Ignaty Leshchiner

This study identifies Bloom syndrome helicase (BLM) as a host factor that promotes HIV-1 reverse transcription and integration in macrophages through CRISPR screening and functional assays.

The paper identifies structural variations in TP53 that inactivate TCAB1, a telomerase chaperone, and show these variations are prevalent in ALT-positive osteosarcoma tumors.

The paper benchmarks 31 subclonal reconstruction algorithms on simulated tumours, finding that algorithm choice significantly impacts performance and no single algorithm excels across all tasks.

This study identifies molecular and immune features associated with response to anti-PD-(L)1 therapy in NSCLC using a cohort of 393 patients.

The paper develops DNA- and RNA-based models combining immune and tumor features to predict outcomes of checkpoint inhibition in melanoma.

This study identifies Osr1's role in maintaining renal progenitors and regulating podocyte development through Wnt2ba expression, revealing its antagonistic relationship with Hand2.

This study shows that Slc7a7 is essential for tissue macrophages with sustained efferocytic activity, as its expression is induced during efferocytosis and supports their survival.

PhylogicNDT statistically reconstructs cancer driver timing, subclonal phylogenies, and population dynamics from single- or multi-timepoint sequencing, revealing subtype-specific trajectories and therapy resistance evolution across 498 lung adenocarcinomas.

This study identifies tfap2a as a key regulator of distal nephron segment differentiation in zebrafish, revealing its role in controlling gene regulatory networks and specialized metabolic functions.

Four levers for cheaper cloud genomics on FireCloud: size virtual disks dynamically, tune VM provisioning from monitoring data, buy preemptible machines, and parallelise tasks at the right width.

The paper describes the PCAWG project's large-scale analysis of cancer whole genomes across multiple computing environments, producing validated consensus variants for downstream research.