Publications

Selected Publications

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Glinos, Dafni A; Garborcauskas, Garrett; Hoffman, Paul; Ehsan, Nava; Jiang, Lihua; Gokden, Alper; Dai, Xiaoguang; Aguet, Francois; Brown, Kathleen L; Garimella, Kiran; Bowers, Tera; Costello, Maura; Ardlie, Kristin; Jian, Ruiqi; Tucker, Nathan R; Ellinor, Patrick T; Harrington, Eoghan D; Tang, Hua; Snyder, Michael; Juul, Sissel; Mohammadi, Pejman; MacArthur, Daniel G; Lappalainen, Tuuli; Cummings, Beryl

Transcriptome variation in human tissues revealed by long-read sequencing Journal Article

biorxiv, 2021.

Links | BibTeX | Tags: human tissues, transcriptome

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

GTEx Consortium,

The GTEx Consortium atlas of genetic regulatory effects across human tissues Journal Article

Science, 369 (6509), pp. 1318–1330, 2020.

Links | BibTeX | Tags: gene expression, GTEx, human tissues, pleiotropy, regulatory mechanisms, RNA, splicing, transcriptome

Oliva, Meritxell; Muñoz-Aguirre, Manuel; Kim-Hellmuth, Sarah; Wucher, Valentin; Gewirtz, Ariel DH; Cotter, Daniel J; Parsana, Princy; Kasela, Silva; Balliu, Brunilda; Viñuela, Ana; others,

The impact of sex on gene expression across human tissues Journal Article

Science, 369 (6509), 2020.

Links | BibTeX | Tags: GTEx, sex-specific, transcriptome

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

Mohammadi, Pejman; Iulio, Julia Di; Munoz, Miguel; Martinez, Raquel; Bartha, Istvan; Cavassini, Matthias; Thorball, Christian; Fellay, Jacques; Beerenwinkel, Niko; Ciuffi, Angela; others,

Dynamics of HIV latency and reactivation in a primary CD4+ T cell model Journal Article

PLoS Pathogens, 10 (5), pp. e1004156, 2014.

Links | BibTeX | Tags: CD4+, HIV, transcriptome, translation

Mohammadi, Pejman; Desfarges, Sébastien; Bartha, István; Joos, Beda; Zangger, Nadine; Munoz, Miguel; Günthard, Huldrych F; Beerenwinkel, Niko; Telenti, Amalio; Ciuffi, Angela

24 hours in the life of HIV-1 in a T cell line Journal Article

PLoS Pathogens, 9 (1), pp. e1003161, 2013.

Links | BibTeX | Tags: CD4+, disease, HIV, miRNAs, modeling, transcriptome