Pejman Mohammadi
A5009782162- RNA Research and Splicing
- Genetic Associations and Epidemiology
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Genetic Mapping and Diversity in Plants and Animals
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Cancer-related molecular mechanisms research
- Genomics and Rare Diseases
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- HIV Research and Treatment
- Molecular Biology Techniques and Applications
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- Genetic and phenotypic traits in livestock
- Adipose Tissue and Metabolism
- Immune Cell Function and Interaction
- SARS-CoV-2 and COVID-19 Research
- Epigenetics and DNA Methylation
- Computational Physics and Python Applications
- HIV/AIDS drug development and treatment
- Neuroendocrine regulation and behavior
- Receptor Mechanisms and Signaling
- Corneal surgery and disorders
University of Washington
2023-2025
Seattle Children's Hospital
2025
Scripps Institution of Oceanography
2020-2024
Seattle University
2024
Scripps Research Institute
2018-2023
Scripps (United States)
2022-2023
KTH Royal Institute of Technology
2023
University of California, San Diego
2022
University of Colorado Anschutz Medical Campus
2022
University of Tennessee Health Science Center
2022
The Genotype-Tissue Expression (GTEx) project dissects how genetic variation affects gene expression and splicing.
Abstract Scalable, integrative methods to understand mechanisms that link genetic variants with phenotypes are needed. Here we derive a mathematical expression compute PrediXcan (a gene mapping approach) results using summary data (S-PrediXcan) and show its accuracy general robustness misspecified reference sets. We apply this framework 44 GTEx tissues 100+ from GWAS meta-analysis studies, creating growing public catalog of associations seeks capture the effects variation on human...
Many complex human phenotypes exhibit sex-differentiated characteristics. However, the molecular mechanisms underlying these differences remain largely unknown. We generated a catalog of sex in gene expression and genetic regulation across 44 tissue sources surveyed by Genotype-Tissue Expression project (GTEx, v8 release). demonstrate that influences levels cellular composition samples body. A total 37% all genes sex-biased at least one tissue. identify cis quantitative trait loci (eQTLs)...
Cell type composition, estimated from bulk tissue, maps the cellular specificity of genetic variants.
Telomere length within an individual varies in a correlated manner across most tissues.
Allelic expression analysis has become important for integrating genome and transcriptome data to characterize various biological phenomena such as cis-regulatory variation nonsense-mediated decay. We analyze the properties of allelic read count technical sources error, low-quality or double-counted RNA-seq reads, genotyping errors, mapping bias, covariates due sample preparation sequencing, in total depth. provide guidelines correcting show that our quality control measures improve...
Abstract Innate immune activation by macrophages is an essential part of host defence against infection. Cytosolic recognition microbial DNA in leads to induction interferons and cytokines through cyclic GMP-AMP synthase (cGAS) stimulator interferon genes (STING). Other factors, including interferon-gamma inducible factor 16 (IFI16), have been proposed contribute DNA. However, their relation the cGAS-STING pathway not clear. Here, we show that IFI16 functions on two distinct levels....
Abstract The Genotype-Tissue Expression (GTEx) project was established to characterize genetic effects on the transcriptome across human tissues, and link these regulatory mechanisms trait disease associations. Here, we present analyses of v8 data, based 17,382 RNA-sequencing samples from 54 tissues 948 post-mortem donors. We comprehensively associations for gene expression splicing in cis trans , showing that are found almost all genes, describe underlying molecular their contribution...
The immune system plays a major role in human health and disease, understanding genetic causes of interindividual variability responses is vital. Here, we isolate monocytes from 134 genotyped individuals, stimulate these cells with three defined microbe-associated molecular patterns (LPS, MDP, 5'-ppp-dsRNA), profile the transcriptomes at time points. Mapping expression quantitative trait loci (eQTL), identify 417 response eQTLs (reQTLs) varying effects between conditions. We characterize...
HIV-1 infects CD4+ T cells and completes its replication cycle in approximately 24 hours. We employed repeated measurements a standardized cell system rigorous mathematical modeling to characterize the emergence of viral intermediates their impact on cellular transcriptional response with high temporal resolution. observed 7,991 (73%) 10,958 expressed genes be modulated concordance key steps replication. Fifty-two percent overall variability host transcriptome was explained by linear...
Mapping cis -acting expression quantitative trait loci ( -eQTL) has become a popular approach for characterizing proximal genetic regulatory variants. In this paper, we describe and characterize log allelic fold change (aFC), the magnitude of associated with given variant, as biologically interpretable unit quantifying effect size -eQTLs mathematically convenient systematic modeling -regulation. This measure is independent from level allele frequency, additive, applicable to multiallelic...
Abstract Haplotype phasing of genetic variants is important for clinical interpretation the genome, population analysis and functional genomic allelic activity. Here we present phASER, an accurate approach that are overlapped by sequencing reads, including those from RNA (RNA-seq), which often span multiple exons due to splicing. Using diverse RNA-seq data demonstrate this provides more rare compared with population-based allows in same gene up hundreds kilobases away cannot be obtained DNA...
Outliers in the human transcriptome reveal functional effects of rare genetic variants.
Abstract Allele expression (AE) analysis robustly measures cis -regulatory effects. Here, we present and demonstrate the utility of a vast AE resource generated from GTEx v8 release, containing 15,253 samples spanning 54 human tissues for total 431 million measurements at SNP level 153 haplotype level. In addition, develop an extension our tool phASER that allows effect sizes variants to be estimated using haplotype-level data. This is largest date, are able make data publicly available. We...
Transcriptome data can facilitate the interpretation of effects rare genetic variants. Here, we introduce ANEVA (analysis expression variation) to quantify variation in gene dosage from allelic (AE) a population. Application Genotype-Tissues Expression (GTEx) showed that this variance estimate is robust and correlated with selective constraint gene. Using these estimates outlier test (ANEVA-DOT) applied AE 70 Mendelian muscular disease patients accuracy detecting genes pathogenic variants...
Despite rapid progress in characterizing the role of host genetics SARS-Cov-2 infection, there is limited understanding genes and pathways that contribute to COVID-19. Here, we integrate a genome-wide association study COVID-19 hospitalization (7,885 cases 961,804 controls from Host Genetics Initiative) with mRNA expression, splicing, protein levels (n = 18,502). We identify 27 related inflammation coagulation whose genetically predicted expression was associated hospitalization....
The seventh iteration of the reference genome assembly for Rattus norvegicus-mRatBN7.2-corrects numerous misplaced segments and reduces base-level errors by approximately 9-fold increases contiguity 290-fold compared with its predecessor. Gene annotations are now more complete, improving mapping precision genomic, transcriptomic, proteomics datasets. We jointly analyzed 163 short-read whole-genome sequencing datasets representing 120 laboratory rat strains substrains using mRatBN7.2. defined...