Alexey A. Gurevich

BGC-QUAST evaluates and compares BGC predictions across samples, assemblies, and tools to facilitate biosynthetic potential analysis.

The paper presents 154 new Myxococcota genomes, expands taxonomy, and identifies novel natural products, highlighting their biosynthetic potential for drug discovery.

Nerpa 2 links biosynthetic gene clusters to nonribosomal peptides using probabilistic models, improving accuracy and scalability in pathway reconstruction.

GRIP predicts gradient retention times using physics-informed neural networks, showing zero-shot generalization and performance comparable to transfer learning baselines.

The paper introduces the BGC Atlas, a web resource that explores BGC diversity in metagenomes, identifying nearly 1.8 million BGCs and showing RiPPs as the most abundant compound class.

ABC-HuMi catalogs 19,218 biosynthetic gene clusters from the human microbiome, offering a comprehensive resource for exploring bioactive compound potential.

NPOmix connects mass spectrometry fragmentation data to biosynthetic gene clusters using a k-nearest neighbor classifier, improving metabolite discovery and structure prediction.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

molDiscovery improves small molecule identification by learning fragmentation patterns from mass spectra, achieving higher efficiency and accuracy than existing methods.

This tutorial explains how to use the CAMI benchmarking toolkit to evaluate metagenomics software performance using standardized datasets and metrics.

metaFlye improves metagenome assembly using long-read sequencing, producing more contiguous and accurate assemblies with better reconstruction of 16S RNA genes and novel plasmids/viruses.

The paper introduces FBMN, a method for improving molecular networking by enhancing quantitative analysis and isomer distinction using feature detection and alignment tools in the GNPS platform.

The paper introduces tandemMapper and tandemQUAST to map long reads to extra-long tandem repeats and improve their assembly quality.

The paper introduces CycloNovo, a de novo cyclopeptide sequencing algorithm, revealing a vast hidden cyclopeptidome in the human gut and other environments.

MetaRiPPquest identifies RiPPs by combining genome/metagenome mining with mass spectrometry analysis, discovering 5 novel natural products from 6 datasets.

The paper benchmarks computational metagenomics software using complex datasets, showing strengths and limitations in assembly, binning, and taxonomic profiling.