Harun Mustafa

The Ocean Microbiomics Database reveals thermal niches and projected pressure on marine microbes in a warming ocean

The paper introduces the Ocean Microbiomics Database (OMDB) to analyze microbial thermal niches and predict their response to ocean warming, showing richness declines faster than abundance.

Improving Metagenomics Classification with Kmask: Entropy-Based Masking of Low-Complexity Regions

Kmask reduces misclassifications in metagenomics by masking low-complexity regions, improving accuracy in bacterial, archaeal, viral, and fungal classification.

Indexing All Life's Known Biological Sequences

The paper develops a scalable indexing framework for biological sequences, enabling efficient and cost-effective full-text search across vast genomic datasets.

Aligning Distant Sequences to Graphs using Long Seed Sketches

The paper introduces a long seed sketch method for sequence-to-graph alignment, improving time-accuracy trade-offs in high mutation rate scenarios.

Label-guided seed-chain-extend alignment on annotated De Bruijn graphs

This paper introduces a new alignment method for annotated De Bruijn graphs that improves taxonomic classification accuracy and coverage for long reads.

Lossless Indexing with Counting de Bruijn Graphs

This paper introduces Counting de Bruijn graphs for efficiently indexing and querying sequencing data, achieving smaller storage and faster construction compared to existing methods.

Topology-based Sparsification of Graph Annotations

The paper introduces RowDiff, a method to compactly store graph labels by exploiting annotation similarities, achieving significant space reductions when combined with compression techniques.

AStarix: Fast and Optimal Sequence-to-Graph Alignment

AStarix provides a fast and optimal algorithm for aligning sequences to genome graphs, outperforming existing methods by 1-2 orders of magnitude.

Sparse Binary Relation Representations for Genome Graph Annotation

This paper introduces a new compression method for de Bruijn graph labels, showing improved performance over existing methods on real-world datasets.

Dynamic compression schemes for graph coloring

The paper introduces two compression methods for graph coloring in sequencing data, reducing memory use by up to three orders of magnitude while maintaining dynamic graph topology.

Metannot: A succinct data structure for compression of colors in dynamic de Bruijn graphs

The paper introduces a dynamic data structure called Metannot for compressing and indexing graph metadata in HTS data, achieving better compression ratios than existing methods.