Natural Antisense Transcripts and Long Non-Coding RNA in Neurospora crassa

Natural Antisense Transcript: A Concomitant Engagement with Protein-Coding Transcript

(2015)   Oncotarget

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

Identification and function of long non-coding RNAs

(2013) Robert S. Young et al.   Essays in Biochemistry

Ribonucleoprotein Complexes That Control Circadian Clocks

(2013) Dongni Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Convergent Transcription Induces Dynamic DNA Methylation at disiRNA Loci

(2013) Yunkun Dang et al.   PLoS Genetics

Genome Wide Association Identifies Novel Loci Involved in Fungal Communication

(2013) Javier Palma-Guerrero et al.   PLoS Genetics

Identification and Properties of 1,119 Candidate LincRNA Loci in the Drosophila melanogaster Genome

(2012) Robert S. Young et al.   Genome Biology and Evolution

Pervasive Antisense Transcription Is Evolutionarily Conserved in Budding Yeast

(2012) A. J. Goodman et al.   MOLECULAR BIOLOGY AND EVOLUTION

RNA Polymerase II Collision Interrupts Convergent Transcription

(2012) David J. Hobson et al.   MOLECULAR CELL

Natural antisense transcripts in fungi

(2012) Michael E. Donaldson et al.   MOLECULAR MICROBIOLOGY

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A pre-initiation complex at the 3′-end of genes drives antisense transcription independent of divergent sense transcription

(2011) Struan C. Murray et al.   NUCLEIC ACIDS RESEARCH

Comparative Functional Genomics of the Fission Yeasts

(2011) N. Rhind et al.   SCIENCE

Genome-Wide Analysis of Nascent Transcription in Saccharomyces cerevisiae

(2011) Anastasia McKinlay et al.   G3-Genes Genomes Genetics

CHD1 Remodels Chromatin and Influences Transient DNA Methylation at the Clock Gene frequency

(2011) William J. Belden et al.   PLoS Genetics

Filtering error from SOLiD Output

(2010) Ariella Sasson et al.   BIOINFORMATICS

Diverse Pathways Generate MicroRNA-like RNAs and Dicer-Independent Small Interfering RNAs in Fungi

(2010) Heng-Chi Lee et al.   MOLECULAR CELL

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

The Prevalence and Regulation of Antisense Transcripts in Schizosaccharomyces pombe

(2010) Ting Ni et al.   PLoS One

An exonic splicing enhancer within a bidirectional coding sequence regulates alternative splicing of an antisense mRNA

(2010) Valerie K. Salato et al.   RNA Biology

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

(2010) Moran Yassour et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Tools for Fungal Proteomics: Multifunctional Neurospora Vectors for Gene Replacement, Protein Expression and Protein Purification

(2009) S. Honda et al.   GENETICS

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

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

(2009) Helen Neil et al.   NATURE

Regulatory roles of natural antisense transcripts

(2009) Mohammad Ali Faghihi et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The effect of temperature on Natural Antisense Transcript (NAT) expression in Aspergillus flavus

(2008) Carrie A. Smith et al.   CURRENT GENETICS

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE