Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

Human pre-implantation embryo development

(2012) K. K. Niakan et al.   DEVELOPMENT

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Tracking the progression of the human inner cell mass during embryonic stem cell derivation

(2012) Thomas O'Leary et al.   NATURE BIOTECHNOLOGY

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Transcriptome Analysis during Human Trophectoderm Specification Suggests New Roles of Metabolic and Epigenetic Genes

(2012) Said Assou et al.   PLoS One

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

The Long Non-Coding RNAs: A New (P)layer in the “Dark Matter”

(2012) Thomas Derrien et al.   Frontiers in Genetics

Comparative Transcriptome Analysis of Human Trophectoderm and Embryonic Stem Cell-Derived Trophoblasts Reveal Key Participants in Early Implantation1

(2011) Lusine Aghajanova et al.   BIOLOGY OF REPRODUCTION

An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming

(2011) Mathieu Gabut et al.   CELL

Gene expression heterogeneities in embryonic stem cell populations: origin and function

(2011) Alfonso Martinez Arias et al.   CURRENT OPINION IN CELL BIOLOGY

Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development

(2011) R. Vassena et al.   DEVELOPMENT

Human hypoblast formation is not dependent on FGF signalling

(2011) Mila Roode et al.   DEVELOPMENTAL BIOLOGY

Transcriptome analysis reveals dialogues between human trophectoderm and endometrial cells during the implantation period

(2011) D. Haouzi et al.   HUMAN REPRODUCTION

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Microbial environments confound antibiotic efficacy

(2011) Henry H Lee et al.   Nature Chemical Biology

Non-invasive imaging of human embryos to predict developmental competence

(2011) R.A. Reijo Pera   PLACENTA

Dissecting the First Transcriptional Divergence During Human Embryonic Development

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

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

(2010) Fuchou Tang et al.   Cell Stem Cell

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

Rewirable gene regulatory networks in the preimplantation embryonic development of three mammalian species

(2010) D. Xie et al.   GENOME RESEARCH

Dynamic changes in gene expression during human early embryo development: from fundamental aspects to clinical applications

(2010) S. Assou et al.   HUMAN REPRODUCTION UPDATE

Genome-wide microarray evidence that 8-cell human blastomeres over-express cell cycle drivers and under-express checkpoints

(2010) Ann A. Kiessling et al.   JOURNAL OF ASSISTED REPRODUCTION AND GENETICS

Making the blastocyst: lessons from the mouse

(2010) Katie Cockburn et al.   JOURNAL OF CLINICAL INVESTIGATION

Non-invasive imaging of human embryos before embryonic genome activation predicts development to the blastocyst stage

(2010) Connie C Wong et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

RNA-Seq analysis to capture the transcriptome landscape of a single cell

(2010) Fuchou Tang et al.   Nature Protocols

Functional Genomics of 5- to 8-Cell Stage Human Embryos by Blastomere Single-Cell cDNA Analysis

(2010) Amparo Galán et al.   PLoS One

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A gene expression signature shared by human mature oocytes and embryonic stem cells

(2009) Said Assou et al.   BMC GENOMICS

Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse

(2009) J. Rossant et al.   DEVELOPMENT

Gene expression profiles of human inner cell mass cells and embryonic stem cells

(2009) Renee A. Reijo Pera et al.   DIFFERENTIATION

Evidence that human blastomere cleavage is under unique cell cycle control

(2009) Ann A. Kiessling et al.   JOURNAL OF ASSISTED REPRODUCTION AND GENETICS

Epigenetic reversion of post-implantation epiblast to pluripotent embryonic stem cells

(2009) Siqin Bao et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Characteristics of embryo development in Robertsonian translocations' preimplantation genetic diagnosis cycles

(2009) Jin Huang et al.   PRENATAL DIAGNOSIS

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gene expression profiling of human oocytes at different maturational stages and after in vitro maturation

(2008) Dagan Wells et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS