Large-scale profiling of noncoding RNA function in yeast

A resource for functional profiling of noncoding RNA in the yeast Saccharomyces cerevisiae

(2017) Steven Parker et al.   RNA

Non-coding RNAs and disease: the classical ncRNAs make a comeback

(2016) R. A. de Almeida et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Functional characterisation of long intergenic non-coding RNAs through genetic interaction profiling in Saccharomyces cerevisiae

(2016) Dimitris Kyriakou et al.   BMC BIOLOGY

Nonsense-Mediated Decay Restricts LncRNA Levels in Yeast Unless Blocked by Double-Stranded RNA Structure

(2016) Maxime Wery et al.   MOLECULAR CELL

Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library

(2016) Shiyou Zhu et al.   NATURE BIOTECHNOLOGY

Mutations in SNORD118 cause the cerebral microangiopathy leukoencephalopathy with calcifications and cysts

(2016) Emma M Jenkinson et al.   NATURE GENETICS

Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer

(2016) Supipi Duffy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assembly and trafficking of box C/D and H/ACA snoRNPs

(2016) Séverine Massenet et al.   RNA Biology

Correction to: The Spliceosome: The Ultimate RNA Chaperone and Sculptor

(2016) Panagiotis Papasaikas et al.   TRENDS IN BIOCHEMICAL SCIENCES

Selective suppression of antisense transcription by Set2-mediated H3K36 methylation

(2016) Swaminathan Venkatesh et al.   Nature Communications

Protein Abundance Control by Non-coding Antisense Transcription

(2016) Florian Huber et al.   Cell Reports

DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs

(2015) Estel Aparicio-Prat et al.   BMC GENOMICS

Functional Analysis and Characterization of Differential Coexpression Networks

(2015) Chia-Lang Hsu et al.   Scientific Reports

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

Elongator, a conserved complex required for wobble uridine modifications in Eukaryotes

(2015) Tony Karlsborn et al.   RNA Biology

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Environmental systems biology of cold-tolerant phenotype inSaccharomycesspecies adapted to grow at different temperatures

(2014) Caroline Mary Paget et al.   MOLECULAR ECOLOGY

The translational landscape of fission-yeast meiosis and sporulation

(2014) Caia D S Duncan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines

(2014) Tsui-Ting Ho et al.   NUCLEIC ACIDS RESEARCH

Translation of Small Open Reading Frames within Unannotated RNA Transcripts in Saccharomyces cerevisiae

(2014) Jenna E. Smith et al.   Cell Reports

A Comprehensive tRNA Deletion Library Unravels the Genetic Architecture of the tRNA Pool

(2014) Zohar Bloom-Ackermann et al.   PLoS Genetics

Cotranscriptional events in eukaryotic ribosome synthesis

(2014) Tomasz W. Turowski et al.   Wiley Interdisciplinary Reviews-RNA

Elucidating gene function and function evolution through comparison of co-expression networks of plants

(2014) Bjoern O. Hansen et al.   Frontiers in Plant Science

Leveraging gene co-expression networks to pinpoint the regulation of complex traits and disease, with a focus on cardiovascular traits

(2013) M. Rotival et al.   Briefings in Functional Genomics

A Transcriptome-wide Atlas of RNP Composition Reveals Diverse Classes of mRNAs and lncRNAs

(2013) Alex Charles Tuck et al.   CELL

Transcriptome Surveillance by Selective Termination of Noncoding RNA Synthesis

(2013) Daniel Schulz et al.   CELL

Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast

(2013) G. G. Zampar et al.   Molecular Systems Biology

RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts

(2013) Sarah Geisler et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

SGAtools: one-stop analysis and visualization of array-based genetic interaction screens

(2013) Omar Wagih et al.   NUCLEIC ACIDS RESEARCH

A Yeast Purification System for Human Translation Initiation Factors eIF2 and eIF2Bε and Their Use in the Diagnosis of CACH/VWM Disease

(2013) Rogerio A. de Almeida et al.   PLoS One

Genome Regulation by Long Noncoding RNAs

(2012) John L. Rinn et al.   Annual Review of Biochemistry

Non-coding RNAs inSaccharomyces cerevisiae: what is the function?

(2012) Jian Wu et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Impact of Chromosomal Inversions on the Yeast DAL Cluster

(2012) Samina Naseeb et al.   PLoS One

lincRNAs act in the circuitry controlling pluripotency and differentiation

(2011) Mitchell Guttman et al.   NATURE

XUTs are a class of Xrn1-sensitive antisense regulatory non-coding RNA in yeast

(2011) E. L. van Dijk et al.   NATURE

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

(2011) G. A. Brar et al.   SCIENCE

Comprehensive phenotypic analysis of single-gene deletion and overexpression strains of Saccharomyces cerevisiae

(2011) Katsunori Yoshikawa et al.   YEAST

Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples

(2010) A. M. Smith et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae

(2009) J. Camblong et al.   GENES & DEVELOPMENT

Quantitative phenotyping via deep barcode sequencing

(2009) A. M. Smith et al.   GENOME RESEARCH

Non-coding RNAs: regulators of disease

(2009) Ryan J Taft et al.   JOURNAL OF PATHOLOGY

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

DRYGIN: a database of quantitative genetic interaction networks in yeast

(2009) Judice L. Y. Koh et al.   NUCLEIC ACIDS RESEARCH

Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast

(2009) S. L. Bumgarner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Non-Coding RNA Prediction and Verification in Saccharomyces cerevisiae

(2009) Laura A. Kavanaugh et al.   PLoS Genetics

A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae

(2008) J. Berretta et al.   GENES & DEVELOPMENT

A ncRNA Modulates Histone Modification and mRNA Induction in the Yeast GAL Gene Cluster

(2008) Jonathan Houseley et al.   MOLECULAR CELL