A5022202018- Bioinformatics and Genomic Networks
- Immunotherapy and Immune Responses
- SARS-CoV-2 and COVID-19 Research
- Monoclonal and Polyclonal Antibodies Research
- vaccines and immunoinformatics approaches
- Biomedical Text Mining and Ontologies
- Advanced Proteomics Techniques and Applications
- Cancer Immunotherapy and Biomarkers
- COVID-19 Clinical Research Studies
- Gene expression and cancer classification
- Systemic Lupus Erythematosus Research
- T-cell and B-cell Immunology
- Genetics, Bioinformatics, and Biomedical Research
- Metabolomics and Mass Spectrometry Studies
- Genomics and Phylogenetic Studies
- Single-cell and spatial transcriptomics
- CAR-T cell therapy research
- Machine Learning in Bioinformatics
- Viral gastroenteritis research and epidemiology
- Immune Cell Function and Interaction
- Identification and Quantification in Food
- Molecular Biology Techniques and Applications
- Statistical Methods in Clinical Trials
- Cell Adhesion Molecules Research
- Cancer Genomics and Diagnostics
LabGenius (United Kingdom)
2024
Serimmune (United States)
2020-2022
Yale University
2021
Translational Research Informatics Center (Japan)
2020
Institute of Infection and Immunity
2020
Stanford University
2013-2019
Dalian University of Technology
2017
Seattle Children's Hospital
2013-2016
Health Alliance International
2013
Seattle University
2011-2013
To find and validate generalizable sepsis subtypes using data-driven clustering.We used advanced informatics techniques to pool data from 14 bacterial transcriptomic datasets eight different countries (n = 700).Retrospective analysis.Persons admitted the hospital with sepsis.None.A unified clustering analysis across discovery revealed three subtypes, which, based on functional analysis, we termed "Inflammopathic, Adaptive, Coagulopathic." We then validated these in nine independent five...
Abstract We found tremendous inequality across gene and protein annotation resources. observed that this bias leads biomedical researchers to focus on richly annotated genes instead of those with the strongest molecular data. advocate reduce these biases by pursuing data-driven hypotheses.
Abstract Gene Ontology (GO) enrichment analysis is ubiquitously used for interpreting high throughput molecular data and generating hypotheses about underlying biological phenomena of experiments. However, the two building blocks this — ontology annotations evolve rapidly. We gene signatures derived from 104 disease analyses to systematically evaluate how results were affected by evolution GO over a decade. found low consistency between obtained with early more recent versions. Furthermore,...
Abstract In silico quantification of cell proportions from mixed-cell transcriptomics data (deconvolution) requires a reference expression matrix, called basis matrix. We hypothesize that matrices created using only healthy samples single microarray platform would introduce biological and technical biases in deconvolution. show presence such two existing matrices, IRIS LM22, irrespective deconvolution method. Here, we present immunoStates, matrix built 6160 with different disease states...
Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number hypotheses relatively small sample sizes, results whole-genome expression particular reproducible. Compared single-study analysis, gene meta-analysis can improve reproducibility by integrating data multiple studies. However, there choices designing carrying out meta-analysis. Yet, clear guidelines on best practices scarce. Here, we hypothesized...
Large numbers of mass spectrometry proteomics studies are being conducted to understand all types biological processes. The size and complexity data hinders efforts easily share, integrate, query compare the studies. Model Organism Protein Expression Database (MOPED, htttp://moped.proteinspire.org) is a new expanding resource that enables rapid browsing protein expression information from publicly available on humans model organisms. MOPED designed simplify comparison sharing for greater...
Abstract Patients with cancer are currently prioritized in coronavirus disease 2019 (COVID-19) vaccination programs globally, which includes administration of mRNA vaccines. Cytokine release syndrome (CRS) has not been reported vaccines and is an extremely rare immune-related adverse event immune checkpoint inhibitors. We present a case CRS that occurred 5 d after BTN162b2 (tozinameran)—the Pfizer-BioNTech COVID-19 vaccine—in patient colorectal on long-standing anti-PD-1 monotherapy. The was...
Life science technologies generate a deluge of data that hold the keys to unlocking secrets important biological functions and disease mechanisms. We present DEAP, Differential Expression Analysis for Pathways, which capitalizes on information about pathways identify regulatory patterns from differential expression data. DEAP makes significant improvements over existing approaches by including pathway structure discovering most differentially expressed portion pathway. On simulated data,...
As Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) continues to spread, characterization of its antibody epitopes, emerging strains, related coronaviruses, and even the human proteome in naturally infected patients can guide development effective vaccines therapies. Since traditional epitope identification tools are dependent upon pre-defined peptide sequences, they not readily adaptable diverse viral proteomes. The Serum Epitope Repertoire Analysis (SERA) platform leverages a...
T follicular helper (T
The integrative personal omics profile (iPOP) is a pioneering study that combines genomics, transcriptomics, proteomics, metabolomics and autoantibody profiles from single individual over 14-month period. observation period includes two episodes of viral infection: human rhinovirus respiratory syncytial virus. studies give an informative snapshot into the biological functioning organism. We hypothesize pathway expression levels are associated with disease status. To test this hypothesis, we...
Systemic lupus erythematosus (SLE) is a complex autoimmune disease that follows an unpredictable course and affects multiple organs tissues. We performed integrated, multicohort analysis of 7,471 transcriptomic profiles from 40 independent studies to identify robust gene expression changes associated with SLE. identified 93-gene signature (SLE MetaSignature) differentially expressed in the blood patients SLE compared healthy volunteers; distinguishes other autoimmune, inflammatory,...
Abstract In 579 COVID patients’ samples collected between March and July of 2020, we examined the effects non-synonymous mutations harbored by circulating B.1.1.7 strain on linear antibody epitope signal for spike glycoprotein nucleoprotein. At antigen level, only substantially reduced in 0.5% population. Although some reduce measured up to 6% population, these are not dominant epitopes their antigens. Given patterns observed, our data suggest that would result immune evasion a large...
The development of bispecific antibodies that bind at least two different targets relies on bringing together multiple binding domains with properties and biophysical characteristics to produce a drug-like therapeutic. These building blocks play an important role in the overall quality molecule can influence many aspects from potency specificity stability half-life. Single-domain antibodies, particularly camelid-derived variable heavy domain chain (VHH) are becoming increasingly popular...
The life sciences have entered into the realm of big data and data-enabled science, where can either empower or overwhelm. These bring challenges 5 Vs data: volume, veracity, velocity, variety, value. Both independently through our involvement with DELSA Global (Data-Enabled Life Sciences Alliance, DELSAglobal.org), Kolker Lab ( kolkerlab.org ) is creating partnerships that identify solve community needs. We specialize in solutions to complex biological challenges, as exemplified by resource...
Combining an immune checkpoint inhibitor with a tumor vaccine may modulate the system to leverage complementary mechanisms of action that lead sustained T-cell activation and potent prolonged immunotherapeutic response in metastatic castration resistant prostate cancer (mCRPC).Subjects asymptomatic or minimally symptomatic mCRPC were randomly assigned 1:1 ratio receive either atezolizumab followed by sipuleucel-T (Arm 1) 2). The primary endpoint was safety, while secondary endpoints included...
To gauge the current commitment to scientific research in United States of America (US), we compared federal funding (FRF) with US gross domestic product (GDP) and industry spending during past six decades. In order address recent globalization research, also focused on four key indicators activities: development (R&D) funding, total science engineering doctoral degrees, patents, publications. We these across three major population economic regions: US, European Union (EU) People's Republic...
Identification of the antigens associated with antibodies is vital to understanding immune responses in context infection, autoimmunity, and cancer. Discovering at a proteome scale could enable broader identification that are responsible for generating an response or driving disease state. Although targeted tests known can be straightforward, discovering using protein peptide arrays time consuming expensive. We leverage Serum Epitope Repertoire Analysis (SERA), assay based on random...