Deepali L. Kundnani

MutQA: A Cross-Validated Q&A Dataset for Genetic Mutations

The paper introduces MutQA, a cross-validated Q&A dataset linking genetic mutations to their functional consequences, and demonstrates its utility in improving LLM performance.

Tumor γδ T-cell abundance is associated with favorable cancer treatment outcomes

This study finds that higher pretreatment γδ T-cell abundance is linked to better outcomes in cancer patients receiving immune checkpoint blockade and improved survival across multiple tumor types.

Genome-wide ribonucleotide detection in Archaea

The paper investigates the role of RNase H types 1 and 2 in removing ribonucleotides from the genomes of two archaeal species using combined experimental and sequencing approaches.

Human ribomes reveal DNA-embedded ribonucleotides as a new type of epigenetic mark

The paper maps DNA-embedded ribonucleotides (rNMPs) across human cell types, revealing their non-random distribution and role as a novel epigenetic mark affecting gene expression.

rNMPID: a database for riboNucleoside Mono-Phosphates In DNA

The paper introduces rNMPID, a database that compiles rNMP-embedment data across species, providing insights into their genomic characteristics and potential roles in disease.

Distinct features of ribonucleotides within genomic DNA in Aicardi-Goutieres syndrome (AGS)-ortholog mutants of Saccharomyces cerevisiae

This study examines rNMP incorporation in AGS-ortholog yeast mutants, revealing differences in rNMP abundance and strand-specific patterns.

Gene co-expression analysis of human RNASEH2A reveals functional networks associated with DNA replication, DNA damage response, and cell cycle regulation

This study identifies co-expressed genes of RNASEH2A and reveals its involvement in DNA replication, DNA damage response, and cell cycle regulation, with increased expression in cancer cells.

Testing the Gene Expression Classification of the EMT Spectrum

The paper uses computational methods to classify gene expression profiles into epithelial, hybrid E/M, and mesenchymal categories based on EMT dynamics and scoring metrics.