Epigenetics Analysis and Integrated Analysis of Multiomics Data, Including Epigenetic Data, Using Artificial Intelligence in the Era of Precision Medicine

A State-of-the-Art Survey on Deep Learning Theory and Architectures

(2019) Md Zahangir Alom et al.   Electronics

DeepTACT: predicting 3D chromatin contacts via bootstrapping deep learning

(2019) Wenran Li et al.   NUCLEIC ACIDS RESEARCH

Integrated phenotype-genotype approach in diagnosis and classification of common CNS tumours

(2019) Ashirwad Merve et al.   HISTOPATHOLOGY

Histone methyltransferase SMYD2 selective inhibitor LLY-507 in combination with poly ADP ribose polymerase inhibitor has therapeutic potential against high-grade serous ovarian carcinomas

(2019) Asako Kukita et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The histone methyltransferase WHSC1 is regulated by EZH2 and is important for ovarian clear cell carcinoma cell proliferation

(2019) Machiko Kojima et al.   BMC CANCER

Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing

(2019) Li Zhou et al.   Scientific Reports

Challenges and future of precision medicine strategies for breast cancer based on a database on drug reactions

(2019) Xiping Zhang et al.   BIOSCIENCE REPORTS

Cost-effectiveness of precision medicine: a scoping review

(2019) Miriam Kasztura et al.   International Journal of Public Health

Development of a real-time endoscopic image diagnosis support system using deep learning technology in colonoscopy

(2019) Masayoshi Yamada et al.   Scientific Reports

DNA methylation-based classification of central nervous system tumours

(2018) David Capper et al.   NATURE

DNA methylation loss in late-replicating domains is linked to mitotic cell division

(2018) Wanding Zhou et al.   NATURE GENETICS

Transcript-indexed ATAC-seq for precision immune profiling

(2018) Ansuman T. Satpathy et al.   NATURE MEDICINE

ATAC-Seq analysis reveals a widespread decrease of chromatin accessibility in age-related macular degeneration

(2018) Jie Wang et al.   Nature Communications

A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia

(2018) Su-In Lee et al.   Nature Communications

Enhancing Hi-C data resolution with deep convolutional neural network HiCPlus

(2018) Yan Zhang et al.   Nature Communications

Three-dimensional Epigenome Statistical Model: Genome-wide Chromatin Looping Prediction

(2018) Ziad Al Bkhetan et al.   Scientific Reports

Overexpression of KDM5B/JARID1B is associated with poor prognosis in hepatocellular carcinoma

(2018) Yoshinobu Shigekawa et al.   Oncotarget

Gene Selection in Cancer Classification Using Sparse Logistic Regression with L1/2 Regularization

(2018) Shengbing Wu et al.   Applied Sciences-Basel

A semi-supervised deep learning method based on stacked sparse auto-encoder for cancer prediction using RNA-seq data

(2018) Yawen Xiao et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

The novel prognostic marker, EHMT2, is involved in cell proliferation via HSPD1 regulation in breast cancer

(2018) Seon‑Kyu Kim et al.   INTERNATIONAL JOURNAL OF ONCOLOGY

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Single cell RNA-seq and ATAC-seq analysis of cardiac progenitor cell transition states and lineage settlement

(2018) Guangshuai Jia et al.   Nature Communications

Mastering the game of Go without human knowledge

(2017) David Silver et al.   NATURE

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms

(2017) Sierra S. Nishizaki et al.   TRENDS IN GENETICS

Less Is More: Cross-Validation Testing of Simplified Nonlinear Regression Model Specifications for EQ-5D-5L Health State Values

(2017) Kim Rand-Hendriksen et al.   VALUE IN HEALTH

Novel prognostic marker PRMT1 regulates cell growth via downregulation of CDKN1A in HCC

(2017) Jea-Woon Ryu et al.   Oncotarget

Integrating Clinical and Multiple Omics Data for Prognostic Assessment across Human Cancers

(2017) Bin Zhu et al.   Scientific Reports

Advancements in Next-Generation Sequencing

(2016) Shawn E. Levy et al.   Annual Review of Genomics and Human Genetics

Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes

(2016) Pascal D. Johann et al.   CANCER CELL

Dysregulation of protein methyltransferases in human cancer: An emerging target class for anticancer therapy

(2016) Ryuji Hamamoto et al.   CANCER SCIENCE

New Brain Tumor Entities Emerge from Molecular Classification of CNS-PNETs

(2016) Dominik Sturm et al.   CELL

Perspective: The precision-oncology illusion

(2016) Vinay Prasad   NATURE

Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

(2016) Sean Whalen et al.   NATURE GENETICS

Regularization

(2016) Jake Lever et al.   NATURE METHODS

Genome-wide mapping and analysis of chromosome architecture

(2016) Anthony D. Schmitt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

(2016) Zefu Lu et al.   NUCLEIC ACIDS RESEARCH

MappingSLCO1B1Genetic Variation for Global Precision Medicine in Understudied Regions in Africa: A Focus on Zulu and Cape Admixed Populations

(2016) Nisreen Hoosain et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Toward an Integration of Deep Learning and Neuroscience

(2016) Adam H. Marblestone et al.   Frontiers in Computational Neuroscience

ChIP-seq in studying epigenetic mechanisms of disease and promoting precision medicine: progresses and future directions

(2016) Huihuang Yan et al.   Epigenomics

Constructing 3D interaction maps from 1D epigenomes

(2016) Yun Zhu et al.   Nature Communications

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

Integration of ATAC-seq and RNA-seq identifies human alpha cell and beta cell signature genes

(2016) Amanda M. Ackermann et al.   Molecular Metabolism

ATAC-seq on biobanked specimens defines a unique chromatin accessibility structure in naïve SLE B cells

(2016) Christopher D. Scharer et al.   Scientific Reports

Multitask learning improves prediction of cancer drug sensitivity

(2016) Han Yuan et al.   Scientific Reports

Adult IDH wild type astrocytomas biologically and clinically resolve into other tumor entities

(2015) David E. Reuss et al.   ACTA NEUROPATHOLOGICA

Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups

(2015) Kristian W. Pajtler et al.   CANCER CELL

Feasibility of Large-Scale Genomic Testing to Facilitate Enrollment Onto Genomically Matched Clinical Trials

(2015) Funda Meric-Bernstam et al.   JOURNAL OF CLINICAL ONCOLOGY

Deep learning

(2015) Yann LeCun et al.   NATURE

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

(2015) Natsuhiko Kumasaka et al.   NATURE GENETICS

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Biological context of Hebb learning in artificial neural networks, a review

(2015) Eduard Kuriscak et al.   NEUROCOMPUTING

SUV39H2 methylates and stabilizes LSD1 by inhibiting polyubiquitination in human cancer cells

(2015) Lianhua Piao et al.   Oncotarget

Predicting Anticancer Drug Responses Using a Dual-Layer Integrated Cell Line-Drug Network Model

(2015) Naiqian Zhang et al.   PLoS Computational Biology

Enhanced Expression of EHMT2 Is Involved in the Proliferation of Cancer Cells through Negative Regulation of SIAH1

(2015) Hyun-Soo Cho et al.   NEOPLASIA

Histone Lysine Methyltransferase Wolf-Hirschhorn Syndrome Candidate 1 Is Involved in Human Carcinogenesis through Regulation of the Wnt Pathway

(2015) Gouji Toyokawa et al.   NEOPLASIA

RB1 Methylation by SMYD2 Enhances Cell Cycle Progression through an Increase of RB1 Phosphorylation

(2015) Hyun-Soo Cho et al.   NEOPLASIA

The Oncogenic Polycomb Histone Methyltransferase EZH2Methylates Lysine 120 on Histone H2B and Competes Ubiquitination

(2015) Masaharu Kogure et al.   NEOPLASIA

Integrated DNA methylation and copy-number profiling identify three clinically and biologically relevant groups of anaplastic glioma

(2014) Benedikt Wiestler et al.   ACTA NEUROPATHOLOGICA

Epigenetics: Relevance and Implications for Public Health

(2014) Laura S. Rozek et al.   Annual Review of Public Health

Drug susceptibility prediction against a panel of drugs using kernelized Bayesian multitask learning

(2014) Mehmet Gönen et al.   BIOINFORMATICS

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C

(2014) Nicola H. Dryden et al.   GENOME RESEARCH

Epigenetic markers for noninvasive early detection of nasopharyngeal carcinoma by methylation-sensitive high resolution melting

(2014) Xuesong Yang et al.   INTERNATIONAL JOURNAL OF CANCER

WHSC1 Promotes Oncogenesis through Regulation of NIMA-Related Kinase-7 in Squamous Cell Carcinoma of the Head and Neck

(2014) Vassiliki Saloura et al.   MOLECULAR CANCER RESEARCH

Epigenomic alterations define lethal CIMP-positive ependymomas of infancy

(2014) S. C. Mack et al.   NATURE

A community effort to assess and improve drug sensitivity prediction algorithms

(2014) James C Costello et al.   NATURE BIOTECHNOLOGY

Critical role of lysine 134 methylation on histone H2AX for γ-H2AX production and DNA repair

(2014) Kenbun Sone et al.   Nature Communications

Differential expression and methylation of brain developmental genes define location-specific subsets of pilocytic astrocytoma

(2013) Sally R. Lambert et al.   ACTA NEUROPATHOLOGICA

Robust molecular subgrouping and copy-number profiling of medulloblastoma from small amounts of archival tumour material using high-density DNA methylation arrays

(2013) Volker Hovestadt et al.   ACTA NEUROPATHOLOGICA

Multilabel classification for exploiting cross-resistance information in HIV-1 drug resistance prediction

(2013) Dominik Heider et al.   BIOINFORMATICS

An RNAi-based screen reveals PLK1, CDK1 and NDC80 as potential therapeutic targets in malignant pleural mesothelioma

(2013) A Linton et al.   BRITISH JOURNAL OF CANCER

Deregulation of the histone demethylase JMJD2A is involved in human carcinogenesis through regulation of the G1/S transition

(2013) Masaharu Kogure et al.   CANCER LETTERS

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

(2013) M. Stevens et al.   GENOME RESEARCH

Representation Learning: A Review and New Perspectives

(2013) Y. Bengio et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Chemical Genomics Identifies Small-Molecule MCL1 Repressors and BCL-xL as a Predictor of MCL1 Dependency

(2012) Guo Wei et al.   CANCER CELL

SnapShot: Chromosome Conformation Capture

(2012) Ofir Hakim et al.   CELL

The histone methyltransferase Wolf-Hirschhorn syndrome candidate 1-like 1 (WHSC1L1) is involved in human carcinogenesis

(2012) Daechun Kang et al.   GENES CHROMOSOMES & CANCER

Quantitative profiling of CpG island methylation in human stool for colorectal cancer detection

(2012) Giles O. Elliott et al.   INTERNATIONAL JOURNAL OF COLORECTAL DISEASE

Technical Considerations for Reduced Representation Bisulfite Sequencing with Multiplexed Libraries

(2012) Aniruddha Chatterjee et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

The histone methyltransferase MMSET/WHSC1 activates TWIST1 to promote an epithelial–mesenchymal transition and invasive properties of prostate cancer

(2012) T Ezponda et al.   ONCOGENE

Semi-supervised learning improves gene expression-based prediction of cancer recurrence

(2011) Mingguang Shi et al.   BIOINFORMATICS

The Histone Demethylase JMJD2B Plays an Essential Role in Human Carcinogenesis through Positive Regulation of Cyclin-Dependent Kinase 6

(2011) G. Toyokawa et al.   Cancer Prevention Research

Validation of the histone methyltransferase EZH2 as a therapeutic target for various types of human cancer and as a prognostic marker

(2011) Masashi Takawa et al.   CANCER SCIENCE

The JmjC domain-containing histone demethylase KDM3A is a positive regulator of the G1/S transition in cancer cells via transcriptional regulation of the HOXA1 gene

(2011) Hyun-Soo Cho et al.   INTERNATIONAL JOURNAL OF CANCER

Resistance, epigenetics and the cancer ecosystem

(2011) Stephen B Baylin   NATURE MEDICINE

Interobserver variation of the histopathological diagnosis in clinical trials on glioma: a clinician’s perspective

(2010) Martin J. van den Bent   ACTA NEUROPATHOLOGICA

Demethylation of RB Regulator MYPT1 by Histone Demethylase LSD1 Promotes Cell Cycle Progression in Cancer Cells

(2010) H.-S. Cho et al.   CANCER RESEARCH

Dysregulation of PRMT1 and PRMT6, Type I arginine methyltransferases, is involved in various types of human cancers

(2010) Masanori Yoshimatsu et al.   INTERNATIONAL JOURNAL OF CANCER

Overexpression of LSD1 contributes to human carcinogenesis through chromatin regulation in various cancers

(2010) Shinya Hayami et al.   INTERNATIONAL JOURNAL OF CANCER

The Current State of Chromatin Immunoprecipitation

(2010) Philippe Collas   MOLECULAR BIOTECHNOLOGY

Overexpression of the JmjC histone demethylase KDM5B in human carcinogenesis: involvement in the proliferation of cancer cells through the E2F/RB pathway

(2010) Shinya Hayami et al.   Molecular Cancer

Linking cell signaling and the epigenetic machinery

(2010) Helai P Mohammad et al.   NATURE BIOTECHNOLOGY

ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing

(2010) Guoliang Li et al.   GENOME BIOLOGY

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Epigenetics: Definition, Mechanisms and Clinical Perspective

(2009) Cathérine Dupont et al.   SEMINARS IN REPRODUCTIVE MEDICINE

Methods in DNA methylation profiling

(2009) Tao Zuo et al.   Epigenomics