Three‐dimensional genome structure shapes the recombination landscape of chromatin features during female germline stem cell development

Integrative analysis of the 3D genome structure reveals that CTCF maintains the properties of mouse female germline stem cells

(2022) Geng G. Tian et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Offspring production of ovarian organoids derived from spermatogonial stem cells by defined factors with chromatin reorganization

(2021) Huacheng Luo et al.   Journal of Advanced Research

Generation of offspring-producing 3D ovarian organoids derived from female germline stem cells and their application in toxicological detection

(2021) Xiaoyong Li et al.   BIOMATERIALS

Parental-to-embryo switch of chromosome organization in early embryogenesis

(2020) Samuel Collombet et al.   NATURE

Alternative splicing signatures in preimplantation embryo development

(2020) Geng G. Tian et al.   Cell and Bioscience

Diverse motif ensembles specify non-redundant DNA binding activities of AP-1 family members in macrophages

(2019) Gregory J. Fonseca et al.   Nature Communications

Reprogramming of Meiotic Chromatin Architecture during Spermatogenesis

(2019) Yao Wang et al.   MOLECULAR CELL

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos

(2019) Zhenhai Du et al.   MOLECULAR CELL

Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation

(2019) She Zhang et al.   NUCLEIC ACIDS RESEARCH

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development

(2017) Douglas H. Phanstiel et al.   MOLECULAR CELL

Transcriptional control of genes mediating ovarian follicular growth, differentiation, and steroidogenesis in pigs

(2017) Holly A. LaVoie   MOLECULAR REPRODUCTION AND DEVELOPMENT

Tracing and Characterizing the Development of Transplanted Female Germline Stem Cells In Vivo

(2017) Changqing Wu et al.   MOLECULAR THERAPY

Bladder Cancer: 4 Big questions

(2017) Chris Berdik   NATURE

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

Dosage compensation in the process of inactivation/reactivation during both germ cell development and early embryogenesis in mouse

(2017) Xiaoyong Li et al.   Scientific Reports

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

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

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

Human GV oocytes generated by mitotically active germ cells obtained from follicular aspirates

(2016) Xinbao Ding et al.   Scientific Reports

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

Nuclear Organization and Genome Function

(2012) Kevin Van Bortle et al.   Annual Review of Cell and Developmental Biology

HiTC: exploration of high-throughput ‘C’ experiments

(2012) Nicolas Servant et al.   BIOINFORMATICS

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

Production of offspring from a germline stem cell line derived from neonatal ovaries

(2009) Kang Zou et al.   NATURE CELL BIOLOGY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Genomic imprinting at the mammalian Dlk1-Dio3 domain

(2008) Simao Teixeira da Rocha et al.   TRENDS IN GENETICS