İnanç Birol

biHash is a rolling hash algorithm designed for bisulfite-sequenced data, offering faster hashing by recognizing bisulfite-compatible sequence states.

ntSynt-viz sorts genomes and chromosomes by synteny, normalizes strands, and draws chromosome-painting ribbon plots easier to interpret than NGenomeSyn output for human and hoverfly genomes.

The paper analyzes disease-associated tandem repeat loci across diverse populations using long-read data, revealing ancestry-specific variation and complex genotype-phenotype relationships.

The paper introduces Stash, a hash-based data structure for detecting genome misassemblies using Pacbio HiFi reads, showing it reduces misassemblies in human genome assemblies.

The paper introduces triAMPh, a framework for predicting pathogen-specific antimicrobial peptide activity using biological large language models, showing it matches or outperforms existing methods.

aaKomp provides a fast, memory-efficient, alignment-free method for genome completeness assessment, outperforming existing tools in speed and scalability.

The paper creates a comprehensive catalog of tandem repeat loci in the human genome using long-read sequencing data from 272 genomes.

The paper compares self-declared and genome-inferred ancestry in 10,250 HostSeq participants, finding high concordance for some groups and lower for others, highlighting the complexity of admixture and the need for complementary approaches.

The paper introduces ntSynt, a tool for detecting multi-genome synteny blocks using minimizer graphs, showing high coverage and efficiency across diverse genomes.

This study evaluates three AI-identified antimicrobial peptides for efficacy and safety against avian pathogenic Escherichia coli in poultry, showing improved survival and immune modulation without adverse effects.

The paper uses long-read sequencing to analyze HPV integration sites in cervical cancer genomes, identifying structural and epigenetic impacts of integration.

The paper identifies novel antimicrobial peptides from the UniProtKB/Swiss-Prot database using AMPlify, prioritizing 40 for chicken applications and testing 38 for antimicrobial activity.

GoldPolish-Target polishes targeted regions of genome assemblies, reducing errors and improving accuracy with lower computational demands.

ntRoot infers human super-population ancestry from genomic data with high accuracy and efficiency, outperforming traditional methods on large datasets.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

The paper identifies dense NLR gene clusters on single chromosomes in conifers, showing widespread genomic architecture and evolutionary significance.

ntEmbd is a deep learning tool for nucleotide sequence embedding, demonstrating utility in RNA classification and adapter sequence identification.

GoldRush is a de novo long read genome assembler with linear time complexity, achieving efficient assembly of large genomes with high contiguity and low memory usage.

RNA-Bloom2 is a reference-free transcriptome assembler for long-read data, showing competitive performance with reference-based methods and lower resource usage.

aaHash is a recursive amino acid sequence hashing algorithm that improves speed and sensitivity for protein sequence analysis.

Meta-NanoSim simulates and characterizes nanopore metagenomic data to improve microbial abundance estimation and guide algorithm development.

AMPlify is a deep learning model that predicts antimicrobial peptides from bullfrog genomes, identifying novel peptides effective against WHO priority pathogens including drug-resistant bacteria.

LongStitch improves draft genome assemblies using long reads, significantly increasing contiguity and accuracy compared to existing methods.

The paper uses in silico HLA predictions from COVID-19 patients to identify alleles associated with disease prognosis, finding significant associations with A*11:01, C*04:01, and DQA1*01:02.

The paper evaluates STR detection tools and develops a pipeline to identify pathogenic expansions in exome/genome data, finding 27 samples with STR mutations in 306 families.

ntHits identifies repeat elements in genomics data using a streaming algorithm, efficiently detecting repetitive k-mers with high accuracy and low resource usage.

RNA-Bloom is a de novo RNA-seq assembler for scRNA-seq data that reconstructs cell-specific isoforms and detects gene fusions, outperforming bulk RNA-seq methods.

Trans-NanoSim simulates nanopore RNA-seq reads using features learned from real data, enabling cost-effective development of analytical tools.

The paper sequences and assembles the largest complete mitochondrial genome of a gymnosperm, Sitka spruce, revealing a complex multipartite structure.

Terminitor predicts polyadenylation cleavage sites from RNA-seq data, outperforming existing tools in sensitivity and precision on experimental data.