Serghei Mangul
A5017101305- Genomics and Phylogenetic Studies
- Scientific Computing and Data Management
- Single-cell and spatial transcriptomics
- Gene expression and cancer classification
- Cancer-related molecular mechanisms research
- Genetics, Bioinformatics, and Biomedical Research
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Cancer Genomics and Diagnostics
- Research Data Management Practices
- Immune Cell Function and Interaction
- SARS-CoV-2 and COVID-19 Research
- Bioinformatics and Genomic Networks
- Bacteriophages and microbial interactions
- Gut microbiota and health
- Molecular Biology Techniques and Applications
- Cell Image Analysis Techniques
- Microbial Community Ecology and Physiology
- Genetic Associations and Epidemiology
- T-cell and B-cell Immunology
- Metabolomics and Mass Spectrometry Studies
- RNA Research and Splicing
- HIV Research and Treatment
- Genomics and Rare Diseases
- Epigenetics and DNA Methylation
University of Southern California
2018-2025
Ştefan cel Mare University of Suceava
2025
University of California, Los Angeles
2013-2024
Southern California University for Professional Studies
2023-2024
QB3
2016-2023
UCLA Health
2016-2022
King Abdulaziz City for Science and Technology
2021
University of North Carolina at Chapel Hill
2021
Thermo Fisher Scientific (Sweden)
2020
University of Santa Monica
2018
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...
Responses to anti-PD-1 immunotherapy occur but are infrequent in bladder cancer. The specific T cells that mediate tumor rejection unknown. from human tumors and non-malignant tissue were assessed with single-cell RNA paired cell receptor (TCR) sequencing of 30,604 7 patients. We find the states repertoires CD8+ not distinct compared tissues. In contrast, analysis CD4+ demonstrates several tumor-specific states, including multiple regulatory cells. Surprisingly, we also cytotoxic clonally...
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.
Abstract Evaluating metagenomic software is key for optimizing metagenome interpretation and focus of the Initiative Critical Assessment Metagenome Interpretation (CAMI). The CAMI II challenge engaged community to assess methods on realistic complex datasets with long- short-read sequences, created computationally from around 1,700 new known genomes, as well 600 plasmids viruses. Here we analyze 5,002 results by 76 program versions. Substantial improvements were seen in assembly, some due...
Massively parallel whole transcriptome sequencing, commonly referred as RNA-Seq, is quickly becoming the technology of choice for gene expression profiling. However, due to short read length delivered by current sequencing technologies, estimation levels alternative splicing isoforms remains challenging.In this paper we present a novel expectation-maximization algorithm inference isoform- and gene-specific from RNA-Seq data. Our algorithm, IsoEM, based on disambiguating information provided...
Outliers in the human transcriptome reveal functional effects of rare genetic variants.
RNA viruses infecting a host usually exist as set of closely related sequences, referred to quasispecies. The genomic diversity viral quasispecies is subject great interest, particularly for chronic infections, since it can lead resistance existing therapies. High-throughput sequencing promising approach characterizing diversity, but unfortunately standard assembly software was originally designed single genome and cannot be used simultaneously assemble estimate the abundance multiple...
Abstract Biomedical research depends increasingly on computational tools, but mechanisms ensuring open data, software, and reproducibility are variably enforced by academic institutions, funders, publishers. Publications may present software for which source code or documentation become unavailable; this compromises the role of peer review in evaluating technical strength scientific contribution. Incomplete ancillary information an package bias limit subsequent work. We provide 8...
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...
The role of the human microbiome in health and disease is increasingly appreciated. We studied composition microbial communities present blood across 192 individuals, including healthy controls patients with three disorders affecting brain: schizophrenia, amyotrophic lateral sclerosis, bipolar disorder. By using high-quality unmapped RNA sequencing reads as candidate reads, we performed profiling transcripts detected whole blood. were able to detect a wide range bacterial archaeal phyla...
Abstract Profiling immunoglobulin (Ig) receptor repertoires with specialized assays can be cost-ineffective and time-consuming. Here we report ImReP, a computational method for rapid accurate profiling of the Ig repertoire, including complementary-determining region 3 (CDR3), using regular RNA sequencing data such as those from 8,555 samples across 53 tissues types 544 individuals in Genotype-Tissue Expression (GTEx v6) project. Using ImReP GTEx v6 data, generate collection 3.6 million...
A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole-genome sequencing 1,864 cases (713 with 1,151 mild disease) 15,033 ancestry-matched population controls 4 independent biobanks. tested whether pLOF these were associated COVID-19. identified only 1 mutation among 713 observed no enrichment pLOFs compared evidence...
As are most non-European populations, the Han Chinese relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 women we present a catalog 25,057,223 variants, including 548,401 novel variants that seen at least 10 times our data set. Individuals from this set came 24 out 33 administrative divisions across China (including 19 provinces, 4 municipalities, 1 autonomous region), thus allowing us to study structure, genetic ancestry,...