Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control

Small RNAs in development – insights from plants

(2012) Xuemei Chen   CURRENT OPINION IN GENETICS & DEVELOPMENT

Comprehensive analysis of RNA-Seq data reveals extensive RNA editing in a human transcriptome

(2012) Zhiyu Peng et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation

(2012) Alexander Sherstnev et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification of a novel α-L-arabinofuranosidase gene associated with mealiness in apple

(2011) Paula Macedo Nobile et al.   JOURNAL OF EXPERIMENTAL BOTANY

RNA 3' processing functions of Arabidopsis FCA and FPA limit intergenic transcription

(2011) C. Sonmez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome of the domesticated apple (Malus × domestica Borkh.)

(2010) Riccardo Velasco et al.   NATURE GENETICS

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

22-nucleotide RNAs trigger secondary siRNA biogenesis in plants

(2010) H.-M. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Roles of Plant Small RNAs in Biotic Stress Responses

(2009) Virginia Ruiz-Ferrer et al.   Annual Review of Plant Biology

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide and Organ-Specific Landscapes of Epigenetic Modifications and Their Relationships to mRNA and Small RNA Transcriptomes in Maize

(2009) X. Wang et al.   PLANT CELL

Genome-Wide Medicago truncatula Small RNA Analysis Revealed Novel MicroRNAs and Isoforms Differentially Regulated in Roots and Nodules

(2009) C. Lelandais-Briere et al.   PLANT CELL

An Integrated Genomics Approach to Define Niche Establishment by Rhodococcus fascians

(2009) S. Depuydt et al.   PLANT PHYSIOLOGY

Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids

(2009) M. Ha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Targeted 3' Processing of Antisense Transcripts Triggers Arabidopsis FLC Chromatin Silencing

(2009) F. Liu et al.   SCIENCE

Antisense transcription: A critical look in both directions

(2008) T. Beiter et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5'-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes

(2008) J. G. Reid et al.   GENOME RESEARCH

Genome-wide identification and analysis of small RNAs originated from natural antisense transcripts in Oryza sativa

(2008) X. Zhou et al.   GENOME RESEARCH

Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster

(2008) Katsutomo Okamura et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Antisense Transcriptomes of Human Cells

(2008) Yiping He et al.   SCIENCE