Publications

1. Shlemov A. , Dvorkina T. , Antipov D. , Nurk S. , Korobeynikov A. Tools for assembly graph analysis via SPAdes toolbox and more (talk), 2019
2. Antipov D. , Bushmanova E. , Dvorkina T. , Gurevich A. , Kunyavskaya O. , Shlemov A., Lapidus A. , Meleshko D. , Nurk S. , Prjibelski A. , Korobeynikov A. SPAdes Family of Tools for Genome Assembly and Analysis (poster), 2019
3. Korobeynikov A. , Antipov D. , Bushmanova E. , Gurevich A. , Lapidus A. , Meleshko D. , Mikheenko A. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2018
4. Korobeynikov A. , Antipov D. , Bushmanova E. , Gurevich A. , Lapidus A. L. , Meleshko D. , Mikheenko A. , Nurk S. , Prjibelski A. , and Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: Current Status (poster), 2018
5. Nurk S., Meleshko D., Korobeynikov A., Pevzner P. A. metaSPAdes: a new versatile de novo metagenomics assembler. Genome Research, 2017
6. Nurk S., Gorshkov Y., Pevzner P.A. Reconstructing individual genomes from multiple metagenomic samples with MTS pipeline. Manuscript in preparation., 2017
7. Korobeynikov A. , Antipov D. , Bankevich A. , Bushmanova E. , Lapidus A. , Meleshko D. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes: is there anything new we could develop? (talk), 2017
8. Lapidus A. , Antipov D. , Bankevich A. , Bushmanova E. , Korobeynikov A. , Meleshko D. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2017
9. Korobeynikov A. , Antipov D. , Bankevich A. , Bushmanova E. , Gurevich A. , Lapidus A. , Meleshko D. , Nurk S. , Prjibelski A. , Pevzner P. A. SPAdes Family of Tools for Genome Assembly and Analysis: What’s New? (poster), 2017
10. Nurk S. Assembly of metagenomic (series) data with SPAdes instruments (talk), 2017
11. Nurk S. Past, present and future of metaSPAdes metagenomic assembler (talk), 2017
12. Guzman G. I., Utrilla J., Nurk S., Brunk E., Monk J. M., Ebrahim A., Palsson B. A., Feist A. M. Model-driven discovery of underground metabolic functions in Escherichia coli. Proceedings of the National Academy of Sciences, 2015
13. Prjibelski A., Vasilinetc I., Bankevich A., Gurevich A., Krivosheeva T., Nurk S., Pham S., Korobeynikov A., Lapidus A., Pevzner P. A. ExSPAnder: a universal repeat resolver for DNA fragment assembly. Bioinformatics, 2014
14. Lin Y., Nurk S., Pevzner P. A. What is the difference between the breakpoint graph and the de Bruijn graph? BMC Genomics, 2014
15. Nurk S., Bankevich A., Antipov D., Gurevich A., Korobeynikov A., Lapidus A., Prjibelski A., Pyshkin A., Sirotkin A., Sirotkin Y., Stepanauskas R., Clingenpeel S. R., Woyke T., Mclean J. S., Lasken R., Tesler G., Alekseyev M. A., Pevzner P. A. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. Journal of Computational Biology, 2013
16. McLean J. S., Lombardo M.-J., Ziegler M. G., Novotny M., Yee-Greenbaum J., Badger J. H., Tesler G., Nurk S., Lesin V., Brami D., Hall A. P., Edlund A., Allen L. Z., Durkin S., Reed S., Torriani F., Nealson K. H., Pevzner P. A., Friedman R. M., Venter J. C., Lasken R. S. Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform. Genome Research, 2013
17. Bankevich A., Nurk S., Antipov D., Gurevich A., Dvorkin M., Kulikov A. S., Lesin V., Nikolenko S., Pham S., Prjibelski A., Pyshkin A., Sirotkin A., Vyahhi N., Tesler G., Alekseyev M. A., Pevzner P. A. SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing. Journal of Computational Biology, 2012
18. Nurk S. An Upper Bound for Circuit SAT. PDMI preprint 10/2009, 2009