An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo

The developmental proteome of Drosophila melanogaster

(2017) Nuria Casas-Vila et al.   GENOME RESEARCH

Protein Expression Landscape of Mouse Embryos during Pre-implantation Development

(2017) Yawei Gao et al.   Cell Reports

Secretome of in vitro cultured human embryos contains extracellular vesicles that are uptaken by the maternal side

(2017) Elisa Giacomini et al.   Scientific Reports

Totipotency segregates between the sister blastomeres of two-cell stage mouse embryos

(2017) E. Casser et al.   Scientific Reports

Oocyte-expressed yes-associated protein is a key activator of the early zygotic genome in mouse

(2016) Chao Yu et al.   CELL RESEARCH

Proteomic Analysis of Mouse Oocytes Identifies PRMT7 as a Reprogramming Factor that Replaces SOX2 in the Induction of Pluripotent Stem Cells

(2016) Bingyuan Wang et al.   JOURNAL OF PROTEOME RESEARCH

Identifying the role of Wilms tumor 1 associated protein in cancer prediction using integrative genomic analyses

(2016) Li-Sheng Wu et al.   Molecular Medicine Reports

Reconstitution in vitro of the entire cycle of the mouse female germ line

(2016) Orie Hikabe et al.   NATURE

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

IGF2BP2/IMP2-Deficient Mice Resist Obesity through Enhanced Translation of Ucp1 mRNA and Other mRNAs Encoding Mitochondrial Proteins

(2015) Ning Dai et al.   Cell Metabolism

On the Relationship of Protein and mRNA Dynamics in Vertebrate Embryonic Development

(2015) Leonid Peshkin et al.   DEVELOPMENTAL CELL

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Differences in embryo quality are associated with differences in oocyte composition: A proteomic study in inbred mice

(2015) Martin J. Pfeiffer et al.   PROTEOMICS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Integral Proteomic Analysis of Blastocysts Reveals Key Molecular Machinery Governing Embryonic Diapause and Reactivation for Implantation in Mice1

(2014) Zheng Fu et al.   BIOLOGY OF REPRODUCTION

Improvement of Cloned Embryos Development by Co-Culturing with Parthenotes: A Possible Role of Exosomes/Microvesicles for Embryos Paracrine Communication

(2014) Islam M. Saadeldin et al.   Cellular Reprogramming

Stage-Specific Proteome Signatures in Early Bovine Embryo Development

(2014) Daniela R. Deutsch et al.   JOURNAL OF PROTEOME RESEARCH

A promoter-level mammalian expression atlas

(2014)   NATURE

Global absolute quantification reveals tight regulation of protein expression in single Xenopus eggs

(2014) Arne H. Smits et al.   NUCLEIC ACIDS RESEARCH

Impaired Bone Formation in Pdia3 Deficient Mice

(2014) Yun Wang et al.   PLoS One

Quantitative proteomics reveals the dynamics of protein changes duringDrosophilaoocyte maturation and the oocyte-to-embryo transition

(2014) Iva Kronja et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteome analysis of early lineage specification in bovine embryos

(2014) Myriam Demant et al.   PROTEOMICS

Blastocyst implantation failure relates to impaired translational machinery gene expression

(2014) Vicki Plaks et al.   REPRODUCTION

Identification and characterization of an oocyte factor required for sperm decondensation in pig

(2014) Jingyu Li et al.   REPRODUCTION

Maternal age effect on mouse oocytes: new biological insight from proteomic analysis

(2014) Caroline Schwarzer et al.   REPRODUCTION

Quantitative proteomics of Xenopus laevis embryos: expression kinetics of nearly 4000 proteins during early development

(2014) Liangliang Sun et al.   Scientific Reports

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

(2013) Weijun Luo et al.   BIOINFORMATICS

The role of MATER in endoplasmic reticulum distribution and calcium homeostasis in mouse oocytes

(2013) Boram Kim et al.   DEVELOPMENTAL BIOLOGY

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

ART culture conditions change the probability of mouse embryo gestation through defined cellular and molecular responses

(2012) C. Schwarzer et al.   HUMAN REPRODUCTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

(2012) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

P-Bodies and Stress Granules: Possible Roles in the Control of Translation and mRNA Degradation

(2012) C. J. Decker et al.   Cold Spring Harbor Perspectives in Biology

Proteomic Analysis of Mouse Oocytes Reveals 28 Candidate Factors of the “Reprogrammome”

(2011) Martin J. Pfeiffer et al.   JOURNAL OF PROTEOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Dissecting the First Transcriptional Divergence During Human Embryonic Development

(2011) Qiang Bai et al.   Stem Cell Reviews and Reports

Deficiency of Suppressor Enhancer Lin12 1 Like (SEL1L) in Mice Leads to Systemic Endoplasmic Reticulum Stress and Embryonic Lethality

(2010) Adam B. Francisco et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Proteome of mouse oocytes at different developmental stages

(2010) Shufang Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Mouse ZAR1-like (XM_359149) colocalizes with mRNA processing components and its dominant-negative mutant caused two-cell-stage embryonic arrest

(2009) Jianjun Hu et al.   DEVELOPMENTAL DYNAMICS

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

(2009) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Embryonic arrest at midgestation and disruption of Notch signaling produced by the absence of both epsin 1 and epsin 2 in mice

(2009) H. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role for PADI6 and the cytoplasmic lattices in ribosomal storage in oocytes and translational control in the early mouse embryo

(2008) P. Yurttas et al.   DEVELOPMENT

A Subcortical Maternal Complex Essential for Preimplantation Mouse Embryogenesis

(2008) Lei Li et al.   DEVELOPMENTAL CELL

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Diverse RNA-Binding Proteins Interact with Functionally Related Sets of RNAs, Suggesting an Extensive Regulatory System

(2008) Daniel J Hogan et al.   PLOS BIOLOGY