Generation of lineage-resolved complete metagenome-assembled genomes by precision phasing. Nature Biotechnology, in press (2021)

Derek M. Bickhart*, Mikhail Kolmogorov*, Elizabeth Tseng, Daniel Portik, Anton Korobeynikov, Ivan Tolstoganov, Gherman Uritskiy, Ivan Liachko, Shawn T. Sullivan, Sung Bong Shin, Alvah Zorea, Victòria Pascal Andreu, Kevin Panke-Buisse, Marnix H. Medema, Itzik Mizrahi, Pavel Pevzner & Tim Smith

Assembling viruses and identifying their hosts from long-read metagenomics data. Genome Biology, in press (2021)

Dmitry Antipov, Mikhail Rayko, Mikhail Kolmogorov & Pavel Pevzner

Haplotype-aware variant calling with PEPPER-Margin-DeepVariant enables high accuracy in nanopore long-reads. Nature Methods (18) 1322–1332 (2021)

Shafin, K., Pesout, T., Chang, P.C., Nattestad, M., Kolesnikov, A., Goel, S., Baid, G., Kolmogorov, M., Eizenga, J.M., Miga, K.H., Carnevali, P., Jain, M., Carroll, A. & Benedict Paten

Critical Assessment of Metagenome Interpretation - the second round of challenges. bioRxiv (2021)

Meyer, F., Fritz, A., Deng, Z. L., Koslicki, D., Gurevich, A., Robertson, G., (…), Kolmogorov M., (…), McHardy, A. C

The complete sequence of a human genome. bioRxiv (2021)

Nurk, S., Koren, S., Rhie, A., Rautiainen, M., Bzikadze, A. V., Mikheenko, A., (…), Kolmogorov. M, (…), Phillippy, A. M.

Assembling Long and Accurate Reads Using de Bruijn Graphs. bioRxiv (2021)

A Bankevich, A Bzikadze, M Kolmogorov, D. Antipov & PA Pevzner.

metaFlye: scalable and accurate long-read metagenome assembler, Nature Methods (2020)

Mikhail Kolmogorov, Derek M. Bickhart, Bahar Behsaz, Alexey Gurevich, Mikhail Rayko, Sung Bong Shin, Kristen Kuhn, Jeffrey Yuan, Evgeny Polevikov, Timothy P. L. Smith and Pavel A. Pevzner.

Synteny paths for assembly graphs comparison, WABI 24:1-24:14 (2019)

Evgeny Polevikov and Mikhail Kolmogorov

Assembly of long error-prone reads using repeat graphs, Nature Biotechnology 37, 540–546 (2019)

Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin & Pavel Pevzner

Assembly Graph Browser: interactive visualization of assembly graphs. Bioinformatics 35 (18), 3476-3478 (2019)

Alla Mikheenko & Mikhail Kolmogorov

Chromosome assembly of large and complex genomes using multiple references. Genome Research 28 (11), 1720-1732 (2018)

Mikhail Kolmogorov, Joel Armstrong, Brian J. Raney, Ian Streeter, Matthew Dunn, Fengtang Yang, Duncan Odom, Paul Flicek, Thomas Keane, David Thybert, Benedict Paten & Son Pham.

High-quality genome sequences of uncultured microbes by assembly of read clouds. Nature Biotechnology 36, 1067–1075 (2018)

Alex Bishara, Eli L Moss, Mikhail Kolmogorov, Alma Parada, Ziming Weng, Arend Sidow, Anne E Dekas, Serafim Batzoglou, Ami S Bhatt.

Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional loci. Nature Genetics 50, 1574–1583 (2018)

Jingtao Lilue, Anthony G Doran, Ian T Fiddes, Monica Abrudan, (…), Mikhail Kolmogorov, (…), Benedict Paten, Thomas M Keane

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes. Genome Research 28 (4), 448-459 (2018)

David Thybert, Maša Roller, Fábio CP Navarro, Ian Fiddes, Ian Streeter, Christine Feig, David Martin-Galvez, Mikhail Kolmogorov, (…), Paul Flicek

Single-Molecule Protein Identification by Sub-Nanopore Sensors. PloS Computational Biology 13 (5), e1005356 (2017)

Mikhail Kolmogorov, Eamonn Kennedy, Zhuxin Dong, Gregory Timp and Pavel Pevzner

Assembly of long error-prone reads using de Bruijn graphs. PNAS 113 (52), E8396-E8405, (2016),

Yu Lin*, Jeffrey Yuan*, Mikhail Kolmogorov*, Max Shen and Pavel Pevzner

SpectroGene: a tool for proteogenomic annotations using top-down spectra. Journal of Proteome Research 15 (1), 144-151 (2015)

Mikhail Kolmogorov, Xiaowen Liu and Pavel Pevzner

Ragout - a reference-assisted assembly tool for bacterial genomes. Bioinformatics 30 (12), i302-i309 (2014)

Mikhail Kolmogorov, Brian Raney, Benedict Paten, Son Pham

Sibelia: a scalable and comprehensive synteny block generation tool for closely related microbial genomes. WABI (2013)

Ilya Minkin, Anand Patel, Mikhail Kolmogorov, Nikolay Vyahhi, Son Pham