Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro

Modeling Human TBX5 Haploinsufficiency Predicts Regulatory Networks for Congenital Heart Disease

(2020) Irfan S. Kathiriya et al.   DEVELOPMENTAL CELL

Predictability of human differential gene expression

(2019) Megan Crow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pathogenesis and Cells of Origin of Barrett's Esophagus

(2019) Jianwen Que et al.   GASTROENTEROLOGY

Bromodomain inhibition of the coactivators CBP/EP300 facilitate cellular reprogramming

(2019) Ayyub Ebrahimi et al.   Nature Chemical Biology

Restriction of Cellular Plasticity of Differentiated Cells Mediated by Chromatin Modifiers, Transcription Factors and Protein Kinases

(2019) Dylan Rahe et al.   G3-Genes Genomes Genetics

Transcription factor autoregulation is required for acquisition and maintenance of neuronal identity

(2019) Eduardo Leyva-Díaz et al.   DEVELOPMENT

Metformin induces lipogenic differentiation in myofibroblasts to reverse lung fibrosis

(2019) Vahid Kheirollahi et al.   Nature Communications

A Multi-center Study on the Reproducibility of Drug-Response Assays in Mammalian Cell Lines

(2019) Mario Niepel et al.   Cell Systems

Signatures of cell death and proliferation in perturbation transcriptomics data—from confounding factor to effective prediction

(2019) Bence Szalai et al.   NUCLEIC ACIDS RESEARCH

Massively multiplex chemical transcriptomics at single-cell resolution

(2019) Sanjay R. Srivatsan et al.   SCIENCE

The Library of Integrated Network-Based Cellular Signatures NIH Program: System-Level Cataloging of Human Cells Response to Perturbations

(2018) Alexandra B. Keenan et al.   Cell Systems

FOXD1-dependent MICU1 expression regulates mitochondrial activity and cell differentiation

(2018) Santhanam Shanmughapriya et al.   Nature Communications

Genome-Scale Oscillations in DNA Methylation during Exit from Pluripotency

(2018) Steffen Rulands et al.   Cell Systems

CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming

(2018) Yanxia Liu et al.   Cell Stem Cell

Genetic and epigenetic regulation of cardiomyocytes in development, regeneration and disease

(2018) Miao Cui et al.   DEVELOPMENT

Mapping Cellular Reprogramming via Pooled Overexpression Screens with Paired Fitness and Single-Cell RNA-Sequencing Readout

(2018) Udit Parekh et al.   Cell Systems

ZNF281 enhances cardiac reprogramming by modulating cardiac and inflammatory gene expression

(2017) Huanyu Zhou et al.   GENES & DEVELOPMENT

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates

(2017) Moritz Mall et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Assessment of engineered cells using CellNet and RNA-seq

(2017) Arthur H Radley et al.   Nature Protocols

Coordinated control of terminal differentiation and restriction of cellular plasticity

(2017) Tulsi Patel et al.   eLife

Mouse embryonic stem cells can differentiate via multiple paths to the same state

(2017) James Alexander Briggs et al.   eLife

Disease Model of GATA4 Mutation Reveals Transcription Factor Cooperativity in Human Cardiogenesis

(2016) Yen-Sin Ang et al.   CELL

Chemical Enhancement of In Vitro and In Vivo Direct Cardiac ReprogrammingClinical Perspective

(2016) Tamer M. A. Mohamed et al.   CIRCULATION

A predictive computational framework for direct reprogramming between human cell types

(2016) Owen J L Rackham et al.   NATURE GENETICS

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

(2016) Daniel Marbach et al.   NATURE METHODS

The origin and evolution of cell types

(2016) Detlev Arendt et al.   NATURE REVIEWS GENETICS

A Serial shRNA Screen for Roadblocks to Reprogramming Identifies the Protein Modifier SUMO2

(2016) Marti Borkent et al.   Stem Cell Reports

Enhanced efficiency of genetic programming toward cardiomyocyte creation through topographical cues

(2015) Constant Morez et al.   BIOMATERIALS

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

(2015) Davide Cacchiarelli et al.   CELL

Half dozen of one, six billion of the other: What can small- and large-scale molecular systems biology learn from one another?

(2015) Ian A. Mellis et al.   GENOME RESEARCH

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

(2015) Olivia Padovan-Merhar et al.   MOLECULAR CELL

Simultaneous generation of many RNA-seq libraries in a single reaction

(2015) Alexander A Shishkin et al.   NATURE METHODS

A Non-invasive Platform for Functional Characterization of Stem-Cell-Derived Cardiomyocytes with Applications in Cardiotoxicity Testing

(2015) Mahnaz Maddah et al.   Stem Cell Reports

A Systematic Approach to Identify Candidate Transcription Factors that Control Cell Identity

(2015) Ana C. D’Alessio et al.   Stem Cell Reports

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

(2014) S. Anders et al.   BIOINFORMATICS

Dissecting Engineered Cell Types and Enhancing Cell Fate Conversion via CellNet

(2014) Samantha A. Morris et al.   CELL

CellNet: Network Biology Applied to Stem Cell Engineering

(2014) Patrick Cahan et al.   CELL

Induction of diverse cardiac cell types by reprogramming fibroblasts with cardiac transcription factors

(2014) Y.-J. Nam et al.   DEVELOPMENT

How to make a cardiomyocyte

(2014) D. Spater et al.   DEVELOPMENT

Isolation of single-base genome-edited human iPS cells without antibiotic selection

(2014) Yuichiro Miyaoka et al.   NATURE METHODS

A transient disruption of fibroblastic transcriptional regulatory network facilitatestrans-differentiation

(2014) Yasuhiro Tomaru et al.   NUCLEIC ACIDS RESEARCH

Nkx genes are essential for maintenance of ventricular identity

(2013) K. L. Targoff et al.   DEVELOPMENT

Optimization of direct fibroblast reprogramming to cardiomyocytes using calcium activity as a functional measure of success

(2013) Russell C. Addis et al.   JOURNAL OF MOLECULAR AND CELLULAR CARDIOLOGY

Nkx2-1 Represses a Latent Gastric Differentiation Program in Lung Adenocarcinoma

(2013) Eric L. Snyder et al.   MOLECULAR CELL

Reprogramming of mouse fibroblasts into cardiomyocyte-like cells in vitro

(2013) Li Qian et al.   Nature Protocols

Reprogramming of human fibroblasts toward a cardiac fate

(2013) Y.-J. Nam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Direct Reprogramming of Human Fibroblasts toward a Cardiomyocyte-like State

(2013) Ji-Dong Fu et al.   Stem Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Distinct Metabolic Flow Enables Large-Scale Purification of Mouse and Human Pluripotent Stem Cell-Derived Cardiomyocytes

(2012) Shugo Tohyama et al.   Cell Stem Cell

Maintaining differentiated cellular identity

(2012) Johan Holmberg et al.   NATURE REVIEWS GENETICS

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

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

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Dedifferentiation, transdifferentiation and reprogramming: three routes to regeneration

(2011) Chris Jopling et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Role of Oct4 in maintaining and regaining stem cell pluripotency

(2011) Guilai Shi et al.   Stem Cell Research & Therapy

Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes by Defined Factors

(2010) Masaki Ieda et al.   CELL

Neuregulin/ErbB Signaling Regulates Cardiac Subtype Specification in Differentiating Human Embryonic Stem Cells

(2010) Wei-Zhong Zhu et al.   CIRCULATION RESEARCH

Primary contribution to zebrafish heart regeneration by gata4 + cardiomyocytes

(2010) Kazu Kikuchi et al.   NATURE

Zebrafish heart regeneration occurs by cardiomyocyte dedifferentiation and proliferation

(2010) Chris Jopling et al.   NATURE

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

Suppression of induced pluripotent stem cell generation by the p53–p21 pathway

(2009) Hyenjong Hong et al.   NATURE

Directed transdifferentiation of mouse mesoderm to heart tissue by defined factors

(2009) Jun K. Takeuchi et al.   NATURE

Live cell imaging distinguishes bona fide human iPS cells from partially reprogrammed cells

(2009) Elayne M Chan et al.   NATURE BIOTECHNOLOGY

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS