Русская версия English version   
О журнале
Редакционная коллегия
Правила для авторов
Информация для читателей и авторов
Оглавление текущего номера
Архив
Контакты
Поиск

Отправить статью
 


Том 20   Выпуск 1   Год 2025
Список литературы

  1. Roychoudhury Sh., Das A., Sengupta P., Dutta S., Roychoudhury Sh., Choudhury A.P., Ahmed A.B.F., Bhattacharjee S., Slama P. Viral pandemics of the last four decades: pathophysiology, health impacts and perspectives. International Journal of Environmental Research and Public Health. 2020;17. No. 24. Article No. 9411. doi: 10.3390/ijerph17249411
  2. Speranskaya A.S., Samoilov A.E., Korneenko E.V., Khabudaev K.V., Artyushin I.V., Yusefovich A.P., Dolgova A.S., Dedkov V.G. The characterization of complete genome of MERS-related coronavirus from bat (Pipistrellus nathusii) from Moscow region, prediction and analysis their Spike glycoprotein with DPP4 receptors of the different mammalian species. Bioinformatics of Genome Regulation and Structure/Systems Biology (BGRS/SB-2022). 2022:892-892.
  3. Lau S.K.P., Li K.S.M., Tsang A.K.L., Lam C.S.F., Ahmed S., Chen H., Chan K.-H., Woo P.C.Y., Yuen K.-Y. Genetic characterization of Betacoronavirus lineage C viruses in bats reveals marked sequence divergence in the spike protein of pipistrellus bat coronavirus HKU5 in Japanese pipistrelle: implications for the origin of the novel Middle East respiratory syndrome coronavirus. Journal of Virology. 2013;87(15):8638-8650. doi: 10.1128/JVI.01055-13
  4. Speranskaya A.S., Artiushin I.V., Samoilov A.E., Korneenko E.V., Khabudaev K.V., Ilina E.N., Yusefovich A.P., Safonova M.V., Dolgova A.S., Gladkikh A.S., et al. Identification and genetic characterization of MERS-related coronavirus isolated from Nathusius' pipistrelle (Pipistrellus nathusii) near Zvenigorod (Moscow region, Russia). International Journal of Environmental Research and Public Health. 2023;20. No. 4. Article No. 3702. doi: 10.3390/ijerph20043702
  5. Carroll D.S., Daszak P., Wolfe N.D., Gao G.F., Morel C.M., Morzaria S., Pablos-Mendez A., Tomori O.Y., Mazet J.A.K. The global virome project. Science. 2018;359(6378):872-874. doi: 10.1126/science.aap7463
  6. Koster J., Rahmann S. Snakemake -- a scalable bioinformatics workflow engine. Bioinformatics. 2012;28(19):2520-2522. doi: 10.1093/bioinformatics/bts480
  7. Di Tommaso P., Chatzou M., Floden E.W., Barja P.P., Palumbo E., Notredame C. Nextflow enables reproducible computational workflows. Nature Biotechnology. 2017;35(4):316-319. doi: 10.1038/nbt.3820
  8. Ewels P.A., Peltzer A., Fillinger S., Patel H., Alneberg J., Wilm A., Garcia M.U., Di Tommaso P., Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology. 2020;38(3):276-278. doi: 10.1038/s41587-020-0439-x
  9. Patel H., Monzon S., Varona S., Espinosa-Carrasco J., Garcia M.U., Heuer M.L., Underwood A., Gabernet G., Ewels P., Miguel J., et al. nf-core/viralrecon: nf-core/viralrecon v2. 6.0-Rhodium Raccoon. 2023. doi: Cite to nonCR doi: 10.5281/zenodo.7764938
  10. Kieft K., Zhou Z., Anantharaman K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome. 2020;8. Article No. 90. doi: 10.1186/s40168-020-00867-0
  11. Rampelli S., Soverini M., Turroni S., Quercia S., Biagi E., Brigidi P., Candela M. ViromeScan: a new tool for metagenomic viral community profiling. BMC Genomics. 2016;17. Article No. 165. doi: 10.1186/s12864-016-2446-3
  12. Vilsker M., Moosa Y., Nooij S., Fonseca V., Ghysens Y., Dumon K., Pauwels R., Alcantara L.C., Vanden Eynden E., Vandamme A.-M., et al. Genome Detective: an automated system for virus identification from high-throughput sequencing data. Bioinformatics. 2019;35(5):871-873. doi: 10.1093/bioinformatics/bty695
  13. Ren J., Song K., Deng C., Ahlgren N.A., Fuhrman J.A., Li Y., Xie X., Poplin R., Sun F. Identifying viruses from metagenomic data using deep learning. Quantitative Biology. 2020;8(1):64-77. doi: 10.1007/s40484-019-0187-4
  14. O'Leary N.A., Cox E., Holmes J.B., Anderson W.R., Falk R., Hem V., Tsuchiya M.T.N., Schuler G.D., Zhang X., Torcivia J., et al. Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets. Scientific Data. 2024;11. Article No. 732. doi: 10.1038/s41597-024-03571-y
  15. O'Leary N.A., Wright M.W., Brister J.R., Ciufo S., Haddad D., McVeigh R., Rajput B., Robbertse B., Smith-White B., Ako-Adjei D., et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Research. 2016;44(D1):D733-D745. doi: 10.1093/nar/gkv1189
  16. Paez-Espino D., Eloe-Fadrosh E.A., Pavlopoulos G.A., Thomas A.D., Huntemann M., Mikhailova N., Rubin E., Ivanova N.N., Kyrpides N.C. Uncovering Earth's virome. Nature. 2016;536(7617):425-430. doi: 10.1038/nature19094
  17. Guo J., Bolduc B., Zayed A.A., Varsani A., Dominguez-Huerta G., Delmont T.O., Pratama A.A., Gazitua M.C., Vik D., Sullivan M.B., et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome. 2021;9. Article No. 1-13. doi: 10.1186/s40168-020-00990-y
  18. Bukin Yu.S., Bondaryuk A.N., Butina T.V. Performance Analysis of Cross-Assembly of Metatranscriptomic Datasets in Viral Community Studies. Mathematical Biology and Bioinformatics. 2023;18(2):418-433. doi: 10.17537/2023.18.418
  19. Speranskaya A.S., Dorokhin A.V., Korneenko E.V., Chudinov I.K., Samoilov A.E., Kruskop S.V. A Novel Mastadenovirus from Nyctalus noctula Which Represents a Distinct Evolutionary Branch of Viruses from Bats in Europe. Viruses. 2024;16. No. 8. Article No. 1207. doi: 10.3390/v16081207
  20. Korneenko E.V., Samoilov A.E., Chudinov I.K., Butenko I.O., Sonets I.V., Artyushin I.V., Yusefovich A.P., Kruskop S.V., Sinitsyn S.O., Klyuchnikova E.O., et al. Alphacoronaviruses from bats captured in European Russia in 2015 and 2021 are closely related to those of Northern Europe. Frontiers in Ecology and Evolution. 2024;12. doi: 10.3389/fevo.2024.1324605
  21. Lukina-Gronskaya A.V., Chudinov I.K., Korneenko E.V., Mashkova S.D., Semashko T.A., Sinkova M.A., Penkin L.N., Litvinova E.M., Feoktistova N.Yu., Speranskaya A.S. Novel coronaviruses and mammarenaviruses of hedgehogs from Russia including the comparison of viral communities of hibernating and active specimens. Frontiers in Veterinary Science. 2024;11. doi: 10.3389/fvets.2024.1486635
  22. Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nature Methods. 2012;9(4):357-359. doi: 10.1038/nmeth.1923
  23. nf-core/modules. https://nf-co.re/modules/ (accessed 06.05.2025).
  24. Chen S., Zhou Y., Chen Y., Gu J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34(17):i884-i890. doi: 10.1093/bioinformatics/bty560
  25. Andrews S. FastQC. Babraham Bioinformatics. https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ (accessed 06.05.2025).
  26. GNU Gzip: General file (de)compression: Free Software Foundation, Inc. gunzip. https://www.gnu.org/software/gzip/manual/gzip.html (accessed 06.05.2025).
  27. Wood D.E., Lu J., Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biology. 2019;20. Article No. 257. doi: 10.1186/s13059-019-1891-0
  28. MultiQC overview. Seqera. https://docs.seqera.io/multiqc (accessed 06.05.2025).
  29. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. 1000 Genome Project Data Processing Subgroup. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078-2079. doi: 10.1093/bioinformatics/btp352
  30. Shen W., Le S., Li Y., Hu F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PloS One. 2016;11(10). doi: 10.1371/journal.pone.0163962
  31. Shen W., Sipos B., Zhao L. SeqKit2: A Swiss army knife for sequence and alignment processing. iMeta. 2024;3. No. 3. Article No. e191. doi: 10.1002/imt2.191
  32. Prjibelski A., Antipov D., Meleshko D., Lapidus A., Korobeynikov A. Using SPAdes de novo assembler. Current Protocols in Bioinformatics. 2020;70(1):e102. doi: 10.1002/cpbi.102
  33. Van Rossum G., Drake F.L. Python 3 Reference Manual. CreateSpace Independent Publishing Platform. 2009.
  34. Steinegger M., Soding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology. 2017;35:1026-1028. doi: 10.1038/nbt.3988
  35. Steinegger M., Soding J. Clustering huge protein sequence sets in linear time. Nature Communications. 2018;9. Article No. 2542. doi: 10.1038/s41467-018-04964-5
  36. da Veiga Leprevost F., Gruning B., Alves A.S., Sondergaard H., Rost H.L., Uszkoreit J., Barsnes H., Vaudel M., Moreno P., Gatto L., et al. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192
  37. Gruening B., Sallou O., Moreno P., da Veiga Leprevost F., Menager H., Sondergaard D., Rost H., Sachsenberg T., O'connor B., Madeira F., et al. Recommendations for the packaging and containerizing of bioinformatics software. F1000Research. 2019;7. doi: 10.12688/f1000research.15140.2
  38. Reback J., McKinney W., Jbrockmendel, Van Den Bossche J., Augspurger T., Cloud Ph., Gfyoung, Sinhrks, Klein A., Hawkins S., et al. pandas-dev/pandas: Pandas 1.0.5. 2020. doi: Cite to nonCR doi: 10.5281/zenodo.3898987
  39. Suzek B.E., Huang H., McGarvey P., Mazumder R., Wu C.H. UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics. 2007;23(10):1282-1288. doi: 10.1093/bioinformatics/btm098
  40. Sayers E.W., Bolton E.E., Brister J.R., Canese K., Chan J., Comeau D.C., Connor R., Funk K., Kelly C., Kim S., et al. Database resources of the national center for biotechnology information. Nucleic Acids Research. 2022;50(D1):D20-D26. doi: 10.1093/nar/gkm1000
  41. NCBI. sra-tools. https://github.com/ncbi/sra-tools (accessed 06.05.2025).
  42. Kluyver T., Ragan-Kelley B., Perez F., Granger B., Bussonnier M., Frederic J., Kelley K., Hamrick J., Grout J., Corlay S., et al. Jupyter notebooks-a publishing format for reproducible computational workflows. Positioning and Power in Academic Publishing: Players, Agents and Agendas. 2016:87-90. doi: 10.3233/978-1-61499-649-1-87
  43. McKinney W. Data Structures for Statistical Computing in Python. In: Proceedings of the 9th Python in Science Conference (SciPy 2010). Eds. Van Der Walt S.J. and Millman K.J. Austin, Texas, 2010:56-61. doi: 10.25080/Majora-92bf1922-00a
  44. Hunter J.D. Matplotlib: A 2D graphics environment. Computing in Science & Engineering. 2007;9(03):90-95. doi: 10.1109/MCSE.2007.55
  45. Hagberg A., Chult D.S., Swart P. Exploring Network Structure, Dynamics, and Function using NetworkX. In: Proceedings of the 7th Python in Science Conference (SciPy 2008). Eds. Varoquaux G., Vaught T., Millman J. Pasadena, California, 2008:11-16. doi: 10.25080/TCWV9851
  46. Harris C.R., Millman K.J., Van Der Walt S.J., Gommers R., Virtanen P., Cournapeau D., Wieser E., Taylor J., Berg S., Smith N.J., et al. Array programming with NumPy. Nature. 2020;585:357-362. doi: 10.1038/s41586-020-2649-2
  47. Waskom M.L. Seaborn: statistical data visualization. Journal of Open Source Software. 2021;6(60):3021. doi: 10.21105/joss.03021
  48. Inkscape project. https://inkscape.org (accessed 06.05.2025).
  49. PDFgear. https://www.pdfgear.com (accessed 06.05.2025).
  50. Camacho C., Coulouris G., Avagyan V., Ma N., Papadopoulos J., Bealer K., Madden T.L. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10. doi: 10.1186/1471-2105-10-421
  51. Budkina A.Y., Korneenko E.V., Kotov I.A., Kiselev D.A., Artyushin I.V., Speranskaya A.S., Khafizov K., Akimkin V.G. Utilizing the VirIdAl pipeline to search for viruses in the metagenomic data of bat samples. Viruses. 2021;13. No. 10. Article No. 2006. doi: 10.3390/v13102006
  52. Huggett J.F., Benes V., Bustin S.A., Garson J.A., Harris K., Kammel M., Kubista M., McHugh T.D., Moran-Gilad J., Nolan T., et al. Cautionary note on contamination of reagents used for molecular detection of SARS-CoV-2. Clinical Chemistry. 2020;66(11):1369-1372. doi: 10.1093/clinchem/hvaa214
  53. Healy B., Khan A., Metezai H., Blyth I., Asad H. The impact of false positive COVID-19 results in an area of low prevalence. Clinical Medicine. 2021;21(1):e54-e56. doi: 10.7861/clinmed.2020-0839
  54. Ahmed W., Simpson S.L., Bertsch P.M., Bibby K., Bivins A., Blackall L., Bofill-Mas S., Bosch A., Brandao J., Choi P.M., et al. Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance. Science of the Total Environment. 2022;805. Article No. 149877. doi: 10.1016/j.scitotenv.2021.149877
  55. Wang C.Y.T., Buckley C., Bletchly C., Harris P., Whiley D. Contamination of SARS-CoV-2 RT-PCR probes at the oligonucleotide manufacturer. Pathology. 2020;52(7):814-816. doi: 10.1016/j.pathol.2020.08.002
  56. Volynkina A.S., Ryazanova A.G., Rusanova D.V., Kulichenko A.N. The Problem of DNA/RNA Contamination in the Laboratory during PCR Testing for COVID-19. Public Health and Life Environment – PH&LE.. 2021(7):76-81 (in Russ.). doi: 10.35627/2219-5238/2021-29-7-76-81
  57. Chen L.X., Banfield J.F. COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes. Nature Microbiology. 2024;9:737-750. doi: 10.1038/s41564-023-01598-2
  58. Aksamentov I., Roemer C., Hodcroft E.B., Neher R.A. Nextclade: clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software. 2021;6. No. 67. Article No. 3773. doi: 10.21105/joss.03773
  59. O'Toole A., Scher E., Underwood A., Jackson B., Hill V., McCrone J.T., Colquhoun R., Ruis C., Abu-Dahab K., Taylor B., et al. Assignment of epidemiological lineages in an emerging pandemic using the pangolin tool. Virus Evolution. 2021;7. No. 2. Article No. veab064. doi: 10.1093/ve/veab064
  60. Mistry J., Chuguransky S., Williams L., Qureshi M., Salazar G.A., Sonnhammer E.L.L., Tosatto S.E.C., Paladin L., Raj S., Richardson L.J., et al. Pfam: the protein families database in 2021. Nucleic Acids Research. 2021;49(D1):D412-D419. doi: 10.1093/nar/gkaa913
  61. Kans J. Entrez direct: E-utilities on the UNIX command line. Entrez Programming Utilities Help [Internet]. 2024. https://www.ncbi.nlm.nih.gov/books/NBK25499/ (accessed 06.05.2025).
Содержание
Оригинальная статья
Chudinov I.K., Speranskaya A.S. Facilitating Rapid Screening of Metaviral Data with the VERA Pipeline. Маthematical biology and bioinformatics. 2025;20(1):100-121. doi: 10.17537/2025.20.100
(опубликована на англ. яз.)

Аннотация (англ.)
Аннотация (рус.)
Полный текст (англ., pdf)
Список литературы

 
  Copyright ИМПБ РАН © 2005-2026