Paul Medvedev

The paper derives a formula (Z-value) to predict contig length from read length, coverage, and genome properties, showing high accuracy and practical applications for assembler choice and experimental design.

The paper introduces resources for large-scale metagenome comparison in the SRA, revealing trends in microbial discovery and improving assembly quality.

This paper develops k-mer-based estimators for substitution, insertion, and deletion mutation rates, showing improved accuracy when accounting for indels in mutation models.

This paper introduces a k-mer-based estimator for substitution rates between repetitive sequences, showing it remains accurate for repetitive genomic regions like centromeres.

This paper introduces three repeat-robust k-mer-based mutation rate estimators and evaluates them on highly repetitive alpha satellite sequences, finding that the strongest estimator outperforms existing methods.

The paper introduces CaPLa, a measure to predict the performance of learned indexes on genomic k-mer data, showing it varies across genomes and can predict space bounds.

Assembling the Sequence Read Archive (27.3 million accessions) with over 100-fold compression enables minutes-scale k-mer search and mining of enzymes, plasmids, proteins and viral reactivation.

The paper produces gapless assemblies of ape sex chromosomes for five great apes and a lesser ape, revealing divergence in Y chromosomes and evolutionary dynamics.

This paper introduces an exact sketch-based read mapping algorithm that finds all mapping positions above a similarity threshold, achieving higher recall than minimap2 on long reads of the human Y chromosome.

The paper introduces PLA-complexity as a measure of k-mer multiset structure and presents PLA-index for efficient approximation and querying of rank functions in genomic data.

The paper introduces an efficient algorithm for assessing annotation colocalization with genomic context, improving speed and handling new statistical models.

The paper analyzes transcript isoform diversity of Y-chromosomal ampliconic genes in six great ape species using long-read sequencing and identifies evolutionary patterns and pseudogenization trends.

The paper presents the complete sequence of a human Y chromosome, correcting errors in the GRCh38 reference and adding over 30 million base pairs.

mapquik accelerates long-read mapping by using minimizer-space seeding and a pseudo-chaining algorithm, achieving high sensitivity and speed on human and maize genomes.

The paper introduces a new compression tool for colored de Bruijn graphs, achieving better compression than existing tools across various datasets.

The paper improves genome assembly contiguity by integrating the omnitig framework into existing assemblers using simplified algorithms, showing better alignment-based contiguity with minimal computational cost.

This paper identifies theoretical and practical issues with unitig-based genome assembly, showing that unitigs can be unsafe and lead to under-assembly even with error-free data.

The paper shows that the minimizer Jaccard estimator is biased and inconsistent, affecting the accuracy of sequence similarity estimation and a read mapping tool.

The paper introduces MCDP, a tool that computes p-values for genome annotation overlaps using Markov chains, improving efficiency and accuracy over existing methods.

The paper analyzes the statistical properties of k-mers under a mutation process and develops hypothesis tests and confidence intervals for mutation rates using k-mer counts and Jaccard similarity.

kmtricks improves Bloom filter construction for large sequencing data by efficiently counting k-mers and preserving low-abundant ones, enhancing metagenomics analysis.

The paper studies the molecular evolution of a recently endogenized retrovirus in mule deer, showing increased diversity through horizontal acquisition and recombination.

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

The paper introduces isONcorrect, a method to error correct Oxford Nanopore cDNA data, enabling reference-free transcriptome analysis with high accuracy.

The paper surveys computational methods for indexing and querying large sequencing datasets using k-mer-based data structures.

SibeliaZ improves scalability of multiple whole-genome alignment and collinear block reconstruction on a single machine.

The paper introduces isONclust, a greedy, quality-value based algorithm for clustering long-read transcriptome data, showing improved accuracy and scalability over existing methods.

The paper introduces HowDe-SBT, an improved indexing method for RNA-seq data that reduces construction time, space, and query time compared to existing SBT methods.

Pacasus corrects artificial palindromic errors in long reads after whole-genome amplification, improving mapping and assembly results.

IsoCon improves transcript reconstruction of highly similar multigene family transcripts using long-read sequencing, detecting rare variants and novel isoforms in Y ampliconic gene families.