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List of works by Edward R. Dougherty

A CoD-based reduction algorithm for designing stationary control policies on Boolean networks

scientific article published on 25 April 2010

A CoD-based stationary control policy for intervening in large gene regulatory networks ⬇️

scientific article published on October 18, 2011

A Systems Biology Approach in Therapeutic Response Study for Different Dosing Regimens—a Modeling Study of Drug Effects on Tumor Growth using Hybrid Systems ⬇️

scientific article published on February 27, 2012

A comparison study of optimal and suboptimal intervention policies for gene regulatory networks in the presence of uncertainty

scientific article published on 3 April 2014

A fast Branch-and-Bound algorithm for U-curve feature selection ⬇️

scholarly article

A systematic model of the LC-MS proteomics pipeline

scientific article

Accelerated search for BaTiO3-based piezoelectrics with vertical morphotropic phase boundary using Bayesian learning

scientific article

Accurate and reliable cancer classification based on probabilistic inference of pathway activity

scientific article

Adaptive intervention in probabilistic boolean networks

scientific article published on 8 June 2009

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

scientific article published on November 2015

An experimental design framework for Markovian gene regulatory networks under stationary control policy

article

Analysis and modeling of time-course gene-expression profiles from nanomaterial-exposed primary human epidermal keratinocytes

scientific article

Analytical Study of Performance of Linear Discriminant Analysis in Stochastic Settings

scientific article

Application of the Bayesian MMSE estimator for classification error to gene expression microarray data ⬇️

scientific article published on May 5, 2011

Assessing the efficacy of molecularly targeted agents on cell line-based platforms by using system identification

scientific article

BPDA - A Bayesian peptide detection algorithm for mass spectrometry ⬇️

scientific article published on September 29, 2010

BPDA2d—a 2D global optimization-based Bayesian peptide detection algorithm for liquid chromatograph–mass spectrometry ⬇️

scientific article published on December 6, 2011

Bayesian Regression with Network Prior: Optimal Bayesian Filtering Perspective

scientific article

Big data need big theory too

scientific article

Binarization of microarray data on the basis of a mixture model.

scientific article

Bolstered error estimation

Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS.

scientific article

Cancer therapy design based on pathway logic ⬇️

scientific article published on December 30, 2010

Causality, Randomness, Intelligibility, and the Epistemology of the Cell ⬇️

scientific article (publication date: June 2010)

Characterization of drug efficacy regions based on dosage and frequency schedules

scientific article published on November 9, 2010

Characterization of the effectiveness of reporting lists of small feature sets relative to the accuracy of the prior biological knowledge.

scientific article published on 18 March 2010

Chemopreventive n-3 polyunsaturated fatty acids reprogram genetic signatures during colon cancer initiation and progression in the rat.

scientific article published on September 2004

Classification of quantized small sample data

Classification with reject option in gene expression data

scientific article

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

scientific article

Coefficient of determination in nonlinear signal processing

article

Comparing automatic and manual image processing in FLARE assay analysis for colon carcinogenesis.

scientific article

Comparison of gene regulatory networks via steady-state trajectories

scientific article published on January 2007

Conditioning-based modeling of contextual genomic regulation

scientific article published on April 2009

Confidence intervals for the true classification error conditioned on the estimated error

scientific article published in December 2006

Corrected small-sample estimation of the Bayes error

scientific article published in May 2003

Cross-validation under separate sampling: strong bias and how to correct it

scientific article

Decorrelation of the true and estimated classifier errors in high-dimensional settings

scientific article published on January 2007

Design of binary filters by sequential basis expansion

Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification

scientific article

Detecting periodic genes from irregularly sampled gene expressions: a comparison study

scientific article

Dynamical modeling of drug effect using hybrid systems

scientific article published on 26 December 2012

Dynamical modeling of uncertain interaction-based genomic networks

scientific article published on 25 September 2015

Effect of separate sampling on classification accuracy

scientific article

Efficient experimental design for uncertainty reduction in gene regulatory networks

scientific article published on 25 September 2015

Erratum to: Efficient experimental design for uncertainty reduction in gene regulatory networks

scientific article

Estimating conditional probabilities for the detection of unfavorable copy number alterations in a targeted therapy

scientific article published on 5 June 2013

Evaluating dynamic effects of copy number alterations on gene expression using a single transcription model

scientific article

Evaluating gene set enrichment analysis via a hybrid data model

scientific article

External control in Markovian genetic regulatory networks: the imperfect information case

scientific article published on 29 January 2004

From biological pathways to regulatory networks ⬇️

scientific article published on December 15, 2010

Fuzzy intervention in biological phenomena

scientific article published in November 2012

Gene clustering based on clusterwide mutual information

scientific article published in January 2004

Gene perturbation and intervention in probabilistic Boolean networks

scientific article

Gene selection: a Bayesian variable selection approach

scientific article published on January 2003

Generating Boolean networks with a prescribed attractor structure

scientific article published on 8 September 2005

Genetic regulatory networks

scientific article published on January 2007

Genetic test bed for feature selection

scientific article published on 20 January 2006

Genomic signal processing

scientific article published on September 2009

Growing genetic regulatory networks from seed genes

scientific article published on 10 February 2004

Guest Editorial-Special Collection Topic: Statistical Systems Theory in Cancer Modeling, Diagnosis, and Therapy.

scientific article published on 5 March 2018

High-dimensional bolstered error estimation

scientific article

How many samples are needed to build a classifier: a general sequential approach

scientific article

Identification of combination gene sets for glioma classification.

scientific article

Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network ⬇️

scientific article published on October 7, 2010

Identification of signature genes by microarray for acute myeloid leukemia without maturation and acute promyelocytic leukemia with t(15;17)(q22;q12)(PML/RARalpha).

scientific article

Identifying genes involved in cyclic processes by combining gene expression analysis and prior knowledge

scientific article published on 15 April 2009

Identifying mechanistic similarities in drug responses ⬇️

scientific article published on May 15, 2012

Impact of missing value imputation on classification for DNA microarray gene expression data--a model-based study

scientific article

Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors

scientific article published on 28 December 2017

Incorporating prior knowledge induced from stochastic differential equations in the classification of stochastic observations

scientific article

Incorporation of Biological Pathway Knowledge in the Construction of Priors for Optimal Bayesian Classification

scientific article published in January 2014

Inference from clustering with application to gene-expression microarrays

scientific article

Inference of Boolean networks using sensitivity regularization

scientific article published on January 2008

Inference of a probabilistic Boolean network from a single observed temporal sequence

scientific article published on January 2007

Inferring connectivity of genetic regulatory networks using information-theoretic criteria

scientific article

Inferring gene regulatory networks from time series data using the minimum description length principle

scientific article

Insight into redox-regulated gene networks in vascular cells

scientific article published on 10 April 2007

Integrating Multiscale Modeling with Drug Effects for Cancer Treatment

scientific article

Intervention in Biological Phenomena Modeled by S-Systems ⬇️

scientific article published on December 17, 2010

Intervention in a family of Boolean networks

scientific article published on 12 November 2005

Intervention in context-sensitive probabilistic Boolean networks

scientific article

Intervention in context-sensitive probabilistic Boolean networks revisited

scientific article

Intervention in gene regulatory networks via a stationary mean-first-passage-time control policy

scientific article published in October 2008

Intervention in gene regulatory networks via greedy control policies based on long-run behavior

scientific article

Intervention in gene regulatory networks via phenotypically constrained control policies based on long-run behavior

scientific article published on 20 July 2011

Intervention in gene regulatory networks with maximal phenotype alteration

scientific article published on 29 April 2013

Intrinsically Bayesian robust classifier for single-cell gene expression trajectories in gene regulatory networks.

scientific article published on 21 March 2018

Intrinsically Multivariate Predictive Genes

article

Is cross-validation better than resubstitution for ranking genes?

scientific article published in January 2004

Is cross-validation valid for small-sample microarray classification?

scientific article published in February 2004

Learning restricted Boolean network model by time-series data

scientific article

MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification

scientific article

Missing-value estimation using linear and non-linear regression with Bayesian gene selection

scientific article published in November 2003

Modeling and systematic analysis of biomarker validation using selected reaction monitoring

scientific article

Modeling the next generation sequencing sample processing pipeline for the purposes of classification

scientific article

Moments and Root-Mean-Square Error of the Bayesian MMSE Estimator of Classification Error in the Gaussian Model

scientific article published on June 2014

Morphological spot counting from stacked images for automated analysis of gene copy numbers by fluorescence in situ hybridization

scientific article published on January 2002

Multiple-rule bias in the comparison of classification rules ⬇️

scientific article published on May 5, 2011

Newton, laplace, and the epistemology of systems biology

scientific article published on 30 October 2012

Noise factor analysis for cDNA microarrays

scientific article published in July 2004

Noise-injected neural networks show promise for use on small-sample expression data

scientific article

Noninvasive detection of candidate molecular biomarkers in subjects with a history of insulin resistance and colorectal adenomas

scientific article published on 26 May 2009

Normalization benefits microarray-based classification

scientific article

On the epistemological crisis in genomics

scientific article

On the impoverishment of scientific education

scientific article

On the limitations of biological knowledge

scientific article published on November 2012

On the long-run sensitivity of probabilistic Boolean networks

scientific article published on 31 December 2008

On the number of close-to-optimal feature sets.

scientific article published in January 2006

Optimal clustering with missing values.

scientific article published on 20 June 2019

Optimal constrained stationary intervention in gene regulatory networks

scientific article

Optimal intervention strategies for cyclic therapeutic methods

scientific article published on 15 August 2008

Optimal number of features as a function of sample size for various classification rules

scientific article published on 30 November 2004

Performance of feature selection methods

scientific article published on September 2009

Performance reproducibility index for classification ⬇️

scientific article published on September 6, 2012

Phenotype Classification Using Moment Features of Single-Cell Data.

scientific article

Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks

scientific article published in February 2002

Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty

scientific article

Quantification of the impact of feature selection on the variance of cross-validation error estimation

scientific article published on January 2007

RNAi microarray analysis in cultured mammalian cells

scientific article

Ratio statistics of gene expression levels and applications to microarray data analysis

scientific article

Recent advances in intervention in markovian regulatory networks

scientific article

Recovering genetic regulatory networks from chromatin immunoprecipitation and steady-state microarray data

scientific article

Reducing confounding and suppression effects in TCGA data: an integrated analysis of chemotherapy response in ovarian cancer

scientific article

Reporting bias when using real data sets to analyze classification performance

scientific article

Review of stochastic hybrid systems with applications in biological systems modeling and analysis

scientific article

Scalable Optimal Bayesian Classification of Single-Cell Trajectories under Regulatory Model Uncertainty

Scientific knowledge is possible with small-sample classification

scientific article published on 20 August 2013

Sequential Experimental Design for Optimal Structural Intervention in Gene Regulatory Networks Based on the Mean Objective Cost of Uncertainty

article

Sequential Therapeutic Response Modeling for Tumor Treatment Using Computational Hybrid Control Systems Approach

scientific article

Simulation of cDNA microarrays via a parameterized random signal model

scientific article published in July 2002

Small-sample precision of ROC-related estimates

scientific article published on 3 February 2010

Spectral analysis on time-course expression data: detecting periodic genes using a real-valued iterative adaptive approach

scientific article

Spectral preprocessing for clustering time-series gene expressions

scientific article

State reduction for network intervention in probabilistic Boolean networks ⬇️

scientific article published on October 17, 2010

Steady-state analysis of genetic regulatory networks modelled by probabilistic boolean networks

scientific article

Stochastic modeling of the relationship between copy number and gene expression based on transcriptional logic

scientific article

Strong feature sets from small samples

scientific article published in January 2002

Superior feature-set ranking for small samples using bolstered error estimation

scientific article

Systematic reverse engineering of network topologies: a case study of resettable bistable cellular responses

scientific article

Systems biology for organotypic cell cultures

scientific article published on 14 November 2016

The Illusion of Distribution-Free Small-Sample Classification in Genomics ⬇️

scientific article published on August 1, 2011

The Model-Based Study of the Effectiveness of Reporting Lists of Small Feature Sets Using RNA-Seq Data

scientific article

The impact of function perturbations in Boolean networks

scientific article published on 22 March 2007

The role of certain Post classes in Boolean network models of genetic networks

scientific article

Time-Based Switching Control of Genetic Regulatory Networks: Toward Sequential Drug Intake for Cancer Therapy

scientific article

Tracking transcriptional activities with high-content epifluorescent imaging ⬇️

scientific article published on April 1, 2012

Translational science: epistemology and the investigative process

scientific article published on April 2009

Unbiased bootstrap error estimation for linear discriminant analysis

scientific article published on 03 October 2014

Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor

scientific article

Unraveling gene-gene interactions regulated by ligands of the aryl hydrocarbon receptor

article

Using the minimum description length principle to reduce the rate of false positives of best-fit algorithms

scientific article published on 03 July 2014

Validation of gene regulatory network inference based on controllability

scientific article

Validation of gene regulatory networks: scientific and inferential ⬇️

scientific article published on December 22, 2010

Validation of inference procedures for gene regulatory networks

scientific article published on September 2007

What should be expected from feature selection in small-sample settings

scientific article published on 26 July 2006

Which is better for cDNA-microarray-based classification: ratios or direct intensities

scientific article published on 28 September 2004

Which is better: holdout or full-sample classifier design?

scientific article published on January 2008

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