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1. Genetic diversity of Escherichia coli in gut microbiota of patients with Crohn’s disease discovered using metagenomic and genomic analyses

Author

Tyakht, Alexander V., Manolov, Alexander I., Kanygina, Alexandra V., Ischenko, Dmitry S., Kovarsky, Boris A., Popenko, Anna S., Pavlenko, Alexander V., Elizarova, Anna V., Rakitina, Daria V., Baikova, Julia P., Ladygina, Valentina G., Kostryukova, Elena S., Karpova, Irina Y., Semashko, Tatyana A., Larin, Andrei K., Grigoryeva, Tatyana V., Sinyagina, Mariya N., Malanin, Sergei Y., Shcherbakov, Petr L., Kharitonova, Anastasiya Y., Khalif, Igor L., Shapina, Marina V., Maev, Igor V., Andreev, Dmitriy N., Belousova, Elena A., Buzunova, Yulia M., Alexeev, Dmitry G., and Govorun, Vadim M.

Published
2018
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3. Proteomic dataset: Profiling of cultivated Echerichia coli isolates from Crohn's disease patients and healthy individuals

Author

Rakitina, Daria, primary, Baikova, Julia, additional, Pobeguts, Olga, additional, Bukato, Olga, additional, Butenko, Ivan, additional, Garanina, Irina, additional, Levites, Mark, additional, Manolov, Alexander, additional, Kanygina, Alexandra, additional, Kostryukova, Elena, additional, Semashko, Tatiana, additional, Karpova, Irina, additional, Babenko, Vladislav, additional, Scherbakov, Petr, additional, Khalif, Igor, additional, Shapina, Marina, additional, Parfenov, Asfold, additional, Ruchkina, Irina, additional, Knyazev, Oleg, additional, Fadeeva, Nina, additional, Subbotin, Alexandr, additional, Chamkin, Sergey, additional, Pyrkh, Alexandr, additional, Ivantsova, Marina, additional, and Govorun, Vadim, additional

Published
2019
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4. Additional file 5: of Genome analysis of E. coli isolated from Crohnâ s disease patients

Author

Rakitina, Daria, Manolov, Alexander, Kanygina, Alexandra, Garushyants, Sofya, Baikova, Julia, Alexeev, Dmitry, Ladygina, Valentina, Kostryukova, Elena, Larin, Andrei, Semashko, Tatiana, Karpova, Irina, Babenko, Vladislav, Ruzilya Ismagilova, Malanin, Sergei, Gelfand, Mikhail, Ilina, Elena, Gorodnichev, Roman, Lisitsyna, Eugenia, Aleshkin, Gennady, Scherbakov, Petr, Khalif, Igor, Shapina, Marina, Maev, Igor, Andreev, Dmitry, and Govorun, Vadim

Subjects
viruses
Abstract

Phage sensitivity test of E. coli CD-isolates (see Methods). (DOC 45Â kb)

Published
2017
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5. Additional file 4: of Genome analysis of E. coli isolated from Crohnâ s disease patients

Author

Rakitina, Daria, Manolov, Alexander, Kanygina, Alexandra, Garushyants, Sofya, Baikova, Julia, Alexeev, Dmitry, Ladygina, Valentina, Kostryukova, Elena, Larin, Andrei, Semashko, Tatiana, Karpova, Irina, Babenko, Vladislav, Ruzilya Ismagilova, Malanin, Sergei, Gelfand, Mikhail, Ilina, Elena, Gorodnichev, Roman, Lisitsyna, Eugenia, Aleshkin, Gennady, Scherbakov, Petr, Khalif, Igor, Shapina, Marina, Maev, Igor, Andreev, Dmitry, and Govorun, Vadim

Abstract

(A) Mauve alignment of CD-E. coli isolates from one patient (alignment made for RCE01, RCE02, RCE03, RCE03 and RCE06). (B) Heatmap of the phylogenetic distance between E. coli strains. Distances between strains are calculated as the median distance of core genes (see Methods). Phylogroups of E. coli are designated (A, B1, E, B2, D, F). RCE03 is not shown because of its low similarity to other E. coli strains. (DOC 4350Â kb)

Published
2017
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6. Additional file 12: of Genome analysis of E. coli isolated from Crohnâ s disease patients

Author

Rakitina, Daria, Manolov, Alexander, Kanygina, Alexandra, Garushyants, Sofya, Baikova, Julia, Alexeev, Dmitry, Ladygina, Valentina, Kostryukova, Elena, Larin, Andrei, Semashko, Tatiana, Karpova, Irina, Babenko, Vladislav, Ruzilya Ismagilova, Malanin, Sergei, Gelfand, Mikhail, Ilina, Elena, Gorodnichev, Roman, Lisitsyna, Eugenia, Aleshkin, Gennady, Scherbakov, Petr, Khalif, Igor, Shapina, Marina, Maev, Igor, Andreev, Dmitry, and Govorun, Vadim

Abstract

Competition co-culture of CD-E. coli and isolates from healthy individuals. (DOC 56Â kb)

Published
2017
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7. Additional file 7: of Genome analysis of E. coli isolated from Crohnâ s disease patients

Author

Rakitina, Daria, Manolov, Alexander, Kanygina, Alexandra, Garushyants, Sofya, Baikova, Julia, Alexeev, Dmitry, Ladygina, Valentina, Kostryukova, Elena, Larin, Andrei, Semashko, Tatiana, Karpova, Irina, Babenko, Vladislav, Ruzilya Ismagilova, Malanin, Sergei, Gelfand, Mikhail, Ilina, Elena, Gorodnichev, Roman, Lisitsyna, Eugenia, Aleshkin, Gennady, Scherbakov, Petr, Khalif, Igor, Shapina, Marina, Maev, Igor, Andreev, Dmitry, and Govorun, Vadim

Abstract

plLF82 homologs in CD-associated E. coli. (A) Sequence similarity of CD isolates with the plasmid pLF82 (100Â kb), (B) and (C) functions of proteins common between pLF82 or pJJ1886_4 and CD isolates The functions were obtained from original annotation, complemented by Prokka annotation and BLAST protein similarity search. (D) Sequence similarity of commensal E. coli isolates with plasmids plLF82 and pJJ1886_4 (script for the data is described in supplementary data https://github.com/paraslonic/Rakitina_etal_Crohn_paper/tree/master/plasmidCoverage [41]. (DOC 228Â kb)

Published
2017
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8. Additional file 9: of Genome analysis of E. coli isolated from Crohnâ s disease patients

Author

Rakitina, Daria, Manolov, Alexander, Kanygina, Alexandra, Garushyants, Sofya, Baikova, Julia, Alexeev, Dmitry, Ladygina, Valentina, Kostryukova, Elena, Larin, Andrei, Semashko, Tatiana, Karpova, Irina, Babenko, Vladislav, Ruzilya Ismagilova, Malanin, Sergei, Gelfand, Mikhail, Ilina, Elena, Gorodnichev, Roman, Lisitsyna, Eugenia, Aleshkin, Gennady, Scherbakov, Petr, Khalif, Igor, Shapina, Marina, Maev, Igor, Andreev, Dmitry, and Govorun, Vadim

Subjects
bacteria
Abstract

Test of non randomness of the operon enrichment. (DOC 871Â kb)

Published
2017
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9. Genome analysis of E. coli isolated from Crohn’s disease patients

Author

Rakitina, Daria V., primary, Manolov, Alexander I., additional, Kanygina, Alexandra V., additional, Garushyants, Sofya K., additional, Baikova, Julia P., additional, Alexeev, Dmitry G., additional, Ladygina, Valentina G., additional, Kostryukova, Elena S., additional, Larin, Andrei K., additional, Semashko, Tatiana A., additional, Karpova, Irina Y., additional, Babenko, Vladislav V., additional, Ismagilova, Ruzilya K., additional, Malanin, Sergei Y., additional, Gelfand, Mikhail S., additional, Ilina, Elena N., additional, Gorodnichev, Roman B., additional, Lisitsyna, Eugenia S., additional, Aleshkin, Gennady I., additional, Scherbakov, Petr L., additional, Khalif, Igor L., additional, Shapina, Marina V., additional, Maev, Igor V., additional, Andreev, Dmitry N., additional, and Govorun, Vadim M., additional

Published
2017
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