RIP-PEN-seq identifies a class of kink-turn RNAs as splicing regulators

Structure and folding of four putative kink turns identified in structured RNA species in a test of structural prediction rules

(2021) Lin Huang et al.   NUCLEIC ACIDS RESEARCH

RNA structure probing reveals the structural basis of Dicer binding and cleavage

(2021) Qing-Jun Luo et al.   Nature Communications

Expanding the phenotype of biallelic RNPC3 variants associated with growth hormone deficiency

(2020) Eline A. Verberne et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Binding specificities of human RNA-binding proteins toward structured and linear RNA sequences

(2020) Arttu Jolma et al.   GENOME RESEARCH

Nuclease-mediated depletion biases in ribosome footprint profiling libraries

(2020) Boris Zinshteyn et al.   RNA

Optimized design of antisense oligomers for targeted rRNA depletion

(2020) Wesley A Phelps et al.   NUCLEIC ACIDS RESEARCH

Effect of methylation of adenine N6 on kink turn structure depends on location

(2019) Saira Ashraf et al.   RNA Biology

New insights into minor splicing – A transcriptomic analysis of cells derived from TALS patients

(2019) Audric Cologne et al.   RNA

Minor intron splicing revisited: identification of new minor intron-containing genes and tissue-dependent retention and alternative splicing of minor introns

(2019) Anouk M. Olthof et al.   BMC GENOMICS

An LTR retrotransposon‐derived lnc RNA interacts with RNF 169 to promote homologous recombination

(2019) Bing Deng et al.   EMBO REPORTS

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity

(2018) Michelle Percharde et al.   CELL

Response to growth hormone in patients with RNPC3 mutations

(2018) Gabriel Á Martos‐Moreno et al.   EMBO Molecular Medicine

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins

(2018) Daniel Dominguez et al.   MOLECULAR CELL

The UCSC Genome Browser database: 2019 update

(2018) Maximilian Haeussler et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

RMBase v2.0: deciphering the map of RNA modifications from epitranscriptome sequencing data

(2017) Jia-Jia Xuan et al.   NUCLEIC ACIDS RESEARCH

Exome sequencing reveals a novelCWF19L1mutation associated with intellectual disability and cerebellar atrophy

(2016) Christina Evers et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

Improvements to the HITS-CLIP protocol eliminate widespread mispriming artifacts

(2016) Austin E. Gillen et al.   BMC GENOMICS

RNA Duplex Map in Living Cells Reveals Higher-Order Transcriptome Structure

(2016) Zhipeng Lu et al.   CELL

Minor intron splicing is regulated by FUS and affected by ALS‐associated FUS mutants

(2016) Stefan Reber et al.   EMBO JOURNAL

Local regulation of gene expression by lncRNA promoters, transcription and splicing

(2016) Jesse M. Engreitz et al.   NATURE

An updated human snoRNAome

(2016) Hadi Jorjani et al.   NUCLEIC ACIDS RESEARCH

A critical base pair in k-turns determines the conformational class adopted, and correlates with biological function

(2016) Lin Huang et al.   NUCLEIC ACIDS RESEARCH

Systematic Discovery of Xist RNA Binding Proteins

(2015) Ci Chu et al.   CELL

Pathogenic CWF19L1 variants as a novel cause of autosomal recessive cerebellar ataxia and atrophy

(2015) Minh Nguyen et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Structural imprints in vivo decode RNA regulatory mechanisms

(2015) Robert C. Spitale et al.   NATURE

Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly

(2015) Yury S Polikanov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies

(2015) Mohit Chawla et al.   NUCLEIC ACIDS RESEARCH

Aberrant splicing of U12-type introns is the hallmark of ZRSR2 mutant myelodysplastic syndrome

(2015) Vikas Madan et al.   Nature Communications

Compound heterozygous mutations in the noncoding RNU4ATAC cause Roifman Syndrome by disrupting minor intron splicing

(2015) Daniele Merico et al.   Nature Communications

Structural insights into the role of rRNA modifications in protein synthesis and ribosome assembly

(2015) Yury S Polikanov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The K-turn motif in riboswitches and other RNA species

(2014) David M.J. Lilley   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Defective minor spliceosome mRNA processing results in isolated familial growth hormone deficiency

(2014) J. Argente et al.   EMBO Molecular Medicine

Photo-cross-linking and high-resolution mass spectrometry for assignment of RNA-binding sites in RNA-binding proteins

(2014) Katharina Kramer et al.   NATURE METHODS

RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP)

(2014) Nathan A Siegfried et al.   NATURE METHODS

Homozygous splice mutation in CWF19L1 in a Turkish family with recessive ataxia syndrome

(2014) R. Burns et al.   NEUROLOGY

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biochemical defects in minor spliceosome function in the developmental disorder MOPD I

(2014) F. Jafarifar et al.   RNA

A critical base pair in k-turns that confers folding characteristics and correlates with biological function

(2014) Scott A. McPhee et al.   Nature Communications

The structure of the box C/D enzyme reveals regulation of RNA methylation

(2013) Audrone Lapinaite et al.   NATURE

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Insights into snoRNA biogenesis and processing from PAR-CLIP of snoRNA core proteins and small RNA sequencing

(2013) Shivendra Kishore et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue

(2012) John D. Morlan et al.   PLoS One

YbxF and YlxQ are bacterial homologs of L7Ae and bind K-turns but not K-loops

(2012) N. J. Baird et al.   RNA

The Molecular Interactions That Stabilize RNA Tertiary Structure: RNA Motifs, Patterns, and Networks

(2011) Samuel E. Butcher et al.   ACCOUNTS OF CHEMICAL RESEARCH

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Structural basis for the dual U4 and U4atac snRNA-binding specificity of spliceosomal protein hPrp31

(2011) S. Liu et al.   RNA

Association of TALS Developmental Disorder with Defect in Minor Splicing Component U4atac snRNA

(2011) P. Edery et al.   SCIENCE

Mutations in U4atac snRNA, a Component of the Minor Spliceosome, in the Developmental Disorder MOPD I

(2011) H. He et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

A structural database for k-turn motifs in RNA

(2010) K. T. Schroeder et al.   RNA

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

deepBase: a database for deeply annotating and mining deep sequencing data

(2009) Jian-Hua Yang et al.   NUCLEIC ACIDS RESEARCH