SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks

(2023) Aryan Kamal et al.   Molecular Systems Biology

Dissecting cell identity via network inference and in silico gene perturbation

(2023) Kenji Kamimoto et al.   NATURE

Decoding gene regulation in the fly brain

(2022) Jasper Janssens et al.   NATURE

HyDrop enables droplet based single-cell ATAC-seq and single-cell RNA-seq using dissolvable hydrogel beads

(2022) Florian De Rop et al.   eLife

NanoDam identifies Homeobrain (ARX) and Scarecrow (NKX2.1) as conserved temporal factors in the Drosophila central brain and visual system

(2022) Jocelyn L.Y. Tang et al.   DEVELOPMENTAL CELL

Nonlinear control of transcription through enhancer–promoter interactions

(2022) Jessica Zuin et al.   NATURE

<i>Meis1</i> plays roles in cortical development through regulation of cellular proliferative capacity in the embryonic cerebrum

(2022) Eriko ISOGAI et al.   BIOMEDICAL RESEARCH-TOKYO

Inferring and perturbing cell fate regulomes in human brain organoids

(2022) Jonas Simon Fleck et al.   NATURE

Multi-omic single-cell velocity models epigenome–transcriptome interactions and improves cell fate prediction

(2022) Chen Li et al.   NATURE BIOTECHNOLOGY

Obtaining genetics insights from deep learning via explainable artificial intelligence

(2022) Gherman Novakovsky et al.   NATURE REVIEWS GENETICS

The spatial organization of transcriptional control

(2022) Antonina Hafner et al.   NATURE REVIEWS GENETICS

Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag

(2022) Marek Bartosovic et al.   NATURE BIOTECHNOLOGY

Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution

(2022) Tim Stuart et al.   NATURE BIOTECHNOLOGY

Current challenges in understanding the role of enhancers in disease

(2022) Judith Barbara Zaugg et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MITF reprograms the extracellular matrix and focal adhesion in melanoma

(2021) Ramile Dilshat et al.   eLife

ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis

(2021) Jeffrey M. Granja et al.   NATURE GENETICS

Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues

(2021) Marek Bartosovic et al.   NATURE BIOTECHNOLOGY

Chromatin occupancy and target genes of the haematopoietic master transcription factor MYB

(2021) Roza B. Lemma et al.   Scientific Reports

Mapping single-cell atlases throughout Metazoa unravels cell type evolution

(2021) Alexander J Tarashansky et al.   eLife

UniBind: maps of high-confidence direct TF-DNA interactions across nine species

(2021) Rafael Riudavets Puig et al.   BMC GENOMICS

How subtle changes in 3D structure can create large changes in transcription

(2021) Jordan Yupeng Xiao et al.   eLife

Single-cell and single-nucleus RNA-seq uncovers shared and distinct axes of variation in dorsal LGN neurons in mice, non-human primates, and humans

(2021) Trygve E Bakken et al.   eLife

Comparative cellular analysis of motor cortex in human, marmoset and mouse

(2021) Trygve E. Bakken et al.   NATURE

Effective gene expression prediction from sequence by integrating long-range interactions

(2021) Žiga Avsec et al.   NATURE METHODS

Single-cell chromatin state analysis with Signac

(2021) Tim Stuart et al.   NATURE METHODS

Analysis of long and short enhancers in melanoma cell states

(2021) David Mauduit et al.   eLife

The origin of animal body plans: a view from fossil evidence and the regulatory genome

(2020) Douglas H. Erwin   DEVELOPMENT

Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data

(2020) Aditya Pratapa et al.   NATURE METHODS

Identification of genomic enhancers through spatial integration of single‐cell transcriptomics and epigenomics

(2020) Carmen Bravo González‐Blas et al.   Molecular Systems Biology

Cross-species analysis of enhancer logic using deep learning

(2020) Liesbeth Minnoye et al.   GENOME RESEARCH

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Robust gene expression programs underlie recurrent cell states and phenotype switching in melanoma

(2020) Jasper Wouters et al.   NATURE CELL BIOLOGY

A scalable SCENIC workflow for single-cell gene regulatory network analysis

(2020) Bram Van de Sande et al.   Nature Protocols

Transcriptional Regulation of Natural Killer Cell Development and Functions

(2020) Dandan Wang et al.   Cancers

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

(2020) Sai Ma et al.   CELL

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

(2019) Carmen Bravo González-Blas et al.   NATURE METHODS

Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity

(2019) Jeffrey M Alexander et al.   eLife

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Crazy Little Thing Called Sox—New Insights in Oligodendroglial Sox Protein Function

(2019) Jan Wittstatt et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

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

New developments on the Encyclopedia of DNA Elements (ENCODE) data portal

(2019) Yunhai Luo et al.   NUCLEIC ACIDS RESEARCH

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq

(2018) Arnau Sebé-Pedrós et al.   CELL

Role of Smad3 signaling in the epithelial‑mesenchymal transition of the lens epithelium following injury

(2018) Fanlan Meng et al.   INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE

Enhancer Logic and Mechanics in Development and Disease

(2018) Ryan Rickels et al.   TRENDS IN CELL BIOLOGY

Enhancer and Transcription Factor Dynamics during Myeloid Differentiation Reveal an Early Differentiation Block in Cebpa null Progenitors

(2018) Sachin Pundhir et al.   Cell Reports

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

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

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks

(2018) Thomas Moerman et al.   BIOINFORMATICS

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

A map of direct TF–DNA interactions in the human genome

(2018) Marius Gheorghe et al.   NUCLEIC ACIDS RESEARCH

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas

(2018) Shengbao Suo et al.   Cell Reports

Paired Related Homeobox Protein 1 Regulates Quiescence in Human Oligodendrocyte Progenitors

(2018) Jing Wang et al.   Cell Reports

Runx3 is a key modulator during the epithelial-mesenchymal transition of alveolar type II cells in animal models of BPD

(2017) Haiping Yang et al.   INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

APPRIS 2017: principal isoforms for multiple gene sets

(2017) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

Regulation of normal B-cell differentiation and malignant B-cell survival by OCT2

(2016) Daniel J. Hodson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

ZEB1: At the crossroads of epithelial-mesenchymal transition, metastasis and therapy resistance

(2015) Peijing Zhang et al.   CELL CYCLE

Genome-wide organization of GATA1 and TAL1 determined at high resolution

(2015) G. Celine Han et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2015) Hana Imrichová et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Annelien Verfaillie et al.   Nature Communications

Transcriptional Control of Early T and B Cell Developmental Choices

(2014) Ellen V. Rothenberg   Annual Review of Immunology

Conservation of trans-acting circuitry during mammalian regulatory evolution

(2014) Andrew B. Stergachis et al.   NATURE

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

A Switch in the Expression of Embryonic EMT-Inducers Drives the Development of Malignant Melanoma

(2013) Julie Caramel et al.   CANCER CELL

Sox4 Is a Master Regulator of Epithelial-Mesenchymal Transition by Controlling Ezh2 Expression and Epigenetic Reprogramming

(2013) Neha Tiwari et al.   CANCER CELL

Elucidation of the role of LMO2 in human erythroid cells

(2013) Ai Inoue et al.   EXPERIMENTAL HEMATOLOGY

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model

(2013) Robin P Smith et al.   NATURE GENETICS

Segregation of eye and antenna fates maintained by mutual antagonism in Drosophila

(2012) C.-W. Wang et al.   DEVELOPMENT

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Transcriptional Regulation of Dendritic Cell Diversity

(2012) Michaël Chopin et al.   Frontiers in Immunology

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Multiscale Binarization of Gene Expression Data for Reconstructing Boolean Networks

(2011) M. Hopfensitz et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

Cancer stem cells versus phenotype-switching in melanoma

(2010) Keith S. Hoek et al.   Pigment Cell & Melanoma Research

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

A density-based method for adaptive LDA model selection

(2008) Juan Cao et al.   NEUROCOMPUTING

Improved assay-dependent searching of nucleic acid sequence databases

(2008) J. D. Gans et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY