User profiles for Alexander Dobin
Alexander DobinCold Spring Harbor Laboratory Verified email at cshl.edu Cited by 70314 |
STAR: ultrafast universal RNA-seq aligner
A Dobin, CA Davis, F Schlesinger, J Drenkow… - …, 2013 - academic.oup.com
Motivation: Accurate alignment of high-throughput RNA-seq data is a challenging and yet
unsolved problem because of the non-contiguous transcript structure, relatively short read …
unsolved problem because of the non-contiguous transcript structure, relatively short read …
[HTML][HTML] A comparative encyclopedia of DNA elements in the mouse genome
…, LH See, M Fastuca, J Drenkow, C Zaleski, A Dobin… - Nature, 2014 - nature.com
The laboratory mouse shares the majority of its protein-coding genes with humans, making
it the premier model organism in biomedical research, yet the two mammals differ in …
it the premier model organism in biomedical research, yet the two mammals differ in …
[HTML][HTML] Expanded encyclopaedias of DNA elements in the human and mouse genomes
The human and mouse genomes contain instructions that specify RNAs and proteins and
govern the timing, magnitude, and cellular context of their production. To better delineate these …
govern the timing, magnitude, and cellular context of their production. To better delineate these …
[HTML][HTML] Comparative cellular analysis of motor cortex in human, marmoset and mouse
The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally
conserved across mammals 1 . Here, using high-throughput transcriptomic and epigenomic …
conserved across mammals 1 . Here, using high-throughput transcriptomic and epigenomic …
Mapping RNA‐seq reads with STAR
A Dobin, TR Gingeras - Current protocols in bioinformatics, 2015 - Wiley Online Library
Mapping of large sets of high‐throughput sequencing reads to a reference genome is one
of the foundational steps in RNA‐seq data analysis. The STAR software package performs …
of the foundational steps in RNA‐seq data analysis. The STAR software package performs …
Comparison of the transcriptional landscapes between human and mouse tissues
Although the similarities between humans and mice are typically highlighted, morphologically
and genetically, there are many differences. To better understand these two species on a …
and genetically, there are many differences. To better understand these two species on a …
[HTML][HTML] Comparative analysis of the transcriptome across distant species
The transcriptome is the readout of the genome. Identifying common features in it across distant
species can reveal fundamental principles. To this end, the ENCODE and modENCODE …
species can reveal fundamental principles. To this end, the ENCODE and modENCODE …
[HTML][HTML] Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods
Background Accurate fusion transcript detection is essential for comprehensive characterization
of cancer transcriptomes. Over the last decade, multiple bioinformatic tools have been …
of cancer transcriptomes. Over the last decade, multiple bioinformatic tools have been …
[HTML][HTML] Landscape of transcription in human cells
Eukaryotic cells make many types of primary and processed RNAs that are found either in
specific subcellular compartments or throughout the cells. A complete catalogue of these …
specific subcellular compartments or throughout the cells. A complete catalogue of these …
The developmental transcriptome of Drosophila melanogaster
Drosophila melanogaster is one of the most well studied genetic model organisms; nonetheless,
its genome still contains unannotated coding and non-coding genes, transcripts, exons …
its genome still contains unannotated coding and non-coding genes, transcripts, exons …