Volume 33, Issue 2 | February 2023

Research
- - The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory
    Varsha Poondi Krishnan
    Barbara Morone
    Shir Toubiana
    Monika Krzak
    Salvatore Fioriniello
    Floriana Della Ragione
    ...[+1 authors]...,
    Maria Strazzullo
    Claudia Angelini
    Sara Selig
    Maria R. Matarazzo
    First Published February 24, 2023
  - Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
    Alejandro Martin-Trujillo
    Paras Garg
    Nihir Patel
    Bharati Jadhav
    Andrew J. Sharp
    First Published December 28, 2022
  - Regulation of endogenous retrovirus–derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells
    Cui Du
    Jing Jiang
    Yuzhuo Li
    Miao Yu
    Jian Jin
    Shuai Chen
    ...[+1 authors]...,
    Hairui Fan
    Todd S. Macfarlan
    Bin Cao
    Ming-an Sun
    First Published February 17, 2023
Methods
- - Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing
    Brendan L. O'Connell
    Ruth V. Nichols
    Dmitry Pokholok
    Jerushah Thomas
    Sonia N. Acharya
    Andrew Nishida Casey A. Thornton
    ...[+2 authors]...,
    Marissa Co
    Andrew J. Fields
    Frank J. Steemers
    Andrew C. Adey
    First Published February 15, 2023
  - Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis
    Shreya Mishra
    Neetesh Pandey
    Smriti Chawla
    Madhu Sharma
    Omkar Chandra
    First Published January 18, 2023
  - Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learning
    Tian Tian
    Cheng Zhong
    Xiang Lin
    Zhi Wei
    Hakon Hakonarson
    First Published February 27, 2023
  - Characterization of network hierarchy reflects cell state specificity in genome organization
    Jingyao Wang
    Yue Xue
    Yueying He
    Hui Quan
    Jun Zhang
    First Published February 24, 2023
Resources
- - The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond
    Simon Bray
    John Chilton
    Matthias Bernt
    Nicola Soranzo
    Marius van den Beek
    Bérénice Batut Helena Rasche
    ...[+2 authors]...,
    Martin Čech
    Peter J.A. Cock
    Björn Grüning
    Anton Nekrutenko
    First Published February 24, 2023
  - A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements
    Salam Idriss
    Mohammad Hallal
    Abdullah El-Kurdi
    Hasan Zalzali
    Inaam El-Rassi
    Erik A. Ehli Christel M. Davis Philip E.D. Chung
    ...[+3 authors]...,
    Deena M.A. Gendoo
    Eldad Zacksenhaus
    Raya Saab
    Pierre Khoueiry
    First Published January 17, 2023
  - A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state
    Jack F. Cazet
    Stefan Siebert
    Hannah Morris Little
    Philip Bertemes
    Abby S. Primack
    Peter Ladurner Matthias Achrainer Mark T. Fredriksen R. Travis Moreland Sumeeta Singh Suiyuan Zhang Tyra G. Wolfsberg Christine E. Schnitzler
    ...[+8 authors]...,
    Andreas D. Baxevanis
    Oleg Simakov
    Bert Hobmayer
    Celina E. Juliano
    First Published January 13, 2023

Table of Contents

Volume 33, Issue 2 | February 2023

Research

The aberrant epigenome of DNMT3B-mutated ICF1 patient iPSCs is amenable to correction, with the exception of a subset of regions with H3K4me3- and/or CTCF-based epigenetic memory

Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation

Regulation of endogenous retrovirus–derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells

Methods

Atlas-scale single-cell chromatin accessibility using nanowell-based combinatorial indexing

Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis

Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learning

Characterization of network hierarchy reflects cell state specificity in genome organization

Resources

The Planemo toolkit for developing, deploying, and executing scientific data analyses in Galaxy and beyond

A temporal in vivo catalog of chromatin accessibility and expression profiles in pineoblastoma reveals a prevalent role for repressor elements

A chromosome-scale epigenetic map of the Hydra genome reveals conserved regulators of cell state

Table of Contents

Volume 33, Issue 2 | February 2023

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Research

Methods

Resources