Fast gapped-read alignment with Bowtie 2

Ben Langmead, Steven L. Salzberg

Nature Methods

Long-read SequencingSequence AssemblyNatural SciencesComputational BiologyMolecular Biology +5

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

Da Wei Huang, Brad T. Sherman, Richard A. Lempicki

Nature Protocols

BiologyFunctional GenomicsLarge Gene ListsEngineeringBiological Database +13

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

Jo Vandesompele, Katleen De Preter, Filip Pattyn, +4

Genome biology

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

Cole Trapnell, Brian A. Williams, Geo Pertea, +6

Nature Biotechnology

Developmental BiologyFunctional GenomicsRna BiologyRna-seq RevealsTranscriptomics Technology +8

Mapping and quantifying mammalian transcriptomes by RNA-Seq

A Mortazavi, Brian A. Williams, Kenneth McCue, +2

Nature Methods

Functional GenomicsGeneticsTranscriptomics TechnologyMammalian TranscriptomesLong Non-coding Rna +5

A comparison of normalization methods for high densityoligonucleotide array data based on variance and bias

Benjamin M. Bolstad, Rafael A. Irizarry, Magnus Åstrand, +1

Bioinformatics

A scaling normalization method for differential expression analysis of RNA-seq data

Mark D. Robinson, Alicia Oshlack

Genome biology

Summaries of Affymetrix GeneChip probe level data

Rafael A. Irizarry

Nucleic Acids Research

mRNA-Seq whole-transcriptome analysis of a single cell

Fuchou Tang, Cátálin Bárbácioru, Yangzhou Wang, +9

Nature Methods

Single Cell SequencingMedicineSingle-cell BiologySingle-cell GenomicsTranscriptomics Technology +7

The Minimal Gene Complement of <i>Mycoplasma genitalium</i>

Claire M. Fraser, Jeannine D. Gocayne, Owen White, +26

Science

GeneticsMolecular GeneticsMinimal Gene ComplementGenomicsMolecular Ecology +17