Michael Baudis

CNVSIM: an interpretable copy-number reference atlas for cancer subtyping

CNVSIM creates a reference atlas of copy-number variations for cancer subtyping, identifying 112 subtypes across 19 cancer types using the Progenetix dataset.

High-resolution population structure inference using genome-wide short tandem repeat variations

This paper introduces a framework using STR variations for high-resolution population structure inference, showing STRs provide finer resolution than SNPs.

CNAttention: an attention-based deep multiple-instance method for uncovering CNA signatures across cancers

CNAttention identifies cancer-specific CNA patterns across 30 cancer types using an attention-based deep learning method, revealing both common and distinct genomic features.

Multicancer analyses of short tandem repeat variations reveal shared gene regulatory mechanisms

The paper identifies STR variations associated with gene expression and DNA methylation across three cancer types and finds shared regulatory mechanisms.

pgxRpi: an R/Bioconductor package for user-friendly access to the Beacon v2 API

pgxRpi provides an R/Bioconductor package for accessing the Beacon v2 API, enabling genomic data retrieval and analysis.

In Search of the Perfect Model: How Cancer Cell Lines Relate to Native Cancers

This study compares cancer cell lines to native cancers using CNV profiles and ML to identify cell lines that best represent specific cancer types.

cancercelllines.org - a Novel Resource for Genomic Variants in Cancer Cell Lines

The paper introduces cancercelllines.org, a resource curating genomic variants in cancer cell lines, providing copy number and SNV data for over 16,000 cell lines.

labelSeg: segment annotation for tumor copy number alteration profiles

labelSeg annotates tumor copy number alteration segments to improve interpretation of SCNA profiles, showing strong correlation between SCNA and mRNA expression.

The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

The paper introduces the GA4GH Phenopacket schema to standardize the exchange of phenotypic data for precision medicine applications.

The GA4GH Variation Representation Specification (VRS): a Computational Framework for the Precise Representation and Federated Identification of Molecular Variation

The paper introduces the GA4GH Variation Representation Specification (VRS), a framework for precise and federated representation of molecular variation, with a reference implementation and community resources available online.

Signatures of Discriminative Copy Number Aberrations in 31 Cancer Subtypes

This study develops a bioinformatics pipeline to generate CNA signatures for 31 cancer subtypes and constructs a classifier to identify cancer type and origin from copy number data.

Minimum Error Calibration and Normalization for Genomic Copy Number Analysis

This paper introduces Mecan4CNA, a method for normalizing copy number variation data, showing improved accuracy and performance in detecting focal regions in cancer genomes.

A harmonized meta-knowledgebase of clinical interpretations of cancer genomic variants

The paper harmonizes clinical interpretations of cancer genomic variants across six knowledgebases, improving overlap and matching with patient cohorts.

Enabling population assignment from cancer genomes with SNP2pop

The paper develops a tool for population assignment from cancer genomes and validates its accuracy across healthy and mutated samples.

Geographic assessment of cancer genome profiling studies

This study assesses geographic information in cancer genome profiling publications to identify gaps in representation and highlight inequalities in cancer research geographies.

segment_liftover: a Python tool to convert segments between genome assemblies

segment_liftover converts genome segments between assemblies while preserving continuity, enabling accurate analysis of structural variations.