Ales Varabyou

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

Bramble improves transcript quantification by projecting spliced genomic alignments into transcriptomic coordinates, enhancing accuracy across simulated datasets.

Isocall is a scalable method for joint transcript identification from long-read RNA-seq data, showing high precision and handling large datasets efficiently.

The paper presents HIV Atlas, a reference-quality annotation of HIV-1 and SIV transcriptional diversity, and demonstrates its utility in improving transcriptome analysis.

SPIT detects differential transcript usage in complex diseases by quantifying population heterogeneity and identifying subgroups with distinct DTU events, revealing new events in schizophrenia brain samples.

CHESS 3 improves upon previous versions by using better algorithms and filtering to create a more accurate catalog of human genes and transcripts.

ORFanage identifies ORFs in known and novel transcripts, improving annotations in RefSeq and GENCODE databases and enabling analysis of large RNA-seq datasets.

The paper uses 3D protein structures to evaluate human protein isoforms for biological functionality, refining genome annotations.

This paper introduces Bolotie, a method to detect recombination in SARS-CoV-2 genomes, identifying hundreds of recombinant isolates and showing some persist in the population.

The paper compiles RNA sequencing data from 9,795 experiments to create a new human gene catalog, identifying novel genes and transcripts while highlighting extensive transcriptional noise.