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

Analyzing real-time PCR data by the comparative CT method

Thomas D. Schmittgen, Kenneth J. Livak

Nature Protocols

Computed TomographyImage AnalysisEngineeringMedical ImagingBiomedical Imaging +6

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

Cole Trapnell, Adam Roberts, Loyal A. Goff, +7

Nature Protocols

Differential GeneNatural SciencesGeneticsRna BiologyMolecular Biology +9

Genome engineering using the CRISPR-Cas9 system

F. Ann Ran, Patrick D. Hsu, Jason Wright, +3

Nature Protocols

EngineeringGenome SurgeryGeneticsSynthetic BiologyGenetic Engineering +5

The Phyre2 web portal for protein modeling, prediction and analysis

Lawrence A. Kelley, Stefans Mezulis, Christopher M. Yates, +2

Nature Protocols

Phyre2 Web PortalBiochemistryBiomolecular Structure PredictionNatural SciencesMedicine +11

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

Brian J. Haas, Alexie Papanicolaou, Moran Yassour, +20

Nature Protocols

Functional GenomicsMedicineGeneticsNatural SciencesSequence Analysis +12

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

Mihaela Pertea, Daehwan Kim, Geo Pertea, +2

Nature Protocols

Functional GenomicsNatural SciencesGeneticsRna BiologyMolecular Biology +8

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

P. Naresh Kumar, Steven Henikoff, Pauline C. Ng

Nature Protocols

Protein FunctionFunctional GenomicsNon-synonymous VariantsGene RecognitionGenetics +11

I-TASSER: a unified platform for automated protein structure and function prediction

Ambrish Roy, Alper Küçükural, Yang Zhang

Nature Protocols

Unified PlatformAutomated Protein StructureStructural BioinformaticsBiomolecular Structure PredictionProtein Folding +12

Agar and broth dilution methods to determine the minimal inhibitory concentration (MIC) of antimicrobial substances

Irith Wiegand, Kai Hilpert, Robert E. W. Hancock

Nature Protocols

Antimicrobial SusceptibilityAntibioticsBioassay-guided IsolationMedicineBioanalysis +11