Concepedia

Large-Scale Transcriptional Response to Hypoxia in Aspergillus fumigatus Observed Using RNAseq Identifies a Novel Hypoxia Regulated ncRNA

Liliana Losada, Bridget M. Barker, Suman Pakala, Suchitra Pakala, Vinita Joardar, Nikhat Zafar, Stephanie Mounaud, Natalie D. Fedorova, William C. Nierman, Robert A. Cramer

Mycopathologia · 2014 · 43 citations · 22 references

DOIFull text

Open access

Concepts

References

22

Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg · Nature Methods · 2012 · 61.1K citations

, , +11

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Cole Trapnell, Brian A. Williams, Geo Pertea et al. · Nature Biotechnology · 2010 · 16.5K citations

, , +16

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Cole Trapnell, Adam Roberts, Loyal A. Goff et al. · Nature Protocols · 2012 · 12.9K citations · Full text

, , +12

TopHat: discovering splice junctions with RNA-Seq

Cole Trapnell, Lior Pachter, Steven L. Salzberg · Bioinformatics · 2009 · 12.1K citations · Full text

, , +16

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

Brian J. Haas, Steven L. Salzberg, Wei Zhu et al. · Genome biology · 2008 · 4.4K citations · Full text

, , +15