Single-cell roadmap of human gonadal development

Single-cell analysis of the developing human testis reveals somatic niche cell specification and fetal germline stem cell establishment

(2021) Jingtao Guo et al.   Cell Stem Cell

Blastocyst complementation using Prdm14-deficient rats enables efficient germline transmission and generation of functional mouse spermatids in rats

(2021) Toshihiro Kobayashi et al.   Nature Communications

Single‐cell transcriptomics reveal temporal dynamics of critical regulators of germ cell fate during mouse sex determination

(2021) Chloé Mayère et al.   FASEB JOURNAL

Blood and immune development in human fetal bone marrow and Down syndrome

(2021) Laura Jardine et al.   NATURE

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

ZGLP1 is a determinant for the oogenic fate in mice

(2020) So I. Nagaoka et al.   SCIENCE

Single-cell analysis of human ovarian cortex identifies distinct cell populations but no oogonial stem cells

(2020) Magdalena Wagner et al.   Nature Communications

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

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

Deciphering human macrophage development at single-cell resolution

(2020) Zhilei Bian et al.   NATURE

Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

(2020) Omer Ali Bayraktar et al.   NATURE NEUROSCIENCE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Two distinct pathways of pregranulosa cell differentiation support follicle formation in the mouse ovary

(2020) Wanbao Niu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human fetal microglia acquire homeostatic immune-sensing properties early in development

(2020) L. Kracht et al.   SCIENCE

Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s Disease

(2020) Rasa Elmentaite et al.   DEVELOPMENTAL CELL

Reconstitution of the oocyte transcriptional network with transcription factors

(2020) Nobuhiko Hamazaki et al.   NATURE

Female human primordial germ cells display X-chromosome dosage compensation despite the absence of X-inactivation

(2020) Tsotne Chitiashvili et al.   NATURE CELL BIOLOGY

SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data

(2020) Matthew D Young et al.   GigaScience

Single-cell RNA sequencing reveals regulation of fetal ovary development in the monkey (Macaca fascicularis)

(2020) Zheng-Hui Zhao et al.   Cell Discovery

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

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

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

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

Benchmark and integration of resources for the estimation of human transcription factor activities

(2019) Luz Garcia-Alonso et al.   GENOME RESEARCH

Addressing gaps in care of people with conditions affecting sex development and maturation

(2019) Olaf Hiort et al.   Nature Reviews Endocrinology

Decoding human fetal liver haematopoiesis

(2019) Dorin-Mirel Popescu et al.   NATURE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Testicular macrophages: Guardians of fertility

(2018) Noushin Mossadegh-Keller et al.   CELLULAR IMMUNOLOGY

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

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

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Tracing the transitions from pluripotency to germ cell fate with CRISPR screening

(2018) Jamie A. Hackett et al.   Nature Communications

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

(2017) Alicia N Schep et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

An environment-dependent transcriptional network specifies human microglia identity

(2017) David Gosselin et al.   SCIENCE

The prevalence and phenotypic features of polycystic ovary syndrome: a systematic review and meta-analysis

(2016) Gurkan Bozdag et al.   HUMAN REPRODUCTION

Functional characterization of somatic mutations in cancer using network-based inference of protein activity

(2016) Mariano J Alvarez et al.   NATURE GENETICS

Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons

(2016) Suguna Rani Krishnaswami et al.   Nature Protocols

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Testicular immunoregulation and spermatogenesis

(2016) Qiaoyuan Chen et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

A Unique Gene Regulatory Network Resets the Human Germline Epigenome for Development

(2015) Walfred W.C. Tang et al.   CELL

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models

(2015) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

Zic1 controls placode progenitor formation non-cell autonomously by regulating retinoic acid production and transport

(2015) Maria Belen Jaurena et al.   Nature Communications

Marker genes identify three somatic cell types in the fetal mouse ovary

(2014) Raphael H. Rastetter et al.   DEVELOPMENTAL BIOLOGY

DMRT1 Protects Male Gonadal Cells from Retinoid-Dependent Sexual Transdifferentiation

(2014) Anna Minkina et al.   DEVELOPMENTAL CELL

Yolk-sac-derived macrophages regulate fetal testis vascularization and morphogenesis

(2014) T. DeFalco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temporal Differences in Granulosa Cell Specification in the Ovary Reflect Distinct Follicle Fates in Mice1

(2011) Lindsey Mork et al.   BIOLOGY OF REPRODUCTION

Immunological, paracrine and endocrine aspects of testicular immune privilege

(2010) Andreas Meinhardt et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

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

Somatic Sex Reprogramming of Adult Ovaries to Testes by FOXL2 Ablation

(2009) N. Henriette Uhlenhaut et al.   CELL

Endothelial cell migration directs testis cord formation

(2008) Alexander N. Combes et al.   DEVELOPMENTAL BIOLOGY

Primordial follicular assembly in humans – revisited

(2008) A. Maheshwari et al.   ZYGOTE