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

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

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

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