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.
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.
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.
Aifred Werner's Periodic Table
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.
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.
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.
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.
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.
Barua S., Komissarov A., Kaur H., Brodsky E. Transcriptomic analysis of DNA damage response in zebrafish embryos under simulated microgravity. BioRxiv [база препринтов]. 2021.
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.
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.
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.
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.
Identification and comparison of somatic antigen structures of symbiotic and pathogenic bacteria from Morganellaceae family
Innovative approaches to computational methods across diets, microbiomes and health care
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.
Усовершенствование GINOFIP – алгоритма для идентификации оперонов интереса. Сборник тезисов XXI Всероссийской конференции молодых ученых «Биотехнология в растениеводстве, животноводстве и сельскохозяйственной микробиологии»
Сравнительная геномика соматических антигенов симбиотических и условно-патогенных бактерий рода Herbaspirillum
Применение методов машинного обучения для метагеномного и полногеномного анализов микробиоты кишечника
GINOFIP-пайплайн для поиска оперонов с генами интереса
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.
Особенности структурной организации оперонов О-антигена в геноме Herbaspirillum frisingense
Pannopi: a tool for pangenome based prokaryotic genome assembly and annotation
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.
Митогеномика и молекулярная филогенетика попугаев рода Aratinga и Psittacus
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.
Interoperable whole genome sequencing and metagenomics of colon biopsy samples from patients with ulcerative colitis
Metagenomic analysis of colon biopsy samples in patients with ulcerative colitis
MGELSE: ПАЙПЛАЙН ДЛЯ ПОИСКА И АННОТАЦИИ МОБИЛЬНЫХ ГЕНЕТИЧЕСКИХ ЭЛЕМЕНТОВ У ПРОКАРИОТ
Comparative genomics analysis of o-antigen related genes in prokaryotic genomes
МЕТАГЕНОМНЫЙ АНАЛИЗ БИОПТАТОВ ТОЛСТОЙ КИШКИ ПАЦИЕНТОВ С ЯЗВЕННЫМ КОЛИТОМ
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.
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.
Automatic annotation of operons responsible for O-antigen synthesis
Zilov D.S., Komissarov A.S. Pannopi: prokaryotic genome assembly and annotation pipeline. BMC Bioinformatics. 2020. Vol. 21. No. Suppl20. pp. 6-7.
CONTERA: A TOOL FOR PREPARATION DATA FOR PANGENOMIC ANALYSIS
Rayko M., Komissarov A.S. Quality control of low-frequency variants in SARS-CoV-2 genomes. BioRxiv [база препринтов]. 2020.
Анализ состава транскриптома травяной лягушки Rana Temporaria
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.
Влияние человеческого фактора на результативность генетических исследований в рамках прогнозирования атеросклероза
Mitogenomics and phylogenetics of vulnerable and endangered birds of genera Aratinga and Psittacus
TRANSCRIPTOME ANALYSIS OF RANA TEMPORARIA IN THE EARLY STAGES OF EMBRYOGENESIS
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.
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.
Гетерохроматиновые районы в хромосомах японского перепела
THE GENOME RUSSIA PROJECT-2019
Молекулярные основы классических признаков у кур: факты и гипотезы
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.
Long-Read sequencing and de novo genome assembly of the Manila clam, Ruditapes philippinarum (Bivalvia, Veneridae)
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.
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.
Diversity of genomic variants and population genetics of ethnic and regional groups across Russia
Annotation of genetic variation within Genome Russia project
Assembly and comparative analysis of some apomicticBoechera species genomes
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.
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.
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.
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.
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.
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.
Assembly and annotation of genomes of some species from the apomictic genus Boechera and evolutionary analysis of apomixis-associated genes
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.
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.
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.
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.
The Japanese quail genome a cytogenetic revision
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.
Российская Федерация, Санкт-Петербург