Publications

Selected Publications

Robles-Espinoza, Carla Daniela; Mohammadi, Pejman; Bonilla, Ximena; Gutierrez-Arcelus, Maria

Allele-specific expression: applications in cancer and technical considerations Journal Article Forthcoming

Current Opinion in Genetics & Development - VOLUME 66: CANCER GENOMICS 2021, Forthcoming.

BibTeX | Tags: allele-specific expression, cancer

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

Deshpande, Dhrithi; Chhugani, Karishma; Chang, Yutong; Karlsberg, Aaron; Loeffler, Caitlin; Zhang, Jinyang; Muszynska, Agata; Rotman, Jeremy; Tao, Laura; Martin, Lana S; Balliu, Brunilda; Tseng, Elizabeth; Eskin, Eleazar; Zhao, Fangqing; Mohammadi, Pejman; Labaj, Pawel P; Mangul, Serghei

A comprehensive overview of computational tools for RNA-seq analysis Journal Article

arXiv.org, 2020.

Links | BibTeX | Tags: RNA-sequencing

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

Yahi, A; Hoffman, P; Brandt, M; Mohammadi, P; Tatonetti, NP; Lappalainen, T

EdiTyper: a high-throughput tool for analysis of targeted sequencing data from genome editing experiments Journal Article

bioRxiv, 2020.

Links | BibTeX | Tags: genome, targeted sequencing

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

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

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

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

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

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

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

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

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

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

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

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

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