J. West

Evolutionary double-bind treatment using radiotherapy and NK cell-based immunotherapy in prostate cancer

This study combines radiotherapy and NK cell immunotherapy to exploit an evolutionary double-bind strategy in prostate cancer, showing that RT-resistant cells become more vulnerable to NK cell killing.

Droplet microfluidics for time-resolved serial crystallography

This paper develops a droplet microfluidics approach to produce uniform crystals and enable rapid micromixing for time-resolved serial crystallography.

Spatial interactions modulate tumor growth and immune infiltration

This study uses computational modeling to explore how spatial interactions between immune cells and collagen fibers influence tumor growth and immune infiltration.

Second-order effects of chemotherapy pharmacodynamics and pharmacokinetics on tumor regression and cachexia

This study examines how varying chemotherapy dose schedules affect tumor regression and cachexia, finding that high variance schedules can improve outcomes without increasing total dose.

Ribosomal protein control of hematopoietic stem cell transformation through regulation of metabolism.

This study shows that reduced RPL22 expression in hematopoietic stem cells promotes leukemia by altering metabolism and increasing lipid synthesis via Lin28b.

Adaptive therapy for ovarian cancer: An integrated approach to PARP inhibitor scheduling

This study develops an adaptive therapy protocol for PARP inhibitors by combining mathematical modeling and experiments to optimize treatment scheduling and mitigate resistance.

Games and the treatment convexity of cancer

The paper connects evolutionary game theory to cancer treatment convexity, showing how game types influence treatment response convexity and potential response discontinuities or hysteresis.

Mechanisms of SARS-CoV-2 Inactivation using UVC Laser Radiation

This study investigates the inactivation of SARS-CoV-2 using UVC laser radiation and identifies mechanisms involving RNA damage and disruption of spike protein function.

Cigarette smoke exposed airway epithelial cell-derived EVs promote pro-inflammatory macrophage activation in alpha-1 antitrypsin deficiency

This study shows that cigarette smoke-exposed airway epithelial cell-derived EVs enhance pro-inflammatory activation of AATD macrophages, increasing cytokine production and neutrophil chemoattractant release.

Tumor-immune metaphenotypes orchestrate an evolutionary bottleneck that promotes metabolic transformation

This paper presents a multiscale mathematical model of tumor-immune interactions that identifies metaphenotypes driving immune escape and metabolic transformation in cancer.

Gattaca: Base pair resolution mutation tracking for somatic evolution studies using agent-based models

Gattaca generates base-pair resolution artificial genomes to track somatic mutations in agent-based models, enabling in-silico studies comparable to human somatic evolution.

Mistic: an open-source multiplexed image t-SNE viewer

Mistic provides an open-source tool to visualize multiplexed images using t-SNE or UMAP layouts for exploratory analysis of tumor tissue ecology.

Characterization of changes in the hemagglutinin that accompanied the emergence of H3N2/1968 pandemic influenza viruses

The paper characterizes amino acid substitutions in the hemagglutinin of H3N2/1968 influenza viruses and their effects on receptor binding, stability, and replication.

Dual Dean entrainment with volume ratio modulation for efficient co-encapsulation: Extreme single-cell indexing

This paper introduces Pirouette-seq, a method for efficient single-cell co-encapsulation with improved throughput and signal-to-noise ratio.

Spatial structure impacts adaptive therapy by shaping intra-tumoral competition

This study shows how spatial structure affects adaptive therapy by influencing intra-tumoral competition between drug-sensitive and resistant cells.

Antifragile therapy

This paper introduces a mathematical framework to quantify cancer cell line fragility or antifragility to treatment variability and applies it to treatment resistance and collateral sensitivity.

IsoMaTrix: a framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations

IsoMaTrix visualizes isoclines of matrix games and quantifies uncertainty in structured populations, showing spatial configuration impacts cancer model dynamics under treatment.

Single cell RNA sequence analysis of human bone marrow samples reveals new targets for isolation of skeletal stem cells using DNA-coated gold nanoparticles

The paper uses single-cell RNA sequencing to identify new targets for isolating skeletal stem cells from human bone marrow using DNA-coated gold nanoparticles.

Spatially discrete signalling niches regulate fibroblast heterogeneity in human lung cancer

The paper identifies fibroblast subpopulations in lung cancer using single-cell RNA sequencing and shows their spatial distribution and regulation by TGF-β1 and IL-1.

The Harsh Microenvironment in Early Breast Cancer Selects for a Warburg Phenotype

The paper investigates how harsh microenvironments in early breast cancer select for a Warburg phenotype through metabolic and transcriptomic changes.

Sensory neurons sprouting is dependent on osteoclast-derived extracellular vesicles involving the activation of epidermal growth factor receptors

This study shows that osteoclast-derived extracellular vesicles promote sensory neuron sprouting and electrophysiology via EGFR activation.

Turnover modulates the need for a cost of resistance in adaptive therapy

This study investigates whether a cost of resistance is necessary for adaptive therapy to delay cancer progression, finding that cell turnover modulates this requirement depending on tumor growth conditions.

Single platelet variability governs population sensitivity and initiates intrinsic heterotypic behaviours

The paper shows that single platelet variability drives population-level sensitivity and heterotypic behaviors in platelet aggregation and coagulation.

Revisiting Australian Ectocarpus subulatus (Phaeophyceae) from the Hopkins River: distribution, abiotic environment, and associated microbiota

The paper revisits Ectocarpus subulatus in the Hopkins River, finding it has stably colonized the area and reports new microbiota associated with the algae.

Towards multi-drug adaptive therapy

This paper introduces three novel concepts to aid in designing multi-drug adaptive therapies for cancer by analyzing tumor evolution dynamics and treatment strategies.

Tissue structure accelerates evolution: premalignant sweeps precede neutral expansion

This study shows that tissue structure influences tumor evolution by accelerating neutral expansion through spatial constraints and dispersal events.

How Homeostasis Limits Keratinocyte Evolution

This study presents a mechanistic epidermal model showing homeostasis leads to log-linear subclone size distributions in skin cells, with larger subclones being older due to persistence of driver mutations.

Macrophage-mediated immunoediting drives ductal carcinoma evolution: Space is the game changer

This study uses immunohistochemistry data to model how macrophages influence tumor evolution through spatial dynamics and immune escape strategies in ductal carcinomas.

Genomic programming of antigen cross-presentation in IRF4-expressing human Langerhans cells

The paper identifies IRF4 as a key transcription factor driving antigen cross-presentation in human Langerhans cells, distinguishing them from conventional dendritic cells.

A multidisciplinary approach towards identification of novel antibiotic scaffolds for Acinetobacter baumannii

This study identifies DcaP as a key outer membrane channel in Acinetobacter baumannii and explores its potential as a scaffold for new antibiotics.