Pinstripe: a suite of programs for integrating transcriptomic and proteomic datasets identifies novel proteins and improves differentiation of protein-coding and non-coding genes

The evolution of RNAs with multiple functions

(2011) Marcel E. Dinger et al.   BIOCHIMIE

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

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

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

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

(2011) M. Brosch et al.   GENOME RESEARCH

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

A nucleolar protein, H19 opposite tumor suppressor (HOTS), is a tumor growth inhibitor encoded by a human imprinted H19 antisense transcript

(2011) P. Onyango et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

The Reality of Pervasive Transcription

(2011) Michael B. Clark et al.   PLOS BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome-wide Identification of Polycomb-Associated RNAs by RIP-seq

(2010) Jing Zhao 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

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

lncRNAdb: a reference database for long noncoding RNAs

(2010) Paulo P. Amaral et al.   NUCLEIC ACIDS RESEARCH

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

A novel mutation in Hr causes abnormal hair follicle morphogenesis in hairpoor mouse, an animal model for Marie Unna Hereditary Hypotrichosis

(2009) In Cheol Baek et al.   MAMMALIAN GENOME

Loss-of-function mutations of an inhibitory upstream ORF in the human hairless transcript cause Marie Unna hereditary hypotrichosis

(2009) Yaran Wen et al.   NATURE GENETICS

A guide to the Proteomics Identifications Database proteomics data repository

(2009) Juan Antonio Vizcaíno et al.   PROTEOMICS

PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows

(2008) Eric W Deutsch et al.   EMBO REPORTS

mrtl-A translation/localization regulatory protein encoded within the human c-myclocus and distributed throughout the endoplasmic and nucleoplasmic reticular network

(2008) Hyoungsoo Choi et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Conservation of the H19 noncoding RNA and H19-IGF2 imprinting mechanism in therians

(2008) Guillaume Smits et al.   NATURE GENETICS

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differentiating Protein-Coding and Noncoding RNA: Challenges and Ambiguities

(2008) Marcel E. Dinger et al.   PLoS Computational Biology