A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation

Pervasive functional translation of noncanonical human open reading frames

(2020) Jin Chen et al.   SCIENCE

The long noncoding RNA Falcor regulates Foxa2 expression to maintain lung epithelial homeostasis and promote regeneration

(2019) Daniel T. Swarr et al.   GENES & DEVELOPMENT

Genetic compensation triggered by mutant mRNA degradation

(2019) Mohamed A. El-Brolosy et al.   NATURE

The Translational Landscape of the Human Heart

(2019) Sebastiaan van Heesch et al.   CELL

Overexpression of LINC00261 inhibits non–small cell lung cancer cells progression by interacting with miR‐522‐3p and suppressing Wnt signaling

(2019) Jingli Shi et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

LINC00261 suppresses human colon cancer progression via sponging miR‐324‐3p and inactivating the Wnt/β‐catenin pathway

(2019) Dongsheng Yan et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

(2019) Jonathan M. Mudge et al.   GENOME RESEARCH

How evolution builds genes from scratch

(2019) Adam Levy   NATURE

The Long Noncoding RNA Paupar Modulates PAX6 Regulatory Activities to Promote Alpha Cell Development and Function

(2019) Ruth A. Singer et al.   Cell Metabolism

Accurate annotation of human protein-coding small open reading frames

(2019) Thomas F. Martinez et al.   Nature Chemical Biology

The lncRNA GATA6-AS epigenetically regulates endothelial gene expression via interaction with LOXL2

(2018) Philipp Neumann et al.   Nature Communications

Translation of neutrally evolving peptides provides a basis for de novo gene evolution

(2018) Jorge Ruiz-Orera et al.   Nature Ecology & Evolution

Modelling the endocrine pancreas in health and disease

(2018) Mostafa Bakhti et al.   Nature Reviews Endocrinology

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Mining for Micropeptides

(2017) Catherine A. Makarewich et al.   TRENDS IN CELL BIOLOGY

Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells

(2016) Sai Luo et al.   Cell Stem Cell

βlinc1encodes a long noncoding RNA that regulates islet β-cell formation and function

(2016) Luis Arnes et al.   GENES & DEVELOPMENT

g:Profiler—a web server for functional interpretation of gene lists (2016 update)

(2016) Jüri Reimand et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Cytoplasmic long noncoding RNAs are frequently bound to and degraded at ribosomes in human cells

(2016) Joana Carlevaro-Fita et al.   RNA

DIGIT Is a Conserved Long Noncoding RNA that Regulates GSC Expression to Control Definitive Endoderm Differentiation of Embryonic Stem Cells

(2016) Kaveh Daneshvar et al.   Cell Reports

Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling

(2016) Anil Raj et al.   eLife

The Long Noncoding RNA Pnky Regulates Neuronal Differentiation of Embryonic and Postnatal Neural Stem Cells

(2015) Alexander D. Ramos et al.   Cell Stem Cell

Identification of Novel Long Noncoding RNAs Underlying Vertebrate Cardiovascular Development

(2015) L. Kurian et al.   CIRCULATION

Discovery, Annotation, and Functional Analysis of Long Noncoding RNAs Controlling Cell-Cycle Gene Expression and Proliferation in Breast Cancer Cells

(2015) Miao Sun et al.   MOLECULAR CELL

Detecting actively translated open reading frames in ribosome profiling data

(2015) Lorenzo Calviello et al.   NATURE METHODS

sORFs.org: a repository of small ORFs identified by ribosome profiling

(2015) Volodimir Olexiouk et al.   NUCLEIC ACIDS RESEARCH

Pancreatic islet cell development and regeneration

(2015) Anthony I. Romer et al.   Current Opinion in Endocrinology Diabetes and Obesity

The lncRNA DEANR1 Facilitates Human Endoderm Differentiation by Activating FOXA2 Expression

(2015) Wei Jiang et al.   Cell Reports

Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

(2015) Zhe Ji et al.   eLife

Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution

(2015) Moran N Cabili et al.   GENOME BIOLOGY

Generation of β cells from human pluripotent stem cells: Are we there yet?

(2014) Jacqueline V. Schiesser et al.   Annals of the New York Academy of Sciences

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

(2014) S. Anders et al.   BIOINFORMATICS

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation

(2014) A. A. Bazzini et al.   EMBO JOURNAL

An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment

(2014) Nianwei Lin et al.   MOLECULAR CELL

Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells

(2014) Alireza Rezania et al.   NATURE BIOTECHNOLOGY

Long non-coding RNAs as a source of new peptides

(2014) Jorge Ruiz-Orera et al.   eLife

Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes

(2014) Sebastiaan van Heesch et al.   GENOME BIOLOGY

Braveheart, a Long Noncoding RNA Required for Cardiovascular Lineage Commitment

(2013) Carla A. Klattenhoff et al.   CELL

The RNA Degradation Pathway Regulates the Function of GAS5 a Non-Coding RNA in Mammalian Cells

(2013) Hidenori Tani et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Human β Cell Transcriptome Analysis Uncovers lncRNAs That Are Tissue-Specific, Dynamically Regulated, and Abnormally Expressed in Type 2 Diabetes

(2012) Ignasi Morán et al.   Cell Metabolism

Maturation of Human Embryonic Stem Cell-Derived Pancreatic Progenitors Into Functional Islets Capable of Treating Pre-existing Diabetes in Mice

(2012) A. Rezania et al.   DIABETES

Genome-wide analysis of long noncoding RNA stability

(2012) M. B. Clark et al.   GENOME RESEARCH

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY