Samuel A. J. R. Aparicio

G4SCOPE identifies sequence features and epigenetic contexts of chromatin G-quadruplexes

G4SCOPE predicts chromatin G-quadruplex occupancy from DNA sequence, revealing epigenetic differences in BRCA1 and BRCA2 deficient cells.

Serval: A modular framework for decoding imaging based spatial transcriptomics data

Serval is a modular framework for decoding spatial transcriptomics data that introduces Cosine, a method improving transcript recovery and correlation with expression references.

Chromosomal mutational signatures of DNA damaging agents at single cell resolution

This paper develops a framework to analyze chromosomal mutational patterns at single-cell resolution, revealing drug-induced mutational signatures in human tissues.

Single-cell mapping of the fallopian tube reveals a genomically unstable secretory cell state enriched in carriers of germline BRCA1/2 mutations

The paper identifies genomically unstable secretory cells in fallopian tubes of BRCA1/2 carriers using single-cell transcriptomics, linking them to replication stress and early cancer transformation.

Minimally invasive monitoring of clonal evolution through integrated single cell and ctDNA analysis

cfClone, a Bayesian model, deconvolves cfDNA whole-genome sequencing using scWGS-derived haplotype-specific clone copy-number profiles to estimate tumour fraction, clonal prevalence, and flag missed clones.

Single-cell spatial multi-omic characterization of the tumour microenvironment in transformed follicular lymphoma

The paper uses multi-omic single-cell spatial techniques to study FL transformation, finding spatial shifts in B-cell neighborhoods and immunomodulatory interactions linked to disease progression.

EpiATLAS - a reference for human epigenomic research

EpiATLAS provides a comprehensive collection of human reference epigenomes to advance epigenomic research and understanding of cellular function and disease.

Evolution of oncogene amplification across 86,000 cancer cell genomes

The paper analyzes the evolutionary trajectories of high-level copy-number amplifications in cancer cell genomes to distinguish between extrachromosomal and intrachromosomal amplification mechanisms.

The UV potentiated mutational signature of clinical stage G-quadruplex binder CX5461.

The paper investigates the mutational signature of CX5461, a photosensitiser, when combined with UVA light, showing increased SNV burden only in co-exposed cells.

Somatic copy number mutations contribute to fitness in transplantation models of spontaneous human breast cancer metastasis

This study shows that somatic copy number mutations (CNA) influence metastatic fitness in breast cancer by mediating transcriptional changes and affecting clone survival in different sites.

Ongoing genome doubling promotes evolvability and immune dysregulation in ovarian cancer

This study shows that ongoing whole-genome doubling in ovarian cancer promotes cell diversity and immune dysregulation through chromosomal instability and quiescent states.

Luminal breast epithelial cells from wildtype and BRCA mutation carriers harbor copy number alterations commonly associated with breast cancer

The paper analyzes copy number alterations in breast epithelial cells from BRCA mutation carriers and wildtype individuals, finding lineage-specific CNAs that mirror cancer genomes.

Single cell decoding of drug induced transcriptomic reprogramming in triple negative breast cancers

The paper identifies genomic and non-genomic contributions to drug resistance in triple negative breast cancer using single cell transcriptomics and copy number data.

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.

ESQmodel: biologically informed evaluation of 2-D cell segmentation quality in multiplexed tissue images

ESQmodel evaluates single-cell segmentation quality using expression data and a prior belief of cellular composition to compute per-cell entropy.

Cancer phylogenetic tree inference at scale from 1000s of single cell genomes

The paper introduces a scalable Bayesian method for phylogenetic tree inference from single-cell whole genome sequencing data, demonstrating its application on three datasets.

GeneVector: Identification of transcriptional programs using dense vector representations defined by mutual information.

GeneVector uses mutual information-based dimensionality reduction to identify transcriptional programs and classify cell types across single-cell RNA-seq datasets.

PhylEx: Accurate reconstruction of clonal structure via integrated analysis of bulk DNA-seq and single cell RNA-seq data

PhylEx reconstructs clonal structure by integrating bulk DNA-seq and scRNA-seq data, outperforming existing methods in clonal-tree reconstruction and mutation clustering.

Expansion Sequencing: Spatially Precise In Situ Transcriptomics in Intact Biological Systems

ExSeq enables multiplexed RNA mapping at nanoscale resolution by expanding biological specimens for in situ sequencing.

Epiclomal: probabilistic clustering of sparse single-cell DNA methylation data

Epiclomal clusters sparse single-cell DNA methylation data and imputes missing values, outperforming non-probabilistic methods and revealing sub-clonal methylation patterns in tumour genomes.

Germline determinants of the somatic mutation landscape in 2,642 cancer genomes

This study identifies germline genetic variants influencing somatic mutation patterns in 2,642 cancer genomes across 39 cancer types.

Comprehensive Molecular Characterization of Mitochondrial Genomes in Human Cancers

This study characterizes mitochondrial genomes in 2,700 cancer patients across 37 types using whole-genome sequencing and RNA-seq, revealing mutational patterns, truncating mutations, and nuclear transfer of mitochondrial DNA.

Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase associated stress responses

This study identifies transcriptional stress responses in single-cell RNA-seq data from dissociated tumour tissues, showing that collagenase digestion induces a conserved stress response minimized by cold active protease.

clonealign: statistical integration of independent single-cell RNA & DNA-seq from human cancers

clonealign integrates single-cell RNA and DNA sequencing data from cancer samples to identify clone-specific gene expression patterns and dysregulated pathways.

Probabilistic cell type assignment of single-cell transcriptomic data reveals spatiotemporal microenvironment dynamics in human cancers

CellAssign probabilistically assigns cell types to scRNA-seq data, revealing spatiotemporal dynamics in human cancers like ovarian and follicular lymphoma.

Resource: Scalable whole genome sequencing of 40,000 single cells identifies stochastic aneuploidies, genome replication states and clonal repertoires

EIF4A3 associated splicing and nonsense mediated decay defined by a systems analysis with novel small molecule inhibitors

The paper defines eIF4A3's role in splicing and NMD through a systems analysis using novel small molecule inhibitors and shows its link to cell cycle regulation.