Warren Cheung
A5043567132- Epigenetics and DNA Methylation
- Genomics and Rare Diseases
- Cancer-related gene regulation
- Genetic Syndromes and Imprinting
- Genetic Associations and Epidemiology
- Genomic variations and chromosomal abnormalities
- Genomics and Phylogenetic Studies
- Birth, Development, and Health
- RNA modifications and cancer
- Bioinformatics and Genomic Networks
- Image Retrieval and Classification Techniques
- Genetics, Bioinformatics, and Biomedical Research
- Immune Cell Function and Interaction
- Respiratory viral infections research
- Advanced Image and Video Retrieval Techniques
- Biomedical Text Mining and Ontologies
- RNA and protein synthesis mechanisms
- Nutrition, Genetics, and Disease
- Computational Geometry and Mesh Generation
- CRISPR and Genetic Engineering
- Antimicrobial Peptides and Activities
- vaccines and immunoinformatics approaches
- Inflammasome and immune disorders
- IL-33, ST2, and ILC Pathways
- Health, Environment, Cognitive Aging
Children's Mercy Hospital
2019-2025
National Research Council Canada
2024
McGill Genome Centre
2024
McGill University
2015-2024
Mercy Research
2021-2024
Virginia Tech
2024
Mercy Hospital
2019-2022
University of British Columbia
2003-2021
Pacific Biosciences (United States)
2021
University of Missouri–Kansas City
2021
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics medicine. We carried out high-resolution genetic, epigenetic, transcriptomic profiling three immune cell types (CD14+ monocytes, CD16+ neutrophils, naive CD4+ T cells) from up 197 individuals. assess, quantitatively, relative cis-genetic transcription evaluate their impact as potential sources confounding epigenome-wide association studies. Further, we...
Abstract Lys-27-Met mutations in histone 3 genes (H3K27M) characterize a subgroup of deadly gliomas and decrease genome-wide H3K27 trimethylation. Here we use primary H3K27M tumor lines isogenic CRISPR-edited controls to assess effects vitro vivo. We find that whereas H3K27me3 H3K27me2 are normally deposited by PRC2 across broad regions, their deposition is severely reduced H3.3K27M cells. unable spread from large unmethylated CpG islands, while can be outside these high-affinity sites but...
The rise of antibiotic resistant pathogens is one the most pressing global health issues. Discovery new classes antibiotics has not kept pace; agents often suffer from cross-resistance to existing similar structure. Short, cationic peptides with antimicrobial activity are essential host defenses many organisms and represent a promising class antimicrobials. This paper reports successful in silico screening for potent using combination QSAR machine learning techniques. On basis initial...
We propose the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">n</i> -dimensional scale invariant feature transform ( -SIFT) method for extracting and matching salient features from scalar images of arbitrary dimensionality, compare this method's performance to other related features. The proposed extend concepts used 2-D in computer vision SIFT technique distinctive apply dimensionality through use hyperspherical coordinates gradients...
Abstract The incidence of type 1 diabetes (T1D) has substantially increased over the past decade, suggesting a role for non-genetic factors such as epigenetic mechanisms in disease development. Here we present an epigenome-wide association study across 406,365 CpGs 52 monozygotic twin pairs discordant T1D three immune effector cell types. We observe substantial enrichment differentially variable CpG positions (DVPs) twins when compared with their healthy co-twins and healthy, unrelated...
Abstract Here we present the Transcription Factor Encyclopedia (TFe), a new web-based compendium of mini review articles on transcription factors (TFs) that is founded principles open access and collaboration. Our consortium over 100 researchers has collectively contributed 130 pertinent human, mouse rat TFs. Notable features TFe website include high-quality PDF generator web API for programmatic data retrieval. aims to rapidly educate scientists about TFs they encounter through delivery...
CpG methylation variation is involved in human trait formation and disease susceptibility. Analyses within populations have been biased towards CpG-dense regions through the application of targeted arrays. We generate whole-genome bisulfite sequencing data for approximately 30 adipose blood samples from monozygotic dizygotic twins characterization non-genetic genetic effects at single-site resolution. Purely invariable CpGs display a bimodal distribution with enrichment unmethylated...
PurposeThis study aimed to provide comprehensive diagnostic and candidate analyses in a pediatric rare disease cohort through the Genomic Answers for Kids program.MethodsExtensive of 960 families with suspected genetic disorders included short-read exome sequencing genome (srGS); PacBio HiFi long-read (HiFi-GS); variant calling single nucleotide variants (SNV), structural (SV), repeat variants; machine-learning prioritization. Structured phenotypes, prioritized variants, pedigrees were...
Abstract Rare DNA alterations that cause heritable diseases are only partially resolvable by clinical next-generation sequencing due to the difficulty of detecting structural variation (SV) in all genomic contexts. Long-read, high fidelity genome (HiFi-GS) detects SVs with increased sensitivity and enables assembling personal graph genomes. We leverage standard reference genomes, public assemblies ( n = 94) a large collection HiFi-GS data from rare disease program (Genomic Answers for Kids,...
We present a fully automated multimodal medical image matching technique. Our method extends the concepts used in computer vision SIFT technique for extracting and distinctive scale invariant features 2D scalar images to of arbitrary dimensionality. This extension involves using hyperspherical coordinates gradients multidimensional histograms create feature vectors. These were successfully applied determine accurate point correspondence between pairs (3D) dynamic volumetric data (3D+time).
Pathogens resistant to available drug therapies are a pressing global health problem. Short, cationic peptides represent novel class of agents that have lower rates resistance than derivatives current antibiotics. Previously, we created software system utilizing artificial neural networks were trained on quantitative structure‐activity relationship descriptors calculated for total 1400 synthetic which antibacterial activity was determined. Using the system, correctly identified additional...
The functional impact of genetic variation has been extensively surveyed, revealing that changes correlated to phenotypes lie mostly in non-coding genomic regions. Studies have linked allele-specific gene expression, DNA methylation, and histone marks but these investigations only carried out a limited set samples. We describe large-scale coordinated study allelic non-allelic effects on mark deposition, detecting the interrelations between epigenetic features at unprecedented resolution. use...
Abstract The extravillous trophoblast cell lineage is a key feature of placentation and successful pregnancy. Knowledge transcriptional regulation driving development limited. Here, we map the transcriptome epigenome landscape as well chromatin interactions human stem cells their transition into cells. We show that integrating accessibility, long-range interactions, transcriptomic, transcription factor binding motif enrichment enables identification factors regulatory mechanisms critical for...
Long-read HiFi genome sequencing allows for accurate detection and direct phasing of single nucleotide variants, indels, structural variants. Recent algorithmic development enables simultaneous CpG methylation analysis regulatory element activity directly in reads. We present a comprehensive haplotype resolved 5-base dataset from rare disease cohort 276 samples 152 families to identify (~0.5%) hypermethylation events. find that 80% these events are allele-specific predicted cause loss...
The reaction norm linking rearing temperature and size in Drosophila melanogaster results progressively larger flies as the is lowered from 30°C to 18°C, but it has remained unclear whether this phenotypic plasticity part of an adaptive response temperature. We found that female D. reared adulthood at 18°C versus 25°C showed a 12% increase dry weight. Measurements fecundity these two types fly change had no effect on lifetime fecundity, regardless adult test Thus breaks usual positive...
CblX (MIM309541) is an X-linked recessive disorder characterized by defects in cobalamin (vitamin B12) metabolism and other developmental defects. Mutations HCFC1, a transcriptional co-regulator which interacts with multiple transcription factors, have been associated cblX. HCFC1 regulates via the regulation of MMACHC expression through its interaction THAP11, THAP domain-containing factor. The HCFC1/THAP11 complex potentially genes involved diverse cellular functions including cell cycle,...
Abstract Background Children of aged fathers are at a higher risk developing mental disorders. Alterations in sperm DNA methylation have been implicated as potential cause. However, age-dependent modifications the germ cells’ epigenome remain poorly understood. Our objective was to assess profile human spermatozoa during aging. Results We used high throughput, customized methylC-capture sequencing (MCC-seq) approach characterize dynamic from 94 fertile and infertile men, who were categorized...
Abstract Tandem repeat (TR) variation is associated with gene expression changes and over 50 rare monogenic diseases. Recent advances in sequencing have enabled accurate, long reads that can characterize the full-length sequence methylation profile of TRs. However, despite these technology, computational methods to fully tandem repeats across genome do not exist. To address this gap, we introduce tools for genotyping (TRGT), visualization an accompanying TR database. TRGT accurately resolves...
Structural variants (SVs) are omnipresent in human DNA, yet their genotype and methylation statuses rarely characterized due to previous limitations genome assembly detection of modified nucleotides. Also, the extent which SVs act as quantitative trait loci (SV-mQTLs) is largely unknown. Here, we generated a pangenome graph summarizing 782 de novo assemblies obtained from Genomic Answers for Kids, capturing 14.6 million CpG dinucleotides that absent CHM13v2 reference (SV-CpGs), thus...