Imaging, 1999)

Two-stage binary filters. - Octavian V. Sarca; Edward R. Dougherty; Jaakko Astola (J. Electronic Imaging, 1999)

Markovian Analysis of Adaptive Reconstructive Multiparameter tau-Openings. - Yidong Chen 002; Edward R. Dougherty (J. Math. Imaging Vis., 1999)

Design and Analysis of Robust Binary Filters in the Context of a Prior Distribution for the States of Nature. - Artyom M. Grigoryan; Edward R. Dougherty (J. Math. Imaging Vis., 1999)

Maximum-likelihood estimation and optimal filtering in the nondirectional, one-dimensional binomial germ-grain model. - John C. Handley; Edward R. Dougherty (Pattern Recognit., 1999)

Robustness of granulometric moments. - Francis Sand; Edward R. Dougherty (Pattern Recognit., 1999)

Probability distributions for discrete one-dimensional coverage processes. - John C. Handley; Edward R. Dougherty (Signal Process., 1999)

Multiresolution filter design. - Edward R. Dougherty; Junior Barrera; Gerard Mozelle; Seungchan Kim; Marcel Brun (Electronic Imaging: Nonlinear Image Processing, 2000)

Bayesian multiresolution filter design. - Vishnu G. Kamat; Edward R. Dougherty; Junior Barrera (Electronic Imaging: Nonlinear Image Processing, 2000)

Design of statistically optimal morphological operators. - Junior Barrera; Edward R. Dougherty (EUSIPCO, 2000)

Parametric design of nonlinear optimal filters. - Edward R. Dougherty (EUSIPCO, 2000)

Design of gray-scale nonlinear filters via multiresolution apertures. - Roberto Hirata; Edward R. Dougherty; Junior Barrera (EUSIPCO, 2000)

Fibonacci thresholding, signal representation and morphological filters. - Artyom M. Grigoryan; Sos S. Agaian; Edward R. Dougherty (EUSIPCO, 2000)

Small-sample estimation of the error of the optimal binary filter. - David L. Sabbagh; Edward R. Dougherty (EUSIPCO, 2000)

Boosting OCR Classifier by Optimal Edge Noise Filtering. - Junior Barrera; Marcel Brun; Routo Terada; Edward R. Dougherty (ISMM, 2000)

From the Sup-Decomposition to A Sequential Decomposition. - Ronaldo Fumio Hashimoto; Junior Barrera; Edward R. Dougherty (ISMM, 2000)

Some Applications of Aperture Filters. - Roberto Hirata Jr.; Edward R. Dougherty; Junior Barrera (ISMM, 2000)

Multiresolution Bayesian design of binary filters. - Vishnu G. Kamat; Edward R. Dougherty; Junior Barrera (J. Electronic Imaging, 2000)

Heterogeneous morphological granulometries. - Sinan Batman; Edward R. Dougherty; Francis Sand (Pattern Recognit., 2000)

A switching algorithm for design of optimal increasing binary filters over large windows. - Nina S. T. Hirata; Edward R. Dougherty; Junior Barrera (Pattern Recognit., 2000)

A Constant-time Algorithm for Erosions/Dilations with Applications to Morphological Texture Feature Computation. - Krishnamoorthy Sivakumar; Manish J. Patel; Nasser Kehtarnavaz; Yoganand Balagurunathan; Edward R. Dougherty (Real Time Imaging, 2000)

Hybrid human-machine binary morphological operator design. An independent constraint approach. - Junior Barrera; Edward R. Dougherty; Marcel Brun (Signal Process., 2000)

Coefficient of determination in nonlinear signal processing. - Edward R. Dougherty; Seungchan Kim; Yidong Chen 002 (Signal Process., 2000)

Aperture filters. - Roberto Hirata Jr.; Edward R. Dougherty; Junior Barrera (Signal Process., 2000)

Efficient design of minmax ODIF robust stack filters. - Bogdan Dumitrescu; Ioan Tabus; Sari Peltonen; Jaakko Astola; Edward R. Dougherty (ISSPA, 2001)

Hybrid Human-Machine Non-Linear Filter Design Using Envelopes. - Marcel Brun; Roberto Hirata Jr.; Junior Barrera; Edward R. Dougherty (SIBGRAPI, 2001)

Optimal Conjunctive Granulometric Bandpass Filters. - Edward R. Dougherty (J. Math. Imaging Vis., 2001)

Multiresolution Analysis for Optimal Binary Filters. - Edward R. Dougherty; Junior Barrera; Gerard Mozelle; Seungchan Kim; Marcel Brun (J. Math. Imaging Vis., 2001)

Morphological granulometric estimation of random patterns in the context of parameterized random sets. - Sinan Batman; Edward R. Dougherty (Pattern Recognit., 2001)

Non-homothetic granulometric mixing theory with application to blood cell counting. - Nipon Theera-Umpon; Edward R. Dougherty; Paul D. Gader (Pattern Recognit., 2001)

Asymptotic joint normality of the granulometric moments. - Krishnamoorthy Sivakumar; Yoganand Balagurunathan; Edward R. Dougherty (Pattern Recognit. Lett., 2001)

Robust optimal granulometric bandpass filters. - Edward R. Dougherty; Yidong Chen 002 (Signal Process., 2001)

Bayesian robust optimal linear filters. - Artyom M. Grigoryan; Edward R. Dougherty (Signal Process., 2001)

Granulometric classifiers from small samples. - Yoganand Balagurunathan; Ronaldo Fumio Hashimoto; Seungchan Kim; Junior Barrera; Edward R. Dougherty (Image Processing: Algorithms and Systems, 2002)

Clustering granulometric features. - Marcel Brun; Yoganand Balagurunathan; Junior Barrera; Edward R. Dougherty (Image Processing: Algorithms and Systems, 2002)

Automatic counting of illuminated spheres in a random Boolean model. - Artyom M. Grigoryan; Edward R. Dougherty (Image Processing: Algorithms and Systems, 2002)

Ratio statistics of gene expression levels and applications to microarray data analysis. - Yidong Chen 002; Vishnu G. Kamat; Edward R. Dougherty; Michael L. Bittner; Paul S. Meltzer; Jeffrey M. Trent (Bioinform., 2002)

Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. - Ilya Shmulevich; Edward R. Dougherty; Seungchan Kim; Wei Zhang 011 (Bioinform., 2002)

ayesian automatic relevance determination algorithms for classifying gene expression data. - Ilya Shmulevich; Edward R. Dougherty; Wei Zhang 011 (Bioinform., 2002)

Inference from Clustering with Application to Gene-Expression Microarrays. - Edward R. Dougherty; Junior Barrera; Marcel Brun; Seungchan Kim; Roberto Marcondes Cesar Junior; Yidong Chen 002; Michael L. Bittner; Jeffrey M. Trent (J. Comput. Biol., 2002)

Strong Feature Sets from Small Samples. - Seungchan Kim; Edward R. Dougherty; Junior Barrera; Yidong Chen 002; Michael L. Bittner; Jeffrey M. Trent (J. Comput. Biol., 2002)

Granulometric Size Density for Segmented Random-Disk Models. - Edward R. Dougherty (J. Math. Imaging Vis., 2002)

Guest Editorial. - Edward R. Dougherty; Jaakko Astola (J. Math. Imaging Vis., 2002)

Pattern Recognition Theory in Nonlinear Signal Processing. - Edward R. Dougherty; Junior Barrera (J. Math. Imaging Vis., 2002)

Multiresolution Design of Aperture Operators. - Roberto Hirata Jr.; Marcel Brun; Junior Barrera; Edward R. Dougherty (J. Math. Imaging Vis., 2002)

From Boolean to probabilistic Boolean networks as models of genetic regulatory networks. - Ilya Shmulevich; Edward R. Dougherty; Wei Zhang 011 (Proc. IEEE, 2002)

Optimal linear granulometric estimation for random sets. - Yoganand Balagurunathan; Edward R. Dougherty (Pattern Recognit., 2002)

Simulation Toolbox for 3D-FISH Spot-Counting Algorithms. - Artyom M. Grigoryan; Galen Hostetter; Olli-P. Kallioniemi; Edward R. Dougherty (Real Time Imaging, 2002)

Application of dynamic programming in genetic regulatory networks. - Aniruddha Datta; Ashish Choudhary; Michael L. Bittner; Edward R. Dougherty (CDC, 2003)

Corrected Small-sample Estimation of the Bayes Error. - Marcel Brun; David Sabbagh; Seungchan Kim; Edward R. Dougherty (Bioinform., 2003)

Gene selection: a Bayesian variable selection approach. - Kyeong Eun Lee; Naijun Sha; Edward R. Dougherty; Marina Vannucci; Bani K. Mallick (Bioinform., 2003)

Missing-value estimation using linear and non-linear regression with Bayesian gene selection. - Xiaobo Zhou 001; Xiaodong Wang 001; Edward R. Dougherty (Bioinform., 2003)

Morphological Texture Analysis Using the Texture Evolution Function. - J. McKenzie; Stephen Marshall; Alison J. Gray; Edward R. Dougherty (Int. J. Pattern Recognit. Artif. Intell., 2003)

External Control in Markovian Genetic Regulatory Networks. - Aniruddha Datta; Ashish Choudhary; Michael L. Bittner; Edward R. Dougherty (Mach. Learn., 2003)

Relation Between Permutation-Test P Values and Classifier Error Estimates. - Tailen Hsing; Sanju Attoor; Edward R. Dougherty (Mach. Learn., 2003)

Granulometric parametric estimation for the random Boolean model using optimal linear filters and optimal structuring elements. - Yoganand Balagurunathan; Edward R. Dougherty (Pattern Recognit. Lett., 2003)

Design of optimal binary filters under joint multiresolution-envelope constraint. - Marcel Brun; Edward R. Dougherty; Roberto Hirata Jr.; Junior Barrera (Pattern Recognit. Lett., 2003)

Genomic signal processing. - Jaakko Astola; Edward R. Dougherty; Ilya Shmulevich; Ioan Tabus (Signal Process., 2003)

Mappings between probabilistic Boolean networks. - Edward R. Dougherty; Ilya Shmulevich (Signal Process., 2003)

Design of multi-mask aperture filters. - Alan C. Green; Stephen Marshall; David Greenhalgh; Edward R. Dougherty (Signal Process., 2003)

Efficient selection of feature sets possessing high coefficients of determination based on incremental determinations. - Ronaldo Fumio Hashimoto; Edward R. Dougherty; Marcel Brun; Zheng-Zheng Zhou; Michael L. Bittner; Jeffrey M. Trent (Signal Process., 2003)

Construction of genomic networks using mutual-information clustering and reversible-jump Markov-chain-Monte-Carlo predictor design. - Xiaobo Zhou 001; Xiaodong Wang 001; Edward R. Dougherty (Signal Process., 2003)

New challenges in non-linear signal and image processing. - Stephen Marshall; Edward R. Dougherty (EUSIPCO, 2004)

Which is better for cDNA-microarray-based classification: ratios or direct intensities. - Sanju Attoor; Edward R. Dougherty; Yidong Chen 002; Michael L. Bittner; Jeffrey M. Trent (Bioinform., 2004)

Is cross-validation valid for small-sample microarray classification? - Ulisses M. Braga-Neto; Edward R. Dougherty (Bioinform., 2004)

Is cross-validation better than resubstitution for ranking genes? - Ulisses M. Braga-Neto; Ronaldo Fumio Hashimoto; Edward R. Dougherty; Danh V. Nguyen; Raymond J. Carroll (Bioinform., 2004)

External control in Markovian genetic regulatory networks: the imperfect information case. - Aniruddha Datta; Ashish Choudhary; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2004)

Growing genetic regulatory networks from seed genes. - Ronaldo Fumio Hashimoto; Seungchan Kim; Ilya Shmulevich; Wei Zhang 011; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2004)

A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks. - Xiaobo Zhou 001; Xiaodong Wang 001; Ranadip Pal; Ivan Ivanov 001; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2004)

Genomic Signal Processing: The Salient Issues. - Edward R. Dougherty; Ilya Shmulevich; Michael L. Bittner (EURASIP J. Adv. Signal Process., 2004)

Reduction Mappings between Probabilistic Boolean Networks. - Ivan Ivanov 001; Edward R. Dougherty (EURASIP J. Adv. Signal Process., 2004)

Editorial. - Xiaodong Wang 001; Edward R. Dougherty; Yidong Chen 002; Carsten O. Peterson (EURASIP J. Adv. Signal Process., 2004)

Gene Prediction Using Multinomial Probit Regression with Bayesian Gene Selection. - Xiaobo Zhou 001; Xiaodong Wang 001; Edward R. Dougherty (EURASIP J. Adv. Signal Process., 2004)

Gene Clustering Based on Clusterwide Mutual Information. - Xiaobo Zhou 001; Xiaodong Wang 001; Edward R. Dougherty; Daniel E. Russ; Edward Suh (J. Comput. Biol., 2004)

Automatic design of morphological operators. - Edward R. Dougherty (J. Electronic Imaging, 2004)

A Bayesian approach to nonlinear probit gene selection and classification. - Xiaobo Zhou 001; Xiaodong Wang 001; Edward R. Dougherty (J. Frankl. Inst., 2004)

Nonlinear Filter Design Using Envelopes. - Marcel Brun; Roberto Hirata Jr.; Junior Barrera; Edward R. Dougherty (J. Math. Imaging Vis., 2004)

A Lattice-Based Minimal Gray-Scale Switching Algorithm for Obtaining the Optimal Increasing Filter from the Optimal Filter. - Edward R. Dougherty (J. Math. Imaging Vis., 2004)

Optimal Filters with Multiresolution Apertures. - Alan C. Green; Edward R. Dougherty; Stephen Marshall; David Greenhalgh (J. Math. Imaging Vis., 2004)

Classifier performance as a function of distributional complexity. - Sanju Attoor; Edward R. Dougherty (Pattern Recognit., 2004)

Bolstered error estimation. - Ulisses M. Braga-Neto; Edward R. Dougherty (Pattern Recognit., 2004)

A probabilistic theory of clustering. - Edward R. Dougherty; Marcel Brun (Pattern Recognit., 2004)

Assignment of terminal penalties in controlling genetic regulatory networks. - Ashish Choudhary; Aniruddha Datta; Michael L. Bittner; Edward R. Dougherty (ACC, 2005)

External control in a special class of probabilistic Boolean networks. - Ranadip Pal; Aniruddha Datta; Michael L. Bittner; Edward R. Dougherty (ACC, 2005)

How many samples are needed to build a classifier: a general sequential approach. - Wenjiang J. Fu; Edward R. Dougherty; Bani K. Mallick; Raymond J. Carroll (Bioinform., 2005)

Optimal number of features as a function of sample size for various classification rules. - Jianping Hua; Zixiang Xiong; James Lowey; Edward Suh; Edward R. Dougherty (Bioinform., 2005)

Intervention in context-sensitive probabilistic Boolean networks. - Ranadip Pal; Aniruddha Datta; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2005)

Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS. - Ranadip Pal; Aniruddha Datta; Albert J. Fornace Jr.; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2005)

Generating Boolean networks with a prescribed attractor structure. - Ranadip Pal; Ivan Ivanov 001; Aniruddha Datta; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2005)

Superior feature-set ranking for small samples using bolstered error estimation. - Chao Sima; Ulisses M. Braga-Neto; Edward R. Dougherty (Bioinform., 2005)

Evolving Feature Selection. - Huan Liu 001; Edward R. Dougherty; Jennifer G. Dy; Kari Torkkola; Eugene Tuv; Hanchuan Peng; Chris H. Q. Ding; Fuhui Long; Michael E. Berens; Lance Parsons; Zheng Zhao 002; Lei Yu 001; et al. (IEEE Intell. Syst., 2005)

Exact performance of error estimators for discrete classifiers. - Ulisses M. Braga-Neto; Edward R. Dougherty (Pattern Recognit., 2005)

The fundamental role of pattern recognition for gene-expression/microarray data in bioinformatics. - Edward R. Dougherty (Pattern Recognit., 2005)

Optimal robust classifiers. - Edward R. Dougherty; Jianping Hua; Zixiang Xiong; Yidong Chen 002 (Pattern Recognit., 2005)

The coefficient of intrinsic dependence (feature selection using el CID). - Tailen Hsing; Li-Yu Liu; Marcel Brun; Edward R. Dougherty (Pattern Recognit., 2005)

Determination of the optimal number of features for quadratic discriminant analysis via the normal approximation to the discriminant distribution. - Jianping Hua; Zixiang Xiong; Edward R. Dougherty (Pattern Recognit., 2005)

Impact of error estimation on feature selection. - Chao Sima; Sanju Attoor; Ulisses M. Braga-Neto; James Lowey; Edward Suh; Edward R. Dougherty (Pattern Recognit., 2005)

Feature selection algorithms to find strong genes. - Paulo J. S. Silva; Ronaldo Fumio Hashimoto; Seungchan Kim; Junior Barrera; Leônidas de Oliveira Brandão; Edward Suh; Edward R. Dougherty (Pattern Recognit. Lett., 2005)

Steady-state probabilities for attractors in probabilistic Boolean networks. - Marcel Brun; Edward R. Dougherty; Ilya Shmulevich (Signal Process., 2005)

Genomic signal processing: diagnosis and therapy. - Edward R. Dougherty; Anirulddlha Datta (IEEE Signal Process. Mag., 2005)

Research issues in genomic signal processing. - Edward R. Dougherty; Aniruddha Datta; Chao Sima (IEEE Signal Process. Mag., 2005)

Optimal Control in a Family of Boolean Networks. - Ashish Choudhary; Aniruddha Datta; Michael L. Bittner; Edward R. Dougherty (CDC, 2006)

Genetic test bed for feature selection. - Ashish Choudhary; Marcel Brun; Jianping Hua; James Lowey; Edward Suh; Edward R. Dougherty (Bioinform., 2006)

Intervention in a family of Boolean networks. - Ashish Choudhary; Aniruddha Datta; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2006)

What should be expected from feature selection in small-sample settings. - Chao Sima; Edward R. Dougherty (Bioinform., 2006)

Inferring gene regulatory networks from time series data using the minimum description length principle. - Wentao Zhao; Erchin Serpedin; Edward R. Dougherty (Bioinform., 2006)

Noise-injected neural networks show promise for use on small-sample expression data. - Jianping Hua; James Lowey; Zixiang Xiong; Edward R. Dougherty (BMC Bioinform., 2006)

Normalization Benefits Microarray-Based Classification. - Jianping Hua; Yoganand Balagurunathan; Yidong Chen 002; James Lowey; Michael L. Bittner; Zixiang Xiong; Edward Suh; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2006)

Optimal convex error estimators for classification. - Chao Sima; Edward R. Dougherty (Pattern Recognit., 2006)

Optimizing Consistency-Based Design of Context-Sensitive Gene Regulatory Networks. - Yufei Xiao; Edward R. Dougherty (IEEE Trans. Circuits Syst. I Regul. Pap., 2006)

Design of probabilistic Boolean networks under the requirement of contextual data consistency. - Edward R. Dougherty; Yufei Xiao (IEEE Trans. Signal Process., 2006)

Optimal infinite-horizon control for probabilistic Boolean networks. - Ranadip Pal; Aniruddha Datta; Edward R. Dougherty (IEEE Trans. Signal Process., 2006)

Inference of Gene Regulatory Networks using S-System: A Unified Approach. - Haixin Wang 004; Lijun Qian; Edward R. Dougherty (CIBCB, 2007)

Reconstruction of Genetic Regulatory Networks Based on the Posterior Probabilities of Gene Regulations. - Wentao Zhao; Kwadwo Agyepong; Erchin Serpedin; Edward R. Dougherty (ICASSP (1), 2007)

Modeling Genetic Regulatory Networks by Sigmoidal Functions: A Joint Genetic Algorithm and Kalman Filtering Approach. - Haixin Wang 004; Lijun Qian; Edward R. Dougherty (ICNC (2), 2007)

SNiPer-HD: improved genotype calling accuracy by an expectation-maximization algorithm for high-density SNP arrays. - Jianping Hua; David W. Craig; Marcel Brun; Jennifer Webster; Victoria Zismann; Waibhav Tembe; Keta Joshipura; Matthew J. Huentelman; Edward R. Dougherty; Dietrich A. Stephan (Bioinform., 2007)

The impact of function perturbations in Boolean networks. - Yufei Xiao; Edward R. Dougherty (Bioinform., 2007)

Comparison of Gene Regulatory Networks via Steady-State Trajectories. - Marcel Brun; Seungchan Kim; Woonjung Choi; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2007)

Genetic Regulatory Networks. - Edward R. Dougherty; Tatsuya Akutsu; Paul Dan Cristea; Ahmed H. Tewfik (EURASIP J. Bioinform. Syst. Biol., 2007)

Decorrelation of the True and Estimated Classifier Errors in High-Dimensional Settings. - Blaise Hanczar; Jianping Hua; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2007)

Inference of a Probabilistic Boolean Network from a Single Observed Temporal Sequence. - Stephen Marshall; Le Yu 003; Yufei Xiao; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2007)

Quantification of the Impact of Feature Selection on the Variance of Cross-Validation Error Estimation. - Yufei Xiao; Jianping Hua; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2007)

Model-based evaluation of clustering validation measures. - Marcel Brun; Chao Sima; Jianping Hua; James Lowey; Brent Carroll; Edward Suh; Edward R. Dougherty (Pattern Recognit., 2007)

Control approaches for probabilistic gene regulatory networks - What approaches have been developed for addreassinig the issue of intervention? - Anirulddlha Datta; Ranadip Pal; Ashish Choudhary; Edward R. Dougherty (IEEE Signal Process. Mag., 2007)

Dynamics Preserving Size Reduction Mappings for Probabilistic Boolean Networks. - Ivan Ivanov 001; Ranadip Pal; Edward R. Dougherty (IEEE Trans. Signal Process., 2007)

Optimal intervention in semi-Markov-based asynchronous genetic regulatory networks. - Babak Faryabi; Jean-François Chamberland; Golnaz Vahedi; Aniruddha Datta; Edward R. Dougherty (ACC, 2008)

Mean first-passage time control policy versus reinforcement-learning control policy in gene regulatory networks. - Golnaz Vahedi; Babak Faryabi; Jean-François Chamberland; Aniruddha Datta; Edward R. Dougherty (ACC, 2008)

Identifying drosophila cell-cycle regulated genes from irregular microarray data. - Wentao Zhao; Kwadwo Agyepong; Erchin Serpedin; Edward R. Dougherty (ICASSP, 2008)

Classification with reject option in gene expression data. - Blaise Hanczar; Edward R. Dougherty (Bioinform., 2008)

Which Is Better: Holdout or Full-Sample Classifier Design? - Marcel Brun; Qian Xu 001; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2008)

Optimal Constrained Stationary Intervention in Gene Regulatory Networks. - Babak Faryabi; Golnaz Vahedi; Jean-François Chamberland; Aniruddha Datta; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2008)

Inference of Boolean Networks Using Sensitivity Regularization. - Wenbin Liu; Harri Lähdesmäki; Edward R. Dougherty; Ilya Shmulevich (EURASIP J. Bioinform. Syst. Biol., 2008)

Detecting Periodic Genes from Irregularly Sampled Gene Expressions: A Comparison Study. - Wentao Zhao; Kwadwo Agyepong; Erchin Serpedin; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2008)

Recovering Genetic Regulatory Networks from Chromatin Immunoprecipitation and Steady-State Microarray Data. - Wentao Zhao; Erchin Serpedin; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2008)

Optimal Intervention in Asynchronous Genetic Regulatory Networks. - Babak Faryabi; Jean-François Chamberland; Golnaz Vahedi; Aniruddha Datta; Edward R. Dougherty (IEEE J. Sel. Top. Signal Process., 2008)

Intrinsically Multivariate Predictive Genes. - David Correa Martins Jr.; Ulisses M. Braga-Neto; Ronaldo Fumio Hashimoto; Michael L. Bittner; Edward R. Dougherty (IEEE J. Sel. Top. Signal Process., 2008)

The peaking phenomenon in the presence of feature-selection. - Chao Sima; Edward R. Dougherty (Pattern Recognit. Lett., 2008)

Intervention in Gene Regulatory Networks via a Stationary Mean-First-Passage-Time Control Policy. - Golnaz Vahedi; Babak Faryabi; Jean-François Chamberland; Aniruddha Datta; Edward R. Dougherty (IEEE Trans. Biomed. Eng., 2008)

Inferring Connectivity of Genetic Regulatory Networks Using Information-Theoretic Criteria. - Wentao Zhao; Erchin Serpedin; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Robust Intervention in Probabilistic Boolean Networks. - Ranadip Pal; Aniruddha Datta; Edward R. Dougherty (IEEE Trans. Signal Process., 2008)

Effect of Function Perturbation on the Steady-State Distribution of Genetic Regulatory Networks: Optimal Structural Intervention. - Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2008)

Inference of Noisy Nonlinear Differential Equation Models for Gene Regulatory Networks Using Genetic Programming and Kalman Filtering. - Lijun Qian; Haixin Wang 004; Edward R. Dougherty (IEEE Trans. Signal Process., 2008)

Steady-state analysis of genetic regulatory networks modeled by nonlinear ordinary differential equations. - Haixin Wang 004; Lijun Qian; Edward R. Dougherty (CIBCB, 2009)

Open-Loop Feedback Intervention: Control of gene regulatory networks with unmeasurable context. - Babak Faryabi; Golnaz Vahedi; Jean-François Chamberland; Aniruddha Datta; Edward R. Dougherty (GENSiPS, 2009)

A CoD based reduction algorithm for Boolean and probabilistic Boolean networks. - Noushin Ghaffari; Ivan Ivanov 001; Edward R. Dougherty (GENSiPS, 2009)

Quantification of data extraction noise in probabilistic Boolean Network modeling. - Ranadip Pal; Aniruddha Datta; Edward R. Dougherty (GENSiPS, 2009)

Control-compatible state reduction for Boolean networks. - Xiaoning Qian; Edward R. Dougherty (GENSiPS, 2009)

Bolstered error estimator with feature selection. - Chao Sima; Thang T. Vu; Ulisses M. Braga-Neto; Edward R. Dougherty (GENSiPS, 2009)

Critical Boolean networks require minimal intervention rate. - Golnaz Vahedi; Ilya Shmulevich; Wenbin Liu; Edward R. Dougherty (GENSiPS, 2009)

Bagging degrades the performance of linear discriminant classifiers. - Thang T. Vu; Ulisses M. Braga-Neto; Edward R. Dougherty (GENSiPS, 2009)

Sample size calculation from specified RMS of the resubstitution error for linear classifiers. - Amin Zollanvari; Ulisses M. Braga-Neto; Edward R. Dougherty (GENSiPS, 2009)

Adaptive intervention in probabilistic boolean networks. - Ritwik Layek; Aniruddha Datta; Ranadip Pal; Edward R. Dougherty (Bioinform., 2009)

Analysis and modeling of time-course gene-expression profiles from nanomaterial-exposed primary human epidermal keratinocytes. - Amin Zollanvari; Mary Jane Cunningham; Ulisses M. Braga-Neto; Edward R. Dougherty (BMC Bioinform., 2009)

Intervention in gene regulatory networks via greedy control policies based on long-run behavior. - Xiaoning Qian; Ivan Ivanov 001; Noushin Ghaffari; Edward R. Dougherty (BMC Syst. Biol., 2009)

Intervention in Context-Sensitive Probabilistic Boolean Networks Revisited. - Babak Faryabi; Golnaz Vahedi; Jean-François Chamberland; Aniruddha Datta; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2009)

Impact of Missing Value Imputation on Classification for DNA Microarray Gene Expression Data - A Model-Based Study. - Youting Sun; Ulisses M. Braga-Neto; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2009)

Spectral Preprocessing for Clustering Time-Series Gene Expressions. - Wentao Zhao; Erchin Serpedin; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2009)

Identifying Genes Involved in Cyclic Processes by Combining Gene Expression Analysis and Prior Knowledge. - Wentao Zhao; Erchin Serpedin; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2009)

Performance of feature-selection methods in the classification of high-dimension data. - Jianping Hua; Waibhav Tembe; Edward R. Dougherty (Pattern Recognit., 2009)

On the sampling distribution of resubstitution and leave-one-out error estimators for linear classifiers. - Amin Zollanvari; Ulisses M. Braga-Neto; Edward R. Dougherty (Pattern Recognit., 2009)

The effect of microarray image compression on expression-based classification. - Qian Xu 001; Jianping Hua; Zixiang Xiong; Michael L. Bittner; Edward R. Dougherty (Signal Image Video Process., 2009)

Optimal Intervention Strategies for Cyclic Therapeutic Methods. - Golnaz Vahedi; Babak Faryabi; Jean-François Chamberland; Aniruddha Datta; Edward R. Dougherty (IEEE Trans. Biomed. Eng., 2009)

Conditioning-Based Modeling of Contextual Genomic Regulation. - Edward R. Dougherty; Marcel Brun; Jeffrey M. Trent; Michael L. Bittner (IEEE ACM Trans. Comput. Biol. Bioinform., 2009)

Bayesian robustness in the control of gene regulatory networks. - Ranadip Pal; Aniruddha Datta; Edward R. Dougherty (IEEE Trans. Signal Process., 2009)

Probabilistic Boolean Networks - The Modeling and Control of Gene Regulatory Networks. - Ilya Shmulevich; Edward R. Dougherty (SIAM, 2010)

From biological pathways to regulatory networks. - Ritwik Layek; Aniruddha Datta; Edward R. Dougherty (CDC, 2010)

Modeling treatment and drug effects at the molecular level using hybrid system theory. - Xiangfang Li; Lijun Qian; Edward R. Dougherty (CIBCB, 2010)

Bayesian MMSE estimation of classification error and performance on real genomic data. - Lori A. Dalton; Edward R. Dougherty (GENSiPS, 2010)

A comparative study on sensitivities of Boolean networks. - Xiaoning Qian; Edward R. Dougherty (GENSiPS, 2010)

Effects of partial reporting of classification results. - Mohammadmahdi R. Yousefi; Jianping Hua; Chao Sima; Edward R. Dougherty (GENSiPS, 2010)

Conditioning-based model for the regulatory activities of microRNAs in specific dietary contexts. - Chen Zhao; Ivan Ivanov 001; Manasvi Shah; Laurie A. Davidson; Robert S. Chapkin; Edward R. Dougherty (GENSiPS, 2010)

RMS bounds and sample size considerations for error estimation in linear discriminant analysis. - Amin Zollanvari; Ulisses M. Braga-Neto; Edward R. Dougherty (GENSiPS, 2010)

A CoD-based reduction algorithm for designing stationary control policies on Boolean networks. - Noushin Ghaffari; Ivan Ivanov 001; Xiaoning Qian; Edward R. Dougherty (Bioinform., 2010)

Small-sample precision of ROC-related estimates. - Blaise Hanczar; Jianping Hua; Chao Sima; John N. Weinstein; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2010)

State reduction for network intervention in probabilistic Boolean networks. - Xiaoning Qian; Noushin Ghaffari; Ivan Ivanov 001; Edward R. Dougherty (Bioinform., 2010)

Reporting bias when using real data sets to analyze classification performance. - Mohammadmahdi R. Yousefi; Jianping Hua; Chao Sima; Edward R. Dougherty (Bioinform., 2010)

Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network. - Junjie Su; Byung-Jun Yoon; Edward R. Dougherty (BMC Bioinform., 2010)

BPDA - A Bayesian peptide detection algorithm for mass spectrometry. - Youting Sun; Jianqiu Zhang 002; Ulisses M. Braga-Neto; Edward R. Dougherty (BMC Bioinform., 2010)

Stationary and structural control in gene regulatory networks: basic concepts. - Edward R. Dougherty; Ranadip Pal; Xiaoning Qian; Michael L. Bittner; Aniruddha Datta (Int. J. Syst. Sci., 2010)

Exact correlation between actual and estimated errors in discrete classification. - Ulisses M. Braga-Neto; Edward R. Dougherty (Pattern Recognit. Lett., 2010)

Joint sampling distribution between actual and estimated classification errors for linear discriminant analysis. - Amin Zollanvari; Ulisses M. Braga-Neto; Edward R. Dougherty (IEEE Trans. Inf. Theory, 2010)

Selection policy-induced reduction mappings for Boolean networks. - Ivan Ivanov 001; Plamen Simeonov; Noushin Ghaffari; Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2010)

Exact MSE performance of the Bayesian MMSE estimator for classification error. - Lori A. Dalton; Edward R. Dougherty (ACSCC, 2011)

Optimal intervention strategies for cyclic therapeutic methods with fixed-length duration of effect. - Mohammadmahdi R. Yousefi; Aniruddha Datta; Edward R. Dougherty (ACSCC, 2011)

Intervention in biological phenomena modeled by S-systems: A model predictive control approach. - Nader Meskin; Hazem N. Nounou; Mohamed N. Nounou; Aniruddha Datta; Edward R. Dougherty (ACC, 2011)

A parallel programming framework with Markovian messaging for LC-MS peptide detection. - Zhenghao Zhang; Youting Sun; Ulisses M. Braga-Neto; Edward R. Dougherty; Jianqiu Zhang 002 (BIBM Workshops, 2011)

Combination therapy design for cancer: A digital systems approach. - Ritwik Layek; Aniruddha Datta; Michael L. Bittner; Edward R. Dougherty (CDC/ECC, 2011)

Parameter estimation of biological phenomena modeled by S-systems: An Extended Kalman filter approach. - Nader Meskin; Hazem N. Nounou; Mohamed N. Nounou; Aniruddha Datta; Edward R. Dougherty (CDC/ECC, 2011)

Multiple reaction monitoring: Modeling and systematic analysis. - Esmaeil Atashpaz-Gargari; Ulisses M. Braga-Neto; Edward R. Dougherty (GENSiPS, 2011)

Relationship between the accuracy of classifier error estimation and distribution complexity. - Esmaeil Atashpaz-Gargari; Chao Sima; Ulisses M. Braga-Neto; Edward R. Dougherty (GENSiPS, 2011)

Classifier error estimator performance in a Bayesian context. - Lori A. Dalton; Edward R. Dougherty (GENSiPS, 2011)

Designing enhanced classifiers using prior process knowledge: Regularized maximum-likelihood. - Mohammad Shahrokh Esfahani; Amin Zollanvari; Byung-Jun Yoon; Edward R. Dougherty (GENSiPS, 2011)

Stochastic modeling of dynamic effects of copy number alterations upon gene expression levels. - Fang-Han Hsu; Erchin Serpedin; Yidong Chen 002; Edward R. Dougherty (GENSiPS, 2011)

Identifying genes associated with chemotherapy response in ovarian carcinomas based on DNA copy number and expression profiles. - Fang-Han Hsu; Erchin Serpedin; Tzu-Hung Hsiao; Alexander J. R. Bishop; Edward R. Dougherty; Yidong Chen 002 (GENSiPS, 2011)

Attractor estimation and model refinement for stochastic regulatory network models. - Jason M. Knight; Edward R. Dougherty (GENSiPS, 2011)

Assessing the efficacy of molecularly targeted agents by using Kalman filter. - Xiangfang Li; Lijun Qian; Michael L. Bittner; Edward R. Dougherty (GENSiPS, 2011)

Uncertainty-based essentiality in gene regulatory networks. - Xiaoning Qian; Byung-Jun Yoon; Edward R. Dougherty (GENSiPS, 2011)

Modeling and systematic analysis of LC-MS proteomics pipeline. - Youting Sun; Ulisses M. Braga-Neto; Edward R. Dougherty (GENSiPS, 2011)

Modeling cyclic and acyclic therapeutic methods with persistent intervention effect in probabilistic Boolean networks. - Mohammadmahdi R. Yousefi; Aniruddha Datta; Edward R. Dougherty (GENSiPS, 2011)

Pathway analysis in the context of Bayesian networks - mathematical modeling of master and canalizing genes. - Chen Zhao; Ivan Ivanov 001; Michael L. Bittner; Edward R. Dougherty (GENSiPS, 2011)

Validation of gene regulatory networks: scientific and inferential. - Edward R. Dougherty (Briefings Bioinform., 2011)

Application of the Bayesian MMSE estimator for classification error to gene expression microarray data. - Lori A. Dalton; Edward R. Dougherty (Bioinform., 2011)

Cancer therapy design based on pathway logic. - Ritwik Layek; Aniruddha Datta; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2011)

High-dimensional bolstered error estimation. - Chao Sima; Ulisses M. Braga-Neto; Edward R. Dougherty (Bioinform., 2011)

Multiple-rule bias in the comparison of classification rules. - Mohammadmahdi R. Yousefi; Jianping Hua; Edward R. Dougherty (Bioinform., 2011)

Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty. - Mohammad Shahrokh Esfahani; Byung-Jun Yoon; Edward R. Dougherty (BMC Bioinform., 2011)

A CoD-based stationary control policy for intervening in large gene regulatory networks. - Noushin Ghaffari; Ivan Ivanov 001; Xiaoning Qian; Edward R. Dougherty (BMC Bioinform., 2011)

Characterization of Drug Efficacy Regions Based on Dosage and Frequency Schedules. - Xiangfang Li; Lijun Qian; Michael L. Bittner; Edward R. Dougherty (IEEE Trans. Biomed. Eng., 2011)

Intervention in Biological Phenomena Modeled by S-Systems. - Nader Meskin; Hazem N. Nounou; Mohamed N. Nounou; Aniruddha Datta; Edward R. Dougherty (IEEE Trans. Biomed. Eng., 2011)

Bayesian Minimum Mean-Square Error Estimation for Classification Error - Part I: Definition and the Bayesian MMSE Error Estimator for Discrete Classification. - Lori A. Dalton; Edward R. Dougherty (IEEE Trans. Signal Process., 2011)

Bayesian Minimum Mean-Square Error Estimation for Classification Error - Part II: Linear Classification of Gaussian Models. - Lori A. Dalton; Edward R. Dougherty (IEEE Trans. Signal Process., 2011)

Analytic Study of Performance of Error Estimators for Linear Discriminant Analysis. - Amin Zollanvari; Ulisses M. Braga-Neto; Edward R. Dougherty (IEEE Trans. Signal Process., 2011)

Output-feedback model predictive control of biological phenomena modeled by S-systems. - Nader Meskin; Hazem N. Nounou; Mohamed N. Nounou; Aniruddha Datta; Edward R. Dougherty (ACC, 2012)

Optimal Bayesian classification and its application to gene regulatory networks. - Lori A. Dalton; Edward R. Dougherty (GENSiPS, 2012)

Optimal therapeutic methods with random-length response in probabilistic boolean networks. - Mohammadmahdi R. Yousefi; Aniruddha Datta; Edward R. Dougherty (GENSiPS, 2012)

Structural intervention of gene regulatory networks by general rank-k matrix perturbation. - Xiaoning Qian; Byung-Jun Yoon; Edward R. Dougherty (ICASSP, 2012)

Optimal classifiers within a Bayesian framework. - Lori A. Dalton; Edward R. Dougherty (SSP, 2012)

Optimal cancer therapy based on a tumor growth inhibition model. - Mohammadmahdi R. Yousefi; Aniruddha Datta; Edward R. Dougherty (SSP, 2012)

BPDA2d - a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph-mass spectrometry. - Youting Sun; Jianqiu Zhang 002; Ulisses M. Braga-Neto; Edward R. Dougherty (Bioinform., 2012)

Performance reproducibility index for classification. - Mohammadmahdi R. Yousefi; Edward R. Dougherty (Bioinform., 2012)

Identifying mechanistic similarities in drug responses. - Chen Zhao; Jianping Hua; Michael L. Bittner; Ivan Ivanov 001; Edward R. Dougherty (Bioinform., 2012)

Dynamical modeling of drug effect using hybrid systems. - Xiangfang Li; Lijun Qian; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2012)

Optimal mean-square-error calibration of classifier error estimators under Bayesian models. - Lori A. Dalton; Edward R. Dougherty (Pattern Recognit., 2012)

Exact representation of the second-order moments for resubstitution and leave-one-out error estimation for linear discriminant analysis in the univariate heteroskedastic Gaussian model. - Amin Zollanvari; Ulisses M. Braga-Neto; Edward R. Dougherty (Pattern Recognit., 2012)

Genomic Signal Processing [Life Sciences]. - Edward R. Dougherty (IEEE Signal Process. Mag., 2012)

Stochastic Modeling of the Relationship between Copy Number and Gene Expression Based on Transcriptional Logic. - Fang-Han Hsu; Erchin Serpedin; Yidong Chen 002; Edward R. Dougherty (IEEE Trans. Biomed. Eng., 2012)

Evaluating Dynamic Effects of Copy Number Alterations on Gene Expression Using a Single Transcription Model. - Fang-Han Hsu; Erchin Serpedin; Yidong Chen 002; Edward R. Dougherty (IEEE Trans. Biomed. Eng., 2012)

Generating Stochastic Gene Regulatory Networks Consistent With Pathway Information and Steady-State Behavior. - Jason M. Knight; Aniruddha Datta; Edward R. Dougherty (IEEE Trans. Biomed. Eng., 2012)

Multiscale Denoising of Biological Data: A Comparative Analysis. - Mohamed N. Nounou; Hazem N. Nounou; Nader Meskin; Aniruddha Datta; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Fuzzy Intervention in Biological Phenomena. - Hazem N. Nounou; Mohamed N. Nounou; Nader Meskin; Aniruddha Datta; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Intervention in Gene Regulatory Networks via Phenotypically Constrained Control Policies Based on Long-Run Behavior. - Xiaoning Qian; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Exact Sample Conditioned MSE Performance of the Bayesian MMSE Estimator for Classification Error - Part I: Representation. - Lori A. Dalton; Edward R. Dougherty (IEEE Trans. Signal Process., 2012)

Exact Sample Conditioned MSE Performance of the Bayesian MMSE Estimator for Classification Error - Part II: Consistency and Performance Analysis. - Lori A. Dalton; Edward R. Dougherty (IEEE Trans. Signal Process., 2012)

Optimal Intervention Strategies for Therapeutic Methods With Fixed-Length Duration of Drug Effectiveness. - Mohammadmahdi R. Yousefi; Aniruddha Datta; Edward R. Dougherty (IEEE Trans. Signal Process., 2012)

Bayes clustering operators for known random labeled point processes. - Lori A. Dalton; Marco Benalcázar; Marcel Brun; Edward R. Dougherty (ACSSC, 2013)

Sample-based prior probability construction using biological pathway knowledge. - Mohammad Shahrokh Esfahani; Edward R. Dougherty (ACSSC, 2013)

Bayesian optimal control of Markovian genetic regulatory networks. - Mohammadmahdi R. Yousefi; Edward R. Dougherty (ACSSC, 2013)

Random matrix theory in pattern classification: An application to error estimation. - Amin Zollanvari; Edward R. Dougherty (ACSSC, 2013)

Improved branch-and-bound algorithm for U-curve optimization. - Esmaeil Atashpaz-Gargari; Ulisses M. Braga-Neto; Edward R. Dougherty (GENSiPS, 2013)

Designing experiments for optimal reduction of uncertainty in gene regulatory networks. - Roozbeh Dehghannasiri; Byung-Jun Yoon; Edward R. Dougherty (GENSiPS, 2013)

Effect of separate sampling on classification and the minimax criterion. - Mohammad Shahrokh Esfahani; Edward R. Dougherty (GENSiPS, 2013)

Bayesian multivariate Poisson model for RNA-seq classification. - Jason M. Knight; Ivan Ivanov 001; Edward R. Dougherty (GENSiPS, 2013)

Drug effect study on proliferation and survival pathways on cell line-based platform: A stochastic hybrid systems approach. - Xiangfang Li; Lijun Qian; Michael L. Bittner; Edward R. Dougherty (GENSiPS, 2013)

Phenotypically constrained Boolean network inference with prescribed steady states. - Xiaoning Qian; Edward R. Dougherty (GENSiPS, 2013)

Effect of mixing probabilities on the bias of cross-validation under separate sampling. - Amin Zollanvari; Ulisses M. Braga-Neto; Edward R. Dougherty (GENSiPS, 2013)

Robust identification of molecularly targeted drug effect coefficient using H∞ filter. - Lijun Qian; Xiangfang Li; Edward R. Dougherty (GlobalSIP, 2013)

Application of double asymptotics and random matrix theory in error estimation of regularized linear discriminant analysis. - Amin Zollanvari; Edward R. Dougherty (GlobalSIP, 2013)

Performance of linear discriminant analysis in stochastic settings. - Amin Zollanvari; Jianping Hua; Edward R. Dougherty (ICASSP, 2013)

Epidemiological modeling of news and rumors on Twitter. - Fang Jin; Edward R. Dougherty; Parang Saraf; Yang Cao 001; Naren Ramakrishnan (SNAKDD, 2013)

Spectral Analysis on Time-Course Expression Data: Detecting Periodic Genes Using a Real-Valued Iterative Adaptive Approach. - Kwadwo Agyepong; Fang-Han Hsu; Edward R. Dougherty; Erchin Serpedin (Adv. Bioinformatics, 2013)

Intervention in gene regulatory networks with maximal phenotype alteration. - Mohammadmahdi R. Yousefi; Edward R. Dougherty (Bioinform., 2013)

Modeling the Next Generation Sequencing sample processing pipeline for the purposes of classification. - Noushin Ghaffari; Mohammadmahdi R. Yousefi; Charles D. Johnson; Ivan Ivanov 001; Edward R. Dougherty (BMC Bioinform., 2013)

On the impoverishment of scientific education. - Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2013)

Scientific knowledge is possible with small-sample classification. - Edward R. Dougherty; Lori A. Dalton (EURASIP J. Bioinform. Syst. Biol., 2013)

Relationship between the accuracy of classifier error estimation and complexity of decision boundary. - Esmaeil Atashpaz-Gargari; Chao Sima; Ulisses M. Braga-Neto; Edward R. Dougherty (Pattern Recognit., 2013)

Optimal classifiers with minimum expected error within a Bayesian framework - Part II: Properties and performance analysis. - Lori A. Dalton; Edward R. Dougherty (Pattern Recognit., 2013)

Optimal classifiers with minimum expected error within a Bayesian framework - Part I: Discrete and Gaussian models. - Lori A. Dalton; Edward R. Dougherty (Pattern Recognit., 2013)

Classifier design given an uncertainty class of feature distributions via regularized maximum likelihood and the incorporation of biological pathway knowledge in steady-state phenotype classification. - Mohammad Shahrokh Esfahani; Jason M. Knight; Amin Zollanvari; Byung-Jun Yoon; Edward R. Dougherty (Pattern Recognit., 2013)

The reliability of estimated confidence intervals for classification error rates when only a single sample is available. - Blaise Hanczar; Edward R. Dougherty (Pattern Recognit., 2013)

Analytical study of performance of linear discriminant analysis in stochastic settings. - Amin Zollanvari; Jianping Hua; Edward R. Dougherty (Pattern Recognit., 2013)

Estimating Conditional Probabilities for the Detection of Unfavorable Copy Number Alterations in a Targeted Therapy. - Fang-Han Hsu; Edward R. Dougherty; Yidong Chen 002; Erchin Serpedin (IEEE Trans. Biomed. Eng., 2013)

Optimal Intervention in Markovian Gene Regulatory Networks With Random-Length Therapeutic Response to Antitumor Drug. - Mohammadmahdi R. Yousefi; Aniruddha Datta; Edward R. Dougherty (IEEE Trans. Biomed. Eng., 2013)

Quantifying the Objective Cost of Uncertainty in Complex Dynamical Systems. - Byung-Jun Yoon; Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2013)

Computationally efficient experimental design strategy for reducing gene network uncertainty. - Roozbeh Dehghannasiri; Byung-Jun Yoon; Edward R. Dougherty (GlobalSIP, 2014)

Sensitivity analysis for drug effect study: An NF-κB pathway example. - Xiangfang Lindsey Li; Sunday Ogedengbe; Lijun Qian; Edward R. Dougherty (GlobalSIP, 2014)

Modeling mass protest adoption in social network communities using geometric brownian motion. - Fang Jin; Rupinder Paul Khandpur; Nathan Self; Edward R. Dougherty; Sheng Guo 002; Feng Chen 001; B. Aditya Prakash; Naren Ramakrishnan (KDD, 2014)

Cross-validation under separate sampling: strong bias and how to correct it. - Ulisses M. Braga-Neto; Amin Zollanvari; Edward R. Dougherty (Bioinform., 2014)

Effect of separate sampling on classification accuracy. - Mohammad Shahrokh Esfahani; Edward R. Dougherty (Bioinform., 2014)

MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification. - Jason M. Knight; Ivan Ivanov 001; Edward R. Dougherty (BMC Bioinform., 2014)

Misinformation Propagation in the Age of Twitter. - Fang Jin; Wei Wang 064; Liang Zhao 002; Edward R. Dougherty; Yang Cao 001; Chang-Tien Lu; Naren Ramakrishnan (Computer, 2014)

Modeling and systematic analysis of biomarker validation using selected reaction monitoring. - Esmaeil Atashpaz-Gargari; Ulisses M. Braga-Neto; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2014)

Using the minimum description length principle to reduce the rate of false positives of best-fit algorithms. - Jie Fang; Hongjia Ouyang; Liangzhong Shen; Edward R. Dougherty; Wenbin Liu (EURASIP J. Bioinform. Syst. Biol., 2014)

Learning restricted Boolean network model by time-series data. - Hongjia Ouyang; Jie Fang; Liangzhong Shen; Edward R. Dougherty; Wenbin Liu (EURASIP J. Bioinform. Syst. Biol., 2014)

Unbiased bootstrap error estimation for linear discriminant analysis. - Thang T. Vu; Chao Sima; Ulisses M. Braga-Neto; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2014)

A comparison study of optimal and suboptimal intervention policies for gene regulatory networks in the presence of uncertainty. - Mohammadmahdi R. Yousefi; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2014)

Moments and root-mean-square error of the Bayesian MMSE estimator of classification error in the Gaussian model. - Amin Zollanvari; Edward R. Dougherty (Pattern Recognit., 2014)

Incorporation of Biological PathwayKnowledge in the Construction of Priorsfor Optimal Bayesian Classification. - Mohammad Shahrokh Esfahani; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Intrinsically Optimal Bayesian Robust Filtering. - Lori A. Dalton; Edward R. Dougherty (IEEE Trans. Signal Process., 2014)

Small data is the problem. - Edward R. Dougherty; Lori A. Dalton; Francis J. Alexander (ACSSC, 2015)

An experimental design to reduce dynamics uncertainty in genomic networks. - Daniel N. Mohsenizadeh; Roozbeh Dehghannasiri; Edward R. Dougherty (BCB, 2015)

Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks. - Roozbeh Dehghannasiri; Byung-Jun Yoon; Edward R. Dougherty (BMC Bioinform., 2015)

Discrete optimal Bayesian classification with error-conditioned sequential sampling. - Ariana Broumand; Mohammad Shahrokh Esfahani; Byung-Jun Yoon; Edward R. Dougherty (Pattern Recognit., 2015)

Optimal Experimental Design for Gene Regulatory Networks in the Presence of Uncertainty. - Roozbeh Dehghannasiri; Byung-Jun Yoon; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

An Optimization-Based Framework for the Transformation of Incomplete Biological Knowledge into a Probabilistic Structure and Its Application to the Utilization of Gene/Protein Signaling Pathways in Discrete Phenotype Classification. - Mohammad Shahrokh Esfahani; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

Analytic Representation of Bayes Labeling and Bayes Clustering Operators for Random Labeled Point Processes. - Lori A. Dalton; Marco Benalcázar; Marcel Brun; Edward R. Dougherty (IEEE Trans. Signal Process., 2015)

Generalized Consistent Error Estimator of Linear Discriminant Analysis. - Amin Zollanvari; Edward R. Dougherty (IEEE Trans. Signal Process., 2015)

Efficient experimental design for uncertainty reduction in gene regulatory networks. - Roozbeh Dehghannasiri; Byung-Jun Yoon; Edward R. Dougherty (BMC Bioinform., 2015)

Dynamical modeling of uncertain interaction-based genomic networks. - Daniel N. Mohsenizadeh; Jianping Hua; Michael L. Bittner; Edward R. Dougherty (BMC Bioinform., 2015)

Inference of gene regulatory networks: validation and uncertainty. - Xiaoning Qian; Byung-Jun Yoon; Edward R. Dougherty (Big Data over Networks, 2016)

A Bayesian framework for robust Kalman filtering under uncertain noise statistics. - Roozbeh Dehghannasiri; Mohammad Shahrokh Esfahani; Edward R. Dougherty (ACSSC, 2016)

Inference of Nonlinear ODE-Based Gene Regulatory Networks via Intrinsically Bayesian Robust Kalman Filtering. - Roozbeh Dehghannasiri; Mohammad Shahrokh Esfahani; Edward R. Dougherty (BCB, 2016)

Model-based study of the Effectiveness of Reporting Lists of Small Feature Sets using RNA-Seq Data. - Eunji Kim; Ivan Ivanov 001; Jianping Hua; Robert S. Chapkin; Edward R. Dougherty (BCB, 2016)

Optimal dynamics uncertainty reduction in gene networks in the presence of experimental error. - Daniel N. Mohsenizadeh; Roozbeh Dehghannasiri; Edward R. Dougherty (BHI, 2016)

Analysis and control of genetic regulatory systems with switched drug inputs. - Wasiu Opeyemi Oduola; Xiangfang Li; Chang Duan; Lijun Qian; Fen Wu; Edward R. Dougherty (BHI, 2016)

Optimal experimental design in canonical expansions with applications to signal compression. - Roozbeh Dehghannasiri; Xiaoning Qian; Edward R. Dougherty (GlobalSIP, 2016)

Incorporating prior knowledge induced from stochastic differential equations in the classification of stochastic observations. - Amin Zollanvari; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2016)

Optimal Wiener and homomorphic filtration: Review. - Artyom M. Grigoryan; Edward R. Dougherty; Sos S. Agaian (Signal Process., 2016)

Bayesian Regression With Network Prior: Optimal Bayesian Filtering Perspective. - Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2016)

Bayesian Kalman filtering in the presence of unknown noise statistics using factor graphs. - Roozbeh Dehghannasiri; Mohammad Shahrokh Esfahani; Xiaoning Qian; Edward R. Dougherty (ACSSC, 2017)

An objective-based experimental design framework for signal processing in the context of canonical expansions. - Roozbeh Dehghannasiri; Xiaoning Qian; Edward R. Dougherty (ACSSC, 2017)

Nonstationary linear discriminant analysis. - Shuilian Xie; Mahdi Imani; Edward R. Dougherty; Ulisses M. Braga-Neto (ACSSC, 2017)

Intrinsically Bayesian Robust Classifier for Single-Cell Gene Expression Time Series in Gene Regulatory Networks. - Alireza Karbalayghareh; Ulisses M. Braga-Neto; Edward R. Dougherty (BCB, 2017)

Classification of Gaussian trajectories with missing data in Boolean gene regulatory networks. - Alireza Karbalayghareh; Ulisses M. Braga-Neto; Edward R. Dougherty (ICASSP, 2017)

Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors. - Shahin Boluki; Mohammad Shahrokh Esfahani; Xiaoning Qian; Edward R. Dougherty (BMC Bioinform., 2017)

Review of stochastic hybrid systems with applications in biological systems modeling and analysis. - Xiangfang Li; Oluwaseyi Omotere; Lijun Qian; Edward R. Dougherty (EURASIP J. Bioinform. Syst. Biol., 2017)

Optimal experimental design in the context of canonical expansions. - Roozbeh Dehghannasiri; Xiaoning Qian; Edward R. Dougherty (IET Signal Process., 2017)

Robust Smoothing for State-Space Models with Unknown Noise Statistics. - Roozbeh Dehghannasiri; Xiaoning Qian; Edward R. Dougherty (ACSSC, 2018)

Scalable Optimal Bayesian Classification of Single-Cell Trajectories under Regulatory Model Uncertainty. - Ehsan Hajiramezanali; Mahdi Imani; Ulisses M. Braga-Neto; Xiaoning Qian; Edward R. Dougherty (BCB, 2018)

Sequential Experimental Design for Optimal Structural Intervention in Gene Regulatory Networks Based on the Mean Objective Cost of Uncertainty. - Mahdi Imani; Roozbeh Dehghannasiri; Ulisses M. Braga-Neto; Edward R. Dougherty (CoRR, 2018)

Optimal Clustering under Uncertainty. - Lori A. Dalton; Marco E. Benalcázar; Edward R. Dougherty (CoRR, 2018)

A Bayesian robust Kalman smoothing framework for state-space models with uncertain noise statistics. - Roozbeh Dehghannasiri; Xiaoning Qian; Edward R. Dougherty (EURASIP J. Adv. Signal Process., 2018)

A fast Branch-and-Bound algorithm for U-curve feature selection. - Esmaeil Atashpaz-Gargari; Marcelo da Silva Reis; Ulisses M. Braga-Neto; Junior Barrera; Edward R. Dougherty (Pattern Recognit., 2018)

Intrinsically Bayesian robust Karhunen-Loève compression. - Roozbeh Dehghannasiri; Xiaoning Qian; Edward R. Dougherty (Signal Process., 2018)

Optimal Bayesian Transfer Regression. - Alireza Karbalayghareh; Xiaoning Qian; Edward R. Dougherty (IEEE Signal Process. Lett., 2018)

Sequential Therapeutic Response Modeling for Tumor Treatment Using Computational Hybrid Control Systems Approach. - Wasiu Opeyemi Oduola; Xiangfang Li; Chang Duan; Lijun Qian; Edward R. Dougherty (IEEE Trans. Biomed. Eng., 2018)

Classification of State Trajectories in Gene Regulatory Networks. - Alireza Karbalayghareh; Ulisses M. Braga-Neto; Jianping Hua; Edward Russell Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification. - Jason M. Knight; Ivan Ivanov 001; Karen Triff; Robert S. Chapkin; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Optimal Objective-Based Experimental Design for Uncertain Dynamical Gene Networks with Experimental Error. - Daniel N. Mohsenizadeh; Roozbeh Dehghannasiri; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Optimal Bayesian Classification With Missing Values. - Siamak Zamani Dadaneh; Edward R. Dougherty; Xiaoning Qian (IEEE Trans. Signal Process., 2018)

Optimal Bayesian Kalman Filtering With Prior Update. - Roozbeh Dehghannasiri; Mohammad Shahrokh Esfahani; Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2018)

Optimal Bayesian Transfer Learning. - Alireza Karbalayghareh; Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2018)

Experimental Design via Generalized Mean Objective Cost of Uncertainty. - Shahin Boluki; Xiaoning Qian; Edward R. Dougherty (IEEE Access, 2019)

Quantifying the notions of canalizing and master genes in a gene regulatory network - a Boolean network modeling perspective. - Eunji Kim; Ivan Ivanov 001; Edward R. Dougherty (Bioinform., 2019)

Optimal clustering with missing values. - Shahin Boluki; Siamak Zamani Dadaneh; Xiaoning Qian; Edward R. Dougherty (BMC Bioinform., 2019)

Constructing Pathway-Based Priors within a Gaussian Mixture Model for Bayesian Regression and Classification. - Shahin Boluki; Mohammad Shahrokh Esfahani; Xiaoning Qian; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Classification of Single-Cell Gene Expression Trajectories from Incomplete and Noisy Data. - Alireza Karbalayghareh; Ulisses M. Braga-Neto; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Optimal Bayesian Classification With Vector Autoregressive Data Dependency. - Amin Zollanvari; Edward R. Dougherty (IEEE Trans. Signal Process., 2019)

Boolean Kalman filter and smoother under model uncertainty. - Mahdi Imani; Edward R. Dougherty; Ulisses M. Braga-Neto (Autom., 2020)

Machine Learning Requires Probability and Statistics [Perspectives]. - Ulisses M. Braga-Neto; Edward R. Dougherty (IEEE Signal Process. Mag., 2020)

Model-Based Robust Filtering and Experimental Design for Stochastic Differential Equation Systems. - Guang Zhao; Xiaoning Qian; Byung-Jun Yoon; Francis J. Alexander; Edward R. Dougherty (IEEE Trans. Signal Process., 2020)

Bayesian Active Learning by Soft Mean Objective Cost of Uncertainty. - Guang Zhao; Edward R. Dougherty; Byung-Jun Yoon; Francis J. Alexander; Xiaoning Qian (AISTATS, 2021)

Uncertainty-aware Active Learning for Optimal Bayesian Classifier. - Guang Zhao; Edward R. Dougherty; Byung-Jun Yoon; Francis J. Alexander; Xiaoning Qian (ICLR, 2021)

Efficient Active Learning for Gaussian Process Classification by Error Reduction. - Guang Zhao; Edward R. Dougherty; Byung-Jun Yoon; Francis J. Alexander; Xiaoning Qian (NeurIPS, 2021)

Quantifying the Multi-Objective Cost of Uncertainty. - Byung-Jun Yoon; Xiaoning Qian; Edward R. Dougherty (IEEE Access, 2021)

Optimal Bayesian supervised domain adaptation for RNA sequencing data. - Shahin Boluki; Xiaoning Qian; Edward R. Dougherty (Bioinform., 2021)

Optimal Bayesian Transfer Learning for Count Data. - Alireza Karbalayghareh; Xiaoning Qian; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2021)

Comprehensive analysis of gene expression profiles to radiation exposure reveals molecular signatures of low-dose radiation response. - Xihaier Luo; Sean McCorkle; Gilchan Park; Vanessa López-Marrero; Shinjae Yoo; Edward R. Dougherty; Xiaoning Qian; Francis J. Alexander; Byung-Jun Yoon (BIBM, 2022)

Adaptive Group Testing with Mismatched Models. - Mingzhou Fan; Byung-Jun Yoon; Francis J. Alexander; Edward R. Dougherty; Xiaoning Qian (ICASSP, 2022)

Robust importance sampling for error estimation in the context of optimal Bayesian transfer learning. - Omar Maddouri; Xiaoning Qian; Francis J. Alexander; Edward R. Dougherty; Byung-Jun Yoon (Patterns, 2022)

Network Classification Based on Reducibility With Respect to the Stability of Canalizing Power of Genes in a Gene Regulatory Network - A Boolean Network Modeling Perspective. - Eunji Kim; Ivan Ivanov 001; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Sensitivity Analysis of Genome-Scale Metabolic Flux Prediction. - Puhua Niu; Maria J. Soto; Shuai Huang 001; Byung-Jun Yoon; Edward R. Dougherty; Francis J. Alexander; Ian Blaby; Xiaoning Qian (J. Comput. Biol., 2023)

Knowledge-driven learning, optimization, and experimental design under uncertainty for materials discovery. - Xiaoning Qian; Byung-Jun Yoon; Raymundo Arróyave; Xiaofeng Qian; Edward R. Dougherty (Patterns, 2023)

Optimal decision-making in high-throughput virtual screening pipelines. - Hyun-Myung Woo; Xiaoning Qian; Li Tan; Shantenu Jha; Francis J. Alexander; Edward R. Dougherty; Byung-Jun Yoon (Patterns, 2023)

Multi-fidelity Bayesian Optimization with Multiple Information Sources of Input-dependent Fidelity. - Mingzhou Fan; Byung-Jun Yoon; Edward R. Dougherty; Nathan M. Urban; Francis J. Alexander; Raymundo Arróyave; Xiaoning Qian (UAI, 2024)

Pathway-based analyses of gene expression profiles at low doses of ionizing radiation. - Xihaier Luo; Seyednami Niyakan; Patrick R. Johnstone; Sean McCorkle; Gilchan Park; Vanessa López-Marrero; Shinjae Yoo; Edward R. Dougherty; Xiaoning Qian; Francis J. Alexander; Shantenu Jha; Byung-Jun Yoon (Frontiers Bioinform., 2024)

Optimal Bayesian Regression With Vector Autoregressive Data Dependency. - Samira Reihanian; Edward R. Dougherty; Amin Zollanvari (IEEE Trans. Signal Process., 2024)

Bayesian Proper Orthogonal Decomposition for Learnable Reduced-Order Models With Uncertainty Quantification. - Shahin Boluki; Siamak Zamani Dadaneh; Edward R. Dougherty; Xiaoning Qian (IEEE Trans. Artif. Intell., 2024)