Metin Balaban

Genomic alterations in the YAP/TAZ pathway are associated with stem cell-like castration-resistant prostate cancer

The paper identifies genomic alterations in the YAP/TAZ pathway associated with stem cell-like castration-resistant prostate cancer using transcriptomic and whole-genome sequencing data.

Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics

CalicoST infers allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics data, achieving higher accuracy than existing methods.

Greengenes2 enables a shared data universe for microbiome studies

Greengenes2 aligns 16S rRNA and shotgun metagenomic data using a whole-genome phylogeny, showing agreement in principal coordinates, taxonomy, and phenotype effect size.

DEPP: Deep Learning Enables Extending Species Trees using Single Genes

DEPP extends species trees using single genes by learning to place them without pre-specified models, enabling integration of 16S and metagenomic data.

Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model

The paper introduces an alignment-free method for phylogenetic distance estimation under a no-strand bias model, showing high accuracy in simulations and real data.

Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT

RESPECT estimates genome length and repeat spectra from low-coverage genome skims with <1.5% error, outperforming previous methods.

Fast and Accurate Distance-based Phylogenetic Placement using Divide and Conquer

This paper introduces APPLES-2, a distance-based phylogenetic placement method that is more accurate and scalable than existing methods, enabling efficient placement of microbial genomes on large trees.

On the impact of contaminants on the accuracy of genome skimming and the effectiveness of exclusion read filters

The paper evaluates how contaminant DNA affects genome skimming accuracy and proposes a filtering method using Kraken-II to improve sample identification.

APPLES: Scalable Distance-based Phylogenetic Placement with or without Alignments

APPLES is a distance-based phylogenetic placement method that is faster, more memory efficient, and handles large trees and unassembled reads better than maximum likelihood methods.

TreeCluster: clustering biological sequences using phylogenetic trees

TreeCluster uses phylogenetic trees to cluster biological sequences, improving consistency and downstream application effectiveness.