Sam Lee

hoodscanR identifies and analyzes cell neighborhoods in spatial transcriptomics data, revealing transcriptional differences in tumor cells across neighborhoods.

IdentifiHR predicts homologous recombination deficiency in high-grade serous ovarian carcinoma using gene expression, achieving 85% accuracy in TCGA and 91% in an independent cohort.

The paper identifies neurogenesis-related gene expression as a clone-specific hallmark of brain metastasis in breast cancer using a new optical barcoding tool.

The paper investigates the RNA structures and interactions of the 5' and 3' regions of the SARS-CoV-2 frameshifting element, revealing their co-regulatory roles and implications for therapeutic interventions.

This study shows that malin-deficient mice accumulate Lafora bodies without observable neurobehavioral decline, suggesting a delay between LB accumulation and clinical symptoms.

vissE identifies and visualizes higher-order molecular phenotypes from functional enrichment analysis by summarizing redundancies into biological themes.

This study examines the neurobehavioral phenotype of Stargazer mutant mice, revealing a syndrome with ataxia, hyperactivity, and behavioral abnormalities linked to Cacng2 disruptions.

Open flow cell on a circular wafer with mostly natural nucleotides and no reversible terminators: about 300 bp reads at $1/Gb, 99.6% SNP accuracy on reference human genomes.

This paper introduces PAN, a method to create sample-specific gene networks using annotations, improving breast cancer relapse prediction compared to existing methods.

This paper introduces an anomaly detection approach to classify cancer using only healthy tissue transcriptomes, showing improved accuracy with more normal samples.

This paper improves neuropsychiatric condition classification by using gene ontology terms as features, enhancing performance, stability, and interpretability of classifiers.

This study identifies sex-dependent and -independent biomarkers in ASD using post-mortem brain RNA-Seq and blood microarray data, highlighting sex-specific gene expression differences and pathway dysregulation.