Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features

Yutin, N., Benler, S., Shmakov, S. A., Wolf, Y. I., Tolstoy, I., Rayko, M., Antipov, D., Pevzner, P. A. & Koonin, E. V., Dec 2021, In: Nature Communications. 12, 1, 11 p., 1044.

Research output: Contribution to journal › Article › peer-review

Critical Assessment of Metagenome Interpretation: the second round of challenges

Meyer, F., Fritz, A., Deng, Z. L., Koslicki, D., Lesker, T. R., Gurevich, A., Robertson, G., Alser, M., Antipov, D., Beghini, F., Bertrand, D., Brito, J. J., Brown, C. T., Buchmann, J., Buluç, A., Chen, B., Chikhi, R., Clausen, P. T. L. C., Cristian, A., Dabrowski, P. W. & 83 others, Darling, A. E., Egan, R., Eskin, E., Georganas, E., Goltsman, E., Gray, M. A., Hansen, L. H., Hofmeyr, S., Huang, P., Irber, L., Jia, H., Jørgensen, T. S., Kieser, S. D., Klemetsen, T., Kola, A., Kolmogorov, M., Korobeynikov, A., Kwan, J., LaPierre, N., Lemaitre, C., Li, C., Limasset, A., Malcher-Miranda, F., Mangul, S., Marcelino, V. R., Marchet, C., Marijon, P., Meleshko, D., Mende, D. R., Milanese, A., Nagarajan, N., Nissen, J., Nurk, S., Oliker, L., Paoli, L., Peterlongo, P., Piro, V. C., Porter, J. S., Rasmussen, S., Rees, E. R., Reinert, K., Renard, B., Robertsen, E. M., Rosen, G. L., Ruscheweyh, H. J., Sarwal, V., Segata, N., Seiler, E., Shi, L., Sun, F., Sunagawa, S., Sørensen, S. J., Thomas, A., Tong, C., Trajkovski, M., Tremblay, J., Uritskiy, G., Vicedomini, R., Wang, Z., Wang, Z., Wang, Z., Warren, A., Willassen, N. P., Yelick, K., You, R., Zeller, G., Zhao, Z., Zhu, S., Zhu, J., Garrido-Oter, R., Gastmeier, P., Hacquard, S., Häußler, S., Khaledi, A., Maechler, F., Mesny, F., Radutoiu, S., Schulze-Lefert, P., Smit, N., Strowig, T., Bremges, A., Sczyrba, A. & McHardy, A. C., 8 Apr 2022, In: Nature Methods. 19, 4, p. 429-440 12 p.

Research output: Contribution to journal › Article › peer-review

Extending rnaSPAdes functionality for hybrid transcriptome assembly

Prjibelski, A. D., Puglia, G. D., Antipov, D., Bushmanova, E., Giordano, D., Mikheenko, A., Vitale, D. & Lapidus, A., 24 Jul 2020, In: BMC Bioinformatics. 21, Suppl 12, p. 302 9 p., 302.

Research output: Contribution to journal › Article › peer-review

HybridSPAdes: An algorithm for hybrid assembly of short and long reads

Antipov, D., Korobeynikov, A., McLean, J. S. & Pevzner, P. A., 1 Apr 2016, In: Bioinformatics. 32, 7, p. 1009-1015 7 p.

Research output: Contribution to journal › Article › peer-review

METAVIRALSPADES: assembly of viruses from metagenomic data

Antipov, D., Raiko, M., Lapidus, A. & Pevzner, P. A., 15 Jul 2020, In: Bioinformatics. 36, 14, p. 4126-4129 4 p.

Research output: Contribution to journal › Article › peer-review

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

Bankevich, A., Bzikadze, A. V., Kolmogorov, M., Antipov, D. & Pevzner, P. A., Jul 2022, In: Nature Biotechnology. 40, 7, p. 1075-1081 7 p.

Research output: Contribution to journal › Article › peer-review

Plasmid detection and assembly in genomic and metagenomic datasets

Antipov, D., Raiko, M., Lapidus, A. & Pevzner, P. A., 1 Jan 2019, In: Genome Research. 29, 6, p. 961-968 8 p.

Research output: Contribution to journal › Article › peer-review

PlasmidSPAdes: Assembling plasmids from whole genome sequencing data

Antipov, D., Hartwick, N., Shen, M., Raiko, M., Lapidus, A. & Pevzner, P. A., 15 Nov 2016, In: Bioinformatics. 32, 22, p. 3380-3387 8 p.

Research output: Contribution to journal › Article › peer-review

RnaQUAST: A quality assessment tool for de novo transcriptome assemblies

Bushmanova, E., Antipov, D., Lapidus, A., Suvorov, V. & Prjibelski, A. D., 15 Jul 2016, In: Bioinformatics. 32, 14, p. 2210-2212 3 p.

Research output: Contribution to journal › Article › peer-review