Stem cell bioengineering: building from stem cell biology

Physiologically Based Pharmacokinetic and Pharmacodynamic Analysis Enabled by Microfluidically Linked Organs-on-Chips

(2018) Rachelle Prantil-Baun et al.   Annual Review of Pharmacology and Toxicology

A TRACER 3D Co-Culture tumour model for head and neck cancer

(2018) Miki Young et al.   BIOMATERIALS

High-Throughput Screening Enhances Kidney Organoid Differentiation from Human Pluripotent Stem Cells and Enables Automated Multidimensional Phenotyping

(2018) Stefan M. Czerniecki et al.   Cell Stem Cell

Engineered Tissue Folding by Mechanical Compaction of the Mesenchyme

(2018) Alex J. Hughes et al.   DEVELOPMENTAL CELL

Blastocyst-like structures generated solely from stem cells

(2018) Nicolas C. Rivron et al.   NATURE

Live imaging of neurogenesis in the adult mouse hippocampus

(2018) Gregor-Alexander Pilz et al.   SCIENCE

Programming gene and engineered-cell therapies with synthetic biology

(2018) Tasuku Kitada et al.   SCIENCE

Morphogen gradient reconstitution reveals Hedgehog pathway design principles

(2018) Pulin Li et al.   SCIENCE

Micropattern differentiation of mouse pluripotent stem cells recapitulates embryo regionalized cell fate patterning

(2018) Sophie M Morgani et al.   eLife

Diverse mechanisms for endogenous regeneration and repair in mammalian organs

(2018) James M. Wells et al.   NATURE

Interconnected Microphysiological Systems for Quantitative Biology and Pharmacology Studies

(2018) Collin D. Edington et al.   Scientific Reports

Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids

(2018) Magdalena Kasendra et al.   Scientific Reports

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

Regeneration of the entire human epidermis using transgenic stem cells

(2017) Tobias Hirsch et al.   NATURE

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo

(2017) Weike Pei et al.   NATURE

Guided self-organization and cortical plate formation in human brain organoids

(2017) Madeline A Lancaster et al.   NATURE BIOTECHNOLOGY

Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells

(2017) Benjamin H Weinberg et al.   NATURE BIOTECHNOLOGY

Wounding induces dedifferentiation of epidermal Gata6+ cells and acquisition of stem cell properties

(2017) Giacomo Donati et al.   NATURE CELL BIOLOGY

Maintenance of neural progenitor cell stemness in 3D hydrogels requires matrix remodelling

(2017) Christopher M. Madl et al.   NATURE MATERIALS

Progenitor T-cell differentiation from hematopoietic stem cells using Delta-like-4 and VCAM-1

(2017) Shreya Shukla et al.   NATURE METHODS

BMP signaling controls buckling forces to modulate looping morphogenesis of the gut

(2017) Nandan L. Nerurkar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Type XVII collagen coordinates proliferation in the interfollicular epidermis

(2017) Mika Watanabe et al.   eLife

A Blueprint for a Synthetic Genetic Feedback Controller to Reprogram Cell Fate

(2017) Domitilla Del Vecchio et al.   Cell Systems

Multi-tissue interactions in an integrated three-tissue organ-on-a-chip platform

(2017) Aleksander Skardal et al.   Scientific Reports

Interorgan Communication Pathways in Physiology: Focus onDrosophila

(2016) Ilia A. Droujinine et al.   Annual Review of Genetics

Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors

(2016) Leonardo Morsut et al.   CELL

Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors

(2016) Kole T. Roybal et al.   CELL

Engineering Stem Cell Organoids

(2016) Xiaolei Yin et al.   Cell Stem Cell

A Balance between Secreted Inhibitors and Edge Sensing Controls Gastruloid Self-Organization

(2016) Fred Etoc et al.   DEVELOPMENTAL CELL

Organoids: Modeling Development and the Stem Cell Niche in a Dish

(2016) Kai Kretzschmar et al.   DEVELOPMENTAL CELL

Mammalian synthetic biology for studying the cell

(2016) Melina Mathur et al.   JOURNAL OF CELL BIOLOGY

Control theory meets synthetic biology

(2016) Domitilla Del Vecchio et al.   Journal of the Royal Society Interface

Tracing haematopoietic stem cell formation at single-cell resolution

(2016) Fan Zhou et al.   NATURE

A 17-gene stemness score for rapid determination of risk in acute leukaemia

(2016) Stanley W. K. Ng et al.   NATURE

Designer matrices for intestinal stem cell and organoid culture

(2016) Nikolce Gjorevski et al.   NATURE

Quality cell therapy manufacturing by design

(2016) Yonatan Y Lipsitz et al.   NATURE BIOTECHNOLOGY

A 3D bioprinting system to produce human-scale tissue constructs with structural integrity

(2016) Hyun-Wook Kang et al.   NATURE BIOTECHNOLOGY

Self-organized amniogenesis by human pluripotent stem cells in a biomimetic implantation-like niche

(2016) Yue Shao et al.   NATURE MATERIALS

Driving CAR T-cells forward

(2016) Hollie J. Jackson et al.   Nature Reviews Clinical Oncology

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Hair follicle aging is driven by transepidermal elimination of stem cells via COL17A1 proteolysis

(2016) H. Matsumura et al.   SCIENCE

Characterizing responses to CFTR-modulating drugs using rectal organoids derived from subjects with cystic fibrosis

(2016) Johanna F. Dekkers et al.   Science Translational Medicine

Synthetic Morphogenesis

(2016) Brian P. Teague et al.   Cold Spring Harbor Perspectives in Biology

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

(2016) Patrick Guye et al.   Nature Communications

A programmable synthetic lineage-control network that differentiates human IPSCs into glucose-sensitive insulin-secreting beta-like cells

(2016) Pratik Saxena et al.   Nature Communications

Design of a Synthetic Integral Feedback Circuit: Dynamic Analysis and DNA Implementation

(2016) Corentin Briat et al.   ACS Synthetic Biology

Feedback, Lineages and Self-Organizing Morphogenesis

(2016) Sameeran Kunche et al.   PLoS Computational Biology

A Multi-Lineage Screen Reveals mTORC1 Inhibition Enhances Human Pluripotent Stem Cell Mesendoderm and Blood Progenitor Production

(2016) Emanuel Joseph Paul Nazareth et al.   Stem Cell Reports

Antithetic Integral Feedback Ensures Robust Perfect Adaptation in Noisy Biomolecular Networks

(2016) Corentin Briat et al.   Cell Systems

Engineered In Vitro Disease Models

(2015) Kambez H. Benam et al.   Annual Review of Pathology-Mechanisms of Disease

Mechanisms of blood homeostasis: lineage tracking and a neutral model of cell populations in rhesus macaques

(2015) Sidhartha Goyal et al.   BMC BIOLOGY

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

(2015) Meritxell Huch et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Positional information and reaction-diffusion: two big ideas in developmental biology combine

(2015) J. B. A. Green et al.   DEVELOPMENT

Self-renewing diploid Axin2+ cells fuel homeostatic renewal of the liver

(2015) Bruce Wang et al.   NATURE

Interleukin-22 promotes intestinal-stem-cell-mediated epithelial regeneration

(2015) Caroline A. Lindemans et al.   NATURE

Decoding the regulatory network of early blood development from single-cell gene expression measurements

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

A three-dimensional engineered tumour for spatial snapshot analysis of cell metabolism and phenotype in hypoxic gradients

(2015) Darren Rodenhizer et al.   NATURE MATERIALS

Hydrogels with tunable stress relaxation regulate stem cell fate and activity

(2015) Ovijit Chaudhuri et al.   NATURE MATERIALS

Programmed synthesis of three-dimensional tissues

(2015) Michael E Todhunter et al.   NATURE METHODS

A strategy for tissue self-organization that is robust to cellular heterogeneity and plasticity

(2015) Alec E. Cerchiari et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CD24 tracks divergent pluripotent states in mouse and human cells

(2015) Nika Shakiba et al.   Nature Communications

CellNet: Network Biology Applied to Stem Cell Engineering

(2014) Patrick Cahan et al.   CELL

Integrating Biological Redesign: Where Synthetic Biology Came From and Where It Needs to Go

(2014) Jeffrey C. Way et al.   CELL

A review on the computational approaches for gene regulatory network construction

(2014) Lian En Chai et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Stochastic NANOG fluctuations allow mouse embryonic stem cells to explore pluripotency

(2014) Elsa Abranches et al.   DEVELOPMENT

Intercellular network structure and regulatory motifs in the human hematopoietic system

(2014) W. Qiao et al.   Molecular Systems Biology

Genome-wide characterization of the routes to pluripotency

(2014) Samer M. I. Hussein et al.   NATURE

A method to recapitulate early embryonic spatial patterning in human embryonic stem cells

(2014) Aryeh Warmflash et al.   NATURE METHODS

CRISPR transcriptional repression devices and layered circuits in mammalian cells

(2014) Samira Kiani et al.   NATURE METHODS

A brief history of synthetic biology

(2014) D. Ewen Cameron et al.   NATURE REVIEWS MICROBIOLOGY

Synthetic biology in mammalian cells: next generation research tools and therapeutics

(2014) Florian Lienert et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Organogenesis in a dish: Modeling development and disease using organoid technologies

(2014) M. A. Lancaster et al.   SCIENCE

Digit patterning is controlled by a Bmp-Sox9-Wnt Turing network modulated by morphogen gradients

(2014) J. Raspopovic et al.   SCIENCE

Defining an essential transcription factor program for naive pluripotency

(2014) S.- J. Dunn et al.   SCIENCE

Programmable self-assembly in a thousand-robot swarm

(2014) M. Rubenstein et al.   SCIENCE

Vascular and Neurogenic Rejuvenation of the Aging Mouse Brain by Young Systemic Factors

(2014) L. Katsimpardi et al.   SCIENCE

Feedback and redundancy in receptor tyrosine kinase signaling: relevance to cancer therapies

(2014) Chong Sun et al.   TRENDS IN BIOCHEMICAL SCIENCES

Highly modular bow-tie gene circuits with programmable dynamic behaviour

(2014) Laura Prochazka et al.   Nature Communications

Local BMP-SMAD1 Signaling Increases LIF Receptor-Dependent STAT3 Responsiveness and Primed-to-Naive Mouse Pluripotent Stem Cell Conversion Frequency

(2014) Kento Onishi et al.   Stem Cell Reports

Growth Differentiation Factor 11 Is a Circulating Factor that Reverses Age-Related Cardiac Hypertrophy

(2013) Francesco S. Loffredo et al.   CELL

The Epidermis Comprises Autonomous Compartments Maintained by Distinct Stem Cell Populations

(2013) Mahalia E. Page et al.   Cell Stem Cell

Dedifferentiation of committed epithelial cells into stem cells in vivo

(2013) Purushothama Rao Tata et al.   NATURE

High-resolution analysis with novel cell-surface markers identifies routes to iPS cells

(2013) James O’Malley et al.   NATURE

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library

(2013) Hiroko Koike-Yusa et al.   NATURE BIOTECHNOLOGY

A functional CFTR assay using primary cystic fibrosis intestinal organoids

(2013) Johanna F Dekkers et al.   NATURE MEDICINE

High-throughput fingerprinting of human pluripotent stem cell fate responses and lineage bias

(2013) Emanuel J P Nazareth et al.   NATURE METHODS

Microfabrication of human organs-on-chips

(2013) Dongeun Huh et al.   Nature Protocols

Unravelling stem cell dynamics by lineage tracing

(2013) Cédric Blanpain et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Design and formulation of functional pluripotent stem cell-derived cardiac microtissues

(2013) N. Thavandiran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic responses in mouse models poorly mimic human inflammatory diseases

(2013) Junhee Seok et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Chaste: An Open Source C++ Library for Computational Physiology and Biology

(2013) Gary R. Mirams et al.   PLoS Computational Biology

Mosaic Hydrogels: One-Step Formation of Multiscale Soft Materials

(2012) Lian Leng et al.   ADVANCED MATERIALS

Rapid Expansion of Human Hematopoietic Stem Cells by Automated Control of Inhibitory Feedback Signaling

(2012) Elizabeth Csaszar et al.   Cell Stem Cell

A Late Transition in Somatic Cell Reprogramming Requires Regulators Distinct from the Pluripotency Network

(2012) Azadeh Golipour et al.   Cell Stem Cell

Microenvironment-mediated reversion of epiblast stem cells by reactivation of repressed JAK–STAT signaling

(2012) Kento Onishi et al.   Integrative Biology

Dll1+ secretory progenitor cells revert to stem cells upon crypt damage

(2012) Johan H. van Es et al.   NATURE CELL BIOLOGY

Periodic stripe formation by a Turing mechanism operating at growth zones in the mammalian palate

(2012) Andrew D Economou et al.   NATURE GENETICS

Extracellular-matrix tethering regulates stem-cell fate

(2012) Britta Trappmann et al.   NATURE MATERIALS

Synthetic incoherent feedforward circuits show adaptation to the amount of their genetic template

(2011) L. Bleris et al.   Molecular Systems Biology

Role of YAP/TAZ in mechanotransduction

(2011) Sirio Dupont et al.   NATURE

Self-organizing optic-cup morphogenesis in three-dimensional culture

(2011) Mototsugu Eiraku et al.   NATURE

Long-term single-cell imaging of mammalian stem cells

(2011) Timm Schroeder   NATURE METHODS

The productivity crisis in pharmaceutical R&D

(2011) Fabio Pammolli et al.   NATURE REVIEWS DRUG DISCOVERY

Multi-Input RNAi-Based Logic Circuit for Identification of Specific Cancer Cells

(2011) Z. Xie et al.   SCIENCE

Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum

(2011) S. C. Bendall et al.   SCIENCE

Cellular barcoding tool for clonal analysis in the hematopoietic system

(2010) A. Gerrits et al.   BLOOD

Micropatterning as a tool to decipher cell morphogenesis and functions

(2010) M. Thery   JOURNAL OF CELL SCIENCE

Dynamic interaction networks in a hierarchically organized tissue

(2010) Daniel C Kirouac et al.   Molecular Systems Biology

Synthetic biology: applications come of age

(2010) Ahmad S. Khalil et al.   NATURE REVIEWS GENETICS

Substrate Elasticity Regulates Skeletal Muscle Stem Cell Self-Renewal in Culture

(2010) P. M. Gilbert et al.   SCIENCE

Regenerative patterning in Swarm Robots: mutual benefits of research in robotics and stem cell biology

(2009) Michael Rubenstein et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Simple and rapid process for single cell micro-patterning

(2009) Ammar Azioune et al.   LAB ON A CHIP

Cell–cell interaction networks regulate blood stem and progenitor cell fate

(2009) Daniel C Kirouac et al.   Molecular Systems Biology

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Manipulation of Signaling Thresholds in “Engineered Stem Cell Niches” Identifies Design Criteria for Pluripotent Stem Cell Screens

(2009) Raheem Peerani et al.   PLoS One

Stem Cells and Niches: Mechanisms That Promote Stem Cell Maintenance throughout Life

(2008) Sean J. Morrison et al.   CELL

Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences

(2008) Arjun Raj et al.   CELL

Stochastic neuronal cell fate choices

(2008) Robert J Johnston et al.   CURRENT OPINION IN NEUROBIOLOGY

Jak/Stat signalling in niche support cells regulates dpp transcription to control germline stem cell maintenance in the Drosophila ovary

(2008) L. Lopez-Onieva et al.   DEVELOPMENT

Stochasticity and Cell Fate

(2008) R. Losick et al.   SCIENCE

Micropatterning of human embryonic stem cells dissects the mesoderm and endoderm lineages

(2008) Lawrence Haoran Lee et al.   Stem Cell Research

Control of Human Embryonic Stem Cell Colony and Aggregate Size Heterogeneity Influences Differentiation Trajectories

(2008) Céline Liu Bauwens et al.   STEM CELLS