Machine learning and clinical epigenetics: a review of challenges for diagnosis and classification

Better medicine through machine learning: What’s real, and what’s artificial?

(2019) Suchi Saria et al.   PLOS MEDICINE

Machine Learning in Medicine

(2019) Alvin Rajkomar et al.   NEW ENGLAND JOURNAL OF MEDICINE

Magic-BLAST, an accurate RNA-seq aligner for long and short reads

(2019) Grzegorz M. Boratyn et al.   BMC BIOINFORMATICS

Maternal Smoking During Pregnancy Induces Persistent Epigenetic Changes Into Adolescence, Independent of Postnatal Smoke Exposure and Is Associated With Cardiometabolic Risk

(2019) Sebastian Rauschert et al.   Frontiers in Genetics

Genomic DNA Methylation Signatures Enable Concurrent Diagnosis and Clinical Genetic Variant Classification in Neurodevelopmental Syndromes

(2018) Erfan Aref-Eshghi et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Deep-Learning Convolutional Neural Networks Accurately Classify Genetic Mutations in Gliomas

(2018) P. Chang et al.   AMERICAN JOURNAL OF NEURORADIOLOGY

Artificial Intelligence in Surgery

(2018) Daniel A. Hashimoto et al.   ANNALS OF SURGERY

Epigenetic machine learning: utilizing DNA methylation patterns to predict spastic cerebral palsy

(2018) Erin L. Crowgey et al.   BMC BIOINFORMATICS

Machine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation

(2018) Tathiane M. Malta et al.   CELL

DNA methylation-based classification of central nervous system tumours

(2018) David Capper et al.   NATURE

Implementing Machine Learning in Health Care — Addressing Ethical Challenges

(2018) Danton S. Char et al.   NEW ENGLAND JOURNAL OF MEDICINE

Integrated genetic and epigenetic prediction of coronary heart disease in the Framingham Heart Study

(2018) Meeshanthini V. Dogan et al.   PLoS One

Variable selection in omics data: A practical evaluation of small sample sizes

(2018) Alexander Kirpich et al.   PLoS One

Multiple imputation with sequential penalized regression

(2018) Faisal M Zahid et al.   STATISTICAL METHODS IN MEDICAL RESEARCH

Genomic DNA Methylation-Derived Algorithm Enables Accurate Detection of Malignant Prostate Tissues

(2018) Erfan Aref-Eshghi et al.   Frontiers in Oncology

Epigenetic Mechanisms and Hypertension

(2018) Mingyu Liang   HYPERTENSION

High-performance medicine: the convergence of human and artificial intelligence

(2018) Eric J. Topol   NATURE MEDICINE

Clinical epigenetics: seizing opportunities for translation

(2018) María Berdasco et al.   NATURE REVIEWS GENETICS

BAFopathies’ DNA methylation epi-signatures demonstrate diagnostic utility and functional continuum of Coffin–Siris and Nicolaides–Baraitser syndromes

(2018) Erfan Aref-Eshghi et al.   Nature Communications

Epigenetic profiling for the molecular classification of metastatic brain tumors

(2018) Javier I. J. Orozco et al.   Nature Communications

Epigenetically reprogrammed methylation landscape drives the DNA self-assembly and serves as a universal cancer biomarker

(2018) Abu Ali Ibn Sina et al.   Nature Communications

Deep Learning in Medicine—Promise, Progress, and Challenges

(2018) Fei Wang et al.   JAMA Internal Medicine

Machine learning for epigenetics and future medical applications

(2017) Lawrence B. Holder et al.   Epigenetics

Learning from class-imbalanced data: Review of methods and applications

(2017) Guo Haixiang et al.   EXPERT SYSTEMS WITH APPLICATIONS

A Critical Review for Developing Accurate and Dynamic Predictive Models Using Machine Learning Methods in Medicine and Health Care

(2017) Hamdan O. Alanazi et al.   JOURNAL OF MEDICAL SYSTEMS

Artificial Intelligence in Precision Cardiovascular Medicine

(2017) Chayakrit Krittanawong et al.   JOURNAL OF THE AMERICAN COLLEGE OF CARDIOLOGY

Artificial intelligence in medicine

(2017) Pavel Hamet et al.   METABOLISM-CLINICAL AND EXPERIMENTAL

Correcting length-bias in gene set analysis for DNA methylation data

(2017) Shaoyu Li et al.   Statistics and Its Interface

Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks

(2017) Mehrab Ghanat Bari et al.   Scientific Reports

DNA methylation landscape of ocular tissue relative to matched peripheral blood

(2017) Alex W Hewitt et al.   Scientific Reports

DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis

(2016) Bonnie R. Joubert et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Dimension reduction techniques for the integrative analysis of multi-omics data

(2016) Chen Meng et al.   BRIEFINGS IN BIOINFORMATICS

Prognostic impact of epigenetic classification in chronic lymphocytic leukemia: The case of subset #2

(2016) Sujata Bhoi et al.   Epigenetics

Epigenome-wide profiling of DNA methylation in paired samples of adipose tissue and blood

(2016) Yen-Tsung Huang et al.   Epigenetics

Unsupervised Deep Learning Applied to Breast Density Segmentation and Mammographic Risk Scoring

(2016) Michiel Kallenberg et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Targeting the cancer epigenome for therapy

(2016) Peter A. Jones et al.   NATURE REVIEWS GENETICS

Machine Learning in Genomic Medicine: A Review of Computational Problems and Data Sets

(2016) Michael K. K. Leung et al.   PROCEEDINGS OF THE IEEE

Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

(2016) Sebastian Moran et al.   Epigenomics

Predicting DNA Methylation State of CpG Dinucleotide Using Genome Topological Features and Deep Networks

(2016) Yiheng Wang et al.   Scientific Reports

Using epigenomics data to predict gene expression in lung cancer

(2015) Jeffery Li et al.   BMC BIOINFORMATICS

Machine Learning in Medicine

(2015) R. C. Deo   CIRCULATION

Classification of lung cancer using ensemble-based feature selection and machine learning methods

(2015) Zhihua Cai et al.   Molecular BioSystems

Deep learning

(2015) Yann LeCun et al.   NATURE

Performance evaluation of classification algorithms by k-fold and leave-one-out cross validation

(2015) Tzu-Tsung Wong   PATTERN RECOGNITION

Clinical applications of epigenetics in cardiovascular disease: the long road ahead

(2015) Stella Aslibekyan et al.   Translational Research

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

(2014) Martin J. Aryee et al.   BIOINFORMATICS

Imbalanced Class Learning in Epigenetics

(2014) M. Muksitul Haque et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A B-cell epigenetic signature defines three biologic subgroups of chronic lymphocytic leukemia with clinical impact

(2014) A C Queirós et al.   LEUKEMIA

A Brief History of Epigenetics

(2014) G. Felsenfeld   Cold Spring Harbor Perspectives in Biology

Measuring epigenetics as the mediator of gene/environment interactions in DOHaD

(2014) M.-L. Ong et al.   Journal of Developmental Origins of Health and Disease

Paternal obesity is associated with IGF2hypomethylation in newborns: results from a Newborn Epigenetics Study (NEST) cohort

(2013) Adelheid Soubry et al.   BMC Medicine

A comprehensive overview of Infinium HumanMethylation450 data processing

(2013) S. Dedeurwaerder et al.   BRIEFINGS IN BIOINFORMATICS

From promises to practical strategies in epigenetic epidemiology

(2013) Jonathan Mill et al.   NATURE REVIEWS GENETICS

Non-Mendelian etiologic factors in neuropsychiatric illness: Pleiotropy, epigenetics, and convergence

(2012) Curtis K. Deutsch et al.   BEHAVIORAL AND BRAIN SCIENCES

DNA methylation based biomarkers: Practical considerations and applications

(2012) Alexandre How Kit et al.   BIOCHIMIE

450K Epigenome-Wide Scan Identifies Differential DNA Methylation in Newborns Related to Maternal Smoking during Pregnancy

(2012) Bonnie R. Joubert et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies

(2012) Andrew E Jaffe et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Nutrition and epigenetics: an interplay of dietary methyl donors, one-carbon metabolism and DNA methylation

(2012) Olivia S. Anderson et al.   JOURNAL OF NUTRITIONAL BIOCHEMISTRY

DNA methylation profiling in the clinic: applications and challenges

(2012) Holger Heyn et al.   NATURE REVIEWS GENETICS

An other-race effect for face recognition algorithms

(2011) P. Jonathon Phillips et al.   ACM Transactions on Applied Perception

Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

(2011) Juan Sandoval et al.   Epigenetics

Insulin-like growth factor-2 (IGF2) loss of imprinting marks a field defect within human prostates containing cancer

(2011) Sachin Bhusari et al.   PROSTATE

Epigenetics and lifestyle

(2011) Jorge Alejandro Alegría-Torres et al.   Epigenomics

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

From discovery to the clinic: the novel DNA methylation biomarkermSEPT9 for the detection of colorectal cancer in blood

(2010) Shannon R Payne   Epigenomics

A systematic analysis of performance measures for classification tasks

(2009) Marina Sokolova et al.   INFORMATION PROCESSING & MANAGEMENT

Epigenetic mechanisms that underpin metabolic and cardiovascular diseases

(2009) Peter D. Gluckman et al.   Nature Reviews Endocrinology

Genome-wide DNA methylation profiling using Infinium®assay

(2009) Marina Bibikova et al.   Epigenomics

Comparison of classification accuracy using Cohen’s Weighted Kappa

(2006) A BENDAVID   EXPERT SYSTEMS WITH APPLICATIONS