Mark Yu. Borodovsky

HPVarcall: Calling lineages and sublineages for partial DNA sequences of human papillomavirus

HPVarcall assigns HPV variant sequences to lineages and sublineages using statistical models trained on sublineage-specific genomic alignments, achieving high accuracy for sequences of 1000 nucleotides or longer.

A new gene finding tool GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes.

GeneMark-ETP improves gene prediction accuracy in large eukaryotic genomes by integrating genomic, transcriptomic, and protein evidence, outperforming existing tools.

BRAKER3: Fully Automated Genome Annotation Using RNA-Seq and Protein Evidence with GeneMark-ETP, AUGUSTUS and TSEBRA

BRAKER3 improves eukaryotic genome annotation by integrating RNA-seq, protein data, and statistical models, achieving higher accuracy than previous tools.

A chromosome-length genome assembly and annotation of blackberry (Rubus argutus, cv. Hillquist)

The paper presents a chromosome-length genome assembly and annotation of the blackberry species Rubus argutus, identifying candidate genes for primocane-fruiting.

MetaGeneMark-2: Improved Gene Prediction in Metagenomes

Gene caller that models GC-dependent ribosome binding and leaderless-promoter signals and detects TGA stop-codon reassignment, reported as more accurate than existing metagenomic gene finders.

Annotation of Phage Genomes with Multiple Genetic Codes

The paper develops a tool to annotate phage genomes using multiple genetic codes and identifies viral contigs with such features in human gut microbiome data.

TSEBRA: Transcript Selector for BRAKER

TSEBRA selects gene predictions from BRAKER1 and BRAKER2 outputs by comparing transcript scores based on RNA-seq and protein evidence, achieving higher accuracy than either pipeline alone.

BRAKER2: Automatic Eukaryotic Genome Annotation with GeneMark-EP+ and AUGUSTUS Supported by a Protein Database

BRAKER2 improves eukaryotic genome annotation by integrating GeneMark-EP+ and AUGUSTUS with cross-species protein sequences, achieving higher accuracy than MAKER2 and BRAKER1 in certain conditions.

Disproportionate presence of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii

The paper identifies a disproportionate incorporation of adenosine in mitochondrial and chloroplast DNA of Chlamydomonas reinhardtii compared to nuclear DNA, linked to elevated ATP levels.

StartLink+: Prediction of Gene Starts in Prokaryotic Genomes by an Algorithm Integrating Independent Sources of Evidence

StartLink+ improves gene start prediction in prokaryotic genomes by integrating ab initio and multiple sequence alignment methods, achieving 98-99% accuracy on verified genes.

GeneMark-EP and -EP+: eukaryotic gene prediction with self-training in the space of genes and proteins

The paper introduces GeneMark-EP and -EP+, which improve eukaryotic gene prediction by integrating protein database information, showing better accuracy than previous methods, especially in large genomes.

Improved Prokaryotic Gene Prediction Yields Insights into Transcription and Translation Mechanisms on Whole Genome Scale

The paper introduces GeneMarkS-2, an improved gene prediction algorithm that identifies diverse gene expression signals and reveals insights into prokaryotic transcription and translation mechanisms across genomes.