Long non-coding RNA GRASLND enhances chondrogenesis via suppression of the interferon type II signaling pathway

An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance

(2018) Assaf C. Bester et al.   CELL

High-depth transcriptomic profiling reveals the temporal gene signature of human mesenchymal stem cells during chondrogenesis

(2018) Nguyen P. T. Huynh et al.   FASEB JOURNAL

Genetic Engineering of Mesenchymal Stem Cells for Differential Matrix Deposition on 3D Woven Scaffolds

(2018) Nguyen P.T. Huynh et al.   TISSUE ENGINEERING PART A

Clonal Analysis Delineates Transcriptional Programs of Osteogenic and Adipogenic Lineages of Adult Mouse Skeletal Progenitors

(2018) Maria Rostovskaya et al.   Stem Cell Reports

Current prospects of type II interferon γ signaling and autoimmunity

(2017) Daniel S. Green et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Genome Engineering for Personalized Arthritis Therapeutics

(2017) Shaunak S. Adkar et al.   TRENDS IN MOLECULAR MEDICINE

CRISPR/Cas9 Editing of Murine Induced Pluripotent Stem Cells for Engineering Inflammation-Resistant Tissues

(2017) Jonathan M. Brunger et al.   Arthritis & Rheumatology

Genome Engineering of Stem Cells for Autonomously Regulated, Closed-Loop Delivery of Biologic Drugs

(2017) Jonathan M. Brunger et al.   Stem Cell Reports

Interaction of PKR with single-stranded RNA

(2017) Christopher B. Mayo et al.   Scientific Reports

Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells

(2016) Joshua B. Black et al.   Cell Stem Cell

Emerging roles for long noncoding RNAs in skeletal biology and disease

(2016) Nguyen P. T. Huynh et al.   CONNECTIVE TISSUE RESEARCH

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

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

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

Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses

(2016) S.L. Dunn et al.   OSTEOARTHRITIS AND CARTILAGE

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu et al.   SCIENCE

Mechanisms of Long Non-coding RNAs in Mammalian Nervous System Development, Plasticity, Disease, and Evolution

(2015) James A. Briggs et al.   NEURON

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Knockdown of the Cell Cycle Inhibitor p21 Enhances Cartilage Formation by Induced Pluripotent Stem Cells

(2015) Brian O. Diekman et al.   TISSUE ENGINEERING PART A

Distinct Transcriptional Programs Underlie Sox9 Regulation of the Mammalian Chondrocyte

(2015) Shinsuke Ohba et al.   Cell Reports

LncRNA-HIT Functions as an Epigenetic Regulator of Chondrogenesis through Its Recruitment of p100/CBP Complexes

(2015) Hanqian L. Carlson et al.   PLoS Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Tissue-engineered cartilage with inducible and tunable immunomodulatory properties

(2014) Katherine A. Glass et al.   BIOMATERIALS

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector

(2014) Ami M. Kabadi et al.   NUCLEIC ACIDS RESEARCH

Genes Involved in the Osteoarthritis Process Identified through Genome Wide Expression Analysis in Articular Cartilage; the RAAK Study

(2014) Yolande F. M. Ramos et al.   PLoS One

Large, stratified, and mechanically functional human cartilage grown in vitro by mesenchymal condensation

(2014) S. Bhumiratana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Scaffold-mediated lentiviral transduction for functional tissue engineering of cartilage

(2014) Jonathan M. Brunger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease

(2013) Jeannie T. Lee et al.   CELL

FGF-2 addition during expansion of human bone marrow-derived stromal cells alters MSC surface marker distribution and chondrogenic differentiation potential

(2013) S. Hagmann et al.   CELL PROLIFERATION

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

Promotion of Osteoblast Differentiation in Mesenchymal Cells Through Cbl-Mediated Control of STAT5 Activity

(2013) François-Xavier Dieudonne et al.   STEM CELLS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors

(2011) Shi-Yan Ng et al.   EMBO JOURNAL

Gamma Interferon Modulates Myogenesis through the Major Histocompatibility Complex Class II Transactivator, CIITA

(2011) P. Londhe et al.   MOLECULAR AND CELLULAR BIOLOGY

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

Isolation of adipose-derived stem cells and their induction to a chondrogenic phenotype

(2010) Bradley T Estes et al.   Nature Protocols

Cross-regulation of Signaling Pathways by Interferon-γ: Implications for Immune Responses and Autoimmune Diseases

(2009) Xiaoyu Hu et al.   IMMUNITY

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Dynamic refolding of IFN-γ mRNA enables it to function as PKR activator and translation template

(2009) Smadar Cohen-Chalamish et al.   Nature Chemical Biology

MENε/β noncoding RNAs are essential for structural integrity of nuclear paraspeckles

(2009) Yasnory T. F. Sasaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Basic Science of Articular Cartilage: Structure, Composition, and Function

(2009) Alice J. Sophia Fox et al.   Sports Health-A Multidisciplinary Approach

Endogenous interferon-γ is required for efficient skeletal muscle regeneration

(2008) Ming Cheng et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY