Transcriptome sequencing in Sezary syndrome identifies Sezary cell and mycosis fungoides-associated lncRNAs and novel transcripts

Rapid identification of non-human sequences in high-throughput sequencing datasets

(2012) Aparna Bhaduri et al.   BIOINFORMATICS

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

ChimeraScan: a tool for identifying chimeric transcription in sequencing data

(2011) Matthew K. Iyer et al.   BIOINFORMATICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Evolving Insights in the Pathogenesis and Therapy of Cutaneous T-cell lymphoma (Mycosis Fungoides and Sezary Syndrome)

(2011) Henry K. Wong et al.   BRITISH JOURNAL OF HAEMATOLOGY

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

(2011) Nicholas T. Ingolia et al.   CELL

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

RNA-sequence analysis of human B-cells

(2011) J. M. Toung et al.   GENOME RESEARCH

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers

(2011) Christian Steidl et al.   NATURE

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

(2011) John R Prensner et al.   NATURE BIOTECHNOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The Emergence of lncRNAs in Cancer Biology

(2011) J. R. Prensner et al.   Cancer Discovery

Absence of TCR loci chromosomal translocations in cutaneous T-cell lymphomas

(2011) Rocío Salgado et al.   Cancer Genetics

deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data

(2011) Andrew McPherson et al.   PLoS Computational Biology

Increased Programmed Death-1 Expression on CD4+ T Cells in Cutaneous T-Cell Lymphoma

(2010) Sara Samimi et al.   ARCHIVES OF DERMATOLOGY

Notch1 as a potential therapeutic target in cutaneous T-cell lymphoma

(2010) M. R. Kamstrup et al.   BLOOD

PHAST and RPHAST: phylogenetic analysis with space/time models

(2010) M. J. Hubisz et al.   BRIEFINGS IN BIOINFORMATICS

Novel approach to gene expression profiling in Sézary syndrome

(2010) R.G. Pomerantz et al.   BRITISH JOURNAL OF DERMATOLOGY

Infectious agents in cutaneous T-cell lymphoma

(2010) Ezra D. Mirvish et al.   JOURNAL OF THE AMERICAN ACADEMY OF DERMATOLOGY

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma

(2010) Nallasivam Palanisamy et al.   NATURE MEDICINE

3′-End Sequencing for Expression Quantification (3SEQ) from Archival Tumor Samples

(2010) Andrew H. Beck et al.   PLoS One

Inhibition of the K+ channel KCa3.1 ameliorates T cell-mediated colitis

(2010) L. Di et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small Peptides Switch the Transcriptional Activity of Shavenbaby During Drosophila Embryogenesis

(2010) T. Kondo et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

ENCODE whole-genome data in the UCSC Genome Browser

(2009) K. R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Novel and Highly Recurrent Chromosomal Alterations in Sezary Syndrome

(2008) M. H. Vermeer et al.   CANCER RESEARCH

Ensembl 2009

(2008) T. J. P. Hubbard et al.   NUCLEIC ACIDS RESEARCH