Marc Glettig
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View article: Simulation and empirical evaluation of biologically-informed neural network performance
Simulation and empirical evaluation of biologically-informed neural network performance Open
Biologically-informed neural networks (BiNNs) offer interpretable deep learning models for biological data, but the dataset characteristics required for strong performance remain poorly understood. For instance, we previously developed P-N…
View article: CanSig Benchmarks Methods for Reproducible Cancer Cell State Discovery from Single-Cell Transcriptomic Data
CanSig Benchmarks Methods for Reproducible Cancer Cell State Discovery from Single-Cell Transcriptomic Data Open
Single-cell RNA-sequencing (scRNA-seq) facilitates the discovery of gene expression signatures that define cell states across patients, which could be used in patient stratification and precision oncology. However, the lack of standardizat…
View article: H&Enium, Applying Foundation Models to Computational Pathology and Spatial Transcriptomics to Learn an Aligned Latent Space
H&Enium, Applying Foundation Models to Computational Pathology and Spatial Transcriptomics to Learn an Aligned Latent Space Open
Bridging the gap from transcriptomic to imaging data at single-cell resolution is essential for understanding tumor biology and improving cancer diagnostics. Spatial transcriptomics enables mapping gene expression onto H&E images of segmen…
View article: Clinico-genomic features predict distinct metastatic phenotypes in cutaneous melanoma
Clinico-genomic features predict distinct metastatic phenotypes in cutaneous melanoma Open
Metastasis drives mortality and morbidity in cancer. While some patients develop broad metastatic disease across multiple organs, others exhibit organ-specific spread. To identify mechanisms underlying metastatic organotropism, we analyzed…
View article: Genomic heterogeneity and ploidy identify patients with intrinsic resistance to PD-1 blockade in metastatic melanoma
Genomic heterogeneity and ploidy identify patients with intrinsic resistance to PD-1 blockade in metastatic melanoma Open
The introduction of immune checkpoint blockade (ICB) has markedly improved outcomes for advanced melanoma. However, many patients develop resistance through unknown mechanisms. While combination ICB has improved response rate and progressi…
View article: Stratified analysis identifies HIF-2<i>α</i>as a therapeutic target for highly immune-infiltrated melanomas
Stratified analysis identifies HIF-2<i>α</i>as a therapeutic target for highly immune-infiltrated melanomas Open
While immune-checkpoint blockade (ICB) has revolutionized treatment of metastatic melanoma over the last decade, the identification of broadly applicable robust biomarkers has been challenging, driven in large part by the heterogeneity of …
View article: Genomic heterogeneity and ploidy identify patients with intrinsic resistance to PD-1 blockade in metastatic melanoma
Genomic heterogeneity and ploidy identify patients with intrinsic resistance to PD-1 blockade in metastatic melanoma Open
While the introduction of immune checkpoint blockade (ICB) has dramatically improved clinical outcomes for patients with advanced melanoma, a significant proportion of patients develop resistance to therapy, and mechanisms of resistance ar…
View article: CanSig: a tool for benchmarking malignant state discovery in single-cell RNA-Seq data
CanSig: a tool for benchmarking malignant state discovery in single-cell RNA-Seq data Open
Single-cell RNA sequencing (scRNA-seq) facilitates the discovery of gene signatures that define cell states across patients, which could be used in patient stratification and drug discovery. However, the lack of standardization in computat…