Intramolecular circularization increases efficiency of RNA sequencing and enables CLIP-Seq of nuclear RNA from human cells

A Model-Based Approach to Identify Binding Sites in CLIP-Seq Data

(2014) Tao Wang et al.   PLoS One

Capture and Amplification by Tailing and Switching (CATS)

(2014) Andrey Turchinovich et al.   RNA Biology

Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs

(2014) Matthew B Friedersdorf et al.   GENOME BIOLOGY

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Argonaute proteins couple chromatin silencing to alternative splicing

(2012) Maya Ameyar-Zazoua et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural bias in T4 RNA ligase-mediated 3′-adapter ligation

(2012) Fanglei Zhuang et al.   NUCLEIC ACIDS RESEARCH

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

(2012) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

(2012) K. Shiroguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ago HITS-CLIP Expands Understanding of Kaposi's Sarcoma-associated Herpesvirus miRNA Function in Primary Effusion Lymphomas

(2012) Irina Haecker et al.   PLoS Pathogens

The Viral and Cellular MicroRNA Targetome in Lymphoblastoid Cell Lines

(2012) Rebecca L. Skalsky et al.   PLoS Pathogens

T4 RNA Ligase 2 truncated active site mutants: improved tools for RNA analysis

(2011) Sebastien Viollet et al.   BMC BIOTECHNOLOGY

The Human Mitochondrial Transcriptome

(2011) Tim R. Mercer et al.   CELL

Viral MicroRNA Targetome of KSHV-Infected Primary Effusion Lymphoma Cell Lines

(2011) Eva Gottwein et al.   Cell Host & Microbe

Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response

(2011) I. Lipchina et al.   GENES & DEVELOPMENT

Microbial environments confound antibiotic efficacy

(2011) Henry H Lee et al.   Nature Chemical Biology

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

(2011) Shivendra Kishore et al.   NATURE METHODS

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

Deep sequencing of the small RNA transcriptome of normal and malignant human B cells identifies hundreds of novel microRNAs

(2010) D. D. Jima et al.   BLOOD

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

miR-ID: A novel, circularization-based platform for detection of microRNAs

(2010) P. Kumar et al.   RNA

Argonaute HITS-CLIP decodes microRNA–mRNA interaction maps

(2009) Sung Wook Chi et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

(2009) Christopher D Armour et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

A multifunctional human Argonaute2-specific monoclonal antibody

(2008) S. Rudel et al.   RNA