Machine learning for epigenetics and future medical applications

DNA methylation-based forensic age prediction using artificial neural networks and next generation sequencing

(2017) Athina Vidaki et al.   Forensic Science International-Genetics

Enlightening discriminative network functional modules behind Principal Component Analysis separation in differential-omic science studies

(2017) Sara Ciucci et al.   Scientific Reports

Identify High-Quality Protein Structural Models by EnhancedK-Means

(2017) Hongjie Wu et al.   Biomed Research International

Imbalanced multi-label learning for identifying antimicrobial peptides and their functional types

(2016) Weizhong Lin et al.   BIOINFORMATICS

Computational inference of a genomic pluripotency signature in human and mouse stem cells

(2016) Esra Kurum et al.   Biology Direct

The parameter sensitivity of random forests

(2016) Barbara F.F. Huang et al.   BMC BIOINFORMATICS

Deep learning in bioinformatics

(2016) Seonwoo Min et al.   BRIEFINGS IN BIOINFORMATICS

Big Data and machine learning in radiation oncology: State of the art and future prospects

(2016) Jean-Emmanuel Bibault et al.   CANCER LETTERS

A Landscape of Pharmacogenomic Interactions in Cancer

(2016) Francesco Iorio et al.   CELL

Machine Learning Techniques in Clinical Vision Sciences

(2016) Miguel Caixinha et al.   CURRENT EYE RESEARCH

Presence of an epigenetic signature of prenatal cigarette smoke exposure in childhood

(2016) Christine Ladd-Acosta et al.   ENVIRONMENTAL RESEARCH

Moving beyond regression techniques in cardiovascular risk prediction: applying machine learning to address analytic challenges

(2016) Benjamin A. Goldstein et al.   EUROPEAN HEART JOURNAL

Guest Editorial Deep Learning in Medical Imaging: Overview and Future Promise of an Exciting New Technique

(2016) Hayit Greenspan et al.   IEEE TRANSACTIONS ON MEDICAL IMAGING

Image analysis and machine learning in digital pathology: Challenges and opportunities

(2016) Anant Madabhushi et al.   MEDICAL IMAGE ANALYSIS

Applications of Deep Learning in Biomedicine

(2016) Polina Mamoshina et al.   MOLECULAR PHARMACEUTICS

Machine learning, statistical learning and the future of biological research in psychiatry

(2016) R. Iniesta et al.   PSYCHOLOGICAL MEDICINE

Portraying breast cancers with long noncoding RNAs

(2016) O. Van Grembergen et al.   Science Advances

Comparison of Approaches for Heart Failure Case Identification From Electronic Health Record Data

(2016) Saul Blecker et al.   JAMA Cardiology

Reconstructing Causal Biological Networks through Active Learning

(2016) Hyunghoon Cho et al.   PLoS One

Tertiary Epimutations – A Novel Aspect of Epigenetic Transgenerational Inheritance Promoting Genome Instability

(2016) John R. McCarrey et al.   PLoS One

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

(2016) Yiheng Wang et al.   Scientific Reports

iRNA-Methyl: Identifying N6-methyladenosine sites using pseudo nucleotide composition

(2015) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

DNA Modification Study of Major Depressive Disorder: Beyond Locus-by-Locus Comparisons

(2015) Gabriel Oh et al.   BIOLOGICAL PSYCHIATRY

Using epigenomics data to predict gene expression in lung cancer

(2015) Jeffery Li et al.   BMC BIOINFORMATICS

Extrapolating histone marks across developmental stages, tissues, and species: an enhancer prediction case study

(2015) John A Capra   BMC GENOMICS

Environmentally induced epigenetic transgenerational inheritance of sperm epimutations promote genetic mutations

(2015) Michael K Skinner et al.   Epigenetics

Characterization and machine learning prediction of allele-specific DNA methylation

(2015) Jianlin He et al.   GENOMICS

Semi-supervised prediction of gene regulatory networks using machine learning algorithms

(2015) Nihir Patel et al.   JOURNAL OF BIOSCIENCES

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

(2015) Zhihua Cai et al.   Molecular BioSystems

Bioinformatics approaches to single-cell analysis in developmental biology

(2015) Dicle Yalcin et al.   MOLECULAR HUMAN REPRODUCTION

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

Assessing Dissimilarity Measures for Sample-Based Hierarchical Clustering of RNA Sequencing Data Using Plasmode Datasets

(2015) Pablo D. Reeb et al.   PLoS One

Genome-Wide Locations of Potential Epimutations Associated with Environmentally Induced Epigenetic Transgenerational Inheritance of Disease Using a Sequential Machine Learning Prediction Approach

(2015) M. Muksitul Haque et al.   PLoS One

CompareSVM: supervised, Support Vector Machine (SVM) inference of gene regularity networks

(2014) Zeeshan Gillani et al.   BMC BIOINFORMATICS

Combinatorial epigenetic patterns as quantitative predictors of chromatin biology

(2014) Marcin Cieślik et al.   BMC GENOMICS

Role of CpG deserts in the epigenetic transgenerational inheritance of differential DNA methylation regions

(2014) Michael K Skinner et al.   BMC GENOMICS

Endocrine disruptor induction of epigenetic transgenerational inheritance of disease

(2014) Michael K. Skinner   MOLECULAR AND CELLULAR ENDOCRINOLOGY

An Active Learning Approach for Rapid Characterization of Endothelial Cells in Human Tumors

(2014) Raghav K. Padmanabhan et al.   PLoS One

Pesticide Methoxychlor Promotes the Epigenetic Transgenerational Inheritance of Adult-Onset Disease through the Female Germline

(2014) Mohan Manikkam et al.   PLoS One

Ancestral dichlorodiphenyltrichloroethane (DDT) exposure promotes epigenetic transgenerational inheritance of obesity

(2013) Michael K Skinner et al.   BMC Medicine

Applications of alignment-free methods in epigenomics

(2013) L. Pinello et al.   BRIEFINGS IN BIOINFORMATICS

Generalized Query-Based Active Learning to Identify Differentially Methylated Regions in DNA

(2013) Md. Muksitul Haque et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Comparative analysis using K-mer and K-flank patterns provides evidence for CpG island sequence evolution in mammalian genomes

(2013) H. Chae et al.   NUCLEIC ACIDS RESEARCH

Environmentally Induced Epigenetic Transgenerational Inheritance of Altered Sertoli Cell Transcriptome and Epigenome: Molecular Etiology of Male Infertility

(2013) Carlos Guerrero-Bosagna et al.   PLoS One

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands

(2013) J. Schreiber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine learning applications in proteomics research: How the past can boost the future

(2013) Pieter Kelchtermans et al.   PROTEOMICS

Detection of allele-specific methylation through a generalized heterogeneous epigenome model

(2012) Q. Peng et al.   BIOINFORMATICS

A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform

(2012) Joanna J Zhuang et al.   BMC BIOINFORMATICS

Linking the Epigenome to the Genome: Correlation of Different Features to DNA Methylation of CpG Islands

(2012) Clemens Wrzodek et al.   PLoS One

Environmentally Induced Epigenetic Transgenerational Inheritance of Ovarian Disease

(2012) Eric Nilsson et al.   PLoS One

An active learning based classification strategy for the minority class problem: application to histopathology annotation

(2011) Scott Doyle et al.   BMC BIOINFORMATICS

Perceptual learning in visual hyperacuity: A reweighting model

(2011) Grigorios Sotiropoulos et al.   VISION RESEARCH

Localized motif discovery in gene regulatory sequences

(2010) V. Narang et al.   BIOINFORMATICS

waviCGH: a web application for the analysis and visualization of genomic copy number alterations

(2010) Angel Carro et al.   NUCLEIC ACIDS RESEARCH

A particle swarm based hybrid system for imbalanced medical data sampling

(2009) Pengyi Yang et al.   BMC GENOMICS

Predicting Positive p53 Cancer Rescue Regions Using Most Informative Positive (MIP) Active Learning

(2009) Samuel A. Danziger et al.   PLoS Computational Biology