Publications

Selected Publications

Chandra, V; Bhattacharyya, A; Schmiedel, BJ; Madrigal, A; Gonzalez-Colin, C; Fotsing, S; Crinklaw, A; Seumois, G; Mohammadi, P; Kronenberg, M; Peters, B; Ay, F; Vijayanand, P

Promoter-interacting expression quantitative trait loci (pieQTLs) are enriched for functional genetic variants. Journal Article Forthcoming

Nature Genetics, Forthcoming.

BibTeX | Tags: QTL

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

Thorball, Christian W; Oudot-Mellakh, Tiphaine; Ehsan, Nava; Hammer, Christian; Santoni, Federico A; Niay, Jonathan; Costagliola, Dominique; Goujard, Cécile; Meyer, Laurence; Wang, Sophia S; others,

Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphoma Journal Article

Haematologica, 2020.

Links | BibTeX | Tags: genetic risk loci, GWAS, HIV

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

Zou, James; Huss, Mikael; Abid, Abubakar; Mohammadi, Pejman; Torkamani, Ali; Telenti, Amalio

A primer on deep learning in genomics Journal Article

Nature Genetics, 51 (1), pp. 12–18, 2019.

Links | BibTeX | Tags: deep learning, machine learning, regulatory genomics

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

Yahi, Alexandre; Lappalainen, Tuuli; Mohammadi, Pejman; Tatonetti, Nicholas P

RecNW: A fast pairwise aligner for targeted sequencing Journal Article

bioRxiv, pp. 371989, 2018.

Links | BibTeX | Tags: alignment, RecNW, targeted sequencing

Castel, Stephane E; Cervera, Alejandra; Mohammadi, Pejman; Aguet, François; Reverter, Ferran; Wolman, Aaron; Guigo, Roderic; Iossifov, Ivan; Vasileva, Ana; Lappalainen, Tuuli

Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk Journal Article

Nature Genetics, 50 (9), pp. 1327–1334, 2018.

Links | BibTeX | Tags: autism, cancer, cis-regulatory variation, coding variants, genotype, GTEx, haplotype, penetrance, phenotype, SNP

Kim-Hellmuth, Sarah; Bechheim, Matthias; Pütz, Benno; Mohammadi, Pejman; Nédélec, Yohann; Giangreco, Nicholas; Becker, Jessica; Kaiser, Vera; Fricker, Nadine; Beier, Esther; others,

Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations Journal Article

Nature Communications, 8 (1), pp. 1–10, 2017.

Links | BibTeX | Tags: disease, eQTLs, GWAS, immune system, reQTLs

Jønsson, KL; Laustsen, A; Krapp, C; Skipper, KA; Thavachelvam, K; Hotter, D; Egedal, JH; Kjolby, M; Mohammadi, P; Prabakaran, T; others,

IFI16 is required for DNA sensing in human macrophages by promoting production and function of cGAMP Journal Article

Nature communications, 8 (1), pp. 1–17, 2017.

Links | BibTeX | Tags: disease, immune activation

Mohammadi, Pejman; Beerenwinkel, Niko; Benenson, Yaakov

Automated design of synthetic cell classifier circuits using a two-step optimization strategy Journal Article

Cell Systems, 4 (2), pp. 207–218, 2017.

Links | BibTeX | Tags: cell classifiers, microRNA-based circuits

GTEx Consortium,

Genetic effects on gene expression across human tissues Journal Article

Nature, 550 (7675), pp. 204–213, 2017.

Links | BibTeX | Tags: disease, gene expression, GTEx, molecular function, tissue specificity

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

Golumbeanu, Monica; Mohammadi, Pejman; Beerenwinkel, Niko

BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data Journal Article

Bioinformatics, 32 (7), pp. 976–983, 2016.

Links | BibTeX | Tags: BMix, PAR-CLIP

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

Constantinescu, Simona; Szczurek, Ewa; Mohammadi, Pejman; Rahnenführer, Jörg; Beerenwinkel, Niko

TiMEx: a waiting time model for mutually exclusive cancer alterations Journal Article

Bioinformatics, 32 (7), pp. 968–975, 2016.

Links | BibTeX | Tags: cancer, genetic alterations, TiMEx

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

Bartha, István; Rausell, Antonio; McLaren, Paul J; Mohammadi, Pejman; Tardaguila, Manuel; Chaturvedi, Nimisha; Fellay, Jacques; Telenti, Amalio

The characteristics of heterozygous protein truncating variants in the human genome Journal Article

PLoS Computational Biology, 11 (12), pp. e1004647, 2015.

Links | BibTeX | Tags: frameshift variants, phenotype, truncating variants

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

Rausell, Antonio; Mohammadi, Pejman; McLaren, Paul J; Bartha, Istvan; Xenarios, Ioannis; Fellay, Jacques; Telenti, Amalio

Analysis of stop-gain and frameshift variants in human innate immunity genes Journal Article

PLoS Computational Biology, 10 (7), pp. e1003757, 2014.

Links | BibTeX | Tags: gene expression, genome, loss-of-function, nonsense-mediated decay, OMIM

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