Integrated Analysis of Whole Genome and Epigenome Data Using Machine Learning Technology: Toward the Establishment of Precision Oncology

Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis

(2021) Kirsten A. Reimer et al.   MOLECULAR CELL

Detection of Cardiac Structural Abnormalities in Fetal Ultrasound Videos Using Deep Learning

(2021) Masaaki Komatsu et al.   Applied Sciences-Basel

Shadow Estimation for Ultrasound Images Using Auto-Encoding Structures and Synthetic Shadows

(2021) Suguru Yasutomi et al.   Applied Sciences-Basel

A Targeted Gene Panel for Circulating Tumor DNA Sequencing in Neuroblastoma

(2021) Flora Cimmino et al.   Frontiers in Oncology

Application of Artificial Intelligence for Medical Research

(2021) Ryuji Hamamoto   Biomolecules

Fine-Tuning Approach for Segmentation of Gliomas in Brain Magnetic Resonance Images with a Machine Learning Method to Normalize Image Differences among Facilities

(2021) Satoshi Takahashi et al.   Cancers

Targeting super-enhancer-associated oncogenes in osteosarcoma with THZ2, a covalent CDK7 inhibitor

(2020) Jiajun Zhang et al.   CLINICAL CANCER RESEARCH

Evaluation of haplotype callers for next-generation sequencing of viruses

(2020) Anton Eliseev et al.   INFECTION GENETICS AND EVOLUTION

Pan-cancer analysis of whole genomes

(2020)   NATURE

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns

(2020) Wei Jiao et al.   Nature Communications

DeepWAS: Multivariate genotype-phenotype associations by directly integrating regulatory information using deep learning

(2020) Janine Arloth et al.   PLoS Computational Biology

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

(2020) Ryuji Hamamoto et al.   Biomolecules

A highly accurate platform for clone-specific mutation discovery enables the study of active mutational processes

(2020) Mohammad KaramiNejadRanjbar et al.   eLife

Uncovering Prognosis-Related Genes and Pathways by Multi-Omics Analysis in Lung Cancer

(2020) Ken Asada et al.   Biomolecules

Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes

(2020) Pier Vitale Nuzzo et al.   NATURE MEDICINE

Detection and discrimination of intracranial tumors using plasma cell-free DNA methylomes

(2020) Farshad Nassiri et al.   NATURE MEDICINE

Decoding whole-genome mutational signatures in 37 human pan-cancers by denoising sparse autoencoder neural network

(2020) Guangsheng Pei et al.   ONCOGENE

Using sigLASSO to optimize cancer mutation signatures jointly with sampling likelihood

(2020) Shantao Li et al.   Nature Communications

Critical Roles of N6-Methyladenosine (m6A) in Cancer and Virus Infection

(2020) Ken Asada et al.   Biomolecules

The Development of a Skin Cancer Classification System for Pigmented Skin Lesions Using Deep Learning

(2020) Shunichi Jinnai et al.   Biomolecules

Autoencoded DNA Methylation Data to Predict Breast Cancer Recurrence: Machine Learning Models and Gene-Weight Significance

(2020) Laura Macías-García et al.   ARTIFICIAL INTELLIGENCE IN MEDICINE

Distinct Classes of Complex Structural Variation Uncovered across Thousands of Cancer Genome Graphs

(2020) Kevin Hadi et al.   CELL

Subclonal reconstruction of tumors by using machine learning and population genetics

(2020) Giulio Caravagna et al.   NATURE GENETICS

Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer

(2020) Marie Wong et al.   NATURE MEDICINE

Alternative Enhancer Usage and Targeted Polycomb Marking Hallmark Promoter Choice during T Cell Differentiation

(2020) Muhammad Ahmad Maqbool et al.   Cell Reports

Fully-Connected Neural Networks with Reduced Parameterization for Predicting Histological Types of Lung Cancer from Somatic Mutations

(2020) Kazuma Kobayashi et al.   Biomolecules

Predicting Deep Learning Based Multi-Omics Parallel Integration Survival Subtypes in Lung Cancer Using Reverse Phase Protein Array Data

(2020) Satoshi Takahashi et al.   Biomolecules

Application of Artificial Intelligence Technology in Oncology: Towards the Establishment of Precision Medicine

(2020) Ryuji Hamamoto et al.   Cancers

Model-Agnostic Method for Thoracic Wall Segmentation in Fetal Ultrasound Videos

(2020) Kanto Shozu et al.   Biomolecules

Epigenetic Modifier SETD8 as a Therapeutic Target for High-Grade Serous Ovarian Cancer

(2020) Miku Wada et al.   Biomolecules

Deep convolutional neural networks for accurate somatic mutation detection

(2019) Sayed Mohammad Ebrahim Sahraeian et al.   Nature Communications

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk

(2019) Jian Zhou et al.   NATURE GENETICS

Detecting the mutational signature of homologous recombination deficiency in clinical samples

(2019) Doga C. Gulhan et al.   NATURE GENETICS

Clinical utility of custom-designed NGS panel testing in pediatric tumors

(2019) Lea F. Surrey et al.   Genome Medicine

Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype

(2019) Bojian Yin et al.   BIOINFORMATICS

Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers

(2019) Mizuo Ando et al.   Nature Communications

A practical guide for mutational signature analysis in hematological malignancies

(2019) Francesco Maura et al.   Nature Communications

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

(2019) Xiping Zhang et al.   BIOSCIENCE REPORTS

Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks

(2019) Elizabeth K. Ruzzo et al.   CELL

A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through Alternative Promoters

(2019) Deniz Demircioğlu et al.   CELL

Machine learning analysis of DNA methylation profiles distinguishes primary lung squamous cell carcinomas from head and neck metastases

(2019) Philipp Jurmeister et al.   Science Translational Medicine

Targeted Gene Next-Generation Sequencing Panel in Patients with Advanced Lung Adenocarcinoma: Paving the Way for Clinical Implementation

(2019) Maria Gabriela O. Fernandes et al.   Cancers

GenGraph: a python module for the simple generation and manipulation of genome graphs

(2019) Jon Mitchell Ambler et al.   BMC BIOINFORMATICS

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

(2019) Masayoshi Yamada et al.   Scientific Reports

Deregulation of the Histone Lysine-Specific Demethylase 1 Is Involved in Human Hepatocellular Carcinoma

(2019) Sangchul Kim et al.   Biomolecules

DEEPSEN: a convolutional neural network based method for super-enhancer prediction

(2019) Hongda Bu et al.   BMC BIOINFORMATICS

In silico prediction of high-resolution Hi-C interaction matrices

(2019) Shilu Zhang et al.   Nature Communications

Prediction of enhancer-promoter interactions via natural language processing

(2018) Wanwen Zeng et al.   BMC GENOMICS

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

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

Transcriptional decomposition reveals active chromatin architectures and cell specific regulatory interactions

(2018) Sarah Rennie et al.   Nature Communications

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries

(2018) Yixiao Gong et al.   Nature Communications

Super-enhancers are transcriptionally more active and cell type-specific than stretch enhancers

(2018) Aziz Khan et al.   Epigenetics

A universal SNP and small-indel variant caller using deep neural networks

(2018) Ryan Poplin et al.   NATURE BIOTECHNOLOGY

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 chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Genome graphs and the evolution of genome inference

(2017) Benedict Paten et al.   GENOME RESEARCH

Epi proColon® 2.0 CE: A Blood-Based Screening Test for Colorectal Cancer

(2017) Yvette N. Lamb et al.   Molecular Diagnosis & Therapy

Sequencing and de novo assembly of 150 genomes from Denmark as a population reference

(2017) Lasse Maretty et al.   NATURE

Graphtyper enables population-scale genotyping using pangenome graphs

(2017) Hannes P Eggertsson et al.   NATURE GENETICS

Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines

(2017) Qin Cao et al.   NATURE GENETICS

Genome-wide profiling of heritable and de novo STR variations

(2017) Thomas Willems et al.   NATURE METHODS

Epigenetic drivers of tumourigenesis and cancer metastasis

(2017) Aniruddha Chatterjee et al.   SEMINARS IN CANCER BIOLOGY

Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome

(2017) Andrea J. Cohen et al.   Nature Communications

Oncogenic histone methyltransferase EZH2: A novel prognostic marker with therapeutic potential in endometrial cancer

(2017) Shinya Oki et al.   Oncotarget

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

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

(2017) Bin Zhu et al.   Scientific Reports

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease

(2016) Damian Smedley et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Advancements in Next-Generation Sequencing

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

Gene aberrations for precision medicine against lung adenocarcinoma

(2016) Motonobu Saito et al.   CANCER SCIENCE

Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

(2016) Rongxin Fang et al.   CELL RESEARCH

An Ectopic Network of Transcription Factors Regulated by Hippo Signaling Drives Growth and Invasion of a Malignant Tumor Model

(2016) Mardelle Atkins et al.   CURRENT BIOLOGY

Enhancer methylation dynamics contribute to cancer plasticity and patient mortality

(2016) Rachel E. Bell et al.   GENOME RESEARCH

Cell-free DNA (cfDNA): Clinical Significance and Utility in Cancer Shaped By Emerging Technologies

(2016) S. Volik et al.   MOLECULAR CANCER RESEARCH

Perspective: The precision-oncology illusion

(2016) Vinay Prasad   NATURE

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

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

(2016) Yiheng Wang et al.   Scientific Reports

Multitask learning improves prediction of cancer drug sensitivity

(2016) Han Yuan et al.   Scientific Reports

Combining Multiple Hypothesis Testing with Machine Learning Increases the Statistical Power of Genome-wide Association Studies

(2016) Bettina Mieth et al.   Scientific Reports

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

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

Cell-of-origin chromatin organization shapes the mutational landscape of cancer

(2015) Paz Polak et al.   NATURE

Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR

(2015) Miguel Vizoso et al.   NATURE MEDICINE

Machine learning applications in genetics and genomics

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

Methylation-dependent SOX9 expression mediates invasion in human melanoma cells and is a negative prognostic factor in advanced melanoma

(2015) Phil F Cheng et al.   GENOME BIOLOGY

Inferring regulatory element landscapes and transcription factor networks from cancer methylomes

(2015) Lijing Yao et al.   GENOME BIOLOGY

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

(2015) Masaharu Kogure et al.   NEOPLASIA

Translating Genomics for Precision Cancer Medicine

(2014) Roychowdhury Sameek et al.   Annual Review of Genomics and Human Genetics

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

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

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

PyClone: statistical inference of clonal population structure in cancer

(2014) Andrew Roth et al.   NATURE METHODS

A Randomized Trial of Bevacizumab for Newly Diagnosed Glioblastoma

(2014) Mark R. Gilbert et al.   NEW ENGLAND JOURNAL OF MEDICINE

Multitarget Stool DNA Testing for Colorectal-Cancer Screening

(2014) Thomas F. Imperiale et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2014) Kenbun Sone et al.   Nature Communications

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Representation Learning: A Review and New Perspectives

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

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Momentum grows to make 'personalized' medicine more 'precise'

(2013) Alla Katsnelson   NATURE MEDICINE

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

An empirical Bayesian framework for somatic mutation detection from cancer genome sequencing data

(2013) Yuichi Shiraishi et al.   NUCLEIC ACIDS RESEARCH

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Cancer Genomics: Technology, Discovery, and Translation

(2012) Ben Tran et al.   JOURNAL OF CLINICAL ONCOLOGY

Clinical Utility of an Epigenetic Assay to Detect Occult Prostate Cancer in Histopathologically Negative Biopsies: Results of the MATLOC Study

(2012) Grant D. Stewart et al.   JOURNAL OF UROLOGY

Chromatin organization is a major influence on regional mutation rates in human cancer cells

(2012) Benjamin Schuster-Böckler et al.   NATURE

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Epigenomic Enhancer Profiling Defines a Signature of Colon Cancer

(2012) B. Akhtar-Zaidi et al.   SCIENCE

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

(2011) Mingguang Shi et al.   BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

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

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

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

ChIP-based methods for the identification of long-range chromatin interactions

(2009) Melissa J. Fullwood et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

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

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

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS