Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids

Homeostatic mini-intestines through scaffold-guided organoid morphogenesis

(2020) Mikhail Nikolaev et al.   NATURE

Upgrading the Physiological Relevance of Human Brain Organoids

(2020) Ashley Del Dosso et al.   NEURON

Distinct roles of Dlk1 isoforms in bi-potential differentiation of hepatic stem cells

(2019) Jiefang Huang et al.   Stem Cell Research & Therapy

Flow-enhanced vascularization and maturation of kidney organoids in vitro

(2019) Kimberly A. Homan et al.   NATURE METHODS

Biologically inspired approaches to enhance human organoid complexity

(2019) Emily M. Holloway et al.   DEVELOPMENT

Modeling Steatohepatitis in Humans with Pluripotent Stem Cell-Derived Organoids

(2019) Rie Ouchi et al.   Cell Metabolism

Engineering Stem Cell Self-organization to Build Better Organoids

(2019) Jonathan A. Brassard et al.   Cell Stem Cell

Organoids by design

(2019) Takanori Takebe et al.   SCIENCE

SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species

(2019) Yuqi Tan et al.   Cell Systems

Synthetic developmental biology: build and control multicellular systems

(2019) Mo R Ebrahimkhani et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Robust, Long-Term Culture of Endoderm-Derived Hepatic Organoids for Disease Modeling

(2019) Soheil Akbari et al.   Stem Cell Reports

Generation of Hepatic Stellate Cells from Human Pluripotent Stem Cells Enables In Vitro Modeling of Liver Fibrosis

(2018) Mar Coll et al.   Cell Stem Cell

Update on FXR Biology: Promising Therapeutic Target?

(2018) Chang Han   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Programming Morphogenesis through Systems and Synthetic Biology

(2018) Jeremy J. Velazquez et al.   TRENDS IN BIOTECHNOLOGY

A Roadmap for Human Liver Differentiation from Pluripotent Stem Cells

(2018) Lay Teng Ang et al.   Cell Reports

Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations

(2018) Sonya A. MacParland et al.   Nature Communications

Haematopoietic stem and progenitor cells from human pluripotent stem cells

(2017) Ryohichi Sugimura et al.   NATURE

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Assessment of engineered cells using CellNet and RNA-seq

(2017) Arthur H Radley et al.   Nature Protocols

Massively parallel digital transcriptional profiling of single cells

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

Adult Mouse Liver Contains Two Distinct Populations of Cholangiocytes

(2017) Bin Li et al.   Stem Cell Reports

Direct conversion of human fibroblasts into hepatocyte-like cells by ATF5, PROX1, FOXA2, FOXA3, and HNF4A transduction

(2017) Daiki Nakamori et al.   Scientific Reports

Hepatic maturation of human iPS cell-derived hepatocyte-like cells by ATF5, c/EBPα, and PROX1 transduction

(2016) Daiki Nakamori et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Modeling Development and Disease with Organoids

(2016) Hans Clevers   CELL

Engineering Stem Cell Organoids

(2016) Xiaolei Yin et al.   Cell Stem Cell

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Genetically engineering self-organization of human pluripotent stem cells into a liver bud-like tissue using Gata6

(2016) Patrick Guye et al.   Nature Communications

Long-Term Culture of Genome-Stable Bipotent Stem Cells from Adult Human Liver

(2015) Meritxell Huch et al.   CELL

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Bile acids induce hepatic differentiation of mesenchymal stem cells

(2015) Iris Sawitza et al.   Scientific Reports

KeyGenes, a Tool to Probe Tissue Differentiation Using a Human Fetal Transcriptional Atlas

(2015) Matthias S. Roost et al.   Stem Cell Reports

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

CellNet: Network Biology Applied to Stem Cell Engineering

(2014) Patrick Cahan et al.   CELL

Human Hepatocytes with Drug Metabolic Function Induced from Fibroblasts by Lineage Reprogramming

(2014) Yuanyuan Du et al.   Cell Stem Cell

Prox1 ablation in hepatic progenitors causes defective hepatocyte specification and increases biliary cell commitment

(2014) A. Seth et al.   DEVELOPMENT

Multiplexed and Programmable Regulation of Gene Networks with an Integrated RNA and CRISPR/Cas Toolkit in Human Cells

(2014) Lior Nissim et al.   MOLECULAR CELL

Rapid neurogenesis through transcriptional activation in human stem cells

(2014) V. Busskamp et al.   Molecular Systems Biology

Mouse liver repopulation with hepatocytes generated from human fibroblasts

(2014) Saiyong Zhu et al.   NATURE

CRISPR transcriptional repression devices and layered circuits in mammalian cells

(2014) Samira Kiani et al.   NATURE METHODS

Extensive double humanization of both liver and hematopoiesis in FRGN mice

(2014) Elizabeth M. Wilson et al.   Stem Cell Research

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Vascularized and functional human liver from an iPSC-derived organ bud transplant

(2013) Takanori Takebe et al.   NATURE

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

(2013) Prashant Mali et al.   NATURE BIOTECHNOLOGY

Cytochrome P450 enzymes in drug metabolism: Regulation of gene expression, enzyme activities, and impact of genetic variation

(2013) Ulrich M. Zanger et al.   PHARMACOLOGY & THERAPEUTICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Present state and future perspectives of using pluripotent stem cells in toxicology research

(2011) Anna M. Wobus et al.   ARCHIVES OF TOXICOLOGY

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

A gene regulatory network controlling the embryonic specification of endoderm

(2011) Isabelle S. Peter et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The complement system

(2010) J. Vidya Sarma et al.   CELL AND TISSUE RESEARCH

Organogenesis and Development of the Liver

(2010) Karim Si-Tayeb et al.   DEVELOPMENTAL CELL

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

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

Highly efficient generation of human hepatocyte-like cells from induced pluripotent stem cells

(2009) Karim Si-Tayeb et al.   HEPATOLOGY

ATF5 Is a Highly Abundant Liver-Enriched Transcription Factor that Cooperates with Constitutive Androstane Receptor in the Transactivation of CYP2B6: Implications in Hepatic Stress Responses

(2008) M. Pascual et al.   DRUG METABOLISM AND DISPOSITION

Prospero-related homeobox 1 and liver receptor homolog 1 coordinately regulate long-term proliferation of murine fetal hepatoblasts

(2008) Akihide Kamiya et al.   HEPATOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY