Velichko N.S., Kokoulin M.S., Dmitrenok P.S., Grinev V.S., Kuchur P.D., Komissarov A.S., Fedonenko Y.P. Lipopolysaccharides of Herbaspirillum species and their relevance for bacterium–host interactions. International Journal of Biological Macromolecules. 2024. Vol. 261. No. 1. pp. 129516.
Yakupova A., Tomarovsky A., Totikov A., Beklemisheva V., Logacheva M., Perelman P.L., Komissarov A., Dobrinin P., Krasheninnikova K., Tamazian G., Serdyukova N.A., Rayko M., Bulyonkova T., Cherkasov N., Pylev V., Peterfeld V., Penin A., Balanovska E., Lapidus A., Dna Z., O’Brien S., Graphodatsky A., Koepfli K., Kliver S. Chromosome-Length Assembly of the Baikal Seal (Pusa sibirica) Genome Reveals a Historically Large Population Prior to Isolation in Lake Baikal. Genes. 2023. Vol. 14. No. 3. pp. 619.
Kusakin A.V., Goleva O.V., Danilov L., Krylov A.V., Tsay V.V., Kalinin R.S., Tian N.S., Eismont Y.A., Mukomolova A.L., Chukhlovin A.B., Komissarov A.S., Glotov O.S. The Telomeric Repeats of HHV-6A Do Not Determine the Chromosome into Which the Virus Is Integrated. Genes. 2023. Vol. 14. No. 2. pp. 521.
Kliver S., Houck M.L., Perelman P.L., Totikov A., Tomarovsky A., Dudchenko O., Omer A.D., Colaric Z., Weisz D., Aiden E.L., Chan S., Hastie A., Komissarov A., Ryder O., Graphodatsky A., Johnson W., Maldonado J., Pukazhenthi B., Marinari P.E., Wildt D., Koepfli K. Chromosome-length genome assembly and karyotype of the endangered black-footed ferret (Mustela nigripes). Journal of Heredity. 2023. Vol. 114. No. 5. pp. 539-548.
Majeske A., Mercado Capote A.J., Komissarov A., Bogdanova A., Schizas N.V., Castro Marquez S.O., Hilkert K., Wolfsberger W., Oleksyk T. The first complete mitochondrial genome of Diadema antillarum (Diadematoida, Diadematidae). GigaByte. 2022. Vol. 2022. pp. 12.
Abbas Q., Kusakin A.V., Sharruf K., Komissarov A.S., Dzhiakkhvo S. Follow-up investigation and detailed mutational characterization of the SARS-CoV-2 Omicron variant and its lineages (BA.1, BA.2, and BA.3) and sub-lineage (BA.1.1). BioRxiv [база препринтов]. 2022. pp. 1.
Afonnikova S.D., Komissarov A.S., Kuchur P.D. Unique or not unique? Comparative genetic analysis of bacterial O-antigens from the Oxalobacteraceae family [Сравнительный генетический анализ О-антигенов бактерий семейства Oxalobacteraceae: уникальность или тривиальность?]. Вавиловский журнал генетики и селекции = Vavilovskii Zhurnal Genetiki i Selektsii. 2022. Vol. 26. No. 8. pp. 810-818.
Takki O., Komissarov A., Kulak M., Galkina S. Identification of Centromere-Specific Repeats in the Zebra Finch Genome. Cytogenetic and Genome Research. 2022. Vol. 162. No. 1-2. pp. 55-63.
Ochkalova S., Korchagin V., Vergun A., Urin A., Zilov D., Ryakhovsky S., Girnyk A., Martirosyan I., Zhernakova D.V., Arakelyan M., Danielyan F., Kliver S., Brukhin V., Komissarov A.S., Ryskov A. First Genome of Rock Lizard Darevskia valentini Involved in Formation of Several Parthenogenetic Species. Genes. 2022. Vol. 13. No. 9. pp. 1569.
Ryakhovsky S., Zhernakova D.V., Korchagin V., Vergun A., Girnyk A., Dikaya V., Arakelyan M., Komissarov A.S., Ryskov A. The mixed liver and kidney transcriptome dataset of Darevskia valentini rock lizard. BMC Research Notes. 2022. Vol. 15. No. 1. pp. 345.
Aifred Werner's Periodic Table
Barua S., Komissarov A., Kaur H., Brodsky E. Transcriptomic analysis of DNA damage response in zebrafish embryos under simulated microgravity. BioRxiv [база препринтов]. 2021.
Tamazian G., Dobrynin P.V., Zhuk A.S., Zhernakova D.V., Perelman P.L., Serdyukova N.A., Graphodatsky A., Komissarov A.S., Kliver S.F., Cherkasov N., Scott A.F., Mohr D.W., Koepfli K., O’Brien S., Krasheninnikova K. Draft de novo Genome Assembly of the Elusive Jaguarundi, Puma yagouaroundi. Journal of Heredity. 2021. Vol. 112. No. 6. pp. 540-548.
Сравнительная геномика соматических антигенов симбиотических и условно-патогенных бактерий рода Herbaspirillum
Усовершенствование GINOFIP – алгоритма для идентификации оперонов интереса. Сборник тезисов XXI Всероссийской конференции молодых ученых «Биотехнология в растениеводстве, животноводстве и сельскохозяйственной микробиологии»
GINOFIP-пайплайн для поиска оперонов с генами интереса
Применение методов машинного обучения для метагеномного и полногеномного анализов микробиоты кишечника
Innovative approaches to computational methods across diets, microbiomes and health care
Identification and comparison of somatic antigen structures of symbiotic and pathogenic bacteria from Morganellaceae family
Shevchenko A., Zhernakova D.V., Malov S., Komissarov A., Kolchanova S., Tamazian G., Antonik A., Cherkasov N., Kliver S., Turenko A., Rotkevich M., Evsyukov I., Vlahov D., Thami P., Gaseitsiwe S., Novitsky V., Essex M., O’Brien S. Genome-wide association study reveals genetic variants associated with HIV-1C infection in a Botswana study population. Proceedings of the National Academy of Sciences of the United States of America. 2021. Vol. 118. No. 47. pp. e2107830118.
Dukhinova M.S., Kokinos E., Kuchur P.D., Komissarov A., Shtro A. Macrophage-derived cytokines in pneumonia: Linking cellular immunology and genetics. Cytokine and Growth Factor Reviews. 2021. Vol. 59. pp. 46-61.
Ryakhovsky S., Dikaya V., Korchagin V., Vergun A., Danilov L., Ochkalova S., Girnyk A., Zhernakova D.V., Arakelyan M., Brukhin V., Komissarov A.S., Ryskov A. De novo transcriptome assembly and annotation of parthenogenetic lizard Darevskia unisexualis and its parental ancestors Darevskia valentini and Darevskia raddei nairensis. Data in Brief. 2021. Vol. 39. pp. 107685.
Kolchanova S., Komissarov A., Kliver S., Mazo-Vargas A., Afanador Y., Velez-Valentin J., De La Rosa R., Castro-Marquez S., Rivera-Colon I., Majeske A., Wolfsberger W., Hans T., Corvelo A., Martinez-Cruzado J., Glenn T., Robinson O., Koepfli K., Oleksyk T. Molecular phylogeny and evolution of amazon parrots in the greater antilles. Genes. 2021. Vol. 12. No. 4. pp. 608.
Чеснокова П.Д., Ковтунов Е.А., Величко Н.С., Комиссаров А.С. Особенности структурной организации оперонов о-антигена в геноме herbaspirillum frisingense. Гены и клетки [Genes and Cells]. 2020. Т. 15. № S3. С. 153.
Comparative genomics analysis of o-antigen related genes in prokaryotic genomes
Анализ состава транскриптома травяной лягушки Rana Temporaria
MGELSE: ПАЙПЛАЙН ДЛЯ ПОИСКА И АННОТАЦИИ МОБИЛЬНЫХ ГЕНЕТИЧЕСКИХ ЭЛЕМЕНТОВ У ПРОКАРИОТ
CONTERA: A TOOL FOR PREPARATION DATA FOR PANGENOMIC ANALYSIS
Interoperable whole genome sequencing and metagenomics of colon biopsy samples from patients with ulcerative colitis
Velichko N.S., Kokoulin M.S., Sigida E.N., Kuchur P.D., Komissarov A.S., Kovtunov E.A., Fedonenko Y.P. Structural and genetic characterization of the colitose-containing O-specific polysaccharide from the lipopolysaccharide of Herbaspirillum frisingense GSF30T. International Journal of Biological Macromolecules. 2020. Vol. 161. pp. 891-897.
Митогеномика и молекулярная филогенетика попугаев рода Aratinga и Psittacus
Буланцев Н.А., Комиссаров А.С., Кошель Е.И., Круглов Е.Е., Мякишева Ю.В., Кафтырева Л.А. Метагеномный анализ биоптатов толстой кишки пациентов с язвенным колитом. Гены и клетки [Genes and Cells]. 2020. Т. 15. № S3. С. 128.
Дикая В.А., Травина А.О., Остромышенский Д.И., Подгорная О.И., Комиссаров А.С. Анализ состава транскриптома травяной лягушки rana temporaria. Гены и клетки [Genes and Cells]. 2020. Т. 15. № S3. С. 132.
Rayko M., Komissarov A.S. Quality control of low-frequency variants in SARS-CoV-2 genomes. BioRxiv [база препринтов]. 2020.
Zilov D.S., Komissarov A.S. Pannopi: prokaryotic genome assembly and annotation pipeline. BMC Bioinformatics. 2020. Vol. 21. No. Suppl20. pp. 6-7.
Pannopi: a tool for pangenome based prokaryotic genome assembly and annotation
Rayko M., Komissarov A.S., Kwan J., Lim-Fong G., Rhodes A., Kliver S., Kuchur P.D., O’Brien S., Lopez J. Draft genome of Bugula neritina, a colonial animal packing powerful symbionts and potential medicines. Scientific Data. 2020. Vol. 7. No. 1. pp. 356.
Zhernakova D.A., Brukhin V., Malov S., Oleksyk T., Koepfli K., Zhuk A., Dobrynin P., Klivera S., Cherkasov N., Tamazian G., Rotkevich M., Krasheninnikova K., Evsyukov I., Sidorov S., Gorbunova A., Chernyaeva E., Shevchenko A., Kolchanova S., Komissarov A.S., Simonov S., Antonik A., Logachev A., Polevh D., Pavlovah O., Glotov A., Ulantsev V., Noskova E., Davydova T., Sivtseva T., Limborska S., Balanovsky O., Osakovsky V., Novozhilov A., Puzyrev V., O'Brien S. Genome-wide sequence analyses of ethnic populations across Russia. Genomics. 2020. Vol. 112. No. 1. pp. 442-458.
Metagenomic analysis of colon biopsy samples in patients with ulcerative colitis
МЕТАГЕНОМНЫЙ АНАЛИЗ БИОПТАТОВ ТОЛСТОЙ КИШКИ ПАЦИЕНТОВ С ЯЗВЕННЫМ КОЛИТОМ
Ряховский С.С., Комиссаров А.С. Поиск и визуализация TAAR генов в собранных геномах позвоночных. Гены и клетки [Genes and Cells]. 2020. Т. 15. № S3. С. 147.
TRANSCRIPTOME ANALYSIS OF RANA TEMPORARIA IN THE EARLY STAGES OF EMBRYOGENESIS
Особенности структурной организации оперонов О-антигена в геноме Herbaspirillum frisingense
Влияние человеческого фактора на результативность генетических исследований в рамках прогнозирования атеросклероза
Automatic annotation of operons responsible for O-antigen synthesis
Mitogenomics and phylogenetics of vulnerable and endangered birds of genera Aratinga and Psittacus
Long-Read sequencing and de novo genome assembly of the Manila clam, Ruditapes philippinarum (Bivalvia, Veneridae)
Marra N.J., Stanhope M.J., Jue N.K., Wang M., Sun Q., Bitar P.P., Richards V.P., Komissarov A., Rayko M., Kliver S. White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability. Proceedings of the National Academy of Sciences of the United States of America. 2019. Vol. 116. No. 10. pp. 4446-4455.
Гетерохроматиновые районы в хромосомах японского перепела
Koepfli K., Tamazian G., Wildt D., Dobrynin P., Kim C., Frandsen P.B., Godinho R., Yurchenko A.A., Komissarov A., Krasheninnikova K., Kliver S., Kolchanova S. Whole genome sequencing and re-sequencing of the sable antelope (Hippotragus niger): a resource for monitoring diversity in ex situ and in situ populations. G3: Genes, Genomes, Genetics. 2019. Vol. 9. No. 6. pp. 1785-1793.
Молекулярные основы классических признаков у кур: факты и гипотезы
THE GENOME RUSSIA PROJECT-2019
Kolchanova S., Kliver S., Komissarov A.S., Dobrinin P., Tamazian G., Grigorev K., Wolfsberger W., Majeske A., Velez-Valentin J., De La Rosa R., Paul-Murphy J.R., Guzman D.S., Court M.H., Rodriguez-Flores J.L., Martinez-Cruzado J., Oleksyk T. Genomes of Three Closely Related Caribbean Amazons Provide Insight for Species History and Conservation. Genes. 2019. Vol. 10. No. 1. pp. 54.
Kulak M., Komissarov A.S., Dyomin A., Fillon V., Gaginskaya E., Saifitdinova A., Galkina S. Description of new tandem repeats in the genome of Japanese quail. Molecular Cytogenetics. 2019. Vol. 12. No. S1. pp. 4.
Grigorev K., Kliver S., Dobrynin P., Komissarov A., Wolfsberger W., Krasheninnikova K., Afanador-Hernandez Y.M., Brandt A.L., Paulino L.A., Carreras R., Rodriguez L.E., Nunez A., Brandt J.R., Silva F., Hernandez-Martich J.D., Majeske A., Antunes A., Roca A.L., O'Brien S.J., Martinez-Cruzado J., Oleksyk T. Innovative assembly strategy contributes to understanding the evolution and conservation genetics of the endangered Solenodon paradoxus from the island of Hispaniola. GigaScience. 2018. Vol. 7. No. 6. pp. giy025.
Komissarov A., Vij S., Yurchenko A., Trifonov V., Thevasagayam N., Saju J., Sridatta P.S., Purushothaman K., Graphodatsky A., Orban L., Kuznetsova I. B Chromosomes of the Asian seabass (Lates calcarifer) contribute to genome variations at the level of individuals and populations. Genes. 2018. Vol. 9. No. 10. pp. 464.
Diversity of genomic variants and population genetics of ethnic and regional groups across Russia
Annotation of genetic variation within Genome Russia project
Kliver S., Rayko M., Komissarov A., Bakin E., Zhernakova D.V., Prasad K., Rushworth C., Baskar R., Smetanin D., Schmutz J., Rokhsar D.S., Mitchell-Olds T., Grossniklaus U., Brukhin V. Assembly of the Boechera retrofracta genome and evolutionary analysis of apomixis-associated genes. Genes. 2018. Vol. 9. No. 4. pp. 185.
Volodkina V.A., Kulak M.M., Komissarov A.S., Galkina S.A., Gaginskaya E.R., Saifitdinova A.F. Chicken tandem repeats Ggal10 and Ggal20 are specific to different microchromosomes. Comparative Cytogenetics. 2018. Vol. 12. No. 3. pp. 357-358.
Assembly and annotation of genomes of some species from the apomictic genus Boechera and evolutionary analysis of apomixis-associated genes
O'Brien S.J., Tamazian G., Komissarov A.S., Dobrynin P.V., Krasheninnikova K.V., Kliver S.F., Cherkasov N.A., Koepfli K. A Moving Landscape for Comparative Genomics in Mammals. Comparative Cytogenetics. 2018. Vol. 12. No. 3. pp. 301.
Assembly and comparative analysis of some apomicticBoechera species genomes
Komissarov A.S., Galkina S.A., Koshel E.I., Kulak M.M., Dyomin A.G., O'Brien S.J., Gaginskaya E.R., Saifitdinova A.F. New high copy tandem repeat in the content of the chicken W chromosome. Chromosoma. 2018. Vol. 127. No. 1. pp. 73-83.
Kulak M.M., Dyomin A.G., Komissarov A.S., Fillon V., Saifitdinova A.F., Pavlova O.A., Gaginskaya E.R., Galkina S.A. New pericentromeric repeat identified in the genome of japanese quail. Comparative Cytogenetics. 2018. Vol. 12. No. 3. pp. 337-338.
Filling in the gaps in the chicken sex W chromosome map
Brandt A.L., Grigorev K., Afanador-Hernandez Y.M., Paulino L.A., Murphy W.J., Nunez A., Komissarov A., Brandt J.R., Dobrynin P., Hernandez-Martich J.D., Maria R., O’Brien S.J. Mitogenomic sequences support a north–south subspecies subdivision within Solenodon paradoxus. Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis. 2017. Vol. 28. No. 5. pp. 662-670.
Komissarov A.S., Ghiselli F., Milani L., Dunham J.P., Breton S., Nuzhdin S.V., Passamonti M. The draft genome of Ruditapes philippinarum (the Manila clam), a promising model system for mitochondrial biology. PeerJ PrePrints. 2017.
Biltueva L.S., Prokopov D.Y., Makunin A.I., Komissarov A.S., Kudryavtseva A.V., Lemskaya N.A., Vorobieva N.V., Serdyukova N.A., Romanenko S.A., Gladkikh O.L., Graphodatsky A., Trifonov V.A. Genomic organization and physical mapping of tandemly arranged repetitive DNAs in sterlet (Acipenser ruthenus). Cytogenetic and Genome Research. 2017. Vol. 152. No. 3. pp. 148-157.
Figueiro H.V., Li G., Trindade F.J., Assis J., Pais F., Fernandes G., Santos S.H., Hughes G.M., Komissarov A., Antunes A., Trinca C.S., Rodrigues M., Linderoth T., Bi K., Silveira L., Azevedo F.C., Kantek D., Ramalho E., Brassaloti R.A., Villela P.M., Nunes A.L., Teixeira R.H., Morato R.G., Loska D., Saragueta P., Gabaldon T., Teeling E., O'Brien S.J., Nielsen R., Coutinho L.L., Oliveira G., Murphy W.J., Eizirik E. Genome-wide signatures of complex introgression and adaptive evolution in the big cats. Science Advances. 2017. Vol. 3. No. 7. pp. e1700299.
The Japanese quail genome a cytogenetic revision
Российская Федерация, Санкт-Петербург