Assessment of engineered cells using CellNet and RNA-seq

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Direct Reprogramming of Hepatic Myofibroblasts into Hepatocytes In Vivo Attenuates Liver Fibrosis

(2016) Guangqi Song et al.   Cell Stem Cell

A predictive computational framework for direct reprogramming between human cell types

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

Conversion of human fibroblasts into functional cardiomyocytes by small molecules

(2016) Nan Cao et al.   SCIENCE

Computational Tools for Stem Cell Biology

(2016) Qin Bian et al.   TRENDS IN BIOTECHNOLOGY

Multiphasic and Dynamic Changes in Alternative Splicing during Induction of Pluripotency Are Coordinated by Numerous RNA-Binding Proteins

(2016) Benjamin Cieply et al.   Cell Reports

Engineered Murine HSCs Reconstitute Multi-lineage Hematopoiesis and Adaptive Immunity

(2016) Yi-Fen Lu et al.   Cell Reports

Enhancing the functional maturity of induced pluripotent stem cell-derived human hepatocytes by controlled presentation of cell-cell interactionsin vitro

(2015) Dustin R. Berger et al.   HEPATOLOGY

Gene networks and transcription factor motifs defining the differentiation of stem cells into hepatocyte-like cells

(2015) Patricio Godoy et al.   JOURNAL OF HEPATOLOGY

Differential responses to lithium in hyperexcitable neurons from patients with bipolar disorder

(2015) Jerome Mertens et al.   NATURE

Transcriptional Landscape of Cardiomyocyte Maturation

(2015) Hideki Uosaki et al.   Cell Reports

TeratoScore: Assessing the Differentiation Potential of Human Pluripotent Stem Cells by Quantitative Expression Analysis of Teratomas

(2015) Yishai Avior 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

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

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

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

Genome-wide characterization of the routes to pluripotency

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

The Transcriptional Landscape of Hematopoietic Stem Cell Ontogeny

(2012) Shannon McKinney-Freeman et al.   Cell Stem Cell

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

Reference Maps of Human ES and iPS Cell Variation Enable High-Throughput Characterization of Pluripotent Cell Lines

(2011) Christoph Bock et al.   CELL

A bioinformatic assay for pluripotency in human cells

(2011) Franz-Josef Müller et al.   NATURE METHODS

Generation of mouse ES cell lines engineered for the forced induction of transcription factors

(2011) Lina S. Correa-Cerro et al.   Scientific Reports

Direct Reprogramming of Fibroblasts into Functional Cardiomyocytes by Defined Factors

(2010) Masaki Ieda et al.   CELL

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Differentiation of Embryonic Stem Cells to Clinically Relevant Populations: Lessons from Embryonic Development

(2008) Charles E. Murry et al.   CELL

Carcinoma of unknown primary (CUP)

(2008) Nicholas Pavlidis et al.   CRITICAL REVIEWS IN ONCOLOGY HEMATOLOGY

Maps of random walks on complex networks reveal community structure

(2008) M. Rosvall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA