M. Kolmogorov

发表

High-quality genome sequences of uncultured microbes by assembly of read clouds

Serafim Batzoglou, Arend Sidow, Alex Bishara, 2018, Nature Biotechnology.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Mark Gerstein, Benedict Paten, Paul Flicek, 2017, bioRxiv.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Son K. Pham, Ian T. Fiddes, Bronwen L. Aken, 2017, bioRxiv.

Culture-free generation of microbial genomes from human and marine microbiomes

S. Batzoglou, Alex Bishara, Z. Weng, 2018, bioRxiv.

metaFlye: scalable long-read metagenome assembly using repeat graphs

P. Pevzner, D. Bickhart, Jeffrey Yuan, 2019, Nature Methods.

Chromosome assembly of large and complex genomes using multiple references

Son K. Pham, Thomas M. Keane, Fengtang Yang, 2016, bioRxiv.

Semi-automated assembly of high-quality diploid human reference genomes

Ira M. Hall, Nathan D. Olson, Mark J. P. Chaisson, 2022, bioRxiv.

The complete sequence of a human genome

Aaron M. Streets, Ira M. Hall, Nathan D. Olson, 2021, bioRxiv.

Assembly of long error-prone reads using de Bruijn graphs

Pavel A. Pevzner, Mark Chaisson, Yu Lin, 2016, Proceedings of the National Academy of Sciences.

Assembly of long, error-prone reads using repeat graphs

Yu Lin, Pavel A. Pevzner, Jeffrey Yuan, 2018, Nature Biotechnology.

Assembly of long, error-prone reads using repeat graphs

Yu Lin, Pavel A. Pevzner, Jeffrey Yuan, 2018, Nature Biotechnology.

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads

Jordan M. Eizenga, Karen H. Miga, B. Paten, 2021, Nature Methods.

Sixteen diverse laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Mark Gerstein, Jane Loveland, Dent Earl, 2018, Nature Genetics.

Sixteen diverse laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Son K. Pham, Thomas M. Keane, Ian T. Fiddes, 2018, Nature Genetics.

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities

Victòria Pascal Andreu, P. Pevzner, D. Bickhart, 2022, Nature Biotechnology.

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

Mark Gerstein, Jane Loveland, Dent Earl, 2018, bioRxiv.

viralFlye: assembling viruses and identifying their hosts from long-read metagenomics data

P. Pevzner, M. Kolmogorov, D. Antipov, 2022, Genome biology.

Critical Assessment of Metagenome Interpretation: the second round of challenges

K. Reinert, E. Eskin, F. Beghini, 2021, Nature Methods.

Single-molecule protein identification by sub-nanopore sensors

Pavel A. Pevzner, Eamonn Kennedy, Gregory Timp, 2016, PLoS Comput. Biol..

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities

Victòria Pascal Andreu, P. Pevzner, D. Bickhart, 2022, Nature Biotechnology.

Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing

Victòria Pascal Andreu, P. Pevzner, D. Bickhart, 2021, bioRxiv.

stRainy: assembly-based metagenomic strain phasing using long reads

M. Pop, M. Kolmogorov, Ataberk Donmez, 2023, bioRxiv.

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

Sonja W. Scholz, Mark J. P. Chaisson, Karen H. Miga, 2023, Nature Methods.

Assembly Graph Browser: interactive visualization of assembly graphs

Alla Mikheenko, Mikhail Kolmogorov, M. Kolmogorov, 2019, Bioinform..

Multiplex de Bruijn graphs enable genome assembly from long, high-fidelity reads

P. Pevzner, A. Bzikadze, M. Kolmogorov, 2022, Nature Biotechnology.

Ragout—a reference-assisted assembly tool for bacterial genomes

Brian J. Raney, Benedict Paten, Son K. Pham, 2014, Bioinform..

LJA: Assembling Long and Accurate Reads Using Multiplex de Bruijn Graphs

Pavel A. Pevzner, Anton Bankevich, Andrey Bzikadze, 2020, bioRxiv.

SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra.

Pavel A Pevzner, Xiaowen Liu, Mikhail Kolmogorov, 2016, Journal of proteome research.

Sibelia: A Scalable and Comprehensive Synteny Block Generation Tool for Closely Related Microbial Genomes

Nikolay Vyahhi, Son K. Pham, Ilya Minkin, 2013, WABI.

Scalable Nanopore sequencing of human genomes provides a comprehensive view of haplotype-resolved variation and methylation

Sonja W. Scholz, Mark J. P. Chaisson, Karen H. Miga, 2023, bioRxiv.

Analyzing rare mutations in metagenomes assembled using long and accurate reads

Marcus W. Fedarko, P. Pevzner, M. Kolmogorov, 2022, Genome research.

Assembly of Long Error-Prone Reads Using Repeat Graphs

P. Pevzner, Jeffrey Yuan, M. Kolmogorov, 2018, bioRxiv.

Insights into the Mechanisms and Structure of Breakage-Fusion-Bridge Cycles in Cervical Cancer using Long-Read Sequencing

Daria A. Gaykalova, M. Carrington, C. Blauwendraat, 2023, medRxiv.

Synteny Paths for Assembly Graphs Comparison

Mikhail Kolmogorov, Evgeny Polevikov, M. Kolmogorov, 2019, WABI.

Semi-automated assembly of high-quality diploid human reference genomes

Ira M. Hall, Nathan D. Olson, Mark J. P. Chaisson, 2022, Nature.

Assembly of Long Error-Prone Reads and Repeat Classification

Yu Lin, Pavel A. Pevzner, Jeffrey Yuan, 2018, RECOMB 2018.

metaFlye: scalable long-read metagenome assembly using repeat graphs

Kristen Kuhn, Alexey Gurevich, Bahar Behsaz, 2020, Nature Methods.