Unified single-cell analysis of testis gene regulation and pathology in five mouse strains

Single-cell RNA-seq denoising using a deep count autoencoder

(2019) Gökcen Eraslan et al.   Nature Communications

A meiosis-specific BRCA2 binding protein recruits recombinases to DNA double-strand breaks to ensure homologous recombination

(2019) Jingjing Zhang et al.   Nature Communications

The meiotic TERB1-TERB2-MAJIN complex tethers telomeres to the nuclear envelope

(2019) Yan Wang et al.   Nature Communications

Characterizing mutagenic effects of recombination through a sequence-level genetic map

(2019) Bjarni V. Halldorsson et al.   SCIENCE

REC114 Partner ANKRD31 Controls Number, Timing, and Location of Meiotic DNA Breaks

(2019) Michiel Boekhout et al.   MOLECULAR CELL

Amplification of a broad transcriptional program by a common factor triggers the meiotic cell cycle in mice

(2019) Mina L Kojima et al.   eLife

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

The SS18-SSX Oncoprotein Hijacks KDM2B-PRC1.1 to Drive Synovial Sarcoma

(2018) Ana Banito et al.   CANCER CELL

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

Control of meiotic double-strand-break formation by ATM: local and global views

(2018) Agnieszka Lukaszewicz et al.   CELL CYCLE

PRDM9 Methyltransferase Activity Is Essential for Meiotic DNA Double-Strand Break Formation at Its Binding Sites

(2018) Boubou Diagouraga et al.   MOLECULAR CELL

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations

(2018) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cullin 3-Based Ubiquitin Ligases as Master Regulators of Mammalian Cell Differentiation

(2018) Wolfgang Dubiel et al.   TRENDS IN BIOCHEMICAL SCIENCES

ATR is a multifunctional regulator of male mouse meiosis

(2018) Alexander Widger et al.   Nature Communications

ATR is required to complete meiotic recombination in mice

(2018) Sarai Pacheco et al.   Nature Communications

Characterization of germ cell differentiation in the male mouse through single-cell RNA sequencing

(2018) S. Lukassen et al.   Scientific Reports

SHOC1 is a ERCC4-(HhH)2-like protein, integral to the formation of crossover recombination intermediates during mammalian meiosis

(2018) Michel F. Guiraldelli et al.   PLoS Genetics

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

Single-cell RNA-seq uncovers dynamic processes and critical regulators in mouse spermatogenesis

(2018) Yao Chen et al.   CELL RESEARCH

A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq

(2018) Christopher Daniel Green et al.   DEVELOPMENTAL CELL

Enter the Matrix: Factorization Uncovers Knowledge from Omics

(2018) Genevieve L. Stein-O’Brien et al.   TRENDS IN GENETICS

Reappraising the microscopic anatomy of human testis: identification of telocyte networks in the peritubular and intertubular stromal space

(2018) Mirca Marini et al.   Scientific Reports

The Mammalian Spermatogenesis Single-Cell Transcriptome, from Spermatogonial Stem Cells to Spermatids

(2018) Brian P. Hermann et al.   Cell Reports

NRF1 coordinates with DNA methylation to regulate spermatogenesis

(2017) Junpeng Wang et al.   FASEB JOURNAL

PRDM9 interactions with other proteins provide a link between recombination hotspots and the chromosomal axis in meiosis

(2017) Emil D. Parvanov et al.   MOLECULAR BIOLOGY OF THE CELL

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis

(2017) Ivan V Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

Meiotic Knockdown and Complementation Reveals Essential Role of RAD51 in Mouse Spermatogenesis

(2017) Jieqiong Dai et al.   Cell Reports

Meioc maintains an extended meiotic prophase I in mice

(2017) Y. Q. Shirleen Soh et al.   PLoS Genetics

A map of human PRDM9 binding provides evidence for novel behaviors of PRDM9 and other zinc-finger proteins in meiosis

(2017) Nicolas Altemose et al.   eLife

A Standardized Approach for Multispecies Purification of Mammalian Male Germ Cells by Mechanical Tissue Dissociation and Flow Cytometry

(2017) Ana C. Lima et al.   Jove-Journal of Visualized Experiments

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

(2017) Xun Zhu et al.   PeerJ

Acrosome markers of human sperm

(2016) Chizuru Ito et al.   ANATOMICAL SCIENCE INTERNATIONAL

Robust classification of single-cell transcriptome data by nonnegative matrix factorization

(2016) Chunxuan Shao et al.   BIOINFORMATICS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Transcriptome analysis of highly purified mouse spermatogenic cell populations: gene expression signatures switch from meiotic-to postmeiotic-related processes at pachytene stage

(2016) Irene da Cruz et al.   BMC GENOMICS

Complete Meiosis from Embryonic Stem Cell-Derived Germ Cells In Vitro

(2016) Quan Zhou et al.   Cell Stem Cell

Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice

(2016) Benjamin Davies et al.   NATURE

Meiotic DNA break formation requires the unsynapsed chromosome axis-binding protein IHO1 (CCDC36) in mice

(2016) Marcello Stanzione et al.   NATURE CELL BIOLOGY

Tensor decomposition for multiple-tissue gene expression experiments

(2016) Victoria Hore et al.   NATURE GENETICS

BRCA2 regulates DMC1-mediated recombination through the BRC repeats

(2016) Juan S. Martinez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Speedy A–Cdk2 binding mediates initial telomere–nuclear envelope attachment during meiotic prophase I independent of Cdk2 activation

(2016) Zhaowei Tu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A DNA topoisomerase VI-like complex initiates meiotic recombination

(2016) N. Vrielynck et al.   SCIENCE

The TopoVIB-Like protein family is required for meiotic DNA double-strand break formation

(2016) T. Robert et al.   SCIENCE

Transcription Factor GLIS3: A New and Critical Regulator of Postnatal Stages of Mouse Spermatogenesis

(2016) Hong Soon Kang et al.   STEM CELLS

Expression and epigenomic landscape of the sex chromosomes in mouse post-meiotic male germ cells

(2016) Charlotte Moretti et al.   Epigenetics & Chromatin

C14ORF39/SIX6OS1 is a constituent of the synaptonemal complex and is essential for mouse fertility

(2016) Laura Gómez-H et al.   Nature Communications

Implementation of meiosis prophase I programme requires a conserved retinoid-independent stabilizer of meiotic transcripts

(2016) Emilie Abby et al.   Nature Communications

A High-Density Map for Navigating the Human Polycomb Complexome

(2016) Simon Hauri et al.   Cell Reports

The Meiotic Recombination Activator PRDM9 Trimethylates Both H3K36 and H3K4 at Recombination Hotspots In Vivo

(2016) Natalie R. Powers et al.   PLoS Genetics

Meiotic Silencing in Mammals

(2015) James M.A. Turner   Annual Review of Genetics

oposSOM: R-package for high-dimensional portraying of genome-wide expression landscapes on bioconductor: Fig. 1.

(2015) Henry Löffler-Wirth et al.   BIOINFORMATICS

Poised chromatin and bivalent domains facilitate the mitosis-to-meiosis transition in the male germline

(2015) Ho-Su Sin et al.   BMC BIOLOGY

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

FancJ (Brip1) loss-of-function allele results in spermatogonial cell depletion during embryogenesis and altered processing of crossover sites during meiotic prophase I in mice

(2015) Xianfei Sun et al.   CHROMOSOMA

Complex elaboration: making sense of meiotic cohesin dynamics

(2015) Susannah Rankin   FEBS Journal

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Evolution of haploid selection in predominantly diploid organisms

(2015) Sarah P. Otto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Recombination, Pairing, and Synapsis of Homologs during Meiosis

(2015) Denise Zickler et al.   Cold Spring Harbor Perspectives in Biology

MCM8-9 complex promotes resection of double-strand break ends by MRE11-RAD50-NBS1 complex

(2015) Kyung Yong Lee et al.   Nature Communications

RFX2 Is a Major Transcriptional Regulator of Spermiogenesis

(2015) W. Stephen Kistler et al.   PLoS Genetics

Small Rad51 and Dmc1 Complexes Often Co-occupy Both Ends of a Meiotic DNA Double Strand Break

(2015) M. Scott Brown et al.   PLoS Genetics

Scalable Strategies for Computing with Massive Data

(2015) Michael J. Kane et al.   Journal of Statistical Software

Proteomic analysis of murine testes lipid droplets

(2015) Weiyi Wang et al.   Scientific Reports

Meiosis-specific cohesin mediates homolog recognition in mouse spermatocytes

(2014) K.-i. Ishiguro et al.   GENES & DEVELOPMENT

The human testis-specific proteome defined by transcriptomics and antibody-based profiling

(2014) D. Djureinovic et al.   MOLECULAR HUMAN REPRODUCTION

Fast Principal Component Analysis of Large-Scale Genome-Wide Data

(2014) Gad Abraham et al.   PLoS One

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Strand Exchange and RecA Homologs in Meiosis

(2014) M. Scott Brown et al.   Cold Spring Harbor Perspectives in Biology

Macrophages and Leydig Cells in Testicular Biopsies of Azoospermic Men

(2014) Trpimir Goluža et al.   Biomed Research International

A molecular model for the role of SYCP3 in meiotic chromosome organisation

(2014) Johanna Liinamaria Syrjänen et al.   eLife

Homologous Pairing Preceding SPO11-Mediated Double-Strand Breaks in Mice

(2013) Kingsley A. Boateng et al.   DEVELOPMENTAL CELL

Common and low-frequency variants associated with genome-wide recombination rate

(2013) Augustine Kong et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Structural Insights into Saccharomyces cerevisiae Msh4–Msh5 Complex Function Using Homology Modeling

(2013) Ramaswamy Rakshambikai et al.   PLoS One

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

Mouse HFM1/Mer3 Is Required for Crossover Formation and Complete Synapsis of Homologous Chromosomes during Meiosis

(2013) Michel F. Guiraldelli et al.   PLoS Genetics

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Novel Insights into the Downstream Pathways and Targets Controlled by Transcription Factors CREM in the Testis

(2012) Rok Kosir et al.   PLoS One

Orally applied doxazosin disturbed testosterone homeostasis and changed the transcriptional profile of steroidogenic machinery, cAMP/cGMP signalling and adrenergic receptors in Leydig cells of adult rats

(2012) N. J. Stojkov et al.   Andrology

Testicular biopsy: clinical practice and interpretation

(2011) Gert R Dohle et al.   ASIAN JOURNAL OF ANDROLOGY

A-MYB (MYBL1) transcription factor is a master regulator of male meiosis

(2011) E. Bolcun-Filas et al.   DEVELOPMENT

The E3 ubiquitin ligase Cullin 4A regulates meiotic progression in mouse spermatogenesis

(2011) Yan Yin et al.   DEVELOPMENTAL BIOLOGY

Foxo1 is required in mouse spermatogonial stem cells for their maintenance and the initiation of spermatogenesis

(2011) Meredith J. Goertz et al.   JOURNAL OF CLINICAL INVESTIGATION

Meiotic homologue alignment and its quality surveillance are controlled by mouse HORMAD1

(2011) Katrin Daniel et al.   NATURE CELL BIOLOGY

Germ Cell Intercellular Bridges

(2011) M. P. Greenbaum et al.   Cold Spring Harbor Perspectives in Biology

Flow Cytometry Purification of Mouse Meiotic Cells

(2011) Irina V. Getun et al.   Jove-Journal of Visualized Experiments

Spermatophagy in the Seminiferous Tubules and Excurrent Ducts of the Testis in Rhesus Monkey and in Man*

(2010) A.-F. HOLSTEIN   ANDROLOGIA

Evidence that Meiotic Sex Chromosome Inactivation Is Essential for Male Fertility

(2010) Hélène Royo et al.   CURRENT BIOLOGY

Flow Cytometry for Gene Expression Studies in Mammalian Spermatogenesis

(2010) A. Geisinger et al.   CYTOGENETIC AND GENOME RESEARCH

Sex chromosome inactivation in the male

(2010) Wei Yan et al.   Epigenetics

Prdm9 Controls Activation of Mammalian Recombination Hotspots

(2010) E. D. Parvanov et al.   SCIENCE

Drive Against Hotspot Motifs in Primates Implicates the PRDM9 Gene in Meiotic Recombination

(2010) S. Myers et al.   SCIENCE

PRDM9 Is a Major Determinant of Meiotic Recombination Hotspots in Humans and Mice

(2010) F. Baudat et al.   SCIENCE

Hormad1 Mutation Disrupts Synaptonemal Complex Formation, Recombination, and Chromosome Segregation in Mammalian Meiosis

(2010) Yong-Hyun Shin et al.   PLoS Genetics

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The pluripotency factor LIN28 marks undifferentiated spermatogonia in mouse

(2009) Ke Zheng et al.   BMC DEVELOPMENTAL BIOLOGY

The heterogeneity of spermatogonia is revealed by their topology and expression of marker proteins including the germ cell-specific proteins Nanos2 and Nanos3

(2009) Hitomi Suzuki et al.   DEVELOPMENTAL BIOLOGY

Retention of gene products in syncytial spermatids promotes non-Mendelian inheritance as revealed by the t complex responder

(2009) N. Veron et al.   GENES & DEVELOPMENT

Distinctive chromatin in human sperm packages genes for embryo development

(2009) Saher Sue Hammoud et al.   NATURE

Lineage-Specific Biology Revealed by a Finished Genome Assembly of the Mouse

(2009) Deanna M. Church et al.   PLOS BIOLOGY

Mouse HORMAD1 and HORMAD2, Two Conserved Meiotic Chromosomal Proteins, Are Depleted from Synapsed Chromosome Axes with the Help of TRIP13 AAA-ATPase

(2009) Lukasz Wojtasz et al.   PLoS Genetics

Mouse TEX15 is essential for DNA double-strand break repair and chromosomal synapsis during male meiosis

(2008) Fang Yang et al.   JOURNAL OF CELL BIOLOGY

ZIP4H (TEX11) Deficiency in the Mouse Impairs Meiotic Double Strand Break Repair and the Regulation of Crossing Over

(2008) Carrie A. Adelman et al.   PLoS Genetics