Bidirectional Promoters as Important Drivers for the Emergence of Species-Specific Transcripts

Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome

(2012) C. Howald et al.   GENOME RESEARCH

Proto-genes and de novo gene birth

(2012) Anne-Ruxandra Carvunis et al.   NATURE

Gene Loops Enhance Transcriptional Directionality

(2012) S. M. Tan-Wong et al.   SCIENCE

Long non-coding RNA modifies chromatin

(2011) Alka Saxena et al.   BIOESSAYS

Genome-wide analysis of the transcription factor binding preference of human bi-directional promoters and functional annotation of related gene pairs

(2011) Bingchuan Liu et al.   BMC Systems Biology

De novo origin of new genes with introns inPlasmodium vivax

(2011) Zefeng Yang et al.   FEBS LETTERS

The Role of GC-Biased Gene Conversion in Shaping the Fastest Evolving Regions of the Human Genome

(2011) D. Kostka et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

A comprehensive survey of human polymorphisms at conserved splice dinucleotides and its evolutionary relationship with alternative splicing

(2010) Makoto K Shimada et al.   BMC EVOLUTIONARY BIOLOGY

Long Noncoding RNAs with Enhancer-like Function in Human Cells

(2010) Ulf Andersson Ørom et al.   CELL

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Genome-wide evidence for an essential role of the human Staf/ZNF143 transcription factor in bidirectional transcription

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Detecting positive selection within genomes: the problem of biased gene conversion

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Tissue-Specific and Ubiquitous Expression Patterns from Alternative Promoters of Human Genes

(2010) Edwin Jacox et al.   PLoS One

Most “Dark Matter” Transcripts Are Associated With Known Genes

(2010) Harm van Bakel et al.   PLOS BIOLOGY

GC-Biased Evolution Near Human Accelerated Regions

(2010) Sol Katzman et al.   PLoS Genetics

Genomic features defining exonic variants that modulate splicing

(2010) Adam Woolfe et al.   GENOME BIOLOGY

Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

(2010) Jeremy Goecks et al.   GENOME BIOLOGY

Affy exon tissues: exon levels in normal tissues in human, mouse and rat

(2009) Andrew A. Pohl et al.   BIOINFORMATICS

Inherent promoter bidirectionality facilitates maintenance of sequence integrity and transcription of parasitic DNA in mammalian genomes

(2009) Paul Kalitsis et al.   BMC GENOMICS

Alu repeats increase local recombination rates

(2009) David J Witherspoon et al.   BMC GENOMICS

Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts

(2009) Helen Piontkivska et al.   BMC GENOMICS

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Recent de novo origin of human protein-coding genes

(2009) D. G. Knowles et al.   GENOME RESEARCH

High-throughput sequence-based epigenomic analysis of Alu repeats in human cerebellum

(2009) Hehuang Xie et al.   NUCLEIC ACIDS RESEARCH

De Novo Origination of a New Protein-Coding Gene in Saccharomyces cerevisiae

(2008) J. Cai et al.   GENETICS

On the origin of new genes in Drosophila

(2008) Q. Zhou et al.   GENOME RESEARCH

Origin of Primate Orphan Genes: A Comparative Genomics Approach

(2008) M. Toll-Riera et al.   MOLECULAR BIOLOGY AND EVOLUTION

Transcription-coupled DNA repair: two decades of progress and surprises

(2008) Philip C. Hanawalt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE