Andrey V. Bzikadze

Trex-QTL: A mixture-model for identification of genetic effects with global effects on molecular phenotypes

Trex-QTL identifies trans-eQTLs with global effects on molecular phenotypes, showing improved power and replicating known loci in rat brain data.

A complete diploid human genome benchmark for personalized genomics

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

The complete sequence of a human Y chromosome

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

TandemAligner: a new parameter-free framework for fast sequence alignment

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: automated annotation of human centromeres

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

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

The paper improves a telomere-to-telomere human genome assembly by developing a repeat-aware polishing strategy, fixing 51% of errors and increasing assembly quality.

The complete sequence of a human genome

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.

Complete genomic and epigenetic maps of human centromeres

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

Assembling Long Accurate Reads Using Multiplex de Bruijn Graphs

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

The structure, function, and evolution of a complete human chromosome 8

This paper completes the linear assembly of human chromosome 8, resolves long-standing gaps, and analyzes the evolutionary history of its centromeric regions across great apes.

centroFlye: Assembling Centromeres with Long Error-Prone Reads

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.

Telomere-to-telomere assembly of a complete human X chromosome

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

The String Decomposition Problem and its Applications to Centromere Assembly

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

TandemMapper and TandemQUAST: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats

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