Evaluating genetic causes of azoospermia: What can we learn from a complex cellular structure and single-cell transcriptomics of the human testis?

Monogenic causes of non-obstructive azoospermia: challenges, established knowledge, limitations and perspectives

(2020) Laura Kasak et al.   HUMAN GENETICS

Comparative analysis of differential gene expression analysis tools for single-cell RNA sequencing data

(2019) Tianyu Wang et al.   BMC BIOINFORMATICS

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

(2019) Gökcen Eraslan et al.   Nature Communications

The Neonatal and Adult Human Testis Defined at the Single-Cell Level

(2019) Abhishek Sohni et al.   Cell Reports

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

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

A new MEIOB mutation is a recurrent cause for azoospermia and testicular meiotic arrest

(2019) Moran Gershoni et al.   HUMAN REPRODUCTION

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

(2019) Geoffrey Schiebinger et al.   CELL

Sequencing of a ‘mouse azoospermia’ gene panel in azoospermic men: identification of RNF212 and STAG3 mutations as novel genetic causes of meiotic arrest

(2019) A Riera-Escamilla et al.   HUMAN REPRODUCTION

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Performance Assessment and Selection of Normalization Procedures for Single-Cell RNA-Seq

(2019) Michael B. Cole et al.   Cell Systems

Concepts and limitations for learning developmental trajectories from single cell genomics

(2019) Sophie Tritschler et al.   DEVELOPMENT

RNA profiling of human testicular cells identifies syntenic lncRNAs associated with spermatogenesis

(2019) A D Rolland et al.   HUMAN REPRODUCTION

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Joint analysis of heterogeneous single-cell RNA-seq dataset collections

(2019) Nikolas Barkas et al.   NATURE METHODS

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

(2019) Christopher S. McGinnis et al.   NATURE METHODS

Meiosis I progression in spermatogenesis requires a type of testis-specific 20S core proteasome

(2019) Qianting Zhang et al.   Nature Communications

BBKNN: fast batch alignment of single cell transcriptomes

(2019) Krzysztof Polański et al.   BIOINFORMATICS

A systematic evaluation of single cell RNA-seq analysis pipelines

(2019) Beate Vieth et al.   Nature Communications

The X chromosome and male infertility

(2019) Matthias Vockel et al.   HUMAN GENETICS

Novel ADGRG2 truncating variants in patients with X‐linked congenital absence of vas deferens

(2019) Adrien Pagin et al.   Andrology

DEsingle for detecting three types of differential expression in single-cell RNA-seq data

(2018) Zhun Miao et al.   BIOINFORMATICS

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

(2018) Kelly Street et al.   BMC GENOMICS

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

From exome analysis in idiopathic azoospermia to the identification of a high-risk subgroup for occult Fanconi anemia

(2018) Csilla Krausz et al.   GENETICS IN MEDICINE

Potential roles of the poly(A)-binding proteins in translational regulation during spermatogenesis

(2018) Saffet OZTURK et al.   JOURNAL OF REPRODUCTION AND DEVELOPMENT

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

Genetics of male infertility

(2018) Csilla Krausz et al.   Nature Reviews Urology

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Bi-allelic Recessive Loss-of-Function Variants in FANCM Cause Non-obstructive Azoospermia

(2018) Laura Kasak et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis

(2018) Mei Wang et al.   Cell Stem Cell

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

The adult human testis transcriptional cell atlas

(2018) Jingtao Guo et al.   CELL RESEARCH

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

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

Clinical, genetic, biochemical, and testicular biopsy findings among 1,213 men evaluated for infertility

(2017) Inge Ahlmann Olesen et al.   FERTILITY AND STERILITY

A familial study of azoospermic men identifies three novel causative mutations in three new human azoospermia genes

(2017) Moran Gershoni et al.   GENETICS IN MEDICINE

Spermatogenic failure and the Y chromosome

(2017) C. Krausz et al.   HUMAN GENETICS

Chromosomal abnormalities in 1663 infertile men with azoospermia: the clinical consequences

(2017) R B Donker et al.   HUMAN REPRODUCTION

The diagnosis of male infertility: an analysis of the evidence to support the development of global WHO guidance—challenges and future research opportunities

(2017) Christopher L R Barratt et al.   HUMAN REPRODUCTION UPDATE

Female-to-male sex reversal associated with unique Xp21.2 deletion disrupting genomic regulatory architecture of the dosage-sensitive sex reversal region

(2017) Pankaj Dangle et al.   JOURNAL OF MEDICAL GENETICS

Kallmann syndrome: phenotype and genotype of hypogonadotropic hypogonadism

(2017) Maria I. Stamou et al.   METABOLISM-CLINICAL AND EXPERIMENTAL

Meiotic Genes Are Enriched in Regions of Reduced Archaic Ancestry

(2017) B. Jégou et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

SCnorm: robust normalization of single-cell RNA-seq data

(2017) Rhonda Bacher et al.   NATURE METHODS

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

SC3: consensus clustering of single-cell RNA-seq data

(2017) Vladimir Yu Kiselev et al.   NATURE METHODS

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Congenital bilateral absence of the vas deferens as an atypical form of cystic fibrosis: reproductive implications and genetic counseling

(2017) D. A. S. de Souza et al.   Andrology

Are AZFb deletions always incompatible with sperm production?

(2017) K. Stouffs et al.   Andrology

Novel concepts in the aetiology of male reproductive impairment

(2017) Herman Tournaye et al.   Lancet Diabetes & Endocrinology

ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information

(2016) Alexander Lachmann 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

Tensor decomposition for multiple-tissue gene expression experiments

(2016) Victoria Hore et al.   NATURE GENETICS

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

Male Reproductive Disorders and Fertility Trends: Influences of Environment and Genetic Susceptibility

(2016) Niels E. Skakkebaek et al.   PHYSIOLOGICAL REVIEWS

Dynamics of the Transcriptome during Human Spermatogenesis: Predicting the Potential Key Genes Regulating Male Gametes Generation

(2016) Zijue Zhu et al.   Scientific Reports

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

Trends in Use of and Reproductive Outcomes Associated With Intracytoplasmic Sperm Injection

(2015) Sheree L. Boulet et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

European Consensus Statement on congenital hypogonadotropic hypogonadism—pathogenesis, diagnosis and treatment

(2015) Ulrich Boehm et al.   Nature Reviews Endocrinology

An update on the diagnosis and management of ejaculatory duct obstruction

(2015) Vaibhav Modgil et al.   Nature Reviews Urology

X-Linked TEX11 Mutations, Meiotic Arrest, and Azoospermia in Infertile Men

(2015) Alexander N. Yatsenko et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

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

A unique view on male infertility around the globe

(2015) Ashok Agarwal et al.   Reproductive Biology and Endocrinology

High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis1

(2014) Frédéric Chalmel et al.   BIOLOGY OF REPRODUCTION

Truncating mutations inTAF4BandZMYND15causing recessive azoospermia

(2014) Özgecan Ayhan et al.   JOURNAL OF MEDICAL GENETICS

Deconstructing transcriptional heterogeneity in pluripotent stem cells

(2014) Roshan M. Kumar et al.   NATURE

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

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

(2014) Simone Picelli et al.   Nature Protocols

Conditional density-based analysis of T cell signaling in single-cell data

(2014) S. Krishnaswamy et al.   SCIENCE

Novel Stage Classification of Human Spermatogenesis Based on Acrosome Development1

(2013) Barbara Muciaccia et al.   BIOLOGY OF REPRODUCTION

Clinical relevance of Y-linked CNV screening in male infertility: new insights based on the 8-year experience of a diagnostic genetic laboratory

(2013) Deborah Lo Giacco et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Comprehensive sequence analysis of the NR5A1 gene encoding steroidogenic factor 1 in a large group of infertile males

(2013) Albrecht Röpke et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Human Spermatogenic Failure Purges Deleterious Mutation Load from the Autosomes and Both Sex Chromosomes, including the Gene DMRT1

(2013) Alexandra M. Lopes et al.   PLoS Genetics

EAA/EMQN best practice guidelines for molecular diagnosis of Y-chromosomal microdeletions: state-of-the-art 2013

(2013) C. Krausz et al.   Andrology

A dominant-negative mutation of HSF2 associated with idiopathic azoospermia

(2012) Lisha Mou et al.   HUMAN GENETICS

A Recurrent Deletion of DPY19L2 Causes Infertility in Man by Blocking Sperm Head Elongation and Acrosome Formation

(2011) Radu Harbuz et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Clinical experience with azoospermia: aetiology and chances for spermatozoa detection upon biopsy

(2010) F. Tüttelmann et al.   INTERNATIONAL JOURNAL OF ANDROLOGY

Clinical consequences of microdeletions of the Y chromosome: the extended Münster experience

(2010) Manuela Simoni et al.   REPRODUCTIVE BIOMEDICINE ONLINE

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

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

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

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT