Machine learning for profile prediction in genomics

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

(2021) Yanrong Ji et al.   BIOINFORMATICS

Regulatory genomic circuitry of human disease loci by integrative epigenomics

(2021) Carles A. Boix et al.   NATURE

The dynamics of chromatin architecture in brain development and function

(2021) Izabela Harabula et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Towards a comprehensive catalogue of validated and target-linked human enhancers

(2020) Molly Gasperini et al.   NATURE REVIEWS GENETICS

Realistic in silico generation and augmentation of single-cell RNA-seq data using generative adversarial networks

(2020) Mohamed Marouf et al.   Nature Communications

Interpretable factor models of single-cell RNA-seq via variational autoencoders

(2020) Valentine Svensson et al.   BIOINFORMATICS

scVAE: Variational auto-encoders for single-cell gene expression data

(2020) Christopher Heje Grønbech et al.   BIOINFORMATICS

scIGANs: single-cell RNA-seq imputation using generative adversarial networks

(2020) Yungang Xu et al.   NUCLEIC ACIDS RESEARCH

Enhancing the interpretability of transcription factor binding site prediction using attention mechanism

(2020) Sungjoon Park et al.   Scientific Reports

Cross-species regulatory sequence activity prediction

(2020) David R. Kelley   PLoS Computational Biology

Predicting 3D genome folding from DNA sequence with Akita

(2020) Geoff Fudenberg et al.   NATURE METHODS

Revisiting 3D chromatin architecture in cancer development and progression

(2020) Yuliang Feng et al.   NUCLEIC ACIDS RESEARCH

Genetic variant effects on gene expression in human pancreatic islets and their implications for T2D

(2020) Ana Viñuela et al.   Nature Communications

Predicting transcription factor binding in single cells through deep learning

(2020) Laiyi Fu et al.   Science Advances

FactorNet: a deep learning framework for predicting cell type specific transcription factor binding from nucleotide-resolution sequential data

(2019) Daniel Quang et al.   METHODS

EPIP: a novel approach for condition-specific enhancer–promoter interaction prediction

(2019) Amlan Talukder et al.   BIOINFORMATICS

A compendium of promoter-centered long-range chromatin interactions in the human genome

(2019) Inkyung Jung et al.   NATURE GENETICS

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

(2019)   NATURE

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

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

(2019) Shilu Zhang et al.   Nature Communications

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

(2018) David R. Kelley et al.   GENOME RESEARCH

An accurate and robust imputation method scImpute for single-cell RNA-seq data

(2018) Wei Vivian Li et al.   Nature Communications

PREDICTD PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition

(2018) Timothy J. Durham et al.   Nature Communications

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

(2018) Hongyang Li et al.   GENOME RESEARCH

An efficient method to transcription factor binding sites imputation via simultaneous completion of multiple matrices with positional consistency

(2017) Wei-Li Guo et al.   Molecular BioSystems

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

A critical assessment of topologically associating domain prediction tools

(2017) Rola Dali et al.   NUCLEIC ACIDS RESEARCH

Imputation for transcription factor binding predictions based on deep learning

(2017) Qian Qin et al.   PLoS Computational Biology

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

(2016) Hendrik G. Stunnenberg et al.   CELL

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

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

(2016) Sean Whalen et al.   NATURE GENETICS

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

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

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

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

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

(2015) Jason Ernst et al.   NATURE BIOTECHNOLOGY

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

A predictive modeling approach for cell line-specific long-range regulatory interactions

(2015) Sushmita Roy et al.   NUCLEIC ACIDS RESEARCH

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

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

(2014) Suhas S.P. Rao et al.   CELL

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Sequence and chromatin determinants of cell-type-specific transcription factor binding

(2012) A. Arvey et al.   GENOME RESEARCH

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

To Explain or to Predict?

(2011) Galit Shmueli   STATISTICAL SCIENCE

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Nuclear architecture and gene regulation

(2008) Elena Fedorova et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

(2008) E. Wingender   BRIEFINGS IN BIOINFORMATICS