Publications

(2023). WebQUAST: online evaluation of genome assemblies. Nucleic Acids Research.

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(2023). The complete sequence of a human Y chromosome. Nature.

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(2023). Systematic assessment of long-read RNA-seq methods for transcript identification and quantification. bioRxiv.

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(2023). PolyGR and polyPR knock-in mice reveal a conserved neuroprotective extracellular matrix signature in C9orf72 ALS/FTD neurons. bioRxiv.

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(2023). Accurate isoform discovery with IsoQuant using long reads. Nature Biotechnology.

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(2022). The complete sequence of a human genome. Science.

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(2022). Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Nature biotechnology.

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(2022). Sequencing of individual barcoded cDNAs using Pacific Biosciences and Oxford Nanopore Technologies reveals platform-specific error patterns. Genome Research.

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(2022). NPvis: An Interactive Visualizer of Peptidic Natural Product--MS/MS Matches. Metabolites.

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(2022). Fast and accurate mapping of long reads to complete genome assemblies with VerityMap. Genome Research.

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(2022). Complete genomic and epigenetic maps of human centromeres. Science.

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(2022). Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies. Nature methods.

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(2021). The structure, function and evolution of a complete human chromosome 8. Nature.

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(2020). TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats. Bioinformatics.

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(2020). Extending rnaSPAdes functionality for hybrid transcriptome assembly. BMC bioinformatics.

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(2019). MetaMiner: a scalable peptidogenomics approach for discovery of ribosomal peptide natural products with blind modifications from microbial communities. Cell systems.

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(2019). Assembly Graph Browser: interactive visualization of assembly graphs. Bioinformatics.

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(2018). Versatile genome assembly evaluation with QUAST-LG. Bioinformatics.

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(2018). Increased diversity of peptidic natural products revealed by modification-tolerant database search of mass spectra. Nature microbiology.

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(2018). Dereplication of microbial metabolites through database search of mass spectra. Nature communications.

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(2017). MetaRiPPquest: a peptidogenomics approach for the discovery of ribosomally synthesized and post-translationally modified peptides. BioRxiv.

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(2017). Dereplication of peptidic natural products through database search of mass spectra. Nature chemical biology.

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(2016). MetaQUAST: evaluation of metagenome assemblies. Bioinformatics.

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(2016). Icarus: visualizer for de novo assembly evaluation. Bioinformatics.

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(2015). Using Parameters of Protein Oxidative Modifications for Differential Diagnosis of Progressive Ovarian Cancer. ARCHIVOS DE MEDICINA.

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(2015). Using parameters of protein oxidative modifications for differential diagnosis of progressive ovarian cancer. Translational Biomedicine.

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