- TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20742, USA
Genome Biol 14:R36. 2013
..TopHat2 is available at http://ccb.jhu.edu/software/tophat...
- Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
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 bias
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...
- Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre
1 Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA 2 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA 3 Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA 4
Nat Struct Mol Biol 21:198-206. 2014
..Thus, our data suggest a model in which lncRNAs such as Firre can interface with and modulate nuclear architecture across chromosomes. ..
- Long noncoding RNAs regulate adipogenesis
Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
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-seq
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 subclasses
Moran 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...
- The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
1 Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA 2 The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 3
Nat Biotechnol 32:381-6. 2014
..Monocle can in principle be used to recover single-cell gene expression kinetics from a wide array of cellular processes, including differentiation, proliferation and oncogenic transformation. ..
- Transcriptional and epigenetic dynamics during specification of human embryonic stem cells
Casey A Gifford
Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
Cell 153:1149-63. 2013
- Computational methods for transcriptome annotation and quantification using RNA-seq
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...