A5089176448- T-cell and B-cell Immunology
- Immune Cell Function and Interaction
- Monoclonal and Polyclonal Antibodies Research
- vaccines and immunoinformatics approaches
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- CAR-T cell therapy research
- Gene expression and cancer classification
- Evolution and Genetic Dynamics
- Single-cell and spatial transcriptomics
- Gaussian Processes and Bayesian Inference
- Immunotherapy and Immune Responses
- Probabilistic and Robust Engineering Design
- Markov Chains and Monte Carlo Methods
- Precipitation Measurement and Analysis
- Hydrology and Drought Analysis
- Influenza Virus Research Studies
- Atherosclerosis and Cardiovascular Diseases
- Genetic factors in colorectal cancer
- Cancer Genomics and Diagnostics
- Renal Transplantation Outcomes and Treatments
University of Washington
2017-2022
Fred Hutch Cancer Center
2018-2022
Seattle University
2019
Probabilistic models of adaptive immune repertoire sequence distributions can be used to infer the expansion cells in response stimulus, differentiate genetic from environmental factors that determine sharing, and evaluate suitability various target sequences for stimulation via vaccination. Classically, these are defined terms a probabilistic V(D)J recombination model which is sometimes combined with selection model. In this paper we take different approach, fitting variational autoencoder...
Abstract Summary Antibody repertoires reveal insights into the biology of adaptive immune system and empower diagnostics therapeutics. There are currently multiple tools available for annotation antibody sequences. All downstream analyses such as choosing lead drug candidates depend on correct these sequences; however, a thorough comparison performance has not been investigated. Here, we benchmark commonly used immunoinformatic tools, i.e. IMGT/HighV-QUEST, IgBLAST MiXCR, in terms...
The adaptive immune system generates an incredible diversity of antigen receptors for B and T cells to keep dangerous pathogens at bay. DNA sequences coding these arise by a complex recombination process followed series productivity-based filters, as well affinity maturation cells, giving considerable the circulating pool receptor sequences. Although datasets hold promise medical public health applications, structure resulting repertoire sequencing (AIRR-seq) makes analysis difficult. In...
Abstract Stochastic precipitation generators (SPGs) produce synthetic data and are frequently used to generate inputs for physical models throughout many scientific disciplines. Especially large sets, statistical parameter estimation is difficult due the high dimensionality of likelihood function. We propose techniques estimate SPG parameters spatiotemporal occurrence based on an emerging set methods called Approximate Bayesian computation (ABC), which bypass evaluation a Our model employs...
The complexity of entire T cell receptor (TCR) repertoires makes their comparison a difficult but important task. Current methods TCR repertoire can incur high loss distributional information by considering overly simplistic sequence- or repertoire-level characteristics. Optimal transport form suitable approach for such given some distance metric between values in the sample space, with appealing theoretical and computational properties. In this paper we introduce nonparametric to comparing...
Abstract The adaptive immune system generates an incredible diversity of antigen receptors for B and T cells to keep dangerous pathogens at bay. DNA sequences coding these arise by a complex recombination process followed series productivity-based filters, as well affinity maturation cells, giving considerable the circulating pool receptor sequences. Although datasets hold promise medical public health applications, structure resulting repertoire sequencing (AIRR-seq) makes analysis...
BCR sequences diversify through mutations introduced by purpose-built cellular machinery. A recent paper has concluded that a "templated mutagenesis" process is major contributor to somatic hypermutation and therefore Ig diversification in mice humans. In this proposed process, the locus are copying short segments from other genes. If true, would overturn decades of research on B cell require complete rewrite computational methods analyze data for these species. paper, we re-evaluate...
Abstract Mutations that compromise mismatch repair (MMR) or DNA polymerase ε δ exonuclease domains produce mutator phenotypes capable of fueling cancer evolution. Here, we investigate how combined defects in these pathways expands genetic heterogeneity cells the budding yeast, Saccharomyces cerevisiae , using a single-cell resolution approach tallies all mutations arising from individual divisions. The distribution replication errors present mother after initial S-phase was broader than...
Probabilistic modeling is fundamental to the statistical analysis of complex data. In addition forming a coherent description data-generating process, probabilistic models enable parameter inference about given data sets. This procedure well-developed in Bayesian perspective, which one infers probability distributions describing what extent various possible parameters agree with this paper we motivate and review for adaptive immune receptor repertoire then describe progress prospects future...
B cell receptor sequences diversify through mutations introduced by purpose-built cellular machinery. A recent paper has concluded that a "templated mutagenesis" process is major contributor to somatic hypermutation, and therefore immunoglobulin diversification, in mice humans. In this proposed process, the locus are copying short segments from other genes. If true, would overturn decades of research on require complete re-write computational methods analyze data for these species. paper, we...