Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcriptsJoshua Z Levin
Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA 02141, USA
Genome Biol 10:R115. 2009
..Thus, targeted RNA-Seq produces an enhanced view of the molecular state of a set of "high interest" genes...
- Comprehensive comparative analysis of strand-specific RNA sequencing methods
Joshua Z Levin
Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA
Nat Methods 7:709-15. 2010
..Our analysis provides a comprehensive benchmark, and our computational pipeline is applicable for assessment of future protocols in other organisms...
- Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species
Moran Yassour
Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
Genome Biol 11:R87. 2010
..However, the functional role of antisense transcripts has been demonstrated only in a few cases and it has been suggested that most antisense transcripts may result from promiscuous bi-directional transcription in a dense genome...
- Integrative analysis of the melanoma transcriptome
Michael F Berger
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Genome Res 20:413-27. 2010
..Taken together, these results may indicate new avenues for target discovery in melanoma, while also providing a template for large-scale transcriptome studies across many tumor types...
- Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells
Michal Rabani
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Nat Biotechnol 29:436-42. 2011
..Certain transcripts, including those encoding cytokines and transcription factors, mature faster. Our study provides a quantitative approach to study the integrative process of RNA regulation...
- Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis
Andrea Pauli
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
Genome Res 22:577-91. 2012
..Our study provides the first systematic identification of lncRNAs in a vertebrate embryo and forms the foundation for future genetic, genomic, and evolutionary studies...
- Full-length transcriptome assembly from RNA-Seq data without a reference genome
Manfred G Grabherr
Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
Nat Biotechnol 29:644-52. 2011
..Our approach provides a unified solution for transcriptome reconstruction in any sample, especially in the absence of a reference genome...
- Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs
Mitchell Guttman
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Nat Biotechnol 28:503-10. 2010
..Our results open the way to direct experimental manipulation of thousands of noncoding RNAs and demonstrate the power of ab initio reconstruction to render a comprehensive picture of mammalian transcriptomes...
- RNA-SeQC: RNA-seq metrics for quality control and process optimization
David S DeLuca
Broad Institute of MIT and Harvard, Cambridge, MA, USA
Bioinformatics 28:1530-2. 2012
..Availability and implementation: See www.genepattern.org to run online, or www.broadinstitute.org/rna-seqc/ for a command line tool...
- Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth
Christina A Cuomo
The Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
Genome Res 22:2478-88. 2012
..Together these events may explain the emergence and success of these diverse intracellular parasites...
Peptidomic discovery of short open reading frame-encoded peptides in human cellsSarah A Slavoff
Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
Nat Chem Biol 9:59-64. 2013
..In addition, coding sORFs are present in a small fraction (8 out of 1,866) of long intergenic noncoding RNAs. Together, these results provide strong evidence that the human proteome is more complex than previously appreciated...
- Efficient and robust RNA-seq process for cultured bacteria and complex community transcriptomes
Georgia Giannoukos
Genome Sequencing and Analysis Program, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA
Genome Biol 13:R23. 2012
..The resulting expression profiles were highly reproducible, enriched up to 40-fold for non-rRNA transcripts, and correlated well with profiles representing undepleted total RNA...
