Marcin B. Imielinski

Machine learning guided signal enrichment for ultrasensitive plasma tumor burden monitoring

This paper introduces MRD-EDGE, a machine learning platform for ultrasensitive ctDNA detection in plasma WGS, showing improved sensitivity and broader applicability for MRD monitoring.

APOBEC shapes tumor evolution and age at onset of lung cancer in smokers

The paper identifies two lung cancer subtypes defined by APOBEC mutagenesis levels and shows their association with different genetic mutations, aging, and immune responses.

Detecting significantly recurrent genomic connections from simple and complex rearrangements in the cancer genome

This paper introduces two methods to detect recurrent genomic rearrangements in cancer genomes and identifies 80 simple and 29 complex rearrangements across 2,500 cancers.

Comparison of germline and somatic structural variants in cancers reveal systematic differences in variant generating and selection processes

The paper compares germline and somatic structural variants in cancer, identifying differences in their generating processes and selection, and develops a classifier to distinguish them in tumor samples without matched normals.

Loose ends in cancer genome structure

The paper identifies 'loose ends' in cancer genomes, structural variations missed by short-read WGS, and estimates they account for <3% of large-scale structural variation.

Structural variant evolution after telomere crisis

The paper investigates structural variants (SVs) generated during telomere crisis, showing that BFB cycles and chromothripsis can occur in clones that escape telomere crisis.

Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions

This study uses rapid diagnostics and metatranscriptomics to analyze SARS-CoV-2 infection, revealing viral evolution, host responses, and drug interactions in NYC samples.

Genomic footprints of activated telomere maintenance mechanisms in cancer

The paper analyzes whole-genome sequencing data from cancer samples to identify genomic footprints of telomere maintenance mechanisms, finding specific telomere variant repeat patterns associated with ATRX/DAXX mutations.

Spatial Genome Organization as a Framework for Somatic Alterations in Human Cancer

The paper examines how somatic structural variations affect TAD boundaries and gene regulation in human cancers using whole genome sequencing data.

Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing

This study analyzes chromothripsis in 2,658 cancers using whole-genome sequencing, finding it prevalent across multiple cancer types with complex structural alterations.

Robust foreground detection in somatic copy number data

dryclean improves somatic copy number alteration detection in cancer genomes by reducing read depth waviness through signal processing.

Novel patterns of complex structural variation revealed across thousands of cancer genome graphs

The paper identifies three novel complex structural variation patterns in cancer genomes using genome graph analysis across 2,833 tumor WGS.

Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure

Pore-C reads multi-way chromatin contacts directly off unamplified Nanopore long reads, recovering Hi-C-scale features while also resolving rearranged cancer alleles and supporting de novo assembly.

Genome-wide detection of structural variants and indels by local assembly

SvABA detects structural variants and indels using genome-wide local assembly, showing improved sensitivity and specificity, especially for small variants and complex rearrangements in cancer genomes.

Deep Convolutional Neural Networks Enable Discrimination of Heterogeneous Digital Pathology Images

This study develops a CNN-based pipeline to classify histopathology images across cancer types and biomarkers, achieving high accuracy in distinguishing cancer subtypes and IHC scores.

Selective and mechanistic sources of recurrent rearrangements across the cancer genome

The paper analyzes somatic rearrangements in cancer genomes using whole-genome sequencing data, identifying recurrent breakpoints and their genomic features.

Patterns of structural variation in human cancer

The paper identifies nine structural variation signatures in cancer genomes, revealing patterns of deletions, tandem duplications, and translocations linked to replication mechanisms and oncogenic activation.