Oksana E. Glushchenko, Andrei E. Samoilov, Evgenii I. Olekhnovich, Boris A. Kovarsky, Alexander V. Tyakht, Alexander V. Pavlenko, Vlad V. Babenko, Andrei K. Larin, Elena S. Kostryukova, Maja V. Malakhova, Elena N. Ilina, Rustem A. Abdulkhakov, Dilyara I. Safina, Tatiana V. Grigoryeva, Sayar R. Abdulkhakov, Vadim M. Govorun. Data on gut metagenomes of the patients with Helicobacter pylori infection before and after the antibiotic therapy // Data in Brief. – 2017. – Т. 11. – С. 68-71. 
 
Olekhnovich, E. I., Vasilyev, A. T., Ulyantsev, V. I., Kostryukova, E. S., Tyakht, A. V. (2017). MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota. Bioinformatics. 
 
Terekhov SS, Smirnov IV, Stepanova AV, Bobik TV, Mokrushina YA, Ponomarenko NA, Belogurov AA Jr, Rubtsova MP, Kartseva OV, Gomzikova MO, Moskovtsev AA, Bukatin AS, Dubina MV, Kostryukova ES, Babenko VV, Vakhitova MT, Manolov AI, Malakhova MV, Kornienko MA, Tyakht AV, Vanyushkina AA, Ilina EN, Masson P, Gabibov AG, Altman S. "Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity." Proceedings of the National Academy of Sciences (2017): 201621226.
 
Rakitina, D.V., Manolov, A.I., Kanygina, A.V., Garushyants, S.K., Baikova, J.P., Alexeev, D.G., Ladygina, V.G., Kostryukova, E.S., Larin, A.K., Semashko, T.A. and Karpova, I.Y., 2017. Genome analysis of E. coli isolated from Crohn’s disease patients. BMC genomics, 18(1), p.544. 
 
Zakharzhevskaya, N.B., Vanyushkina, A.A., Altukhov, I.A., Shavarda, A.L., Butenko, I.O., Rakitina, D.V., Nikitina, A.S., Manolov, A.I., Egorova, A.N., Kulikov, E.E. and Vishnyakov, I.E., 2017. Outer membrane vesicles secreted by pathogenic and nonpathogenic Bacteroides fragilis represent different metabolic activities. Scientific Reports, 7. 
 
Bulaev, A.G., Kanygina, A.V. and Manolov, A.I., 2017. Genome analysis of Acidiplasma sp. MBA-1, a polyextremophilic archaeon predominant in the microbial community of a bioleaching reactor. Microbiology, 86(1), pp.89-95. 
 
Veronika B Dubinkina, Alexander V Tyakht, Vera Y Odintsova, Konstantin S Yarygin, Boris A Kovarsky, Alexander V Pavlenko, Dmitry S Ischenko, Anna S Popenko, Dmitry G Alexeev, Anastasiya Y Taraskina, Regina F Nasyrova, Evgeny M Krupitsky, Nino V Shalikiani, Igor G Bakulin, Petr L Shcherbakov, Lyubov O Skorodumova, Andrei K Larin, Elena S Kostryukova, Rustam A Abdulkhakov, Sayar R Abdulkhakov, Sergey Y Malanin, Ruzilya K Ismagilova, Tatiana V Grigoryeva, Elena N Ilina, Vadim M Govorun. (2017). Links of gut microbiota composition with alcohol dependence syndrome and alcoholic liver disease. Microbiome, 5(1), 141.  
 
Данилова Н.А., Абдулхаков С.Р., Григорьева Т.В., Маркелова М.И., Павленко А.В., Тяхт А.В., Дубинкина В.Б., Кострюкова Е.С., Ларин А.К., Скородумова Л.О., Манолов А.И., Одинцова А.Х., Абдулхаков Р.А. Изменения состава микробиоты кишечника у пациентов с язвенным колитом. Экспериментальная и клиническая гастроэнтерология. 2017. № 6 (142). С. 54-60.
 
Yarygin, K. S., Kovarsky, B. A., Bibikova, T. S., Melnikov, D. S., Tyakht, A. V., & Alexeev, D. G. (2017). ResistoMap—online visualization of human gut microbiota antibiotic resistome. Bioinformatics, btx134. 
 
Yarygin, K., Tyakht, A., Larin, A., Kostryukova, E., Kolchenko, S., Bitner, V., & Alexeev, D. (2017). Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses. PloS one, 12(4), e0176154. 
 
Odintsova V., Tyakht A., Alexeev D. Guidelines to Statistical Analysis of Microbial Composition Data Inferred from Metagenomic Sequencing //Current issues in molecular biology. – 2017. – Т. 24. – С. 17-36. 
 
Data on gut metagenomes of the patients with alcoholic dependence syndrome and alcoholic liver cirrhosis. Tyakht AV, Dubinkina VB, Odintsova VY, Yarygin KS, Kovarsky BA, Pavlenko AV, Ischenko DS, Popenko AS, Alexeev DG, Taraskina AY, Nasyrova RF -  Data in Brief. 2017 
 
Shashkova, T., Popenko, A., Tyakht, A., Peskov, K., Kosinsky, Y., Bogolubsky, L., ... & Govorun, V. (2016). Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations. PLOS ONE, 11(2), e0148386.
 
Dubinkina, V. B., Ischenko, D. S., Ulyantsev, V. I., Tyakht, A. V., & Alexeev, D. G. (2016). Assessment of k-mer spectrum applicability for metagenomic dissimilarity analysis. BMC bioinformatics, 17(1), 1.
 
Alexeev D, Bibikova T, Kovarsky B, Melnikov D, Tyakht A, Govorun V. Bacterial rose garden for metagenomic SNP-based phylogeny visualization. BioData Min. 2015 Mar 21;8:10. doi: 10.1186/s13040-015-0045-5. eCollection 2015. 
 
Огородова, Л. М., Говорун, В. М., Федосенко, С. В., Карнаушкина, М. А., Салтыкова, И. В., Алексеев, Д. Г., ... & Попенко, А. С. (2014). Особенности микробиоты кишечника у больных хронической обструктивной болезнью легких. Бюллетень сибирской медицины, 13(5), 55-61.
 
Федосенко, С. В., Огородова, Л. М., Карнаушкина, М. А., Куликов, Е. С., Деев, И. А., & Кириллова, Н. А. (2014). Роль сообщества микроорганизмов дыхательных путей в патогенезе хронической обструктивной болезни легких. Бюллетень сибирской медицины, 13(1), 153-160. 
 
Кострюкова, Е. С., Карпова, И. Ю., Ларин, А. К., Попенко, А. С., Тяхт, А. В., & Ильина, Е. Н. (2014). Вариабельность относительного содержания геномной ДНК человека при метагеномном анализе микробиоты кишечника. Биомедицинская химия, 60(6), 695-701.

Tyakht AV, Alexeev DG, Popenko AS, Kostryukova ES, Govorun VM. Rural and urban microbiota: To be or not to be? Gut Microbes. 2014 May-Jun;5(3):351-6. doi:10.4161/gmic.28685. Epub 2014 Apr 1. 

Tyakht AV, Kostryukova ES, Popenko AS, Belenikin MS, Pavlenko AV, Larin AK, Karpova IY, Selezneva OV, Semashko TA, Ospanova EA, Babenko VV, Maev IV, Cheremushkin SV, Kucheryavyy YA, Shcherbakov PL, Grinevich VB, Efimov OI, Sas EI, Abdulkhakov RA, Abdulkhakov SR, Lyalyukova EA, Livzan MA, Vlassov VV, Sagdeev RZ, Tsukanov VV, Osipenko MF, Kozlova IV, Tkachev AV, Sergienko VI, Alexeev DG, Govorun VM. Human gut microbiota community structures in urban and rural populations in Russia. Nat Commun.2013;4:2469. doi: 10.1038/ncomms3469

Tyakht AV, Popenko AS, Belenikin MS, Altukhov IA, Pavlenko AV, Kostryukova ES, Selezneva OV, Larin AK, Karpova IY, Alexeev DG. MALINA: a web service for visual analytics of human gut microbiota whole-genome
metagenomic reads. Source Code Biol Med. 2012 Dec 7;7(1):13. doi: 10.1186/1751-0473-7-13