4.8 Article

Asymmetric predictive relationships across histone modifications

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Evidence of widespread, independent sequence signature for transcription factor cobinding

Manqi Zhou et al.

Summary: A machine learning algorithm was developed to explore the contributors of transcription factor cobinding patterns, revealing that independent motif sequences play a significant role in shaping these patterns. These independent motif sequences include transcription initiation-related proteins and known TF complexes, contributing to the regulatory language in a hierarchical and directional organization.

GENOME RESEARCH (2021)

Article Biology

DeepSleep convolutional neural network allows accurate and fast detection of sleep arousal

Hongyang Li et al.

Summary: Li and Guan present a deep learning approach for automatically segmenting sleep arousal regions based on polysomnographic recordings. The algorithm, which won an open competition, enables fast and accurate delineation of sleep arousal events and would be useful in the scoring process in clinical studies.

COMMUNICATIONS BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Fast decoding cell type?specific transcription factor binding landscape at single-nucleotide resolution Hongyang Li and Yuanfang Guan

Hongyang Li et al.

Summary: The novel deep learning approach Leopard can predict TF binding sites at single-nucleotide resolution with impressive accuracy, outperforming current state-of-the-art methods by a significant margin.

GENOME RESEARCH (2021)

Review Genetics & Heredity

Mechanisms of tissue and cell-type specificity in heritable traits and diseases

Idan Hekselman et al.

NATURE REVIEWS GENETICS (2020)

Article Multidisciplinary Sciences

Expanded encyclopaedias of DNA elements in the human and mouse genomes

Jill E. Moore et al.

NATURE (2020)

Article Biochemical Research Methods

Cross-species regulatory sequence activity prediction

David R. Kelley

PLOS COMPUTATIONAL BIOLOGY (2020)

Article Biotechnology & Applied Microbiology

Avocado: a multi-scale deep tensor factorization method learns a latent representation of the human epigenome

Jacob Schreiber et al.

GENOME BIOLOGY (2020)

Article Multidisciplinary Sciences

Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse

Vu Ngo et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

Article Biochemistry & Molecular Biology

Identification of DNA motifs that regulate DNA methylation

Mengchi Wang et al.

NUCLEIC ACIDS RESEARCH (2019)

Review Immunology

Interferon target-gene expression and epigenomic signatures in health and disease

Franck J. Barrat et al.

NATURE IMMUNOLOGY (2019)

Article Biochemistry & Molecular Biology

Anchor: trans-cell type prediction of transcription factor binding sites

Hongyang Li et al.

GENOME RESEARCH (2019)

Article Biochemistry & Molecular Biology

GENCODE reference annotation for the human and mouse genomes

Adam Frankish et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Biochemistry & Molecular Biology

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

David R. Kelley et al.

GENOME RESEARCH (2018)

Article Biochemistry & Molecular Biology

Relationship between histone modifications and transcription factor binding is protein family specific

Beibei Xin et al.

GENOME RESEARCH (2018)

Article Multidisciplinary Sciences

PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition

Timothy J. Durham et al.

NATURE COMMUNICATIONS (2018)

Article Engineering, Biomedical

Explainable machine-learning predictions for the prevention of hypoxaemia during surgery

Scott M. Lundberg et al.

NATURE BIOMEDICAL ENGINEERING (2018)

Article Biochemical Research Methods

Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties

Ling Chen et al.

PLOS COMPUTATIONAL BIOLOGY (2018)

Article Biochemistry & Molecular Biology

Modeling co-occupancy of transcription factors using chromatin features

Liang Liu et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Integrative analysis of 111 reference human epigenomes

Anshul Kundaje et al.

NATURE (2015)

Article Biotechnology & Applied Microbiology

Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues

Jason Ernst et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemical Research Methods

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

Jian Zhou et al.

NATURE METHODS (2015)

Article Biochemistry & Molecular Biology

Modeling the relationship of epigenetic modifications to transcription factor binding

Liang Liu et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biotechnology & Applied Microbiology

Gateways to the FANTOM5 promoter level mammalian expression atlas

Marina Lizio et al.

GENOME BIOLOGY (2015)

Article Multidisciplinary Sciences

Transcription factor binding predicts histone modifications in human cell lines

Dan Benveniste et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

Article Biochemical Research Methods

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

Mahmoud Ghandi et al.

PLOS COMPUTATIONAL BIOLOGY (2014)

Review Biochemistry & Molecular Biology

Mapping Human Epigenomes

Chloe M. Rivera et al.

Article Biotechnology & Applied Microbiology

A community-driven global reconstruction of human metabolism

Ines Thiele et al.

NATURE BIOTECHNOLOGY (2013)

Review Genetics & Heredity

DNA methylation: roles in mammalian development

Zachary D. Smith et al.

NATURE REVIEWS GENETICS (2013)

Article Multidisciplinary Sciences

An integrated encyclopedia of DNA elements in the human genome

Ian Dunham et al.

NATURE (2012)

Article Biochemical Research Methods

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

Michael M. Hoffman et al.

NATURE METHODS (2012)

Letter Biochemical Research Methods

ChromHMM: automating chromatin-state discovery and characterization

Jason Ernst et al.

NATURE METHODS (2012)

Review Genetics & Heredity

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

Patricia J. Wittkopp et al.

NATURE REVIEWS GENETICS (2012)

Article Biochemistry & Molecular Biology

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

Roger Pique-Regi et al.

GENOME RESEARCH (2011)

Article Biotechnology & Applied Microbiology

Discovery and characterization of chromatin states for systematic annotation of the human genome

Jason Ernst et al.

NATURE BIOTECHNOLOGY (2010)

Review Genetics & Heredity

RNA-binding proteins in human genetic disease

Kiven E. Lukong et al.

TRENDS IN GENETICS (2008)

Review Multidisciplinary Sciences

The sequence of the human genome

JC Venter et al.

SCIENCE (2001)