Publications

@article{Munro2022,

title = {The regulatory landscape of multiple brain regions in outbred heterogeneous stock rats},

author = {Daniel Munro and Tengfei Wang and Apurva S Chitre and Oksana Polesskaya and Nava Ehsan and Jianjun Gao and Hao Chen and Alexander Gusev and Leah C Solberg Woods and Laura M Saba and Abraham A Palmer and Pejman Mohammadi},

url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkac912/6764417},

doi = {10.1093/nar/gkac912},

year  = {2022},

date = {2022-10-20},

urldate = {2022-04-08},

journal = {Nucleic Acids Research},

pages = {gkac912},

keywords = {cis-eQTLs, cis-regulatory variation, eQTLs, RNA-sequencing, splicing},

pubstate = {published},

tppubtype = {article}

}

@article{Glinos2022,

title = {Transcriptome variation in human tissues revealed by long-read sequencing},

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

doi = {10.1038/s41586-022-05035-y},

year  = {2022},

date = {2022-08-03},

urldate = {2021-01-23},

journal = {Nature},

keywords = {human tissues, transcriptome},

pubstate = {published},

tppubtype = {article}

}

@article{Ehsan2022,

title = {Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data},

author = {Nava Ehsan and Bence M. Kotis and Stephane E. Castel and Eric J. Song and Nicholas Mancuso and Pejman Mohammadi},

url = {https://www.biorxiv.org/content/10.1101/2022.01.28.478116v1.abstract},

doi = {10.1101/2022.01.28.478116},

year  = {2022},

date = {2022-02-28},

journal = {bioRxiv},

keywords = {aFC, cis-regulation, eQTLs, GTEx},

pubstate = {forthcoming},

tppubtype = {article}

}

@article{Flynn2022,

title = {Transcription factor regulation of eQTL activity across individuals and tissues},

author = {Elise D. Flynn and Athena L. Tsu and Silva Kasela and Sarah Kim-Hellmuth and Francois Aguet and Kristin G. Ardlie and Harmen J. Bussemaker and Pejman *Mohammadi and Tuuli *Lappalainen},

url = {https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1009719},

doi = {10.1371/journal.pgen.1009719},

year  = {2022},

date = {2022-01-31},

urldate = {2022-01-06},

journal = {PLOS Genetics},

volume = {18},

issue = {1},

pages = {e1009719},

keywords = {eQTLs, GWAS, transcription factors},

pubstate = {published},

tppubtype = {article}

}

@article{Pathak2021,

title = {Integrative genomic analyses identify susceptibility genes underlying COVID-19 hospitalization},

author = {Gita Pathak and Kritika Singh and Tyne Miller-Fleming and Frank Wendt and Nava Ehsan and Kangcheng Hou and Ruth Johnson and Zeyun Lu and Shyamalika Gopalan and Loic Yengo and Pejman Mohammadi and Bogdan Pasaniuc and Renato Polimanti and Lea Davis and Nicholas Mancuso},

url = {https://www.nature.com/articles/s41467-021-24824-z},

doi = {10.1038/s41467-021-24824-z},

year  = {2021},

date = {2021-07-27},

journal = {Nature Communications},

volume = {12},

number = {4569},

keywords = {COVID-19, GWAS},

pubstate = {published},

tppubtype = {article}

}

@article{Robles-Espinoza2020,

title = {Allele-specific expression: applications in cancer and technical considerations},

author = {Carla Daniela Robles-Espinoza and Pejman Mohammadi and Ximena Bonilla and Maria Gutierrez-Arcelus



},

url = {https://doi.org/10.1016/j.gde.2020.10.007},

doi = {10.1016/j.gde.2020.10.007},

year  = {2020},

date = {2020-12-28},

journal = {Current Opinion in Genetics & Development - VOLUME 66: CANCER GENOMICS 2021},

volume = {66},

pages = {10-19},

keywords = {allele-specific expression, cancer},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Promoter-interacting expression quantitative trait loci (pieQTLs) are enriched for functional genetic variants.},

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

url = {https://doi.org/10.1038/s41588-020-00745-3},

doi = {10.1038/s41588-020-00745-3},

year  = {2020},

date = {2020-12-21},

journal = {Nature Genetics},

keywords = {QTL},

pubstate = {published},

tppubtype = {article}

}

@article{Deshpande2020,

title = {A comprehensive overview of computational tools for RNA-seq analysis},

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

url = {https://arxiv.org/abs/2010.02391},

year  = {2020},

date = {2020-10-05},

journal = {arXiv.org},

keywords = {RNA-sequencing},

pubstate = {published},

tppubtype = {article}

}

@article{ferraro2020transcriptomicb,

title = {Transcriptomic signatures across human tissues identify functional rare genetic variation},

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

url = {https://science.sciencemag.org/content/369/6509/eaaz5900},

year  = {2020},

date = {2020-09-11},

journal = {Science},

volume = {369},

number = {6509},

publisher = {American Association for the Advancement of Science},

keywords = {allele-specific expression, allelic expression, alternative splicing, gene expression, genome, GTEx, precision genomics, rare genetic variants, structural variants, transcriptome, Watershed},

pubstate = {published},

tppubtype = {article}

}

@article{Yahi2020,

title = {EdiTyper: a high-throughput tool for analysis of targeted sequencing data from genome editing experiments},

author = {A Yahi and P Hoffman and M Brandt and P Mohammadi and NP Tatonetti and T Lappalainen},

url = {https://www.biorxiv.org/content/10.1101/2020.07.30.229088v1.abstract},

doi = {10.1101/2020.07.30.229088},

year  = {2020},

date = {2020-07-30},

journal = {bioRxiv},

keywords = {genome, targeted sequencing},

pubstate = {published},

tppubtype = {article}

}

@article{gtex2020gtexb,

title = {The GTEx Consortium atlas of genetic regulatory effects across human tissues},

author = {{GTEx Consortium}},

url = {https://science.sciencemag.org/content/369/6509/1318.full},

year  = {2020},

date = {2020-01-01},

journal = {Science},

volume = {369},

number = {6509},

pages = {1318--1330},

publisher = {American Association for the Advancement of Science},

keywords = {gene expression, GTEx, human tissues, pleiotropy, regulatory mechanisms, RNA, splicing, transcriptome},

pubstate = {published},

tppubtype = {article}

}

@article{castel2020vastb,

title = {A vast resource of allelic expression data spanning human tissues},

author = {Stephane E Castel and François Aguet and Pejman Mohammadi and Kristin G Ardlie and Tuuli Lappalainen},

url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02122-z},

year  = {2020},

date = {2020-01-01},

journal = {Genome Biology},

volume = {21},

number = {1},

pages = {1--12},

publisher = {BioMed Central},

keywords = {allelic expression, cis-regulatory effects, GTEx, haplotype, phASER, SNP},

pubstate = {published},

tppubtype = {article}

}

@article{oliva2020impact,

title = {The impact of sex on gene expression across human tissues},

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

url = {https://science.sciencemag.org/content/369/6509/eaba3066.abstract},

year  = {2020},

date = {2020-01-01},

journal = {Science},

volume = {369},

number = {6509},

publisher = {American Association for the Advancement of Science},

keywords = {GTEx, sex-specific, transcriptome},

pubstate = {published},

tppubtype = {article}

}

@article{thorball2020genetic,

title = {Genetic variation near CXCL12 is associated with susceptibility to HIV-related non-Hodgkin lymphoma},

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

url = {https://haematologica.org/article/view/9813},

year  = {2020},

date = {2020-01-01},

journal = {Haematologica},

publisher = {Haematologica},

keywords = {genetic risk loci, GWAS, HIV},

pubstate = {published},

tppubtype = {article}

}

@article{mohammadi2019geneticb,

title = {Genetic regulatory variation in populations informs transcriptome analysis in rare disease},

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

url = {https://www.science.org/doi/10.1126/science.aay0256

https://www.nature.com/articles/s41576-019-0193-4},

year  = {2019},

date = {2019-01-01},

urldate = {2019-01-01},

journal = {Science},

volume = {366},

number = {6463},

pages = {351--356},

publisher = {American Association for the Advancement of Science},

keywords = {allelic expression, ANEVA, ANEVA-DOT, genetic variation, GTEx, Mendelian, noncoding regions, rare genetic variants, RNA-sequencing, tissue-specific},

pubstate = {published},

tppubtype = {article}

}

@article{zou2019primerb,

title = {A primer on deep learning in genomics},

author = {James Zou and Mikael Huss and Abubakar Abid and Pejman Mohammadi and Ali Torkamani and Amalio Telenti},

url = {https://www.nature.com/articles/s41588-018-0295-5},

year  = {2019},

date = {2019-01-01},

journal = {Nature Genetics},

volume = {51},

number = {1},

pages = {12--18},

publisher = {Nature Publishing Group},

keywords = {deep learning, machine learning, regulatory genomics},

pubstate = {published},

tppubtype = {article}

}

@article{castel2018modifiedb,

title = {Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk},

author = {Stephane E Castel and Alejandra Cervera and Pejman Mohammadi and François Aguet and Ferran Reverter and Aaron Wolman and Roderic Guigo and Ivan Iossifov and Ana Vasileva and Tuuli Lappalainen},

url = {https://www.nature.com/articles/s41588-018-0192-y},

year  = {2018},

date = {2018-01-01},

journal = {Nature Genetics},

volume = {50},

number = {9},

pages = {1327--1334},

publisher = {Nature Publishing Group},

keywords = {autism, cancer, cis-regulatory variation, coding variants, genotype, GTEx, haplotype, penetrance, phenotype, SNP},

pubstate = {published},

tppubtype = {article}

}

@article{yahi2018recnw,

title = {RecNW: A fast pairwise aligner for targeted sequencing},

author = {Alexandre Yahi and Tuuli Lappalainen and Pejman Mohammadi and Nicholas P Tatonetti},

url = {https://www.biorxiv.org/content/10.1101/371989v1.abstract},

year  = {2018},

date = {2018-01-01},

journal = {bioRxiv},

pages = {371989},

publisher = {Cold Spring Harbor Laboratory},

keywords = {alignment, RecNW, targeted sequencing},

pubstate = {published},

tppubtype = {article}

}

@article{gtex2017genetic,

title = {Genetic effects on gene expression across human tissues},

author = {{GTEx Consortium}},

url = {https://www.nature.com/articles/nature24277},

year  = {2017},

date = {2017-01-01},

journal = {Nature},

volume = {550},

number = {7675},

pages = {204--213},

publisher = {Nature Publishing Group},

keywords = {disease, gene expression, GTEx, molecular function, tissue specificity},

pubstate = {published},

tppubtype = {article}

}

@article{mohammadi2017quantifying,

title = {Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change},

author = {Pejman Mohammadi and Stephane E Castel and Andrew A Brown and Tuuli Lappalainen},

url = {https://genome.cshlp.org/content/27/11/1872.short},

year  = {2017},

date = {2017-01-01},

journal = {Genome Research},

volume = {27},

number = {11},

pages = {1872--1884},

publisher = {Cold Spring Harbor Lab},

keywords = {aFC, allelic expression, cis-eQTLs, cis-regulation, gene expression, GTEx},

pubstate = {published},

tppubtype = {article}

}

@article{jonsson2017ifi16,

title = {IFI16 is required for DNA sensing in human macrophages by promoting production and function of cGAMP},

author = {KL Jønsson and A Laustsen and C Krapp and KA Skipper and K Thavachelvam and D Hotter and JH Egedal and M Kjolby and P Mohammadi and T Prabakaran and others},

url = {https://www.nature.com/articles/ncomms14391},

year  = {2017},

date = {2017-01-01},

journal = {Nature communications},

volume = {8},

number = {1},

pages = {1--17},

publisher = {Nature Publishing Group},

keywords = {disease, immune activation},

pubstate = {published},

tppubtype = {article}

}

@article{mohammadi2017automated,

title = {Automated design of synthetic cell classifier circuits using a two-step optimization strategy},

author = {Pejman Mohammadi and Niko Beerenwinkel and Yaakov Benenson},

url = {https://www.cell.com/cell-systems/fulltext/S2405-4712(17)30003-0},

year  = {2017},

date = {2017-01-01},

journal = {Cell Systems},

volume = {4},

number = {2},

pages = {207--218},

publisher = {Elsevier},

keywords = {cell classifiers, microRNA-based circuits},

pubstate = {published},

tppubtype = {article}

}

@article{kim2017genetic,

title = {Genetic regulatory effects modified by immune activation contribute to autoimmune disease associations},

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

url = {https://www.nature.com/articles/s41467-017-00366-1},

year  = {2017},

date = {2017-01-01},

journal = {Nature Communications},

volume = {8},

number = {1},

pages = {1--10},

publisher = {Nature Publishing Group},

keywords = {disease, eQTLs, GWAS, immune system, reQTLs},

pubstate = {published},

tppubtype = {article}

}

@article{castel2016rare,

title = {Rare variant phasing and haplotypic expression from RNA sequencing with phASER},

author = {Stephane E Castel and Pejman Mohammadi and Wendy K Chung and Yufeng Shen and Tuuli Lappalainen},

url = {https://www.nature.com/articles/ncomms12817},

year  = {2016},

date = {2016-01-01},

journal = {Nature communications},

volume = {7},

number = {1},

pages = {1--6},

publisher = {Nature Publishing Group},

keywords = {allelic expression, phASER, RNA-sequencing},

pubstate = {published},

tppubtype = {article}

}

@article{constantinescu2016timex,

title = {TiMEx: a waiting time model for mutually exclusive cancer alterations},

author = {Simona Constantinescu and Ewa Szczurek and Pejman Mohammadi and Jörg Rahnenführer and Niko Beerenwinkel},

url = {https://academic.oup.com/bioinformatics/article-abstract/32/7/968/2288357},

year  = {2016},

date = {2016-01-01},

journal = {Bioinformatics},

volume = {32},

number = {7},

pages = {968--975},

publisher = {Oxford University Press},

keywords = {cancer, genetic alterations, TiMEx},

pubstate = {published},

tppubtype = {article}

}

@article{golumbeanu2016bmix,

title = {BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data},

author = {Monica Golumbeanu and Pejman Mohammadi and Niko Beerenwinkel},

url = {https://academic.oup.com/bioinformatics/article-abstract/32/7/976/2288374},

year  = {2016},

date = {2016-01-01},

journal = {Bioinformatics},

volume = {32},

number = {7},

pages = {976--983},

publisher = {Oxford University Press},

keywords = {BMix, PAR-CLIP},

pubstate = {published},

tppubtype = {article}

}

@article{castel2015tools,

title = {Tools and best practices for data processing in allelic expression analysis},

author = {Stephane E Castel and Ami Levy-Moonshine and Pejman Mohammadi and Eric Banks and Tuuli Lappalainen},

url = {https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0762-6},

year  = {2015},

date = {2015-01-01},

journal = {Genome Biology},

volume = {16},

number = {1},

pages = {195},

publisher = {Springer},

keywords = {allelic expression, cis-regulatory variation, genome, genotype, nonsense-mediated decay, RNA-seq reads, transcriptome},

pubstate = {published},

tppubtype = {article}

}

@article{bartha2015characteristics,

title = {The characteristics of heterozygous protein truncating variants in the human genome},

author = {István Bartha and Antonio Rausell and Paul J McLaren and Pejman Mohammadi and Manuel Tardaguila and Nimisha Chaturvedi and Jacques Fellay and Amalio Telenti},

url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004647},

year  = {2015},

date = {2015-01-01},

journal = {PLoS Computational Biology},

volume = {11},

number = {12},

pages = {e1004647},

publisher = {Public Library of Science San Francisco, CA USA},

keywords = {frameshift variants, phenotype, truncating variants},

pubstate = {published},

tppubtype = {article}

}

@article{mohammadi2014dynamics,

title = {Dynamics of HIV latency and reactivation in a primary CD4+ T cell model},

author = {Pejman Mohammadi and Julia Di Iulio and Miguel Munoz and Raquel Martinez and Istvan Bartha and Matthias Cavassini and Christian Thorball and Jacques Fellay and Niko Beerenwinkel and Angela Ciuffi and others},

url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1004156},

year  = {2014},

date = {2014-01-01},

journal = {PLoS Pathogens},

volume = {10},

number = {5},

pages = {e1004156},

publisher = {Public Library of Science},

keywords = {CD4+, HIV, transcriptome, translation},

pubstate = {published},

tppubtype = {article}

}

@article{rausell2014analysis,

title = {Analysis of stop-gain and frameshift variants in human innate immunity genes},

author = {Antonio Rausell and Pejman Mohammadi and Paul J McLaren and Istvan Bartha and Ioannis Xenarios and Jacques Fellay and Amalio Telenti},

url = {https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003757},

year  = {2014},

date = {2014-01-01},

journal = {PLoS Computational Biology},

volume = {10},

number = {7},

pages = {e1003757},

publisher = {Public Library of Science},

keywords = {gene expression, genome, loss-of-function, nonsense-mediated decay, OMIM},

pubstate = {published},

tppubtype = {article}

}

@article{mohammadi201324,

title = {24 hours in the life of HIV-1 in a T cell line},

author = {Pejman Mohammadi and Sébastien Desfarges and István Bartha and Beda Joos and Nadine Zangger and Miguel Munoz and Huldrych F Günthard and Niko Beerenwinkel and Amalio Telenti and Angela Ciuffi},

url = {https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1003161},

year  = {2013},

date = {2013-01-01},

journal = {PLoS Pathogens},

volume = {9},

number = {1},

pages = {e1003161},

publisher = {Public Library of Science},

keywords = {CD4+, disease, HIV, miRNAs, modeling, transcriptome},

pubstate = {published},

tppubtype = {article}

}