Pavel A. Pevzner

The paper presents haplotype-resolved genomes of six ape species with high accuracy and provides comparative analyses to study evolutionary diversity and gene family evolution.

SpLitteR improves diploid genome assembly using linked TELL-Seq reads and assembly graphs, achieving higher contiguity without additional misassemblies.

TandemAligner provides a parameter-free sequence alignment framework for accurately analyzing extra-long tandem repeats, revealing high mutation rates and structural changes in centromeres.

HORmon automates human centromere annotation by integrating monomer and HOR inference, producing results consistent with prior semi-manual studies.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

The paper presents a comprehensive analysis of fully assembled human centromeres, revealing their architecture, variation, and evolutionary dynamics at high resolution.

This paper introduces LJA, an algorithm that improves genome assembly using long accurate reads by constructing multiplex de Bruijn graphs and reducing error rates.

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 centroFlye, an algorithm for assembling centromeres using long error-prone reads, and applies it to the human X centromere to identify potential breakpoints and improve reference genome gaps.

The paper presents a gapless, telomere-to-telomere assembly of the human X chromosome using ultra-long-read nanopore sequencing and complementary technologies.

The paper introduces a low-cost, high-accuracy method for generating long-range sequencing data using short-read NGS systems, enabling de novo genome assembly and haplotype phasing with minimal DNA input.

The paper introduces a StringDecomposer algorithm to translate long reads into centromere monomers, identifying a novel monomer that improves centromere assembly.

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

mosaicFlye improves genome assemblies by resolving unbridged repeats in human, bacterial, and metagenomic datasets.

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

Building the repeat graph from fast, possibly misassembled contigs lets Flye resolve repeats and produce more contiguous long-read assemblies, with fewer errors than Canu on human and worm genomes.

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

The paper introduces AbScan, a proteogenomic method to identify antibody peptides from RNA-seq data, and applies it to colorectal cancer samples to find correlations between antibody peptides and survival.

This paper introduces a de Bruijn graph-based assembler for long error-prone reads, achieving more accurate genome reconstructions than existing methods.