Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements

The complete sequence of a human genome

(2022) Sergey Nurk et al.   SCIENCE

Single nucleus transcriptome and chromatin accessibility of postmortem human pituitaries reveal diverse stem cell regulatory mechanisms

(2022) Zidong Zhang et al.   Cell Reports

CaBagE: A Cas9-based Background Elimination strategy for targeted, long-read DNA sequencing

(2021) Amelia D. Wallace et al.   PLoS One

Targeted nanopore sequencing with Cas9-guided adapter ligation

(2020) Timothy Gilpatrick et al.   NATURE BIOTECHNOLOGY

Long-range single-molecule mapping of chromatin accessibility in eukaryotes

(2020) Zohar Shipony et al.   NATURE METHODS

Differential 3D chromatin organization and gene activity in genomic imprinting

(2020) Daan Noordermeer et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Single-molecule regulatory architectures captured by chromatin fiber sequencing

(2020) Andrew B. Stergachis et al.   SCIENCE

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer

(2020) Sarah E. Johnstone et al.   CELL

The GTEx Consortium atlas of genetic regulatory effects across human tissues

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Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo

(2020) Can Sönmezer et al.   MOLECULAR CELL

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

(2020) Isac Lee et al.   NATURE METHODS

Massively multiplex single-molecule oligonucleosome footprinting

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Genomic imprinting disorders: lessons on how genome, epigenome and environment interact

(2019) David Monk et al.   NATURE REVIEWS GENETICS

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

Genomic Imprinting and Physiological Processes in Mammals

(2019) Valter Tucci et al.   CELL

A comparison of single-cell trajectory inference methods

(2019) Wouter Saelens et al.   NATURE BIOTECHNOLOGY

Single-molecule long-read sequencing reveals the chromatin basis of gene expression

(2019) Yunhao Wang et al.   GENOME RESEARCH

Advances in epigenetics link genetics to the environment and disease

(2019) Giacomo Cavalli et al.   NATURE

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing

(2019) Pay Giesselmann et al.   NATURE BIOTECHNOLOGY

Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution

(2018) Efrat Shema et al.   NATURE GENETICS

Ablation of Transcription Factor IRF4 Promotes Transplant Acceptance by Driving Allogenic CD4 + T Cell Dysfunction

(2017) Jie Wu et al.   IMMUNITY

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

(2017) Julia Joung et al.   Nature Protocols

Associating cellular epigenetic models with human phenotypes

(2017) Tuuli Lappalainen et al.   NATURE REVIEWS GENETICS

Single-cell transcriptomics to explore the immune system in health and disease

(2017) Michael J. T. Stubbington et al.   SCIENCE

Simultaneous measurement of chromatin accessibility, DNA methylation, and nucleosome phasing in single cells

(2017) Sebastian Pott   eLife

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

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Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

TSCAN: Pseudo-time reconstruction and evaluation in single-cell RNA-seq analysis

(2016) Zhicheng Ji et al.   NUCLEIC ACIDS RESEARCH

17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells

(2016) Benjamin Joachim Schmiedel et al.   Nature Communications

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

IRF4 at the crossroads of effector T-cell fate decision

(2014) Magdalena Huber et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment

(2014) F. Court et al.   GENOME RESEARCH

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

(2012) T. K. Kelly et al.   GENOME RESEARCH

BATF–JUN is critical for IRF4-mediated transcription in T cells

(2012) Peng Li et al.   NATURE