cisTopic: cis-regulatory topic modeling on single-cell ATAC-seq data

BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization

(2018) Carl G. de Boer et al.   BMC BIOINFORMATICS

Mapping gene regulatory networks from single-cell omics data

(2018) Mark W E J Fiers et al.   Briefings in Functional Genomics

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

(2018) Jason D. Buenrostro et al.   CELL

Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation

(2018) Sebastian Preissl et al.   NATURE NEUROSCIENCE

Unsupervised clustering and epigenetic classification of single cells

(2018) Mahdi Zamanighomi et al.   Nature Communications

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons

(2018) Alexey Kozlenkov et al.   Science Advances

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

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

(2017) M Ryan Corces et al.   NATURE METHODS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

Neuronal activity modifies the chromatin accessibility landscape in the adult brain

(2017) Yijing Su et al.   NATURE NEUROSCIENCE

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

(2017) Ivan V Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

Single-cell methylomes identify neuronal subtypes and regulatory elements in mammalian cortex

(2017) Chongyuan Luo et al.   SCIENCE

Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex

(2017) Lucas T Gray et al.   eLife

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

destiny: diffusion maps for large-scale single-cell data in R

(2015) Philipp Angerer et al.   BIOINFORMATICS

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

i-cisTarget 2015 update: generalized cis-regulatory enrichment analysis in human, mouse and fly

(2015) Hana Imrichová et al.   NUCLEIC ACIDS RESEARCH

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

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

Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state

(2015) Annelien Verfaillie et al.   Nature Communications

Transcription factor MITF and remodeller BRG1 define chromatin organisation at regulatory elements in melanoma cells

(2015) Patrick Laurette et al.   eLife

topicmodels: AnRPackage for Fitting Topic Models

(2015) Bettina Grün et al.   Journal of Statistical Software

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

(2014) Rekin's Janky et al.   PLoS Computational Biology

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

Essential role of EBF1 in the generation and function of distinct mature B cell types

(2012) Bojan Vilagos et al.   JOURNAL OF EXPERIMENTAL MEDICINE

MDM4 is a key therapeutic target in cutaneous melanoma

(2012) Agnieszka Gembarska et al.   NATURE MEDICINE

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

(2012) Carl Herrmann et al.   NUCLEIC ACIDS RESEARCH

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

(2011) Morgane Thomas-Chollier et al.   Nature Protocols

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

(2011) Morgane Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

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

PU.1 and partners: regulation of haematopoietic stem cell fate in normal and malignant haematopoiesis

(2009) Pallavi Gupta et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

NRG1 / ERBB3 signaling in melanocyte development and melanoma: inhibition of differentiation and promotion of proliferation

(2009) Kristina Buac et al.   Pigment Cell & Melanoma Research

Transcription Factor E2-2 Is an Essential and Specific Regulator of Plasmacytoid Dendritic Cell Development

(2008) Babacar Cisse et al.   CELL