D. Fenyo

Predicting immune checkpoint therapy response in three independent metastatic melanoma cohorts

The paper identifies six proteins that predict response to immune checkpoint therapy across three melanoma cohorts and correlate with patient survival.

Identifying Ferroptosis Inducers, HDAC, and RTK Inhibitor Sensitivity in Melanoma Subtypes through Unbiased Drug Target Prediction

This paper identifies potential drug targets and predicts treatment efficacy and resistance in melanoma subtypes using proteogenomic data and drug sensitivity analysis.

D-type cyclins regulate DNA mismatch repair in the G1 and S phases of the cell cycle, maintaining genome stability

This study shows D-type cyclins inhibit mismatch repair (MMR) in G1 phase by shielding p21, while their degradation in S phase enables proper MMR function, maintaining genome stability.

The expression profile and tumorigenic mechanisms of CD97 (ADGRE5) in glioblastoma render it a targetable vulnerability

This study identifies CD97 as a targetable vulnerability in glioblastoma through its role in tumor metabolism and signaling, supported by transcriptomic, proteomic, and functional analyses.

Histopathology-assisted proteogenomics provides foundations for stratification of melanoma metastases

This study integrates histopathology and proteogenomic data from melanoma metastases to identify subtypes and risk factors, offering a basis for personalized treatment strategies.

GEMspa: a Napari plugin for analysis of single particle tracking data

GEMspa is a Napari plugin that simplifies single particle tracking analysis for microrheology, providing a user-friendly interface and tools for extracting particle motion parameters.

In vivo metabolomics identifies CD38 as an emergent vulnerability in LKB1-mutant lung cancer

The paper identifies CD38 as a therapeutic target in LKB1-mutant lung cancer through in vivo metabolomics and shows that targeting CD38 inhibits tumor growth.

Modulation of GPR133 (ADGRD1) Signaling by its Intracellular Interaction Partner Extended Synaptotagmin 1 (ESYT1)

This study identifies ESYT1 as an intracellular modulator of GPR133 signaling, showing that Ca2+ levels influence their interaction and affect cAMP levels in glioblastoma cells.

The MTIST platform: a microbiome time series inference standardized test simulation, dataset, and scoring systems

The paper introduces MTIST, a platform for benchmarking microbial ecosystem inference tools using simulated time series data and an ecological sign score.

KaryoCreate: a new CRISPR-based technology to generate chromosome-specific aneuploidy by targeting human centromeres

KaryoCreate generates chromosome-specific aneuploidy by targeting centromeres with CRISPR, showing it can induce gains or losses of targeted chromosomes in human cells.

Lupus disease flares are concordant with immune responses to blooms of lipoglycan-expressing Ruminococcus blautia gnavus strains arising from unstable gut microbiota communities

Proteogenomic analysis of aneuploidy reveals divergent types of gene expression regulation across cellular pathways

This study uses proteogenomic analysis to show that gene expression regulation differs across cellular pathways and tissues, with protein-level regulation dominating in some pathways and RNA-level regulation in others.

nucGEMs probe the biophysical properties of the nucleoplasm

The paper introduces nucGEMs, fluorescent nanoparticles that probe nucleoplasm biophysical properties, revealing differences in motility, exclusion from heterochromatin, and effects of mitotic condensation.

A Deep Learning Approach for Rapid Mutational Screening in Melanoma

This paper develops a deep learning model to detect BRAF mutations in melanoma histopathology images using whole slide images from 256 patients, achieving AUC scores of 0.96 and 0.72.

Discovery of protein modifications using high resolution differential mass spectrometry proteomics

This paper introduces SAMPEI, a spectral alignment method for detecting protein modifications using high-resolution mass spectrometry, demonstrating its effectiveness in identifying sub-stoichiometric modifications in mouse macrophages.

Affinity proteomic dissection of the human nuclear cap-binding-complex interactome

This study maps the human nuclear cap-binding complex interactome using affinity proteomics to clarify the composition and interactions of NCBP1, NCBP2, and NCBP3-related macromolecular assemblies.

Distinct features of human myeloid cell cytokine response profiles identify neutrophil activation by cytokines as a prognostic feature during tuberculosis and cancer

The paper identifies neutrophil cytokine response profiles as prognostic markers in tuberculosis and cancer by analyzing myeloid cell transcriptional responses to various cytokines.

LINE-1 ORF2P EXPRESSION IS NEARLY IMPERCEPTIBLE IN HUMAN CANCERS

The paper reports that ORF2p expression is undetectable in human cancers despite high ORF1p expression and somatic L1 retrotransposition.

BRCA1 Mediated Homologous Recombination and S Phase DNA Repair Pathways Restrict LINE-1 Retrotransposition in Human Cells

This study identifies BRCA1 and other DNA repair factors that suppress LINE-1 retrotransposition in human cells by affecting retrotransposition frequency and ORF2 protein translation.

Quantitative mass spectrometry to interrogate proteomic heterogeneity in metastatic lung adenocarcinoma and validate a novel somatic mutation CDK12-G879V

The paper uses quantitative mass spectrometry to analyze proteomic and phosphoproteomic changes in metastatic lung adenocarcinoma and validates a novel somatic mutation CDK12-G879V associated with chemotherapy sensitivity.

Integration and analysis of CPTAC proteomics data in the context of cancer genomics in the cBioPortal

The paper integrates CPTAC proteomics data into cBioPortal to enable integrative analysis with genomics and clinical data from the same tumors.

Classification and Mutation Prediction from Non-Small Cell Lung Cancer Histopathology Images using Deep Learning

This study uses deep learning to classify lung cancer subtypes and predict gene mutations from histopathology images, achieving high accuracy and outperforming human pathologists.

LINE-1 and the cell cycle: protein localization and functional dynamics

This study identifies L1 protein nuclear entry mechanisms and shows a cell cycle bias for L1 retrotransposition peaking in S phase.