User profiles for Alexander Dobin

Alexander Dobin

Cold 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 …

[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 …

[HTML][HTML] Expanded encyclopaedias of DNA elements in the human and mouse genomes

…, N Shoresh, J Adrian, T Kawli, CA Davis, A Dobin… - Nature, 2020 - nature.com
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 …

[HTML][HTML] Comparative cellular analysis of motor cortex in human, marmoset and mouse

…, SA Ament, MM Behrens, HC Bravo, J Chun, A Dobin… - Nature, 2021 - nature.com
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 …

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 …

Comparison of the transcriptional landscapes between human and mouse tissues

…, A Breschi, CA Davis, A Dobin… - Proceedings of the …, 2014 - National Acad Sciences
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 …

[HTML][HTML] Comparative analysis of the transcriptome across distant species

…, AO Harmanci, MO Duff, S Djebali, RP Alexander… - Nature, 2014 - nature.com
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 …

[HTML][HTML] Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods

BJ Haas, A Dobin, B Li, N Stransky, N Pochet, A Regev - Genome biology, 2019 - Springer
Background Accurate fusion transcript detection is essential for comprehensive characterization
of cancer transcriptomes. Over the last decade, multiple bioinformatic tools have been …

[HTML][HTML] Landscape of transcription in human cells

S Djebali, CA Davis, A Merkel, A Dobin, T Lassmann… - Nature, 2012 - nature.com
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 …

The developmental transcriptome of Drosophila melanogaster

…, BW Booth, JB Brown, L Cherbas, CA Davis, A Dobin… - Nature, 2011 - nature.com
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 …