Ayşe Gökçe Keşküş

APOBEC3-driven neoantigen-rich cancers co-opt 1q23.3 amplification for tumor-intrinsic immune cloaking

The paper identifies a tumor-intrinsic immune-cloaking mechanism in neoantigen-rich cancers driven by APOBEC3 mutagenesis and 1q23.3 amplification, showing NECTIN4's role in suppressing immune responses.

TP53-META, a meta-analysis tool for comparative transcriptomics of TP53 dependency: Examples from target silencing and liver fibrosis

TP53-META enables meta-analysis of TP53-related gene expression datasets to identify dependency patterns in transcriptomic changes across different conditions.

A near-complete human pancreatic cancer genome

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

Chromosome-arm-specific telomere length governs dual modes of structural genome evolution in IDH-mutant astrocytoma

This study uses long-read sequencing to show that telomere length differences between chromosome arms influence structural genome changes in IDH-mutant astrocytomas.

Wakhan: reconstruction of chromosome-scale copy number profiles of tumor genomes with long-read sequencing

Wakhan reconstructs chromosome-scale copy number profiles of tumor genomes using long-read sequencing, showing better consistency with data than existing methods.

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies

DeepSomatic is a deep learning method for detecting somatic variants from short-read and long-read sequencing data, outperforming existing callers, especially for indels.

Long-read sequencing of single cell-derived melanoma subclones reveals divergent and parallel genomic and epigenomic evolutionary trajectories

The paper uses long-read sequencing to analyze genomic and epigenomic changes in melanoma subclones, revealing parallel evolutionary paths and lineage-specific methylation patterns.

Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair

The paper describes a comprehensive genomic dataset from a tumor-normal pair with broad consent, generated using multiple sequencing technologies for benchmarking somatic variant detection.

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

Severus detects and characterizes somatic structural variations in tumor genomes using long reads, outperforming existing methods in accuracy and revealing clinically relevant rearrangements.

Successful classification of clinical pediatric leukemia genetic subtypes via structural variant detection using HiFi long-read sequencing

This study shows that HiFi long-read sequencing can detect clinically relevant structural variants in pediatric leukemia, improving subtype classification.

ace2 expression is higher in intestines and liver while being tightly regulated in development and disease in zebrafish

This study analyzes ace2 expression in zebrafish across development and disease, showing tissue-specific patterns and gender dimorphism.