Cancer Informatics

BioMiner: Paving the Way for Personalized Medicine (Published on 20 Apr 2015)

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Profiling Age-Related Epigenetic Markers of Stomach Adenocarcinoma in Young and Old Subjects (Published on 20 Apr 2015)

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Computing Molecular Signatures as Optima of a Bi-Objective Function: Method and Application to Prediction in Oncogenomics (Published on 19 Apr 2015)

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Catchment Area Analysis Using Bayesian Regression Modeling (Published on 19 Apr 2015)

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RNA-Seq and Network Analysis Revealed Interacting Pathways in TGF-β-Treated Lung Cancer Cell Lines (Published on 01 Apr 2015)

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Prioritization of Cancer-Related Genomic Variants by SNP Association Network (Published on 01 Apr 2015)

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Expression of Polarity Genes in Human Cancer (Published on 30 Mar 2015)

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Design and Implementation of a Comprehensive Web-based Survey for Ovarian Cancer Survivorship with an Analysis of Prediagnosis Symptoms via Text Mining (Published on 23 Mar 2015)

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HCsnip: An R Package for Semi-supervised Snipping of the Hierarchical Clustering Tree (Published on 22 Mar 2015)

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Case-Based Retrieval Framework for Gene Expression Data (Published on 19 Mar 2015)

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GeneMed: An Informatics Hub for the Coordination of Next-Generation Sequencing Studies that Support Precision Oncology Clinical Trials (Published on 19 Mar 2015)

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Introductory Editorial: Network and Pathway Analysis of Cancer Susceptibility (A) (Published on 12 Mar 2015)

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Identification of Medium-Sized Copy Number Alterations in Whole-Genome Sequencing (Published on 05 Mar 2015)

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Introductory Editorial: Sequencing Platform Modeling and Analysis (Published on 02 Mar 2015)

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Modeling Discrete Survival Time Using Genomic Feature Data (Published on 02 Mar 2015)

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Comprehensive Evaluation of Composite Gene Features in Cancer Outcome Prediction (Published on 24 Feb 2015)

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What Tumor Dynamics Modeling Can Teach us About Exploiting the Stem-Cell View for Better Cancer Treatment (Published on 24 Feb 2015)

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Network Analysis of Circular Permutations in Multidomain Proteins Reveals Functional Linkages for Uncharacterized Proteins (Published on 19 Feb 2015)

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Introductory Editorial: Array Platform Modeling and Analysis (A) (Published on 17 Feb 2015)

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Mapping Splicing Quantitative Trait Loci in RNA-Seq (Published on 16 Feb 2015)

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Toolbox for Mobile-Element Insertion Detection on Cancer Genomes (Published on 12 Feb 2015)

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Extending Information Retrieval Methods to Personalized Genomic-Based Studies of Disease (Published on 10 Feb 2015)

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Evaluating Methods for Modeling Epistasis Networks with Application to Head and Neck Cancer (Published on 10 Feb 2015)

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Pathway-based Biomarkers for Breast Cancer in Proteomics (Published on 09 Feb 2015)

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An Improved Version of Logistic Bayesian LASSO for Detecting Rare Haplotype-Environment Interactions with Application to Lung Cancer (Published on 09 Feb 2015)

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Regulation of Epithelial-Mesenchymal Transition in Breast Cancer Cells by Cell Contact and Adhesion (Published on 09 Feb 2015)

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Identifying Driver Genes in Cancer by Triangulating Gene Expression, Gene Location, and Survival Data (Published on 03 Feb 2015)

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Empirical Transition Probability Indexing Sparse-Coding Belief Propagation (ETPI-SCoBeP) Genome Sequence Alignment (Published on 01 Feb 2015)

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sfDM: Open-Source Software for Temporal Analysis and Visualization of Brain Tumor Diffusion MR Using Serial Functional Diffusion Mapping (Published on 01 Feb 2015)

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Hidden Markov Model-Based CNV Detection Algorithms for Illumina Genotyping Microarrays (Published on 27 Jan 2015)

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Prognostic Gene Signature Identification Using Causal Structure Learning: Applications in Kidney Cancer (Published on 27 Jan 2015)

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Mitochondrial Variations in Non-Small Cell Lung Cancer (NSCLC) Survival (Published on 27 Jan 2015)

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Nonparametric Tests for Differential Histone Enrichment with ChIP-Seq Data (Published on 27 Jan 2015)

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Inferring Active and Prognostic Ligand-Receptor Pairs with Interactions in Survival Regression Models (Published on 26 Jan 2015)

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Practical Issues in Screening and Variable Selection in Genome-Wide Association Analysis (Published on 14 Jan 2015)

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Network-Constrained Group Lasso for High-Dimensional Multinomial Classification with Application to Cancer Subtype Prediction (Published on 12 Jan 2015)

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Detection of Pancreatic Cancer Biomarkers Using Mass Spectrometry (Published on 06 Jan 2015)

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Web Tool for Estimating the Cancer Hazard Rates in Aging (Published on 17 Dec 2014)

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Statistical Issues in the Design and Analysis of nCounter Projects (Published on 14 Dec 2014)

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ordinalgmifs: An R Package for Ordinal Regression in High-dimensional Data Settings (Published on 10 Dec 2014)

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Bayesian Hierarchical Models for Protein Networks in Single-Cell Mass Cytometry (Published on 10 Dec 2014)

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Overcome Support Vector Machine Diagnosis Overfitting (Published on 09 Dec 2014)

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Normal Cell-Type Epigenetics and Breast Cancer Classification: A Case Study of Cell Mixture–Adjusted Analysis of DNA Methylation Data from Tumors (Published on 09 Dec 2014)

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Growth Rate Analysis and Efficient Experimental Design for Tumor Xenograft Studies (Published on 09 Dec 2014)

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Stratified Pathway Analysis to Identify Gene Sets Associated with Oral Contraceptive Use and Breast Cancer (Published on 09 Dec 2014)

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CARAT-GxG: CUDA-Accelerated Regression Analysis Toolkit for Large-Scale Gene–Gene Interaction with GPU Computing System (Published on 09 Dec 2014)

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Computational Construction of Antibody–Drug Conjugates Using Surface Lysines as the Antibody Conjugation Site and a Non-cleavable Linker (Published on 08 Dec 2014)

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Semantically Linking In Silico Cancer Models (Published on 08 Dec 2014)

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Bayesian Joint Selection of Genes and Pathways: Applications in Multiple Myeloma Genomics (Published on 07 Dec 2014)

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Trial Prospector: Matching Patients with Cancer Research Studies Using an Automated and Scalable Approach (Published on 04 Dec 2014)

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A Pan-Cancer Analysis of Alternative Splicing Events Reveals Novel Tumor-Associated Splice Variants of Matriptase (Published on 04 Dec 2014)

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Streamlined Genome Sequence Compression using Distributed Source Coding (Published on 02 Dec 2014)

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Assessment of Subnetwork Detection Methods for Breast Cancer (Published on 02 Dec 2014)

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FocalCall: An R Package for the Annotation of Focal Copy Number Aberrations (Published on 01 Dec 2014)

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Supervised Classification by Filter Methods and Recursive Feature Elimination Predicts Risk of Radiotherapy-Related Fatigue in Patients with Prostate Cancer (Published on 01 Dec 2014)

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Health Information Technology in Oncology Practice: A Literature Review (Published on 01 Dec 2014)

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Revealing Biological Pathways Implicated in Lung Cancer from TCGA Gene Expression Data Using Gene Set Enrichment Analysis (Published on 01 Dec 2014)

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Correction to “Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes” (Published on 30 Nov 2014)

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Correction to "Network Analysis of Cancer-focused Association Network Reveals Distinct Network Association Patterns" (Published on 20 Nov 2014)

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A Bayesian Framework to Improve MicroRNA Target Prediction by Incorporating External Information (Published on 18 Nov 2014)

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Type I Error Control for Tree Classification (Published on 16 Nov 2014)

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Conducting Retrospective Ontological Clinical Trials in ICD-9-CM in the Age of ICD-10-CM (Published on 09 Nov 2014)

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In Silico Prediction of Synthetic Lethality by Meta-Analysis of Genetic Interactions, Functions, and Pathways in Yeast and Human Cancer (Published on 05 Nov 2014)

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A Novel Subset of Human Tumors That Simultaneously Overexpress Multiple E2F-responsive Genes Found in Breast, Ovarian, and Prostate Cancers (Published on 03 Nov 2014)

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Correction to: Prognostic Features of Signal Transducer and Activator of Transcription 3 in an ER(+) Breast Cancer Model System (Published on 02 Nov 2014)

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Predicting Cancer Prognosis Using Functional Genomics Data Sets (Published on 02 Nov 2014)

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Propensity Score Method for Partially Matched Omics Studies (Published on 29 Oct 2014)

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A Pan-Cancer Modular Regulatory Network Analysis to Identify Common and Cancer-Specific Network Components (Published on 28 Oct 2014)

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Learning Dysregulated Pathways in Cancers from Differential Variability Analysis (Published on 23 Oct 2014)

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Classification of Images Acquired with Colposcopy Using Artificial Neural Networks (Published on 21 Oct 2014)

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eMBI: Boosting Gene Expression-based Clustering for Cancer Subtypes (Published on 21 Oct 2014)

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Co-expression Network Analysis of Human lncRNAs and Cancer Genes (Published on 19 Oct 2014)

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The Axis of Progression of Disease (Published on 19 Oct 2014)

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A Comprehensive Comparison of Normalization Methods for Loading Control and Variance Stabilization of Reverse-Phase Protein Array Data (Published on 16 Oct 2014)

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Network-Based Identification of Biomarkers Coexpressed with Multiple Pathways (Published on 16 Oct 2014)

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StickWRLD as an Interactive Visual Pre-Filter for Canceromics-Centric Expression Quantitative Trait Locus Data (Published on 16 Oct 2014)

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Developing a Comprehensive Database Management System for Organization and Evaluation of Mammography Datasets (Published on 16 Oct 2014)

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Network Analysis of Cancer-focused Association Network Reveals Distinct Network Association Patterns (Published on 16 Oct 2014)

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Toolbox for Mobile-Element Insertion Detection on Cancer Genomes (Published on 15 Oct 2014)

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Mapping Splicing Quantitative Trait Loci in RNA-Seq (Published on 15 Oct 2014)

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TEGS-CN: A Statistical Method for Pathway Analysis of Genome-wide Copy Number Profile (Published on 15 Oct 2014)

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Unsupervised Outlier Profile Analysis (Published on 15 Oct 2014)

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CORM: An R Package Implementing the Clustering of Regression Models Method for Gene Clustering (Published on 15 Oct 2014)

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Profiling the microRNA Expression in Human iPS and iPS-derived Retinal Pigment Epithelium (Published on 15 Oct 2014)

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Master Regulators, Regulatory Networks, and Pathways of Glioblastoma Subtypes (Published on 15 Oct 2014)

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Network-based Prediction of Cancer under Genetic Storm (Published on 15 Oct 2014)

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Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline (Published on 15 Oct 2014)

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Automated Recommendation for Cervical Cancer Screening and Surveillance (Published on 15 Oct 2014)

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Exploiting Literature-derived Knowledge and Semantics to Identify Potential Prostate Cancer Drugs (Published on 14 Oct 2014)

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Prediction of MicroRNA Precursors Using Parsimonious Feature Sets (Published on 14 Oct 2014)

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Disease Biomarker Query from RNA-Seq Data (Published on 14 Oct 2014)

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Integrated DNA Copy Number and Gene Expression Regulatory Network Analysis of Non-small Cell Lung Cancer Metastasis (Published on 14 Oct 2014)

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CSNK1A1 and Gli2 as Novel Targets Identified Through an Integrative Analysis of Gene Expression Data, Protein-Protein Interaction and Pathways Networks in Glioblastoma Tumors: Can These Two Be Antagonistic Proteins? (Published on 13 Oct 2014)

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Introductory Editorial: Computational Advances in Cancer Informatics (A) (Published on 13 Oct 2014)

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Inferring Aberrant Signal Transduction Pathways in Ovarian Cancer from TCGA Data (Published on 13 Oct 2014)

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Optimization of Network Topology in Computer-Aided Detection Schemes Using Phased Searching with NEAT in a Time-Scaled Framework (Published on 13 Oct 2014)

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Mining Cancer-Specific Disease Comorbidities from a Large Observational Health Database (Published on 13 Oct 2014)

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Text Mining in Cancer Gene and Pathway Prioritization (Published on 13 Oct 2014)

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Modeling Signal Transduction from Protein Phosphorylation to Gene Expression (Published on 13 Oct 2014)

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Feasibility and Implementation of a Literature Information Management System for Human Papillomavirus in Head and Neck Cancers with Imaging (Published on 13 Oct 2014)

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Inferring the Effects of Honokiol on the Notch Signaling Pathway in SW480 Colon Cancer Cells (Published on 13 Oct 2014)

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RNAseqPS: A Web Tool for Estimating Sample Size and Power for RNAseq Experiment (Published on 13 Oct 2014)

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Combined Benefit of Prediction and Treatment: A Criterion for Evaluating Clinical Prediction Models (Published on 05 Oct 2014)

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Bayesian Disease Classification Using Copy Number Data (Published on 01 Oct 2014)

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Introductory Editorial: Classification, Predictive Modelling, and Statistical Analysis of Cancer Data (A) (Published on 21 Sep 2014)

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Functional Annotation of Putative Regulatory Elements at Cancer Susceptibility Loci (Published on 21 Sep 2014)

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A Review of Cancer Risk Prediction Models with Genetic Variants (Published on 21 Sep 2014)

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A Bayesian Integrative Model for Genetical Genomics with Spatially Informed Variable Selection (Published on 21 Sep 2014)

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Integrative Bayesian Network Analysis of Genomic Data (Published on 21 Sep 2014)

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Integrated Analysis of Whole-Genome Paired-End and Mate-Pair Sequencing Data for Identifying Genomic Structural Variations in Multiple Myeloma (Published on 21 Sep 2014)

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Comparative Study of Computational Methods for Reconstructing Genetic Networks of Cancer-Related Pathways (Published on 21 Sep 2014)

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Review of Current Methods, Applications, and Data Management for the Bioinformatics Analysis of Whole Exome Sequencing (Published on 21 Sep 2014)

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Integrative Pathway Analysis Using Graph-Based Learning with Applications to TCGA Colon and Ovarian Data (Published on 28 Jul 2014)

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On the Significance of Fuzzification of the N and M in Cancer Staging (Published on 24 Jul 2014)

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Modeling the Altered Expression Levels of Genes on Signaling Pathways in Tumors As Causal Bayesian Networks (Published on 25 May 2014)

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Nonlinear Optical Microscopy Signal Processing Strategies in Cancer (Published on 02 Apr 2014)

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INsPeCT: INtegrative Platform for Cancer Transcriptomics (Published on 12 Mar 2014)

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A New Method for Predicting Patient Survivorship Using Efficient Bayesian Network Learning (Published on 13 Feb 2014)

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Evaluating Gene Set Enrichment Analysis Via a Hybrid Data Model (Published on 12 Feb 2014)

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Prognostic features of signal transducer and activator of transcription 3 in an ER(+) breast cancer model system (Published on 21 Jan 2014)

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OmicCircos: A Simple-to-Use R Package for the Circular Visualization of Multidimensional Omics Data (Published on 16 Jan 2014)

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stepwiseCM: An R Package for Stepwise Classification of Cancer Samples Using Multiple Heterogeneous Data Sets (Published on 02 Jan 2014)

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Are the Somatic Mutation and Tissue Organization Field Theories of Carcinogenesis Incompatible? (Published on 01 Dec 2013)

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Gene Expression Meta-Analysis Identifies Cytokine Pathways and 5q Aberrations Involved in Metastasis of ERBB2 Amplified and Basal Breast Cancer (Published on 25 Nov 2013)

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Monitoring of Technical Variation in Quantitative High-Throughput Datasets (Published on 23 Sep 2013)

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Comprehensive Assessment and Network Analysis of the Emerging Genetic Susceptibility Landscape of Prostate Cancer (Published on 28 Aug 2013)

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Analysis of Patterns of Gene Expression Variation within and between Ethnic Populations in Pediatric B-ALL (Published on 27 Aug 2013)

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Improved Sparse Multi-Class SVM and Its Application for Gene Selection in Cancer Classification (Published on 04 Aug 2013)

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Novel Integrative Genomics Approach for Associating GWAS Information with Intrinsic Subtypes of Breast Cancer (Published on 15 May 2013)

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Dealing with Diversity in Computational Cancer Modeling (Published on 07 May 2013)

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Prognostic Estimator of Survival for Patients with Localized and Extended Pancreatic Ductal Adenocarcinoma (Published on 18 Mar 2013)

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An Empirical Evaluation of Normalization Methods for MicroRNA Arrays in a Liposarcoma Study (Published on 18 Mar 2013)

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Basic Equations and Computing Procedures for Frailty Modeling of Carcinogenesis: Application to Pancreatic Cancer Data (Published on 18 Feb 2013)

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In Silico Discovery of Mitosis Regulation Networks Associated with Early Distant Metastases in Estrogen Receptor Positive Breast Cancers (Published on 13 Feb 2013)

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Classification of Tumor Samples from Expression Data Using Decision Trunks (Published on 13 Feb 2013)

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Design of an Expert System for Mitigating Trace Element Toxicity in Cancer Risk Management (Published on 04 Feb 2013)

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An Integrative Genomics Approach for Associating GWAS Information with Triple-Negative Breast Cancer (Published on 29 Jan 2013)

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Prediction of Breast Cancer Metastasis by Gene Expression Profiles: A Comparison of Metagenes and Single Genes (Published on 10 Dec 2012)

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Mapping the Future—Merging the Old with the New Across Disciplines (Published on 26 Nov 2012)

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Newton, Laplace, and The Epistemology of Systems Biology (Published on 30 Oct 2012)

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Significance Analysis of Microarrays (SAM) Offers Clues to Differences Between the Genomes of Adult Philadelphia Positive ALL and the Lymphoid Blast Transformation of CML (Published on 12 Sep 2012)

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Haploinsufficiency of Tumor Suppressor Genes is Driven by the Cumulative Effect of microRNAs, microRNA Binding Site Polymorphisms and microRNA Polymorphisms: An In silico Approach (Published on 29 Aug 2012)

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TNBCtype: A Subtyping Tool for Triple-Negative Breast Cancer (Published on 24 Jul 2012)

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Identification of a Gene Expression Signature Common to Distinct Cancer Pathways (Published on 08 May 2012)

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In Silico Prediction for Regulation of Transcription Factors onTheir Shared Target Genes Indicates Relevant Clinical Implications in a Breast Cancer Population (Published on 19 Apr 2012)

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Major Functional Transcriptome of an Inferred Center Regulator of an ER(-) Breast Cancer Model System (Published on 19 Apr 2012)

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Surface Adjustment of Reverse Phase Protein Arrays using Positive Control Spots (Published on 11 Apr 2012)

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Integrated Analysis Reveals hsa-miR-142 as a Representative of a Lymphocyte-Specific Gene Expression and Methylation Signature (Published on 12 Mar 2012)

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A Systems Biology Approach in Therapeutic Response Study for Different Dosing Regimens—a Modeling Study of Drug Effects on Tumor Growth using Hybrid Systems (Published on 27 Feb 2012)

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Gene Selection using a High-Dimensional Regression Model with Microarrays in Cancer Prognostic Studies (Published on 27 Feb 2012)

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