Single-cell transcriptome and translatome dual-omics reveals potential mechanisms of human oocyte maturation

Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition

(2022) Chunxia Zhang et al.   Science Advances

Ultrasensitive Ribo-seq reveals translational landscapes during mammalian oocyte-to-embryo transition and pre-implantation development

(2022) Zhuqing Xiong et al.   NATURE CELL BIOLOGY

Robust single-cell discovery of RNA targets of RNA-binding proteins and ribosomes

(2021) Kristopher W. Brannan et al.   NATURE METHODS

Coordination between Transport and Local Translation in Neurons

(2021) Loïc Broix et al.   TRENDS IN CELL BIOLOGY

Single-cell Ribo-seq reveals cell cycle-dependent translational pausing

(2021) Michael VanInsberghe et al.   NATURE

Correction to ‘The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets’

(2021) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Genome-wide analysis reveals a switch in the translational program upon oocyte meiotic resumption

(2020) Xuan G Luong et al.   NUCLEIC ACIDS RESEARCH

Single-cell multiomic analysis of in vivo and in vitro matured human oocytes

(2020) Min Ye et al.   HUMAN REPRODUCTION

Studying human reproductive biology through single-cell analysis and in vitro differentiation of stem cells into germ cell-like cells

(2020) Lin Li et al.   HUMAN REPRODUCTION UPDATE

The RNA-binding protein DAZL functions as repressor and activator of mRNA translation during oocyte maturation

(2020) Cai-Rong Yang et al.   Nature Communications

CRISPR/Cas9-Mediated Genome Editing Reveals Oosp Family Genes are Dispensable for Female Fertility in Mice

(2020) Ferheen Abbasi et al.   Cells

Translatomics: The Global View of Translation

(2019) Jing Zhao et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

(2019) Yingyao Zhou et al.   Nature Communications

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Ran GTP and importin β regulate meiosis I spindle assembly and function in mouse oocytes

(2019) David Drutovic et al.   EMBO JOURNAL

Assembly of mammalian oxidative phosphorylation complexes I–V and supercomplexes

(2018) Alba Signes et al.   Essays in Biochemistry

Acquisition of oocyte competence to develop as an embryo: integrated nuclear and cytoplasmic events

(2018) Marco Conti et al.   HUMAN REPRODUCTION UPDATE

De novo annotation and characterization of the translatome with ribosome profiling data

(2018) Zhengtao Xiao et al.   NUCLEIC ACIDS RESEARCH

Acute and rapid degradation of endogenous proteins by Trim-Away

(2018) Dean Clift et al.   Nature Protocols

Publisher Correction: Acute and rapid degradation of endogenous proteins by Trim-Away

(2018) Dean Clift et al.   Nature Protocols

Active Ribosome Profiling with RiboLace

(2018) Massimiliano Clamer et al.   Cell Reports

RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins

(2017) Debashish Ray et al.   METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

The Growing Toolbox for Protein Synthesis Studies

(2017) Shintaro Iwasaki et al.   TRENDS IN BIOCHEMICAL SCIENCES

In vitro differentiation of human embryonic stem cells into ovarian follicle-like cells

(2017) Dajung Jung et al.   Nature Communications

Identification of Maturation-Specific Proteins by Single-Cell Proteomics of Human Oocytes

(2016) Irma Virant-Klun et al.   MOLECULAR & CELLULAR PROTEOMICS

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

ATtRACT—a database of RNA-binding proteins and associated motifs

(2016) Girolamo Giudice et al.   Database-The Journal of Biological Databases and Curation

CLIPdb: a CLIP-seq database for protein-RNA interactions

(2015) Yu-Cheng T Yang et al.   BMC GENOMICS

Oocyte maturation: gamete-somatic cells interactions, meiotic resumption, cytoskeletal dynamics and cytoplasmic reorganization

(2015) Giovanni Coticchio et al.   HUMAN REPRODUCTION UPDATE

Simple and inexpensive ribosome profiling analysis of mRNA translation

(2015) David W. Reid et al.   METHODS

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Ribosome profiling reveals the what, when, where and how of protein synthesis

(2015) Gloria A. Brar et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Translational control of immune responses: from transcripts to translatomes

(2014) Ciriaco A Piccirillo et al.   NATURE IMMUNOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Ran GTPase promotes oocyte polarization by regulating ERM (Ezrin/Radixin/Moesin) inactivation

(2013) Benoit Dehapiot et al.   CELL CYCLE

The nuclear F-actin interactome of Xenopus oocytes reveals an actin-bundling kinesin that is essential for meiotic cytokinesis

(2013) Matthias Samwer et al.   EMBO JOURNAL

The study of mammalian oocyte competence by transcriptome analysis: progress and challenges

(2013) R. Labrecque et al.   MOLECULAR HUMAN REPRODUCTION

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

PCBP1 is required for maintenance of the transcriptionally silent state in fully grown mouse oocytes

(2012) Meng Xia et al.   CELL CYCLE

The dynamics of in vitro maturation of germinal vesicle oocytes

(2012) Laura Escrich et al.   FERTILITY AND STERILITY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Genome-wide analysis of translation reveals a critical role for deleted in azoospermia-like (Dazl) at the oocyte-to-zygote transition

(2011) J. Chen et al.   GENES & DEVELOPMENT

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Posttranscriptional activation of gene expression in Xenopus laevis oocytes by microRNA-protein complexes (microRNPs)

(2011) R. D. Mortensen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transmembrane Receptor DCC Associates with Protein Synthesis Machinery and Regulates Translation

(2010) Joseph Tcherkezian et al.   CELL

Mitochondrial function in the human oocyte and embryo and their role in developmental competence

(2010) Jonathan Van Blerkom   MITOCHONDRION

RBPDB: a database of RNA-binding specificities

(2010) K. B. Cook et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE