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Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery
Author / Creator:Barbitoff, Yury A. ; Abasov, Ruslan ; Tvorogova, Varvara E. ; Glotov, Andrey S. ; Predeus, Alexander V.
Publisher:England: BioMed Central Ltd
Journal title:BMC genomics, 2022-02, Vol.23 (1), p.155-17, Article 155
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Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica
Author / Creator:Powers, TuShun R. ; Haeberle, Amanda L. ; Predeus, Alexander V. ; Hammarlöf, Disa L. ; Cundiff, Jennifer A. ; Saldaña-Ahuactzi, Zeus ; Hokamp, Karsten ; Hinton, Jay C. D. ; Knodler, Leigh A.
Publisher:United States: Public Library of Science
Journal title:PLoS pathogens, 2021-08, Vol.17 (8), p.e1009280
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Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors
Author / Creator:Bhatia, Rama P. ; Kirit, Hande A. ; Predeus, Alexander V. ; Bollback, Jonathan P.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2022-05, Vol.12 (1), p.8788-8788, Article 8788
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LMNA R482L mutation causes impairments in C2C12 myoblasts subpopulations, alterations in metabolic reprogramming during differentiation, and oxidative stress
Author / Creator:Ivanova, Oksana A. ; Predeus, Alexander V. ; Sorokina, Margarita Y. ; Ignatieva, Elena V. ; Bobkov, Danila E. ; Sukhareva, Kseniia S. ; Kostareva, Anna A. ; Dmitrieva, Renata I.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2025-02, Vol.15 (1), p.5358-22
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Author Correction: Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors
Author / Creator:Bhatia, Rama P. ; Kirit, Hande A. ; Predeus, Alexander V. ; Bollback, Jonathan P.
Publisher:London: Nature Publishing Group UK
Journal title:Scientific reports, 2022-10, Vol.12 (1), p.16865-16865, Article 16865
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Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580
Author / Creator:Canals, Rocío ; Hammarlöf, Disa L. ; Kröger, Carsten ; Owen, Siân V. ; Fong, Wai Yee ; Lacharme-Lora, Lizeth ; Zhu, Xiaojun ; Wenner, Nicolas ; Carden, Sarah E. ; Honeycutt, Jared ; Monack, Denise M. ; Kingsley, Robert A. ; Brownridge, Philip ; Chaudhuri, Roy R. ; Rowe, Will P. M. ; Predeus, Alexander V. ; Hokamp, Karsten ; Gordon, Melita A. ; Hinton, Jay C. D.
Publisher:United States: Public Library of Science
Journal title:PLoS biology, 2019-01, Vol.17 (1), p.e3000059
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Single-cell and spatially resolved interactomics of tooth-associated keratinocytes in periodontitis
Author / Creator:Easter, Quinn T. ; Fernandes Matuck, Bruno ; Beldorati Stark, Germán ; Worth, Catherine L. ; Predeus, Alexander V. ; Fremin, Brayon ; Huynh, Khoa ; Ranganathan, Vaishnavi ; Ren, Zhi ; Pereira, Diana ; Rupp, Brittany T. ; Weaver, Theresa ; Miller, Kathryn ; Perez, Paola ; Hasuike, Akira ; Chen, Zhaoxu ; Bush, Mandy ; Qu, Xufeng ; Lee, Janice ; Randell, Scott H. ; Wallet, Shannon M. ; Sequeira, Inês ; Koo, Hyun ; Tyc, Katarzyna M. ; Liu, Jinze ; Ko, Kang I. ; Teichmann, Sarah A. ; Byrd, Kevin M.
Publisher:London: Nature Publishing Group UK
Journal title:Nature communications, 2024-06, Vol.15 (1), p.5016-23, Article 5016
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Potential links between human bloodstream infection by Salmonella enterica serovar Typhimurium and international transmission to Colombia
Author / Creator:Li, Yan ; Pulford, Caisey V. ; Díaz, Paula ; Perez-Sepulveda, Blanca M. ; Duarte, Carolina ; Predeus, Alexander V. ; Wiesner, Magdalena ; Heavens, Darren ; Low, Ross ; Schudoma, Christian ; Montaño, Angeline ; Hall, Neil ; Moreno, Jaime ; Hinton, Jay C. D.
Publisher:United States: Public Library of Science
Journal title:PLoS neglected tropical diseases, 2025-01, Vol.19 (1), p.e0012801
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Salmonella identified in pigs in Kenya and Malawi reveals the potential for zoonotic transmission in emerging pork markets
Author / Creator:Wilson, Catherine N. ; Pulford, Caisey V. ; Akoko, James ; Perez Sepulveda, Blanca ; Predeus, Alexander V. ; Bevington, Jessica ; Duncan, Patricia ; Hall, Neil ; Wigley, Paul ; Feasey, Nicholas ; Pinchbeck, Gina ; Hinton, Jay C. D. ; Gordon, Melita A. ; Fèvre, Eric M.
Publisher:United States: Public Library of Science
Journal title:PLoS neglected tropical diseases, 2020-11, Vol.14 (11), p.e0008796
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Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways
Author / Creator:Wang, Beibei ; Francis, Joshua ; Sharma, Monika ; Law, Sean M. ; Predeus, Alexander V. ; Feig, Michael
Publisher:United States: Public Library of Science
Journal title:PLoS computational biology, 2016-10, Vol.12 (10), p.e1005159-e1005159
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New Intranuclear Symbiotic Bacteria from Macronucleus of Paramecium putrinum—“Candidatus Gortzia Yakutica”
Author / Creator:Beliavskaia, Alexandra Y. ; Predeus, Alexander V. ; Garushyants, Sofya K. ; Logacheva, Maria D. ; Gong, Jun ; Zou, Songbao ; Gelfand, Mikhail S. ; Rautian, Maria S.
Publisher:Basel: MDPI AG
Journal title:Diversity (Basel), 2020-05, Vol.12 (5), p.198
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Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage
Author / Creator:Barbitoff, Yury A ; Matveenko, Andrew G ; Matiiv, Anton B ; Maksiutenko, Evgeniia M ; Moskalenko, Svetlana E ; Drozdova, Polina B ; Polev, Dmitrii E ; Beliavskaia, Alexandra Y ; Danilov, Lavrentii G ; Predeus, Alexander V ; Zhouravleva, Galina A
Publisher:England: Oxford University Press
Journal title:G3 : genes - genomes - genetics, 2021-04, Vol.11 (4)
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Species-Specific Proteins in the Oviducts of Snail Sibling Species: Proteotranscriptomic Study of Littorina fabalis and L. obtusata
Author / Creator:Lobov, Arseniy A. ; Babkina, Irina Y. ; Danilov, Lavrentii G. ; Masharskiy, Alexey E. ; Predeus, Alexander V. ; Mikhailova, Natalia A. ; Granovitch, Andrei I. ; Maltseva, Arina L.
Publisher:Basel: MDPI AG
Journal title:Biology (Basel, Switzerland), 2021-10, Vol.10 (11), p.1087
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Whole‐exome sequencing provides insights into monogenic disease prevalence in Northwest Russia
Author / Creator:Barbitoff, Yury A. ; Skitchenko, Rostislav K. ; Poleshchuk, Olga I. ; Shikov, Anton E. ; Serebryakova, Elena A. ; Nasykhova, Yulia A. ; Polev, Dmitrii E. ; Shuvalova, Anna R. ; Shcherbakova, Irina V. ; Fedyakov, Mikhail A. ; Glotov, Oleg S. ; Glotov, Andrey S. ; Predeus, Alexander V.
Publisher:United States: John Wiley & Sons, Inc
Journal title:Molecular genetics & genomic medicine, 2019-11, Vol.7 (11), p.e964-n/a
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Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage
Author / Creator:Barbitoff, Yury A ; Polev, Dmitrii E ; Glotov, Andrey S ; Serebryakova, Elena A ; Shcherbakova, Irina V ; Kiselev, Artem M ; Kostareva, Anna A ; Glotov, Oleg S ; Predeus, Alexander V
Publisher:London: Nature Publishing Group
Journal title:Scientific reports, 2020-02, Vol.10 (1)
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Phenome-wide functional dissection of pleiotropic effects highlights key molecular pathways for human complex traits
Author / Creator:Shikov, Anton E ; Skitchenko, Rostislav K ; Predeus, Alexander V ; Barbitoff, Yury A
Publisher:London: Nature Publishing Group
Journal title:Scientific reports, 2020-01, Vol.10 (1)
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Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges
Author / Creator:Barbitoff, Yury A ; Ushakov, Mikhail O ; Lazareva, Tatyana E ; Nasykhova, Yulia A ; Glotov, Andrey S ; Predeus, Alexander V
Publisher:England: Oxford University Press
Journal title:Briefings in bioinformatics, 2024-01, Vol.25 (2)
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An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes
Author / Creator:Perez-Sepulveda, Blanca M. ; Heavens, Darren ; Pulford, Caisey V. ; Predeus, Alexander V. ; Low, Ross ; Webster, Hermione ; Dykes, Gregory F. ; Schudoma, Christian ; Rowe, Will ; Lipscombe, James ; Watkins, Chris ; Kumwenda, Benjamin ; Shearer, Neil ; Costigan, Karl ; Baker, Kate S. ; Feasey, Nicholas A. ; Hinton, Jay C. D. ; Hall, Neil ; Acuña, María Teresa ; Antic, Dragan ; Antonio, Martin ; Bernal, Johan ; Bolaños, Hilda ; Chattaway, Marie ; Cheesbrough, John ; Chirambo, Angeziwa ; Darboe, Saffiatou ; Díaz, Paula ; Donado, Pilar ; Duarte, Carolina ; Duarte, Francisco ; Everett, Dean ; Fanning, Séamus ; Feglo, Patrick ; Ferreira, Adriano M. ; Floyd, Rachel ; Gavilán, Ronnie G. ; Gordon, Melita A. ; Hall, Neil ; Hernandes, Rodrigo T. ; Hernández-Mora, Gabriela ; Hurley, Daniel ; Kasumba, Irene N. ; Kwambana-Adams, Brenda ; Mattar, Salim ; Montaño, Lucy Angeline ; Moreira, Cristiano Gallina ; Moreno, Jaime ; Muthappa, Dechamma Mundanda ; Nair, Satheesh ; Parry, Chris M. ; Peno, Chikondi ; Permala-Booth, Jasnehta ; Petrović, Jelena ; Puente, José Luis ; Rebrie, Getenet ; Redway, Martha ; Sadatsune, Terue ; Silva, Claudia ; Smith, Anthony M. ; Tennant, Sharon ; Tran-Dien, Alicia ; Weill, François-Xavier ; Wiesner, Magdalena ; Wilson, Catherine
Publisher:England: BioMed Central Ltd
Journal title:Genome Biology, 2021-12, Vol.22 (1), p.349-349, Article 349
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Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa
Author / Creator:Pulford, Caisey V. ; Perez-Sepulveda, Blanca M. ; Canals, Rocío ; Bevington, Jessica A. ; Bengtsson, Rebecca J. ; Wenner, Nicolas ; Rodwell, Ella V. ; Kumwenda, Benjamin ; Zhu, Xiaojun ; Bennett, Rebecca J. ; Stenhouse, George E. ; Malaka De Silva, P. ; Webster, Hermione J. ; Bengoechea, Jose A. ; Dumigan, Amy ; Tran-Dien, Alicia ; Prakash, Reenesh ; Banda, Happy C. ; Alufandika, Lovemore ; Mautanga, Mike P. ; Bowers-Barnard, Arthur ; Beliavskaia, Alexandra Y. ; Predeus, Alexander V. ; Rowe, Will P. M. ; Darby, Alistair C. ; Hall, Neil ; Weill, François-Xavier ; Gordon, Melita A. ; Feasey, Nicholas A. ; Baker, Kate S. ; Hinton, Jay C. D.
Publisher:London: Nature Publishing Group UK
Journal title:Nature microbiology, 2021-03, Vol.6 (3), p.327-338
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Catching hidden variation: systematic correction of reference minor allele annotation in clinical variant calling
Author / Creator:Barbitoff, Yury A ; Bezdvornykh, Igor V ; Polev, Dmitrii E ; Serebryakova, Elena A ; Glotov, Andrey S ; Glotov, Oleg S ; Predeus, Alexander V
Publisher:New York: Nature Publishing Group US
Journal title:Genetics in medicine, 2018-03, Vol.20 (3), p.360-364
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Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery

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Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica

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Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors

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LMNA R482L mutation causes impairments in C2C12 myoblasts subpopulations, alterations in metabolic reprogramming during differentiation, and oxidative stress

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Author Correction: Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors

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Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580

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Single-cell and spatially resolved interactomics of tooth-associated keratinocytes in periodontitis

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Potential links between human bloodstream infection by Salmonella enterica serovar Typhimurium and international transmission to Colombia

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Salmonella identified in pigs in Kenya and Malawi reveals the potential for zoonotic transmission in emerging pork markets

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Long-Range Signaling in MutS and MSH Homologs via Switching of Dynamic Communication Pathways

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New Intranuclear Symbiotic Bacteria from Macronucleus of Paramecium putrinum—“Candidatus Gortzia Yakutica”

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Chromosome-level genome assembly and structural variant analysis of two laboratory yeast strains from the Peterhof Genetic Collection lineage

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Species-Specific Proteins in the Oviducts of Snail Sibling Species: Proteotranscriptomic Study of Littorina fabalis and L. obtusata

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Whole‐exome sequencing provides insights into monogenic disease prevalence in Northwest Russia

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Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage

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Phenome-wide functional dissection of pleiotropic effects highlights key molecular pathways for human complex traits

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Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges

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An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes

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Stepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa

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Catching hidden variation: systematic correction of reference minor allele annotation in clinical variant calling

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