João M. Alves

Expansion, functional diversification and gene fusion events in the Ato protein family

This study investigates the role of Ato proteins in carboxylic acid utilization in Candida albicans, revealing functional diversity and regulatory interactions among Ato family members.

Unraveling the phylogenetic signal of gene expression from single-cell RNA-seq data

This study evaluates six methods for calling single-nucleotide variants from scRNA-seq data and finds that some methods provide phylogenetically informative genotype calls, with implications for understanding cancer progression.

Single-cell phylodynamics reveal rapid late-stage colorectal cancer expansions

The paper uses single-cell whole-genome sequencing and Bayesian phylodynamic modeling to show colorectal tumors often originate decades before diagnosis and expand rapidly in the last two years.

Genomic Insights Guiding Personalized First-Line Immunotherapy Response in Lung and Bladder Tumors

This study identifies mutation patterns, TMB, HLA haplotypes, and LINE-1 activation as potential biomarkers for predicting ICI response in NSCLC and MIBC.

Intraline genomic heterogeneity of the triple-negative breast cancer MDA-MB-231 cell line

The paper examines genomic diversity within the MDA-MB-231 breast cancer cell line across sublines, identifying intraline heterogeneity driven by single nucleotide variants and copy number alterations.

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

SIEVE: joint inference of single-nucleotide variants and cell phylogeny from single-cell DNA sequencing data

SIEVE jointly infers somatic variants and cell phylogeny from scDNA-seq data, showing improved accuracy in both tasks compared to existing methods.

Comparative analysis of capture methods for genomic profiling of circulating tumor cells in colorectal cancer

This study compares genomic profiling of circulating tumor cells (CTCs) using three methods in metastatic colorectal cancer, finding differences in mutational burden and diversity estimates.

Single-cell mtDNA heteroplasmy in colorectal cancer

This study sequences single-cell mitochondrial genomes from colorectal cancer patients to investigate mtDNA heteroplasmy in normal and tumor cells.

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data

CellPhy infers single-cell phylogenies from scDNA-seq data using a maximum likelihood framework, showing robustness to errors and superior accuracy and speed compared to existing methods.

Sensitivity to sequencing depth in single-cell cancer genomics

This study evaluates how sequencing depth affects single-cell cancer genomics, finding that depths >5x do not significantly improve variant detection or phylogenetic reconstruction for large sample sizes.

Biased evolutionary inferences from bulk tumor samples

The paper shows that using bulk tumor data can lead to incorrect evolutionary inferences in cancer studies.