Dissecting primate early post-implantation development using long-term in vitro embryo culture

Deconvolution of single-cell multi-omics layers reveals regulatory heterogeneity

(2019) Longqi Liu et al.   Nature Communications

Self-Renewal and Lineage Transitions

(2018) Sheila Chari   Cell Stem Cell

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Self-assembly of embryonic and two extra-embryonic stem cell types into gastrulating embryo-like structures

(2018) Berna Sozen et al.   NATURE CELL BIOLOGY

Deconstructing and reconstructing the mouse and human early embryo

(2018) Marta N. Shahbazi et al.   NATURE CELL BIOLOGY

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Self-organization of a human organizer by combined Wnt and Nodal signalling

(2018) I. Martyn et al.   NATURE

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep 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

Comprehensive Mapping of Pluripotent Stem Cell Metabolism Using Dynamic Genome-Scale Network Modeling

(2017) Sriram Chandrasekaran et al.   Cell Reports

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

(2017) Hisham Mohammed et al.   Cell Reports

Primate Primordial Germ Cells Acquire Transplantation Potential by Carnegie Stage 23

(2017) Amander T. Clark et al.   Stem Cell Reports

Dynamic quantitative proteomics characterization of TNF-α-induced necroptosis

(2016) Yang Wang et al.   APOPTOSIS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Cellular Metabolism and Induced Pluripotency

(2016) Jun Wu et al.   CELL

Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo

(2016) Guangdun Peng et al.   DEVELOPMENTAL CELL

The Germ Cell Fate of Cynomolgus Monkeys Is Specified in the Nascent Amnion

(2016) Kotaro Sasaki et al.   DEVELOPMENTAL CELL

Single-cell analyses of X Chromosome inactivation dynamics and pluripotency during differentiation

(2016) Geng Chen et al.   GENOME RESEARCH

Self-organization of the in vitro attached human embryo

(2016) Alessia Deglincerti et al.   NATURE

Resolving early mesoderm diversification through single-cell expression profiling

(2016) Antonio Scialdone et al.   NATURE

A developmental coordinate of pluripotency among mice, monkeys and humans

(2016) Tomonori Nakamura et al.   NATURE

Self-organization of the human embryo in the absence of maternal tissues

(2016) Marta N. Shahbazi et al.   NATURE CELL BIOLOGY

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution

(2016) M Ryan Corces et al.   NATURE GENETICS

Placenta: The Forgotten Organ

(2015) Emin Maltepe et al.   Annual Review of Cell and Developmental Biology

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

SOX17 Is a Critical Specifier of Human Primordial Germ Cell Fate

(2015) Naoko Irie et al.   CELL

Robust In Vitro Induction of Human Germ Cell Fate from Pluripotent Stem Cells

(2015) Kotaro Sasaki et al.   Cell Stem Cell

The metabolome regulates the epigenetic landscape during naive-to-primed human embryonic stem cell transition

(2015) Henrik Sperber et al.   NATURE CELL BIOLOGY

The Amniotic Membrane: Development and Potential Applications - A Review

(2015) PO Favaron et al.   REPRODUCTION IN DOMESTIC ANIMALS

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Self-Organizing Properties of Mouse Pluripotent Cells Initiate Morphogenesis upon Implantation

(2014) Ivan Bedzhov et al.   CELL

Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos

(2014) Yuyu Niu et al.   CELL

Mouse and human blastocyst-derived stem cells: vive les differences

(2014) J. Rossant   DEVELOPMENT

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2014) Simone Picelli et al.   Nature Protocols

BMP4-directed trophoblast differentiation of human embryonic stem cells is mediated through a ΔNp63 + cytotrophoblast stem cell state

(2013) Yingchun Li et al.   DEVELOPMENT

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Otx2 is an intrinsic determinant of the embryonic stem cell state and is required for transition to a stable epiblast stem cell condition

(2012) D. Acampora et al.   DEVELOPMENT

Analysis of human embryos from zygote to blastocyst reveals distinct gene expression patterns relative to the mouse

(2012) Kathy K. Niakan et al.   DEVELOPMENTAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

Multiobjective evolutionary algorithms to identify highly autocorrelated areas: the case of spatial distribution in financially compromised farms

(2011) Carlos R. García-Alonso et al.   ANNALS OF OPERATIONS RESEARCH

Gastrulation: Making and Shaping Germ Layers

(2011) Lila Solnica-Krezel et al.   Annual Review of Cell and Developmental Biology

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Cell fate decisions and axis determination in the early mouse embryo

(2011) K. Takaoka et al.   DEVELOPMENT

Mouse primitive streak forms in situ by initiation of epithelial to mesenchymal transition without migration of a cell population

(2011) Margot Williams et al.   DEVELOPMENTAL DYNAMICS

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

CDX2 in the formation of the trophectoderm lineage in primate embryos

(2009) Hathaitip Sritanaudomchai et al.   DEVELOPMENTAL BIOLOGY

Trophoblast Stem Cells: Models for Investigating Trophectoderm Differentiation and Placental Development

(2009) Gordon C. Douglas et al.   ENDOCRINE REVIEWS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY