A5045777431- Genetic Associations and Epidemiology
- RNA Research and Splicing
- Genetic Mapping and Diversity in Plants and Animals
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Gut microbiota and health
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Genomics and Chromatin Dynamics
- Immune Cell Function and Interaction
- Forensic and Genetic Research
- Single-cell and spatial transcriptomics
- T-cell and B-cell Immunology
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- Stress Responses and Cortisol
- Clostridium difficile and Clostridium perfringens research
- Genetic diversity and population structure
- Genetic and phenotypic traits in livestock
- Health, psychology, and well-being
- RNA and protein synthesis mechanisms
- Pregnancy and preeclampsia studies
- Nematode management and characterization studies
- Asthma and respiratory diseases
- Acute Myeloid Leukemia Research
Wayne State University
2016-2025
University of Chicago
2007-2025
Michigan United
2016-2024
University of Rome Tor Vergata
2021-2024
University of Alabama at Birmingham
2022-2023
University of Michigan
2014-2022
Institute for Sustainable Plant Protection
2017
Hospital of Prato
2013
University of Calabria
2003-2008
Institut Pasteur
2008
The pandemic of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome 2 (SARS-CoV-2) has affected more than 10 million people, including pregnant women. To date, no consistent evidence for vertical transmission SARS-CoV-2 exists. novel canonically utilizes angiotensin-converting enzyme (ACE2) receptor and serine protease TMPRSS2 cell entry. Herein, building upon our previous single-cell study (Pique-Regi et al., 2019), another study, new single-cell/nuclei...
We propose a novel statistical framework for integrating the result from molecular quantitative trait loci (QTL) mapping into genome-wide genetic association analysis of complex traits, with primary objectives quantitatively assessing enrichment QTLs in trait-associated variants and colocalizations two types signals. introduce natural Bayesian hierarchical model that treats latent status as SNP-level annotations candidate SNPs traits. detail computational procedure to seamlessly perform...
More than 135 million births occur each year; yet, the molecular underpinnings of human parturition in gestational tissues, and particular placenta, are still poorly understood. The placenta is a complex heterogeneous organ including cells both maternal fetal origin, insults that disrupt maternal-fetal dialogue could result adverse pregnancy outcomes such as preterm birth. There limited knowledge cell type composition transcriptional activity its compartments during physiologic pathologic...
<h3>Objective</h3> Keratin (K)19, a biliary/hepatic progenitor cell (HPC) marker, is expressed in subset of hepatocellular carcinomas (HCC) with poor prognosis. The underlying mechanisms driving this phenotype K19-positive HCC remain elusive. <h3>Design</h3> Clinicopathological value K19 was compared EpCAM, and α-fetoprotein, Caucasian cohort 242 consecutive patients (167 surgical specimens, 75 needle biopsies) different aetiologies. Using microarrays microRNA profiling the molecular HCCs...
DNA methylation is an epigenetic mark thought to be robust environmental perturbations on a short time scale. Here, we challenge that view by demonstrating the infection of human dendritic cells (DCs) with live pathogenic bacteria associated rapid and active demethylation at thousands loci, independent cell division. We performed integrated analysis data genome-wide methylation, histone patterns, chromatin accessibility, gene expression, before after infection. found infection-induced rarely...
Two groups of populations with completely different lifestyles-the Pygmy hunter-gatherers and the Bantu-speaking farmers-coexist in Central Africa. We investigated origins these two interactions between them, by analyzing mtDNA variation 1,404 individuals from 20 farming 9 Africa, aim shedding light on one most fascinating cultural transitions human evolution (the transition hunting gathering to agriculture). Our data indicate that this region was colonized gradually, an initial L1c-rich...
Gene-by-environment (GxE) interactions determine common disease risk factors and biomedically relevant complex traits. However, quantifying how the environment modulates genetic effects on human quantitative phenotypes presents unique challenges. Environmental covariates are difficult to measure control at organismal level, as found in GWAS epidemiological studies. An alternative approach focuses cellular using vitro treatments a proxy for environment. These environments simplify...
Epidemiological, virological and pathogenetic characteristics of SARS-CoV-2 infection are under evaluation. A better understanding the pathophysiology associated with COVID-19 is crucial to improve treatment modalities develop effective prevention strategies. Transcriptomic proteomic data on host response against still have anecdotic character; currently available from other coronavirus infections therefore a key source information.We investigated selected molecular aspects three human...
Mapping expression quantitative trait loci (eQTLs) has been shown as a powerful tool to uncover the genetic underpinnings of many complex traits at molecular level. In this paper, we present an integrative analysis approach that leverages eQTL data collected from multiple population groups. particular, our effectively identifies independent cis-eQTL signals are consistent across populations, accounting for heterogeneity in allele frequencies and linkage disequilibrium patterns. Furthermore,...
The composition of the gut microbiome has been associated with various aspects human health, but mechanism this interaction is still unclear. We utilized a cellular system to characterize effect on gene expression. showed that some these changes in expression may be mediated by chromatin accessibility. Furthermore, we validate role specific microbe and show its abundance can modify host response. These results an important microbiota regulating suggest manipulation could useful future therapies.
Genetic effects on gene expression and splicing can be modulated by cellular environmental factors; yet interactions between genotypes, cell type, treatment have not been comprehensively studied together. We used an induced pluripotent stem system to study multiple types derived from the same individuals exposed them a large panel of treatments. Cellular responses involved different genes pathways for were highly variable across contexts. For thousands genes, we identified allelic contexts...
Humans display substantial interindividual clinical variability after SARS-CoV-2 infection1-3, the genetic and immunological basis of which has begun to be deciphered4. However, extent drivers population differences in immune responses remain unclear. Here we report single-cell RNA-sequencing data for peripheral blood mononuclear cells-from 222 healthy donors diverse ancestries-that were stimulated with or influenza A virus. We show that induces weaker, but more heterogeneous,...
Glucocorticoids (GCs) mediate physiological responses to environmental stress and are commonly used as pharmaceuticals. GCs act primarily through the GC receptor (GR, a transcription factor). Despite their clear biomedical importance, little is known about genetic architecture of variation in response. Here we provide an initial assessment variability cellular response treatment by profiling gene expression protein secretion 114 EBV-transformed B lymphocytes African European ancestry. We...
Abstract Motivation: Expression quantitative trait loci (eQTL) studies have discovered thousands of genetic variants that regulate gene expression, enabling a better understanding the functional role non-coding sequences. However, eQTL are costly, requiring large sample sizes and genome-wide genotyping each sample. In contrast, analysis allele-specific expression (ASE) is becoming popular approach to detect effect variation on even within single individual. This typically achieved by...
Abstract We propose a new computational framework, probabilistic transcriptome-wide association study (PTWAS), to investigate causal relationships between gene expressions and complex traits. PTWAS applies the established principles from instrumental variables analysis takes advantage of eQTL annotations delineate tackle unique challenges arising in TWAS. not only confers higher power than existing methods but also provides novel functionalities evaluate assumptions estimate tissue- or...