RNA secondary structure profiling in zebrafish reveals unique regulatory features

The ins and outs of lncRNA structure: How, why and what comes next?

(2016) Amanda J. Blythe et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Towards structural classification of long non-coding RNAs

(2016) Karissa Y. Sanbonmatsu   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

(2016) Zhipeng Lu et al.   CELL

HOTAIR Forms an Intricate and Modular Secondary Structure

(2015) Srinivas Somarowthu et al.   MOLECULAR CELL

Selective inhibition of miR-21 by phage display screened peptide

(2015) Debojit Bose et al.   NUCLEIC ACIDS RESEARCH

Regulatory Role of Small Nucleolar RNAs in Human Diseases

(2015) Grigory A. Stepanov et al.   Biomed Research International

A Defined Zebrafish Line for High-Throughput Genetics and Genomics: NHGRI-1

(2014) Matthew C. LaFave et al.   GENETICS

Landscape and variation of RNA secondary structure across the human transcriptome

(2014) Yue Wan et al.   NATURE

A day in the life of the spliceosome

(2014) A. Gregory Matera et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dynamic Expression of Long Non-Coding RNAs (lncRNAs) in Adult Zebrafish

(2014) Kriti Kaushik et al.   PLoS One

Secondary Structures of rRNAs from All Three Domains of Life

(2014) Anton S. Petrov et al.   PLoS One

Mature MiRNAs Form Secondary Structure, which Suggests Their Function beyond RISC

(2014) Agnieszka Belter et al.   PLoS One

Short Stories on Zebrafish Long Noncoding RNAs

(2014) Shadabul Haque et al.   Zebrafish

RNA secondary structure-dependent termination of transcription

(2013) Nikolay Zenkin   CELL CYCLE

Tackling Structures of Long Noncoding RNAs

(2013) Irina Novikova et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

(2013) Yiliang Ding et al.   NATURE

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo

(2013) Silvi Rouskin et al.   NATURE

Structure and function of long noncoding RNAs in epigenetic regulation

(2013) Tim R Mercer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

WEB-based GEne SeT AnaLysis Toolkit (WebGestalt): update 2013

(2013) Jing Wang et al.   NUCLEIC ACIDS RESEARCH

A Sequence-Based Variation Map of Zebrafish

(2013) Ashok Patowary et al.   Zebrafish

Targeted Disruption of Hotair Leads to Homeotic Transformation and Gene Derepression

(2013) Lingjie Li et al.   Cell Reports

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

The Role of RNA Structure in Posttranscriptional Regulation of Gene Expression

(2012) Elina Jacobs et al.   Journal of Genetics and Genomics

Functional complexity and regulation through RNA dynamics

(2012) Elizabeth A. Dethoff et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Structural architecture of the human long non-coding RNA, steroid receptor RNA activator

(2012) Irina V. Novikova et al.   NUCLEIC ACIDS RESEARCH

Regulatory Impact of RNA Secondary Structure across the Arabidopsis Transcriptome

(2012) F. Li et al.   PLANT CELL

Reverse Genetics Screen in Zebrafish Identifies a Role of miR-142a-3p in Vascular Development and Integrity

(2012) Mukesh Kumar Lalwani et al.   PLoS One

Genome-wide Analysis of Pre-mRNA 3′ End Processing Reveals a Decisive Role of Human Cleavage Factor I in the Regulation of 3′ UTR Length

(2012) Georges Martin et al.   Cell Reports

Conserved Function of lincRNAs in Vertebrate Embryonic Development despite Rapid Sequence Evolution

(2011) Igor Ulitsky et al.   CELL

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

The Midblastula Transition Defines the Onset of Y RNA-Dependent DNA Replication in Xenopus laevis

(2011) C. Collart et al.   MOLECULAR AND CELLULAR BIOLOGY

RNA secondary structure in mutually exclusive splicing

(2011) Yun Yang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq)

(2011) J. B. Lucks et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Observation of miRNA Gene Expression in Zebrafish Embryos by In Situ Hybridization to MicroRNA Primary Transcripts

(2011) Xinjun He et al.   Zebrafish

Detection of gene pathways with predictive power for breast cancer prognosis

(2010) Shuangge Ma et al.   BMC BIOINFORMATICS

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation

(2010) Fatih Ozsolak et al.   CELL

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

Genome-wide measurement of RNA secondary structure in yeast

(2010) Michael Kertesz et al.   NATURE

Formation, regulation and evolution of Caenorhabditis elegans 3′UTRs

(2010) Calvin H. Jan et al.   NATURE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Role of 5′- and 3′-untranslated regions of mRNAs in human diseases

(2009) Sangeeta Chatterjee et al.   BIOLOGY OF THE CELL

A noncoding antisense RNA in tie-1 locus regulates tie-1 function in vivo

(2009) K. Li et al.   BLOOD

Expression Patterns of Protein Kinases Correlate with Gene Architecture and Evolutionary Rates

(2008) Aleksey Y. Ogurtsov et al.   PLoS One

High-resolution in situ hybridization to whole-mount zebrafish embryos

(2007) Christine Thisse et al.   Nature Protocols