Publications

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Ferraro, Nicole M; Strober, Benjamin J; Einson, Jonah; Abell, Nathan S; Aguet, Francois; Barbeira, Alvaro N; Brandt, Margot; Bucan, Maja; Castel, Stephane E; Davis, Joe R; others,

Transcriptomic signatures across human tissues identify functional rare genetic variation Journal Article

Science, 369 (6509), 2020.

Links | BibTeX | Tags: allele-specific expression, allelic expression, alternative splicing, gene expression, genome, GTEx, precision genomics, rare genetic variants, structural variants, transcriptome, Watershed

Castel, Stephane E; Aguet, François; Mohammadi, Pejman; Ardlie, Kristin G; Lappalainen, Tuuli

A vast resource of allelic expression data spanning human tissues Journal Article

Genome Biology, 21 (1), pp. 1–12, 2020.

Links | BibTeX | Tags: allelic expression, cis-regulatory effects, GTEx, haplotype, phASER, SNP

Mohammadi, Pejman; Castel, Stephane E; Cummings, Beryl B; Einson, Jonah; Sousa, Christina; Hoffman, Paul; Donkervoort, Sandra; Jiang, Zhuoxun; Mohassel, Payam; Foley, Reghan A; others,

Genetic regulatory variation in populations informs transcriptome analysis in rare disease Journal Article

Science, 366 (6463), pp. 351–356, 2019.

Links | BibTeX | Tags: allelic expression, ANEVA, ANEVA-DOT, genetic variation, GTEx, Mendelian, noncoding regions, rare genetic variants, RNA-sequencing, tissue-specific

Mohammadi, Pejman; Castel, Stephane E; Brown, Andrew A; Lappalainen, Tuuli

Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change Journal Article

Genome Research, 27 (11), pp. 1872–1884, 2017.

Links | BibTeX | Tags: aFC, allelic expression, cis-eQTLs, cis-regulation, gene expression, GTEx

Castel, Stephane E; Mohammadi, Pejman; Chung, Wendy K; Shen, Yufeng; Lappalainen, Tuuli

Rare variant phasing and haplotypic expression from RNA sequencing with phASER Journal Article

Nature communications, 7 (1), pp. 1–6, 2016.

Links | BibTeX | Tags: allelic expression, phASER, RNA-sequencing

Castel, Stephane E; Levy-Moonshine, Ami; Mohammadi, Pejman; Banks, Eric; Lappalainen, Tuuli

Tools and best practices for data processing in allelic expression analysis Journal Article

Genome Biology, 16 (1), pp. 195, 2015.

Links | BibTeX | Tags: allelic expression, cis-regulatory variation, genome, genotype, nonsense-mediated decay, RNA-seq reads, transcriptome