Transcriptomics Publications

Publications in Transcriptomics

Explore the most influential research papers and scholarly works that have shaped Transcriptomics. Use the concept filter below to focus on a specific sub-area of research.

Transcriptomics

2.9K

Publications

460.5K

Citations

Showing yearly statistics from 2000-2026.

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	Year	Citations
clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters Guangchuang Yu, Li-Gen Wang, Yanyan Han, OMICS A Journal of Integrative Biology GeneticsGenomicsGene RecognitionBioinformatics DatabaseR Package	2012	36K
Full-length transcriptome assembly from RNA-Seq data without a reference genome Manfred Grabherr, Brian J. Haas, Moran Yassour, Nature Biotechnology Long-read SequencingFunctional GenomicsNatural SciencesGeneticsSequence Analysis	2011	22K
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation Cole Trapnell, Brian A. Williams, Geo Pertea, Nature Biotechnology Developmental BiologyFunctional GenomicsRna BiologyRna-seq RevealsTranscriptomics Technology	2010	16.1K
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads Mihaela Pertea, Geo Pertea, Corina Antonescu, Nature Biotechnology Functional GenomicsNatural SciencesGeneticsRna Structure PredictionRna Biology	2015	14.5K
Integrating single-cell transcriptomic data across different conditions, technologies, and species Andrew Butler, Paul Hoffman, Peter Smibert, Nature Biotechnology EngineeringGeneticsMultiomicsSingle-cell Transcriptomic DataTranscriptomics Technology	2018	14.1K
Mapping and quantifying mammalian transcriptomes by RNA-Seq A Mortazavi, Brian A. Williams, Kenneth McCue, Nature Methods Functional GenomicsGeneticsTranscriptomics TechnologyMammalian TranscriptomesLong Non-coding Rna	2008	14K
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions Daehwan Kim, Geo Pertea, Cole Trapnell, Genome biology BioinformaticsGene Sequence AnnotationNatural SciencesGeneticsSequence Analysis	2013	13.4K
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks Cole Trapnell, Adam Roberts, Loyal A. Goff, Nature Protocols Differential GeneNatural SciencesGeneticsRna BiologyMolecular Biology	2012	12.6K
De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis Brian J. Haas, Alexie Papanicolaou, Moran Yassour, Nature Protocols Functional GenomicsMedicineGeneticsNatural SciencesSequence Analysis	2013	8.7K
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest Damian Szklarczyk, Rebecca Kirsch, Mikaela Koutrouli, Nucleic Acids Research Functional Enrichment AnalysisGeneticsMolecular BiologyGenomicsBioinformatics Database	2022	7.6K
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown Mihaela Pertea, Daehwan Kim, Geo Pertea, Nature Protocols Functional GenomicsNatural SciencesGeneticsRna BiologyMolecular Biology	2016	7.3K
Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs Lee P. Lim, Nelson C. Lau, Philip W. Garrett-Engele, Nature Target MrnasSystems BiologyFunctional GenomicsMedicineGenetics	2005	4.8K

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