A5010334833- Advanced Proteomics Techniques and Applications
- Metabolomics and Mass Spectrometry Studies
- Mass Spectrometry Techniques and Applications
- Statistical Methods and Inference
- Advanced Statistical Methods and Models
- Renal Transplantation Outcomes and Treatments
- Asthma and respiratory diseases
- Genetic Associations and Epidemiology
- Transplantation: Methods and Outcomes
- Advanced biosensing and bioanalysis techniques
- Advanced Biosensing Techniques and Applications
- Statistical Distribution Estimation and Applications
- Molecular Biology Techniques and Applications
- Signaling Pathways in Disease
- Metabolism and Genetic Disorders
- Cell Image Analysis Techniques
- Advanced Causal Inference Techniques
- Machine Learning in Bioinformatics
- Multiple Sclerosis Research Studies
- Viral Infections and Immunology Research
- Nosocomial Infections in ICU
- Sepsis Diagnosis and Treatment
- Hemoglobinopathies and Related Disorders
- IL-33, ST2, and ILC Pathways
- Complement system in diseases
University of British Columbia
2010-2022
Prevention of Organ Failure
2010-2019
Universidad Torcuato Di Tella
2019
University of British Columbia Hospital
2012-2014
University of Victoria
2012
Genome British Columbia
2012
Vancouver Coastal Health
2007
Vancouver Coastal Health Research Institute
2007
Providence Health Care
2007
BackgroundInter-individual variability during sepsis limits appropriate triage of patients. Identifying, at first clinical presentation, gene expression signatures that predict subsequent severity will allow clinicians to identify the most at-risk groups patients and enable antibiotic use.MethodsBlood RNA-Seq data were collected from 348 in four emergency rooms (ER) one intensive-care-unit (ICU), 44 healthy controls. Gene profiles analyzed using machine learning mining clinically relevant...
A highly‐multiplexed MRM ‐based assay for determination of cardiovascular disease ( CVD ) status and classification has been developed clinical research. high‐flow system using ultra‐high performance LC an gilent 6490 triple quadrupole mass spectrometer, equipped with ion funnel, provided ease use increased the robustness assay. The uses 135 stable isotope‐labeled peptide standards quantitation 67 putative biomarkers in tryptic digests whole plasma a 30‐min Eighty‐five analyses same sample...
Acute graft rejection is an important clinical problem in renal transplantation and adverse predictor for long term survival. Plasma biomarkers may offer option post-transplant monitoring permit timely effective therapeutic intervention to minimize damage. This case-control discovery study (n = 32) used isobaric tagging relative absolute protein quantification (iTRAQ) technology quantitate plasma concentrations precise cohorts of patients with without biopsy-confirmed acute (BCAR). samples...
Recent technical advances in the field of quantitative proteomics have stimulated a large number biomarker discovery studies various diseases, providing avenues for new treatments and diagnostics. However, inherent challenges limited successful translation candidate biomarkers into clinical use, thus highlighting need robust analytical methodology to transition from implementation. We developed an end-to-end computational proteomic pipeline studies. At stage, emphasizes different aspects...
In large-scale quantitative proteomic studies, scientists measure the abundance of thousands proteins from human proteome in search novel biomarkers for a given disease. Penalized regression estimators can be used to identify potential among large set molecular features measured. Yet, performance and statistical properties these depend on loss penalty functions define them. Motivated by real plasma study, we propose new class penalized robust based elastic net penalty, which tuned keep...
Abstract Motivation: The process of producing microarray data involves multiple steps, some which may suffer from technical problems and seriously damage the quality data. Thus, it is essential to identify those arrays with low quality. This article addresses two questions: (1) how assess a dataset using measures provided in control (QC) reports; (2) possible sources problems. Results: We propose novel multivariate approach evaluate an array that examines ‘Mahalanobis distance’ its...
The allergen inhalation challenge is used in clinical trials to test the efficacy of new treatments attenuating late-phase asthmatic response (LAR) and associated airway inflammation subjects with allergic asthma. However, not all asthma develop LAR after inhalation. Blood-based transcriptional biomarkers that can identify such individuals may help subject recruitment for as well provide novel molecular insights.To blood-based biomarker panels predict an individual's challenge.We applied RNA...
Instrumental variables estimators are designed to provide consistent parameter estimates for linear regression models when some covariates correlated with the error term. We propose a new robust instrumental estimator (RIV) which is natural robustification of ordinary (OIV). Specifically, we construct RIV using multivariate location and scatter S-estimator robustify solution estimating equations that define OIV. computationally inexpensive readily available applications through R-library...
A highly-multiplexed LC-ESI-multiple reaction monitoring-MS-based assay is developed for the identification of coronary artery disease (CAD) biomarkers in human plasma.The used to measure 107 stable isotope labeled peptide standards and native peptides from 64 putative cardiovascular diseases tryptic digests plasma subjects with (n = 70) without 45) angiographic evidence CAD no subsequent mortality during follow-up.Extensive computational statistical analysis reveals six proteins associated...
Purpose This proteomics study was designed to determine the utility of i TRAQ MALDI ‐ TOF / technology compare plasma samples from carefully phenotyped mild, atopic asthma subjects undergoing allergen inhalation challenge. Experimental design Eight adult with allergic (four early responders (ERs) and four dual (DRs)) participated in Blood were collected prior 2 h after Sixteen (two per subject), technical replicates, pooled controls analyzed using . Technical validation performed LC MRM MS...
Abstract The continuous evolution of metabolomics over the past two decades has stimulated search for metabolic biomarkers many diseases. Metabolomic data measured from urinary samples can provide rich information biological events triggered by organ rejection in pediatric kidney transplant recipients. With additional validation, markers be used to build clinically useful diagnostic tools. However, there are methodological steps ranging processing modeling that influence performance...
The quantitation of proteins using shotgun proteomics has gained popularity in the last decades, simplifying sample handling procedures, removing extensive protein separation steps and achieving a relatively high throughput readout. process starts with digestion mixture into peptides, which are then separated by liquid chromatography sequenced tandem mass spectrometry (MS/MS). At end workflow, recovering identity originally present is often difficult ambiguous process, because more than one...
Abstract We study the benefit of exploiting gene–environment independence (GEI) assumption for inferring joint effect genotype and environmental exposure on disease risk in a case–control study. By transforming problem into constrained maximum likelihood estimation we derive asymptotic distribution estimator (MLE) under GEI (MLE‐GEI) closed form. Our approach uncovers transparent explanation efficiency gained by more general settings, thus bridging an important gap existing literature....
Abstract Diffuse large B-cell lymphoma (DLBCL) is the most common subtype worldwide, accounting for 40% of all non-Hodgkin lymphomas. DLBCL presents as an aggressive disease requiring immediate treatment. Although significant improvement in outcome has been achieved, ~40% patients still experience treatment failure. Here, we characterized recurrent genetic alterations and transcriptomic signatures diagnostic biopsies from a population registry-based cohort 347 with de novo uniformly treated...