Alan DenAdel
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View article: Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance
Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance Open
The success of transformer-based foundation models on natural language and images has motivated their use in single-cell biology. Single-cell foundation models have been trained on increasingly larger transcriptomic datasets, scaling from …
View article: Mutation and cell state compatibility is required and targetable in Ph<i>+</i>acute lymphoblastic leukemia minimal residual disease
Mutation and cell state compatibility is required and targetable in Ph<i>+</i>acute lymphoblastic leukemia minimal residual disease Open
SUMMARY Efforts to cure BCR::ABL1 B cell acute lymphoblastic leukemia (Ph+ ALL) solely through inhibition of ABL1 kinase activity have thus far been insufficient despite the availability of tyrosine kinase inhibitors (TKIs) with broad acti…
View article: A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing
A knockoff calibration method to avoid over-clustering in single-cell RNA-sequencing Open
Standard single-cell RNA-sequencing (scRNA-seq) pipelines nearly always include unsupervised clustering as a key step in identifying biologically distinct cell types. A follow-up step in these pipelines is to test for differential expressi…
View article: Leveraging the genetic correlation between traits improves the detection of epistasis in genome-wide association studies
Leveraging the genetic correlation between traits improves the detection of epistasis in genome-wide association studies Open
Epistasis, commonly defined as the interaction between genetic loci, is known to play an important role in the phenotypic variation of complex traits. As a result, many statistical methods have been developed to identify genetic variants t…
View article: A spectrum of explainable and interpretable machine learning approaches for genomic studies
A spectrum of explainable and interpretable machine learning approaches for genomic studies Open
The advancement of high‐throughput genomic assays has led to enormous growth in the availability of large‐scale biological datasets. Over the last two decades, these increasingly complex data have required statistical approaches that are m…
View article: Leveraging the Genetic Correlation between Traits Improves the Detection of Epistasis in Genome-wide Association Studies
Leveraging the Genetic Correlation between Traits Improves the Detection of Epistasis in Genome-wide Association Studies Open
Epistasis, commonly defined as the interaction between genetic loci, is known to play an important role in the phenotypic variation of complex traits. As a result, many statistical methods have been developed to identify genetic variants t…
View article: The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer
The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer Open
SUMMARY Bulk transcriptomic studies have defined classical and basal-like gene expression subtypes in pancreatic ductal adenocarcinoma (PDAC) that correlate with survival and response to chemotherapy; however, the underlying mechanisms tha…