A5068542468- Metabolomics and Mass Spectrometry Studies
- Plant Pathogens and Fungal Diseases
- Bioinformatics and Genomic Networks
- Advanced Proteomics Techniques and Applications
- Gene expression and cancer classification
- Imbalanced Data Classification Techniques
- Artificial Intelligence in Healthcare
- Advanced biosensing and bioanalysis techniques
- Plant Disease Resistance and Genetics
- Immune Cell Function and Interaction
- Computational Drug Discovery Methods
- Antifungal resistance and susceptibility
- Mass Spectrometry Techniques and Applications
- Machine Learning and Data Classification
- Plant-Microbe Interactions and Immunity
- Mycotoxins in Agriculture and Food
- RNA and protein synthesis mechanisms
- RNA Interference and Gene Delivery
- Extracellular vesicles in disease
- Single-cell and spatial transcriptomics
- IoT and GPS-based Vehicle Safety Systems
- Health, Environment, Cognitive Aging
- Gastrointestinal motility and disorders
- Adipokines, Inflammation, and Metabolic Diseases
- Distributed Sensor Networks and Detection Algorithms
National Research Council Canada
2017-2024
California State University, Fullerton
2024
University of Toronto
2011-2016
Yeasty HIPHOP In order to identify how chemical compounds target genes and affect the physiology of cell, tests perturbations that occur when treated with a range pharmacological chemicals are required. By examining haploinsufficiency profiling (HIP) homozygous (HOP) chemogenomic platforms, Lee et al. (p. 208 ) analyzed response yeast thousands different small molecules, genetic, proteomic, bioinformatic analyses. Over 300 were identified targeted 121 within 45 cellular signature networks....
Abstract NKT cells are unconventional T that respond to self and microbe-derived lipid glycolipid Ags presented by the CD1d molecule. Invariant (iNKT) influence immune responses in numerous diseases. Although only a few studies have examined their role during intestinal inflammation, it appears iNKT protect from Th1-mediated inflammation but exacerbate Th2-mediated inflammation. Studies using cell–deficient mice chemically induced dextran sodium sulfate (DSS) colitis led inconsistent...
The microbiome shapes diverse facets of human biology and disease, with the importance fungi only beginning to be appreciated. Microbial communities infiltrate anatomical sites as respiratory tract healthy humans those diseases such cystic fibrosis, where chronic colonization infection lead clinical decline. Although are frequently recovered from fibrosis patient sputum samples have been associated deterioration lung function, understanding species population dynamics remains in its infancy....
Invasive fungal infections are an increasingly important cause of human morbidity and mortality. We generated a next-generation sequencing (NGS)-based method designed to detect wide range fungi applied it analysis the microbiome (mycobiome) lung during infection. Internal transcribed spacer 1 (ITS1) amplicon custom pipeline detected 96% species from three mock communities comprised potential pathogens with good recapitulation expected distributions (Pearson correlation coefficients r = 0.63,...
Glioblastoma (GBM) is one of the most aggressive cancers central nervous system. Despite current advances in non-invasive imaging and advent novel therapeutic modalities, patient survival remains very low. There a critical need for development effective biomarkers GBM diagnosis monitoring. Extracellular vesicles (EVs) produced by tumors have been shown to play an important role cellular communication modulation tumor microenvironment. As GBM-derived EVs contain specific "molecular...
Genome-wide screening in human and mouse cells using RNA interference open reading frame over-expression libraries is rapidly becoming a viable experimental approach for many research labs. There are variety of gene expression modulation commercially available, however, detailed validated protocols as well the reagents necessary deconvolving genome-scale screens these lacking. As solution, we designed comprehensive platform highly multiplexed functional genetic human, yeast popular,...
Delirium is an acute change in attention and cognition occurring ~ 65% of severe SARS-CoV-2 cases. It also common following surgery indicator brain vulnerability risk for the development dementia. In this work we analyzed underlying role metabolism delirium-susceptibility postoperative setting using metabolomic profiling cerebrospinal fluid blood taken from same patients prior to planned orthopaedic surgery. Distance correlation analysis Random Forest (RF) feature selection were used...
Abstract Motivation There is a need for easily accessible implementations that measure the strength of both linear and non-linear relationships between metabolites in biological systems as an approach data-driven network development. While multiple tools implement Pearson Spearman methods, there are no such assess distance correlation. Results We present here SIgned Distance COrrelation (SiDCo). SiDCo GUI platform calculation correlation omics data, measuring dependencies variables, well...
Chemical biology, the interfacial discipline of using small molecules as probes to investigate is a powerful approach developing specific, rapidly acting tools that can be applied across organisms. The single-celled alga Chlamydomonas reinhardtii an excellent model system because its photosynthetic ability, cilia-related motility and simple genetics. We report results automated fitness screen 5,445 subsequent assays on motility/phototaxis photosynthesis. Cheminformatic analysis revealed...
Abstract Classification of tumors into subtypes can inform personalized approaches to treatment including the choice targeted therapies. The two most common lung cancer histological subtypes, adenocarcinoma and squamous cell carcinoma, have been previously divided transcriptional using microarray data, corresponding signatures were subsequently used classify RNA-seq data. Cross-platform unsupervised classification facilitates identification robust by combining vast amounts publicly available...
Diseases of agricultural crops caused by fungi have devastating economic and health effects. Fusarium head blight ( FHB ) is one the most damaging diseases wheat other small grain cereals. reduces yield while also affecting food supply safety through deposition toxins (mycotoxins/phytotoxins). Control growth toxin accumulation in grains remain major challenges. While ultimate goal battle against development resistant varieties, actual use fully plants that preclude any need for treatment...
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The application of new proteomics and genomics technologies support a view in which few drugs act solely by inhibiting single cellular target. Indeed, drug activity is modulated complex, often incompletely understood mechanisms. Therefore, efforts to decipher mode action through genetic perturbation such as RNAi typically yields "hits" that fall into several categories. Of particular interest the present study, we aimed characterize secondary activities on cells. Inhibiting known target can...
Abstract In differential gene expression data analysis, one objective is to identify groups of co-expressed genes from a large dataset detect the association between such group and phenotypic trait. This often done through clustering approach, as k -means or bipartition hierarchical clustering, based on particular similarity measures in grouping process. dataset, itself an innate attribute that can be used feature extraction For example, consisting multiple treatments versus their controls,...
Abstract Motivation Class imbalance, or unequal sample sizes between classes, is an increasing concern in machine learning for metabolomic and lipidomic data mining, which can result overfitting the over-represented class. Numerous methods have been developed handling class but they are not readily accessible to users with limited computational experience. Moreover, there no resource that enables easily evaluate effect of different over-sampling algorithms. Results METAbolomics Balancing...
Abstract Dementia with Lewy bodies (DLB) is a common form of dementia known genetic and environmental interactions. However, the underlying epigenetic mechanisms which reflect these gene-environment interactions are poorly studied. Herein, we measure genome-wide DNA methylation profiles post-mortem brain tissue (Broadmann area 7) from 15 pathologically confirmed DLB brains compare them 16 cognitively normal controls using Illumina MethylationEPIC arrays. We identify 17 significantly...
Abstract Motivation Bioinformatic tools capable of annotating, rapidly and reproducibly, large, targeted lipidomic datasets are limited. Specifically, few programs enable high-throughput peak assessment liquid chromatography–electrospray ionization tandem mass spectrometry data acquired in either selected or multiple reaction monitoring modes. Results We present here Bayesian Annotations for Targeted Lipidomics, a Gaussian naïve Bayes classifier lipidomics that annotates identities according...
Abstract Motivation Missing values are often unavoidable in modern high-throughput measurements due to various experimental or analytical reasons. Imputation, the process of replacing missing a dataset with estimated values, plays an important role multivariate and machine learning analyses. Three missingness patterns have been conceptualized: completely at random (MCAR), (MAR), not (MNAR). Each describes unique dependencies between observed data. As result, optimal imputation method for...
Abstract Motivation Missing values are prevalent in high-throughput measurements due to various experimental or analytical reasons. Imputation, the process of replacing missing a dataset with estimated values, plays an important role multivariate and machine learning analyses. The three missingness patterns, including completely at random, not describe unique dependencies between observed data. optimal imputation method for each depends on type data, cause missingness, nature relationships...
Traffic accidents remain a leading cause of death globally, with the World Health Organization reporting approximately one million fatalities annually. Drowsy driving significantly contributes to these accidents, dramatically increasing crash risks. This research addresses this critical issue by proposing driver drowsiness detection system that leverages facial recognition technology and machine learning. The continuously analyses driver's features identify signs fatigue. Specifically, it...
Abstract Motivation Unsupervised data projection for the determination of trends in data, visualization multidimensional a reduced dimension space or feature reduction through combination is major step mining. Methods such as Principal Component Analysis t-Distribution Stochastic Neighbor Embedding are regularly used one first steps computational biology omics investigation. However, significance separation sample groups by these methods generally relies on visual assessment. User-friendly...
Abstract Motivation Bioinformatic tools capable of annotating, rapidly and reproducibly, large, targeted lipidomic datasets are limited. Specifically, few programs enable high-throughput peak assessment liquid chromatography-electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) data acquired in either selected or multiple reaction monitoring (SRM MRM) modes. Results We present here Bayesian Annotations for Targeted Lipidomics (BATL), a Gaussian naïve Bayes classifier lipidomics...