Diverse partial reprogramming strategies restore youthful gene expression and transiently suppress cell identity

Semi-supervised adversarial neural networks for single-cell classification

(2021) Jacob C. Kimmel et al.   GENOME RESEARCH

Reversible reprogramming of cardiomyocytes to a fetal state drives heart regeneration in mice

(2021) Yanpu Chen et al.   SCIENCE

In vivo partial reprogramming of myofibers promotes muscle regeneration by remodeling the stem cell niche

(2021) Chao Wang et al.   Nature Communications

Ameliorating the hallmarks of cellular senescence in skeletal muscle myogenic progenitors in vitro and in vivo

(2021) Aref Shahini et al.   Science Advances

Proteome-wide mapping of short-lived proteins in human cells

(2021) Jiaming Li et al.   MOLECULAR CELL

Benchmarking atlas-level data integration in single-cell genomics

(2021) Malte D. Luecken et al.   NATURE METHODS

Transient non-integrative expression of nuclear reprogramming factors promotes multifaceted amelioration of aging in human cells

(2020) Tapash Jay Sarkar et al.   Nature Communications

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

(2020)   NATURE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning

(2020) Nicholas J. Bernstein et al.   Cell Systems

In Vivo Reprogramming Ameliorates Aging Features in Dentate Gyrus Cells and Improves Memory in Mice

(2020) Alberto Rodríguez-Matellán et al.   Stem Cell Reports

Reprogramming to recover youthful epigenetic information and restore vision

(2020) Yuancheng Lu et al.   NATURE

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

Resolving Cell Fate Decisions during Somatic Cell Reprogramming by Single-Cell RNA-Seq

(2019) Lin Guo et al.   MOLECULAR CELL

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

(2019) Geoffrey Schiebinger et al.   CELL

ChEA3: transcription factor enrichment analysis by orthogonal omics integration

(2019) Alexandra B Keenan et al.   NUCLEIC ACIDS RESEARCH

Defining Reprogramming Checkpoints from Single-Cell Analyses of Induced Pluripotency

(2019) Khoa A. Tran et al.   Cell Reports

Single cell RNA-seq identifies the origins of heterogeneity in efficient cell transdifferentiation and reprogramming

(2019) Mirko Francesconi et al.   eLife

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

(2019) Christopher S. McGinnis et al.   NATURE METHODS

Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging

(2019) Jacob C. Kimmel et al.   GENOME RESEARCH

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Excluding Oct4 from Yamanaka Cocktail Unleashes the Developmental Potential of iPSCs

(2019) Sergiy Velychko et al.   Cell Stem Cell

On the design of CRISPR-based single-cell molecular screens

(2018) Andrew J Hill et al.   NATURE METHODS

Massive mining of publicly available RNA-seq data from human and mouse

(2018) Alexander Lachmann et al.   Nature Communications

AAV vector-mediated in vivo reprogramming into pluripotency

(2018) Elena Senís et al.   Nature Communications

Mitochondrial Aging Defects Emerge in Directly Reprogrammed Human Neurons due to Their Metabolic Profile

(2018) Yongsung Kim et al.   Cell Reports

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Partial reprogramming induces a steady decline in epigenetic age before loss of somatic identity

(2018) Nelly Olova et al.   AGING CELL

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Msh homeobox 1 (Msx1)- andMsx2-overexpressing bone marrow-derived mesenchymal stem cells resemble blastema cells and enhance regeneration in mice

(2017) Leila Taghiyar et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Differential analysis of RNA-seq incorporating quantification uncertainty

(2017) Harold Pimentel et al.   NATURE METHODS

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

In Vivo Amelioration of Age-Associated Hallmarks by Partial Reprogramming

(2016) Alejandro Ocampo et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

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

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

Tissue damage and senescence provide critical signals for cellular reprogramming in vivo

(2016) Lluc Mosteiro et al.   SCIENCE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Directly Reprogrammed Human Neurons Retain Aging-Associated Transcriptomic Signatures and Reveal Age-Related Nucleocytoplasmic Defects

(2015) Jerome Mertens et al.   Cell Stem Cell

Transient acquisition of pluripotency during somatic cell transdifferentiation with iPSC reprogramming factors

(2015) Itay Maza et al.   NATURE BIOTECHNOLOGY

Ectopic expression of Msx2 in mammalian myotubes recapitulates aspects of amphibian muscle dedifferentiation

(2015) Atilgan Yilmaz et al.   Stem Cell Research

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

The Hallmarks of Aging

(2013) Carlos López-Otín et al.   CELL

Generation of Rejuvenated Antigen-Specific T Cells by Reprogramming to Pluripotency and Redifferentiation

(2013) Toshinobu Nishimura et al.   Cell Stem Cell

Reprogramming in vivo produces teratomas and iPS cells with totipotency features

(2013) María Abad et al.   NATURE

Cell Reprogramming Requires Silencing of a Core Subset of Polycomb Targets

(2013) Giulia Fragola et al.   PLoS Genetics

A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells

(2012) Jose M. Polo et al.   CELL

Single-Cell Expression Analyses during Cellular Reprogramming Reveal an Early Stochastic and a Late Hierarchic Phase

(2012) Yosef Buganim et al.   CELL

Chromatin-modifying enzymes as modulators of reprogramming

(2012) Tamer T. Onder et al.   NATURE

Reprogramming Factor Stoichiometry Influences the Epigenetic State and Biological Properties of Induced Pluripotent Stem Cells

(2011) Bryce W. Carey et al.   Cell Stem Cell

Rejuvenating senescent and centenarian human cells by reprogramming through the pluripotent state

(2011) L. Lapasset et al.   GENES & DEVELOPMENT

Functional Genomics Reveals a BMP-Driven Mesenchymal-to-Epithelial Transition in the Initiation of Somatic Cell Reprogramming

(2010) Payman Samavarchi-Tehrani et al.   Cell Stem Cell

Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer

(2010) A. E. Teschendorff et al.   GENOME RESEARCH

The genetics of ageing

(2010) Cynthia J. Kenyon   NATURE

Muscle injury activates resident fibro/adipogenic progenitors that facilitate myogenesis

(2010) Aaron W. B. Joe et al.   NATURE CELL BIOLOGY

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

(2010) P. M. Gilbert et al.   SCIENCE

Sox2 is dispensable for the reprogramming of melanocytes and melanoma cells into induced pluripotent stem cells

(2009) J. Utikal et al.   JOURNAL OF CELL SCIENCE

The mysteries of induced pluripotency: where will they lead?

(2009) Andras Nagy et al.   NATURE METHODS

c-Myc Is Dispensable for Direct Reprogramming of Mouse Fibroblasts

(2008) Marius Wernig et al.   Cell Stem Cell

Database for mRNA Half-Life of 19 977 Genes Obtained by DNA Microarray Analysis of Pluripotent and Differentiating Mouse Embryonic Stem Cells

(2008) L. V. Sharova et al.   DNA RESEARCH

Reprogramming of murine and human somatic cells using a single polycistronic vector

(2008) B. W. Carey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA