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Identification and classification of conserved RNA secondary structures in the human genome.

Pedersen JS, Bejerano G, Siepel A, et al. Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol. 2006;2(4):e33. doi:10.1371/journal.pcbi.0020033

Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection.

Henn MR, Boutwell CL, Charlebois P, et al. Whole genome deep sequencing of HIV-1 reveals the impact of early minor variants upon immune recognition during acute infection. PLoS Pathog. 2012;8(3):e1002529. doi:10.1371/journal.ppat.1002529

RNA-SeQC: RNA-seq metrics for quality control and process optimization.

DeLuca DS, Levin JZ, Sivachenko A, et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics. 2012;28(11):1530-2. doi:10.1093/bioinformatics/bts196

Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth.

Cuomo CA, Desjardins CA, Bakowski MA, et al. Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth. Genome Res. 2012;22(12):2478-88. doi:10.1101/gr.142802.112

Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification.

Malboeuf CM, Yang X, Charlebois P, et al. Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification. Nucleic Acids Res. 2013;41(1):e13. doi:10.1093/nar/gks794

Differential analysis of gene regulation at transcript resolution with RNA-seq.

Trapnell C, Hendrickson DG, Sauvageau M, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol. 2013;31(1):46-53. doi:10.1038/nbt.2450

Comparative analysis of RNA sequencing methods for degraded or low-input samples.

Adiconis X, Borges-Rivera D, Satija R, et al. Comparative analysis of RNA sequencing methods for degraded or low-input samples. Nat Methods. 2013;10(7):623-9. doi:10.1038/nmeth.2483

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.

Shalek AK, Satija R, Adiconis X, et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature. 2013;498(7453):236-40. doi:10.1038/nature12172

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis.

Haas BJ, Papanicolaou A, Yassour M, et al. De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis. Nat Protoc. 2013;8(8):1494-512. doi:10.1038/nprot.2013.084

The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations.

Cerqueira GC, Arnaud MB, Inglis DO, et al. The Aspergillus Genome Database: multispecies curation and incorporation of RNA-Seq data to improve structural gene annotations. Nucleic Acids Res. 2014;42(Database issue):D705-10. doi:10.1093/nar/gkt1029