Mahmudur Rahman Hera

Estimation of substitution and indel rates via k-mer statistics

This paper develops k-mer-based estimators for substitution, insertion, and deletion mutation rates, showing improved accuracy when accounting for indels in mutation models.

Leveraging FracMinHash Containment for Genomic dN/dS

This paper introduces FracMinHash dN/dS, an alignment-free method to estimate dN/dS ratios across genomes, showing it is scalable and comparable to traditional methods.

MaxGeomHash: An Algorithm for Variable-Size Random Sampling of Distinct Elements

The paper introduces a new sketching algorithm for genomic sequences that produces sub-linear sketches, balancing efficiency and accuracy between MinHash and FracMinHash.

Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation

This paper introduces a theoretical framework for estimating cosine similarity using FracMinHash sketches and presents a fast implementation called frac-kmc.

Fast, lightweight, and accurate metagenomic functional profiling using FracMinHash sketches

This paper introduces fmh-funprofiler, a fast and lightweight metagenomic functional profiler using FracMinHash sketches, showing improved purity and speed compared to alignment-based methods.

Debiasing FracMinHash and deriving confidence intervals for mutation rates across a wide range of evolutionary distances

This paper analyzes FracMinHash, showing it can be corrected for bias and used to estimate mutation distances with confidence intervals.

Lightweight compositional analysis of metagenomes with FracMinHash and minimum metagenome covers

Greedy minimum set cover over FracMinHash k-mer sketches selects a small set of reference genomes explaining a metagenome, supporting species-level taxonomic profiling and choice of genomes for read mapping.

kRISP-meR: A Reference-free Guide-RNA Design Tool for CRISPR/Cas9

kRISP-meR designs CRISPR/Cas9 guide RNAs without a reference genome, achieving specificity similar to reference-based tools.