ReFeaFi: Genome-wide prediction of regulatory elements driving transcription initiation

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

(2020) Anurag Sethi et al.   NATURE METHODS

Deep learning for genomics using Janggu

(2020) Wolfgang Kopp et al.   Nature Communications

Genome annotation across species using deep convolutional neural networks

(2020) Ghazaleh Khodabandelou et al.   PeerJ Computer Science

Systematic interrogation of human promoters

(2019) Shira Weingarten-Gabbay et al.   GENOME RESEARCH

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

Determinants of enhancer and promoter activities of regulatory elements

(2019) Robin Andersson et al.   NATURE REVIEWS GENETICS

JASPAR 2020: update of the open-access database of transcription factor binding profiles

(2019) Oriol Fornes et al.   NUCLEIC ACIDS RESEARCH

Identification of putative promoters in 48 eukaryotic genomes on the basis of DNA free energy

(2018) Venkata Rajesh Yella et al.   Scientific Reports

DeepGSR: an optimized deep-learning structure for the recognition of genomic signals and regions

(2018) Manal Kalkatawi et al.   BIOINFORMATICS

Promoter analysis and prediction in the human genome using sequence-based deep learning models

(2018) Ramzan Umarov et al.   BIOINFORMATICS

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

(2018) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Improved regulatory element prediction based on tissue-specific local epigenomic signatures

(2017) Yupeng He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

Dry and wet approaches for genome-wide functional annotation of conventional and unconventional transcriptional activators

(2016) Elisabetta Levati et al.   Computational and Structural Biotechnology Journal

EP-DNN: A Deep Neural Network-Based Global Enhancer Prediction Algorithm

(2016) Seong Gon Kim et al.   Scientific Reports

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Core promoters in transcription: old problem, new insights

(2015) Ananda L. Roy et al.   TRENDS IN BIOCHEMICAL SCIENCES

Role of ChIP-seq in the discovery of transcription factor binding sites, differential gene regulation mechanism, epigenetic marks and beyond

(2014) Rasika Mundade et al.   CELL CYCLE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

DEEP: a general computational framework for predicting enhancers

(2014) Dimitrios Kleftogiannis et al.   NUCLEIC ACIDS RESEARCH

Nuclear stability and transcriptional directionality separate functionally distinct RNA species

(2014) Robin Andersson et al.   Nature Communications

Identifying transcriptional cis -regulatory modules in animal genomes

(2014) Kushal Suryamohan et al.   Wiley Interdisciplinary Reviews-Developmental Biology

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

5′ end–centered expression profiling using cap-analysis gene expression and next-generation sequencing

(2012) Hazuki Takahashi et al.   Nature Protocols

Metazoan promoters: emerging characteristics and insights into transcriptional regulation

(2012) Boris Lenhard et al.   NATURE REVIEWS GENETICS

Genome-wide enhancer prediction from epigenetic signatures using genetic algorithm-optimized support vector machines

(2012) Michael Fernández et al.   NUCLEIC ACIDS RESEARCH

FIMO: scanning for occurrences of a given motif

(2011) Charles E. Grant et al.   BIOINFORMATICS

Discriminative prediction of mammalian enhancers from DNA sequence

(2011) D. Lee et al.   GENOME RESEARCH

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generic eukaryotic core promoter prediction using structural features of DNA

(2007) T. Abeel et al.   GENOME RESEARCH