Systematic benchmark of state-of-the-art variant calling pipelines identifies major factors affecting accuracy of coding sequence variant discovery
Barbitoff, Yury A, Abasov, Ruslan, Tvorogova, Varvara E, Glotov, Andrey S, Predeus, Alexander V
Published in BMC genomics (22.02.2022)
Published in BMC genomics (22.02.2022)
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Journal Article
Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica
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
Published in PLoS pathogens (30.08.2021)
Published in PLoS pathogens (30.08.2021)
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Journal Article
Energetic and Structural Details of the Trigger-Loop Closing Transition in RNA Polymerase II
Wang, Beibei, Predeus, Alexander V., Burton, Zachary F., Feig, Michael
Published in Biophysical journal (06.08.2013)
Published in Biophysical journal (06.08.2013)
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Journal Article
Bioinformatics of germline variant discovery for rare disease diagnostics: current approaches and remaining challenges
Barbitoff, Yury A, Ushakov, Mikhail O, Lazareva, Tatyana E, Nasykhova, Yulia A, Glotov, Andrey S, Predeus, Alexander V
Published in Briefings in bioinformatics (22.01.2024)
Published in Briefings in bioinformatics (22.01.2024)
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Journal Article
Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580
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
Published in PLoS biology (01.01.2019)
Published in PLoS biology (01.01.2019)
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Journal Article
Systematic dissection of biases in whole-exome and whole-genome sequencing reveals major determinants of coding sequence coverage
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.
Published in Scientific reports (06.02.2020)
Published in Scientific reports (06.02.2020)
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Journal Article
Differential Mismatch Recognition Specificities of Eukaryotic MutS Homologs, MutSα and MutSβ
Sharma, Monika, Predeus, Alexander V., Kovacs, Nicholas, Feig, Michael
Published in Biophysical journal (03.06.2014)
Published in Biophysical journal (03.06.2014)
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Journal Article
Salmonella identified in pigs in Kenya and Malawi reveals the potential for zoonotic transmission in emerging pork markets
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
Published in PLoS neglected tropical diseases (01.11.2020)
Published in PLoS neglected tropical diseases (01.11.2020)
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Journal Article
Transcriptomic profiling of Escherichia coli K-12 in response to a compendium of stressors
Bhatia, Rama P., Kirit, Hande A., Predeus, Alexander V., Bollback, Jonathan P.
Published in Scientific reports (24.05.2022)
Published in Scientific reports (24.05.2022)
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Journal Article
PRIMO: A Transferable Coarse-Grained Force Field for Proteins
Kar, Parimal, Gopal, Srinivasa Murthy, Cheng, Yi-Ming, Predeus, Alexander, Feig, Michael
Published in Journal of chemical theory and computation (13.08.2013)
Published in Journal of chemical theory and computation (13.08.2013)
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Journal Article
Multiscale spatial mapping of cell populations across anatomical sites in healthy human skin and basal cell carcinoma
Ganier, Clarisse, Mazin, Pavel, Herrera-Oropeza, Gabriel, Du-Harpur, Xinyi, Blakeley, Matthew, Gabriel, Jeyrroy, Predeus, Alexander V, Cakir, Batuhan, Prete, Martin, Harun, Nasrat, Darrigrand, Jean-Francois, Haiser, Alexander, Wyles, Saranya, Shaw, Tanya, Teichmann, Sarah A, Haniffa, Muzlifah, Watt, Fiona M, Lynch, Magnus D
Published in Proceedings of the National Academy of Sciences - PNAS (09.01.2024)
Published in Proceedings of the National Academy of Sciences - PNAS (09.01.2024)
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Journal Article
Modulation of Salmonella virulence by a novel SPI-2 injectisome effector that interacts with the dystrophin-associated protein complex
Yu, Xiu-Jun, Xie, Haixia, Li, Yan, Liu, Mei, Hou, Ruhong, Predeus, Alexander V, Perez Sepulveda, Blanca M, Hinton, Jay C D, Holden, David W, Thurston, Teresa L M
Published in mBio (17.07.2024)
Published in mBio (17.07.2024)
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Journal Article
New Intranuclear Symbiotic Bacteria from Macronucleus of Paramecium putrinum—“Candidatus Gortzia Yakutica”
Beliavskaia, Alexandra Y., Predeus, Alexander V., Garushyants, Sofya K., Logacheva, Maria D., Gong, Jun, Zou, Songbao, Gelfand, Mikhail S., Rautian, Maria S.
Published in Diversity (Basel) (01.05.2020)
Published in Diversity (Basel) (01.05.2020)
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Journal Article
Single-cell and spatially resolved interactomics of tooth-associated keratinocytes in periodontitis
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.
Published in Nature communications (14.06.2024)
Published in Nature communications (14.06.2024)
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Journal Article
Acute response to pathogens in the early human placenta at single-cell resolution
Hoo, Regina, Ruiz-Morales, Elias R., Kelava, Iva, Rawat, Mukul, Mazzeo, Cecilia Icoresi, Tuck, Elizabeth, Sancho-Serra, Carmen, Chelaghma, Sara, Predeus, Alexander V., Murray, Simon, Fernandez-Antoran, David, Waller, Ross F., Álvarez-Errico, Damiana, Lee, Marcus C.S., Vento-Tormo, Roser
Published in Cell systems (15.05.2024)
Published in Cell systems (15.05.2024)
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Journal Article