A5046358574- Genetic Associations and Epidemiology
- Asthma and respiratory diseases
- Genetic Mapping and Diversity in Plants and Animals
- Gene expression and cancer classification
- Indoor Air Quality and Microbial Exposure
- Bioinformatics and Genomic Networks
- Inflammatory Bowel Disease
- Allergic Rhinitis and Sensitization
- Immune Cell Function and Interaction
- Air Quality and Health Impacts
- Food Allergy and Anaphylaxis Research
- T-cell and B-cell Immunology
- Microbial Community Ecology and Physiology
- Health, Environment, Cognitive Aging
- Malaria Research and Control
- Biological Research and Disease Studies
- Human Health and Disease
- Atmospheric and Environmental Gas Dynamics
- Celiac Disease Research and Management
- Genetics and Neurodevelopmental Disorders
- Nutrition, Genetics, and Disease
- Genomics and Phylogenetic Studies
- Genetic and phenotypic traits in livestock
- Alzheimer's disease research and treatments
- Research on Leishmaniasis Studies
Singapore Centre for Environmental Life Sciences Engineering
2017-2025
Nanyang Technological University
2017-2025
Genome Institute of Singapore
2023-2025
Czech Academy of Sciences, Institute of Molecular Genetics
2008-2023
University of Liège
2010-2021
Czech Academy of Sciences
2006-2013
Charles University
2008-2009
Abstract The underrepresentation of non-Europeans in human genetic studies so far has limited the diversity individuals genomic datasets and led to reduced medical relevance for a large proportion world’s population. Population-specific reference genome as well genome-wide association diverse populations are needed address this issue. Here we describe pilot phase GenomeAsia 100K Project. This includes whole-genome sequencing dataset from 1,739 219 population groups 64 countries across Asia....
The atmosphere is vastly underexplored as a habitable ecosystem for microbial organisms. In this study, we investigated 795 time-resolved metagenomes from tropical air, generating 2.27 terabases of data. Despite only 9 to 17% the generated sequence data currently being assignable taxa, air harbored diversity that rivals complexity other planetary ecosystems. airborne organisms followed clear diel cycle, possibly driven by environmental factors. Interday taxonomic exceeded day-to-day and...
The troposphere constitutes the final frontier of global ecosystem research due to technical challenges arising from its size, low biomass, and gaseous state. Using a vertical testing array comprising meteorological tower aircraft, we conducted synchronized measurements parameters airborne biomass ( n = 480) in air column up 3,500 m. taxonomic analysis metagenomic data revealed differing patterns microbial community composition with respect time day height above ground. temporal spatial...
Abstract Investigation of the microbial ecology terrestrial, aquatic and atmospheric ecosystems requires specific sampling analytical technologies, owing to vastly different biomass densities typically encountered. In particular, ultra-low nature air presents an inherent challenge that is confounded by temporal fluctuations in community structure. Our pipeline advances field bioaerosol research significantly reducing times from days/weeks/months minutes/hours, while maintaining ability...
We propose a minimal protocol for exhaustive genome-wide association interaction analysis that involves screening epistasis over large-scale genomic data combining strengths of different methods and statistical tools. The steps this are illustrated on real-life application Alzheimer's disease (AD) (2259 patients 6017 controls from France). Particularly, in the we identified AD-associated interacting SNPs-pair chromosome 6q11.1 (rs6455128, KHDRBS2 gene) 13q12.11 (rs7989332, CRYL1 (p = 0.006,...
In Genome-Wide Association Studies (GWAS), the concept of linkage disequilibrium is important as it allows identifying genetic markers that tag actual causal variants. Interaction (GWAIS), similar principles hold for pairs However, Linkage Disequilibrium (LD) may also interfere with detection genuine epistasis signals in there be complete confounding between Gametic Phase (GPD) and interaction. GPD involve unlinked markers, even residing on different chromosomes. Often eliminated GWAIS, via...
Research in epistasis or gene-gene interaction detection for human complex traits has grown over the last few years. It been marked by promising methodological developments, improved translation efforts of statistical to biological and attempts integrate different omics information sources into screening enhance power. The quest interactions poses severe multiple-testing problems. In this context, maxT algorithm is one technique control false-positive rate. However, memory needed rises...
Genome sequencing of 1537 individuals from 139 ethnic groups reveals the genetic characteristics understudied populations in North Asia and South America. Our analysis demonstrates that West Siberian ancestry, represented by Kets Nenets, contributed to ancestry most populations. Beringians, including Koryaks, Inuit, Luoravetlans, exhibit adaptation Arctic climate, medically relevant variants. In America, early migrants split into four groups—Amazonians, Andeans, Chaco Amerindians,...
Identifying gene-gene interactions or gene-environment in studies of human complex diseases remains a big challenge genetic epidemiology. An additional challenge, often forgotten, is to account for important lower-order effects. These may hamper the identification genuine epistasis. If effects contribute variance trait, identified statistical simply be due signal boost these In this study, we restrict attention quantitative traits and bi-allelic SNPs as markers. Moreover, our interaction...
Abstract Here, we describe taxonomical composition, as well seasonal and diel dynamics of airborne microbial communities in West Siberia. A total 78 biomass samples from 39 time intervals were analysed, within a temperature range 48 °C (26 to − 22 °C). We observed 5–170-fold decrease DNA yield extracted the winter compared summer, nevertheless, yielding sufficient material for metagenomic analysis. The included Actinobacteria Proteobacteria, Ascomycota Basidiomycota fungi major components,...
Applying a statistical method implies identifying underlying (model) assumptions and checking their validity in the particular context. One of these contexts is association modeling for epistasis detection. Here, depending on technique used, violation model may result increased type I error, power loss, or biased parameter estimates. Remedial measures violated conditions include data transformation selecting more relaxed testing strategy. Model-Based Multifactor Dimensionality Reduction...
Abstract Background In genome-wide association studies the extent and impact of confounding due to population structure have been well recognized. Inadequate handling such is likely lead spurious associations, hampering replication, identification causal variants. Several strategies developed for protecting associations against confounding, most popular one based on Principal Component Analysis. contrast, in gene-gene interaction epistasis are much less investigated understood. particular,...
Over the years, a more prominent role has been given to gene–gene interaction (epistasis) detection, in view of precision medicine and hunt for novel drug targets biomarkers complex diseases. Acknowledging data complexity as embodied by epistasis potentially increases power genome-wide association studies (GWAS) may reveal relevant biological biochemical pathways previously undetected. Although confounding GWAS due shared genetic ancestry well recognized, extent impact such is much less...
ABSTRACT Bacillus altitudinis strain SGAir0031 ( Firmicutes ) was isolated from tropical air samples collected in Singapore. Its genome assembled using short reads and single-molecule real-time sequencing, comprising one chromosome with 3.81 Mb plasmid 32 kb. The consists of 3,820 protein-coding genes, 81 tRNAs, 24 rRNAs.
Successful searching for epistasis is much challenging, which generally requires very large sample sizes and/or dense marker information. We exploited the largest Crohn's disease (CD) dataset (18,000 cases + 34,000 controls) and ulcerative colitis (UC) (14,000 to date. Leveraging its information size of this IBD dataset, we employed a two-step approach exhaustively search epistasis. detected abundant genome-wide significant (p < 1 × 10-13) epistatic signals, all within MHC region. These...
Atopy is a predisposition to hyperproduction of immunoglobulin E (IgE) against common environmental allergens. It often associated with development allergic diseases such as asthma, rhinitis, and dermatitis. Production IgE influenced by genetic factors. In spite progress in the study heredity atopy, mechanisms regulation have not yet been completely elucidated. The analysis complex traits can benefit considerably from integration human mouse genetics. Previously, we mapped IgE-controlling...
Leishmaniasis, a disease caused by parasites of Leishmania spp., endangers more than 1 billion people living in endemic countries and has three clinical forms: cutaneous, mucocutaneous, visceral. Understanding individual differences susceptibility to infection heterogeneity its pathology is largely lacking. Different mouse strains show broad heterogeneous range manifestations such as skin lesions, splenomegaly, hepatomegaly, increased serum levels immunoglobulin E several cytokines....