Cancer Genomics and Diagnostics

When neighbours play a role: a systems-level analysis of protein interactions conditioning cancer driver mutation effects

The paper analyzes how neighbour proteins influence cancer driver mutations and survival outcomes across multiple cancer types.

Optical Genome and Epigenome Mapping of Clear Cell Renal Cell Carcinoma

The paper uses optical genome and epigenome mapping to identify somatic alterations in early-stage clear cell renal cell carcinoma, revealing both known and novel genomic and epigenomic changes.

Investigating the genomic landscape of mouse models of breast cancer metastasis

This study examines four mouse breast cancer models to show that oncogenic drivers influence metastasis-specific copy number variations and gene expression, while genetic background also plays a significant role.

RNAsum: a tool for personalised genome and transcriptome interpretation for improved cancer diagnostics

RNAsum integrates WGS and WTS data to improve cancer diagnostics by corroborating clinically relevant variants and supporting therapeutic decisions.

Canopy2: tumor phylogeny inference by bulk DNA and single-cell RNA sequencing

Canopy2 infers tumor phylogeny using bulk DNA and single-cell RNA sequencing data, outperforming existing methods in reconstructing clonal trees.

Landscape of human protein-coding somatic mutations across tissues and individuals

The paper analyzes somatic mutations across tissues and individuals using exome sequencing data from GTEx donors, identifying 8,470 variants and providing insights into mutation rates and mechanisms.

End-to-end deep learning versus machine learning for biomarker discovery in cancer genomes

This study compares deep learning and machine learning for biomarker prediction in cancer genomes, finding DL performs better in cross-assay and data-sparse settings.

Characterizing the Solution Space of Migration Histories of Metastatic Cancers with MACH2

The paper introduces MACH2, a method to systematically enumerate all plausible migration histories of metastatic cancers, outperforming existing methods and detecting extensive uncertainty in real cancer data.

CNSistent integration and feature extraction from somatic copy number profiles

CNSistent integrates and analyzes somatic copy number profiles across cancer cohorts to improve classification accuracy and identify key alterations.

A cost-effective and scalable approach for DNA extraction from FFPE tissues

This paper presents a high-throughput DNA extraction method for FFPE tissues that is cost-effective and scalable, producing methylation profiles comparable to traditional methods.

Pharming: Joint Clonal Tree Reconstruction of SNV and CNAEvolution from Single-cell DNA Sequencing of Tumors

This paper introduces a method to jointly reconstruct the evolutionary history of SNVs and CNAs from low-coverage single-cell DNA sequencing data, demonstrating improved accuracy over single-modality approaches.

The Open Pediatric Cancer Project

The paper introduces OpenPedCan, a harmonized multi-omic dataset of pediatric cancer patients, providing integrated genomic, transcriptomic, and proteomic data for research and clinical applications.

DNA replication initiation drives focal mutagenesis and rearrangements in human cancers

This study shows that DNA replication initiation sites drive mutagenesis and genomic rearrangements in cancers by affecting repair processes and mutational patterns.

OncotreeVIS - an interactive graphical user interface for visualizing mutation tree cohorts

OncotreeVIS provides an interactive tool for visualizing mutation tree cohorts and analyzing their properties at the cohort level.

FinaleToolkit: Accelerating Cell-Free DNA Fragmentation Analysis with a High-Speed Computational Toolkit

FinaleToolkit accelerates cfDNA fragmentation analysis by generating comprehensive features efficiently, improving processing speed by up to 50-fold for large datasets.

Deconvolution and Phylogeny Inference of Diverse Variant Types Integrating Bulk DNA-seq with Single-cell RNA-seq

This paper introduces TUSV-int, a method that integrates bulk DNA-seq and scRNA-seq to improve deconvolution and phylogenetic inference for cancer clonal structure.

PHALCON: phylogeny-aware variant calling from large-scale single-cell panel sequencing datasets

PHALCON improves variant calling and tumor phylogeny reconstruction in large-scale single-cell panel sequencing data by modeling tumor evolution under a finite-sites model.

Genomic diversity and BCL9L mutational status in CTC pools predict overall survival in metastatic colorectal cancer

Analysis of plasma DNA fragmentation patterns from dried blood spots

This study shows that plasma DNA fragmentation analysis from dried blood spots can detect cancer with machine learning, offering a cost-effective method for early cancer detection in resource-limited settings.

Supervised non-negative matrix factorization on cell-free DNA fragmentomic features enhances early cancer detection

This paper uses supervised non-negative matrix factorization on cfDNA fragmentomic features to improve early cancer detection, achieving high AUC scores in both pan-cancer and HCC-specific classifications.

DICE: Fast and Accurate Distance-Based Reconstruction of Single-Cell Copy Number Phylogenies

DICE-bar and DICE-star are distance-based methods for reconstructing single-cell tumor phylogenies from sCNA data, offering improved accuracy and speed over existing methods.

cancerSimCraft: A Multi-resolution Cancer Genome Simulator with Comprehensive Ground Truth Tracking

cancerSimCraft simulates cancer genome data at clonal and single-cell resolution, enabling benchmarking of computational methods under varied conditions.

An artificial intelligence-based model for prediction of Clonal Hematopoiesis mutants in cell-free DNA samples

The paper presents a machine learning framework to classify variants in cell-free DNA as clonal hematopoiesis or tumor origin, achieving better classification rates than existing methods.

Mutation Impact on mRNA Versus Protein Expression across Human Cancers

The paper analyzes how mutations affect mRNA and protein expression in 953 cancer cases across six types, finding that 47.2% of somatic expression quantitative trait loci (seQTLs) impact protein levels, with some mutations showing disproportionate effects.

A regression based approach to phylogenetic reconstruction from multi-sample bulk DNA sequencing of tumors

This paper introduces fastBE, a method for phylogenetic reconstruction from bulk DNA sequencing data that improves accuracy and scalability over existing approaches.

Comprehensive Longitudinal ctDNA Monitoring in Metastatic Cancer Patients Treated with an Individualized Neoantigen-directed Vaccine

This study monitors ctDNA in metastatic cancer patients receiving an individualized vaccine, showing the assay's sensitivity and insights into treatment response.

Coverage landscape of the human genome in nucleus DNA and cell-free DNA

The paper analyzes genome-wide coverage differences between nuclear DNA and cell-free DNA in healthy and cancer samples, identifying factors influencing coverage and developing a new cancer screening method.

Pan-Cancer Genetic Profiles of Mitotic DNA Integrity Checkpoint Protein Kinases

The paper provides pan-cancer profiles of 16 mitotic DNA integrity checkpoint protein kinase genes across multiple omic layers to identify potential biomarkers and therapeutic targets.

GFPrint™: A MACHINE LEARNING TOOL FOR TRANSFORMING GENETIC DATA INTO CLINICAL INSIGHTS

GFPrint transforms genetic sequencing data into clinical insights by clustering and mapping to clinical outcomes in cancer datasets.

SNMF: Integrated Learning of Mutational Signatures and Prediction of DNA Repair Deficiencies

The paper introduces SNMF, a supervised method to learn mutational signatures and predict DNA repair deficiencies, achieving high accuracy in cell lines and predicting DDR status in tumors.