Publications

Publications:

1. Anton Bankevich, Andrey Bzikadze, Mikhail Kolmogorov, Pavel Pevzner, “Assembling Long Accurate Reads Using Multiplex de Bruijn Graphs”, Nat. Biotechnology (2022), presented at RECOMB 2021, SMRT Leiden and PAG 2022.

2. Tatiana Dvorkina, Anton Bankevich, Alexei Sorokin, Fan Yang, Boahemaa Adu-Oppong, Ryan Williams, Keith Turner, Pavel A Pevzner, “ORFograph: search for novel insecticidal protein genes in genomic and metagenomic assembly graphs”, Microbiome (2021)

3. Anton Bankevich, Pavel A. Pevzner, “mosaicFlye: Resolving long mosaic repeats using long error-prone reads”, bioRxiv (2020), presented at RECOMB 2020, under review in Nat. Methods (presented at RECOMB 2020)

4. Jon G. Sanders, Sergey Nurk, Zhenjiang Z. Xu, Qiyun Zhu, Feng Chen, Brigid S. Boland, Greg C. Humphrey, James Gaffney, Kristen Jepsen, Mahdieh Khosroheidari, Cliff Green, Anton Bankevich, Erich Jaeger, Ali Moshrefi, John T. Chang, William J. Sandborn, Larry Smarr, Pavel A. Pevzner, Rob Knight, “Optimizing sequencing protocols for leaderboard metagenomics by combining long and short reads,'' Genome Biology (2019), 20, p. 226.

5. Ivan Tolstoganov, Anton Bankevich, Zhoutao Chen, Pavel A Pevzner, “cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs.”, Bioinformatics (2019), 35(14), pp. i61–i70 (presented at ISMB 2019)

6. Anton Bankevich, Pavel A. Pevzner, “Joint Analysis of Long and Short Reads Enables Accurate Estimates of Microbiome Complexity.”, Cell Systems (2018), 7(2), pp. 192-200 (presented at RECOMB 2018)

7. Soonok Kim, Yun Sung Cho, Hak-Min Kim, Oksung Chung, Hyunho Kim, Sungwoong Jho, Hong Seomun, Jeongho Kim, Woo Young Bang, Changmu Kim, Junghwa An, Chang Hwan Bae, Youngjune Bhak, Sungwon Jeon, Hyejun Yoon, Yumi Kim, JeHoon Jun, HyeJin Lee, Suan Cho, Olga Uphyrkina, Aleksey Kostyria, John Goodrich, Dale Miquelle, Melody Roelke, John Lewis, Andrey Yurchenko, Anton Bankevich, Juok Cho, Semin Lee, Jeremy S Edwards, Jessica A Weber, Jo Cook, Sangsoo Kim, Hang Lee, Andrea Manica, Ilbeum Lee, Stephen J O’Brien, Jong Bhak, Joo-Hong Yeo, “Comparison of carnivore, omnivore, and herbivore mammalian genomes with a new leopard assembly”, Genome Biology (2016), 17(1), p. 211

8. Anton Bankevich, Pavel A. Pevzner, “TruSPAdes: Barcode Assembly of TruSeq Synthetic Long Reads”, Nature Methods (2016), 13, pp. 248–50

9. Yana Safonova, Anton Bankevich, Pavel A. Pevzner, “dipSPAdes: an assembler for highly polymorphic diploid genomes”, Journal of Computational Biology (2015) 22(6), 528-45 (presented at RECOMB 2014)

10. Andrey D. Prjibelski, Irina Vasilinetc, Anton Bankevich, Alexey Gurevich, Tatiana Krivosheeva, Sergey Nurk, Son Pham, Anton Korobeynikov, Alla Lapidus and Pavel A. Pevzner, “ExSPAnder: a universal repeat resolver for DNA fragment assembly”, Bioinformatics (2014), 30 (12), pp. i293-i301 (presented at ISMB 2014)

11. Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey Prjibelsky, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLean, Roger Lasken, Scott R. Clingenpeel, Tanja Woyke, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner,  “Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads”, Journal of Computational Biology (2013), 20(10), pp. 714-37 (presented at RECOMB 2013)

12. Anton Bankevich, Sergey Nurk, Dmitry Antipov, Alexey Gurevich, Mikhail Dvorkin, Alexander Kulikov, Valery Lesin, Sergey Nikolenko, Son Pham, Andrey Prjibelski, Alexey Pyshkin, Alexander Sirotkin, Nikolay Vyahhi, Glenn Tesler, Max Alekseyev and Pavel Pevzner “SPAdes: a New Genome Assembler and its Applications to Single Cell Sequencing”, Journal of Computational Biology (2012), 19(5), pp. 714-37

13. A. V. Bankevich, “Bounds of the number of leaves of spanning trees in graphs without triangles”, Journal of Mathematical Sciences (2012), 184(5), pp 557-563.

14. A. V. Bankevich, D. V. Karpov “Bounds of the number of leaves of spanning trees” Journal of Mathematical Sciences (2012), 184(5), pp 564-572.

Papers accepted at refereed conferences:

1. Anton Bankevich, Pavel Pevzner, "mosaicFlye: Resolving long mosaic repeats using long error-prone reads", RECOMB 2020.

2. Ivan Tolstoganov, Anton Bankevich, Zhoutao Chen, Pavel A Pevzner, “cloudSPAdes: assembly of synthetic long reads using de Bruijn graphs.”, ISMB 2019.

3. Anton Bankevich, Pavel Pevzner, “Long Reads Enable Accurate Estimates of Complexity of Metagenomes.”, RECOMB 2018.

4. Yana Safonova, Anton Bankevich, Pavel A. Pevzner, “dipSPAdes: Assembler for Highly Polymorphic Diploid Genomes”,  RECOMB 2014

5. Andrey D. Prjibelski, Irina Vasilinetc, Anton Bankevich, Alexey Gurevich, Tatiana Krivosheeva, Sergey Nurk, Son Pham, Anton Korobeynikov, Alla Lapidus and Pavel A. Pevzner, “ExSPAnder: a universal repeat resolver for DNA fragment assembly”,  ISMB 2014

6. Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey Prjibelsky, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLeanRoger, LaskenScott R. Clingenpeel, Tanja Woyke, Glenn Tesler, Max A. Alekseyev, Pavel A. Pevzner, “Assembling genomes and mini-metagenomes from highly chimeric reads.”, RECOMB 2013

Papers in preparation:

1. Anton Bankevich, Pavel Pevzner, “mosaicFlye: Resolving long mosaic repeats using long error-prone reads”. under review

2. Chris L. Dupont, Drishti Kaul, Anton Bankevich, Douglas B. Rusch, Alexander R.  Richter, Zhihong Zhang, Jeanine Stuzka, Valerie Montel, Amanda Young, Narin Celepli, Karolina Ininbergs, Pavel Pevzner, “Microbial crowd-sourcing of carbon, nitrogen, and sulfur cycles in an oxygen minimum zone”, under review

3. Anton Bankevich, Sergey Nurk, Pavel Pevzner, "Theoretical aspects of optimal genome assembly problem".