Diversification of reprogramming trajectories revealed by parallel single-cell transcriptome and chromatin accessibility sequencing

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

(2019) Geoffrey Schiebinger et al.   CELL

OVOL2 induces mesenchymal-to-epithelial transition in fibroblasts and enhances cell-state reprogramming towards epithelial lineages

(2019) Kazuhide Watanabe et al.   Scientific Reports

Organoid single-cell genomic atlas uncovers human-specific features of brain development

(2019) Sabina Kanton et al.   NATURE

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Global H3.3 dynamic deposition defines its bimodal role in cell fate transition

(2018) Hai-Tong Fang et al.   Nature Communications

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

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

(2017) Alicia N Schep et al.   NATURE METHODS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

(2016) Sophie Petropoulos et al.   CELL

Single-cell multimodal profiling reveals cellular epigenetic heterogeneity

(2016) Lih Feng Cheow et al.   NATURE METHODS

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

RNAi Reveals Phase-Specific Global Regulators of Human Somatic Cell Reprogramming

(2016) Cheng-Xu Delon Toh et al.   Cell Reports

Mesenchymal to Epithelial Transition Induced by Reprogramming Factors Attenuates the Malignancy of Cancer Cells

(2016) Mikiro Takaishi et al.   PLoS One

Human mesenchymal stem cells - current trends and future prospective

(2015) Imran Ullah et al.   BIOSCIENCE REPORTS

Systematic Identification of Factors for Provirus Silencing in Embryonic Stem Cells

(2015) Bin Xia Yang et al.   CELL

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

(2015) Davide Cacchiarelli et al.   CELL

Induced Pluripotency and Gene Editing in Disease Modelling: Perspectives and Challenges

(2015) Yu Seah et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Systematic Identification of Barriers to Human iPSC Generation

(2014) Han Qin et al.   CELL

Inhibition of Transforming Growth Factor β (TGF-β) Signaling can Substitute for Oct4 Protein in Reprogramming and Maintain Pluripotency

(2014) Fangzhi Tan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Induction of pluripotency in human somatic cells via a transient state resembling primitive streak-like mesendoderm

(2014) Kazutoshi Takahashi et al.   Nature Communications

Genome-wide Functional Analysis Reveals Factors Needed at the Transition Steps of Induced Reprogramming

(2014) Chao-Shun Yang et al.   Cell Reports

Induction of Pluripotency in Mouse Somatic Cells with Lineage Specifiers

(2013) Jian Shu et al.   CELL

Reprogramming of Human Fibroblasts to Pluripotency with Lineage Specifiers

(2013) Nuria Montserrat et al.   Cell Stem Cell

Promoting Reprogramming by FGF2 Reveals that the Extracellular Matrix Is a Barrier for Reprogramming Fibroblasts to Pluripotency

(2013) Jiao Jiao et al.   STEM CELLS

Circuitry and Dynamics of Human Transcription Factor Regulatory Networks

(2012) Shane Neph et al.   CELL

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Neural stem cell specific fluorescent chemical probe binding to FABP7

(2012) S.-W. Yun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High Resolution Genome Wide Binding Event Finding and Motif Discovery Reveals Transcription Factor Spatial Binding Constraints

(2012) Yuchun Guo et al.   PLoS Computational Biology

An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming

(2011) Mathieu Gabut et al.   CELL

A Precarious Balance: Pluripotency Factors as Lineage Specifiers

(2011) Kyle M. Loh et al.   Cell Stem Cell

A High Proliferation Rate Is Required for Cell Reprogramming and Maintenance of Human Embryonic Stem Cell Identity

(2010) Sergio Ruiz et al.   CURRENT BIOLOGY

Induced pluripotency: history, mechanisms, and applications

(2010) M. Stadtfeld et al.   GENES & DEVELOPMENT