- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and CufflinksCole Trapnell
Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
Nat Protoc 7:562-78. 2012..The protocol's execution time depends on the volume of transcriptome sequencing data and available computing resources but takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time...
- Improving RNA-Seq expression estimates by correcting for fragment biasAdam Roberts
Department of Computer Science, 387 Soda Hall, UC Berkeley, Berkeley, CA 94720, USA
Genome Biol 12:R22. 2011..We find improvements in expression estimates as measured by correlation with independently performed qRT-PCR and show that correction of bias leads to improved replicability of results across libraries and sequencing technologies...
- Long noncoding RNAs regulate adipogenesisLei Sun
Whitehead Institute for Biomedical Research, Cambridge, MA 02142
Proc Natl Acad Sci U S A 110:3387-92. 2013..RNAi-mediated loss of function screens identified functional lncRNAs with varying impact on adipogenesis. Collectively, we have identified numerous lncRNAs that are functionally required for proper adipogenesis...
- Differential analysis of gene regulation at transcript resolution with RNA-seqCole Trapnell
Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA
Nat Biotechnol 31:46-53. 2013..Cuffdiff 2 performs robust differential analysis in RNA-seq experiments at transcript resolution, revealing a layer of regulation not readily observable with other high-throughput technologies...
- Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclassesMoran N Cabili
Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts 02142, USA
Genes Dev 25:1915-27. 2011..Our integrated, comprehensive, yet conservative reference catalog of human lincRNAs reveals the global properties of lincRNAs and will facilitate experimental studies and further functional classification of these genes...
- Computational methods for transcriptome annotation and quantification using RNA-seqManuel Garber
Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA
Nat Methods 8:469-77. 2011..Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications...