Ali Osman Berk Şapcı

DecoDiPhy deconvolves phylogenetic distance mixtures to improve interpretability and downstream analysis in metagenomics.

Phlag detects genomic regions with inconsistent evolutionary processes by modeling gene trees as a stochastic process along the genome.

SPrUCE estimates genetic diversity from UCE data by correcting underestimation bias using a Gompertz function model, providing accurate results comparable to whole-genome methods.

The paper introduces krepp, a k-mer-based method for phylogenetic placement of reads on large reference phylogenies, showing improved scalability and accuracy compared to alignment-based methods.

This paper introduces KRANK, a k-mer selection algorithm that reduces memory usage while maintaining classification accuracy in taxonomic profiling.

CONSULT-II improves taxonomic classification and profiling by combining locality-sensitive hashing with heuristics, achieving higher accuracy for novel species.

FlyVISTA is a machine learning platform that identifies sleep-associated microbehaviors in Drosophila by analyzing high-resolution video data and annotating body parts.

MuDCoD detects dynamic gene communities across multiple subjects and time points in scRNA-seq data, revealing subject- and time-specific network variations.