| Time and place: | ||
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| Wednesday 17:20, I-23 or online in MS Teams. | ||
| Instructors: | ||
| doc. Mgr. Tomáš Vinař, PhD | M-163, | ![]() |
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| doc. Mgr. Broňa Brejová, PhD | M-163, | ![]() |
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| Seminar schedule: | ||
| Short talk schedule | ||
| 2026-02-18 Filip Kerák | Pedro Tomaz da Silva, Alexander Karollus, Johannes Hingerl, Gihanna Sta Teresa Galindez, Nils Wagner, Xavier Hernandez-Alias, Danny Incarnato, Julien Gagneur. Nucleotide dependency analysis of genomic language models detects functional elements. Nature genetics, 2025. link |
| 2026-02-25 Tomáš Vinař | Sergio Arredondo-Alonso, Anna K. Pontinen, Joao A. Gama, Rebecca A. Gladstone, Klaus Harms, Gerry Tonkin-Hill, Harry A. Thorpe, Gunnar S. Simonsen, Orjan Samuelsen, Pal J. Johnsen, Jukka Corander. Plasmid-driven strategies for clone success in Escherichia coli. Nat Commun, 2025. link |
| 2026-03-04 Monika Buchalová | Karina Ilchenko, Remy A. Bonnin, Eduardo P. C. Rocha, Eugen Pfeifer. Efficient detection and typing of phage-plasmids. mBio, 2026. link |
| 2026-03-11 Muqadas Baksh | Mislav Acman, Ruobing Wang, Lucy {van Dorp}, Liam P. Shaw, Qi Wang, Nina Luhmann, Yuyao Yin, Shijun Sun, Hongbin Chen, Hui Wang, Francois Balloux. Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene bla(NDM). Nat Commun, 2022. link |
| 2026-03-18 Jana Černíková | James Robertson, John H. E. Nash. MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies. Microb Genom, 2018. link James Robertson, Kyrylo Bessonov, Justin Schonfeld, John H. E. Nash. Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance. Microb Genom, 2020. link |
| 2026-03-25 Alessia Petescia | Sumit Walia, Harsh Motwani, Yu-Hsiang Tseng, Kyle Smith, Russell Corbett-Detig, Yatish Turakhia. Compressive pangenomics using mutation-annotated networks. Nature genetics, 2026. link |
| 2026-04-01 no seminar | |
| 2026-04-08 Luca Denti | Heng Hu, Runtian Gao, Zhongjun Jiang, Shuqi Cao, Yadong Liu, Murong Zhou, Wentao Gao, Shengming Zhou, Tao Jiang, Guohua Wang. SVPG: a pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples. Technical Report, bioRxiv, 2025. link |
| 2026-04-15 no seminar | |
| 2026-04-22 Kristína Galková | Ying Chen, Andre Sim, Yuk Kei Wan, Keith Yeo, Joseph Jing Xian Lee, Min Hao Ling, Michael I. Love, Jonathan Goke. Context-aware transcript quantification from long-read RNA-seq data with Bambu. Nature methods, 2023. link |
| 2026-04-29 Daniela Halmová | |
| 2026-05-06 Victor Epain | Victor Epain, Aniket Mane, Gianluca Della Vedova, Paola Bonizzoni, Cedric Chauve. A multi-flow approach for binning circular plasmids from short-reads assembly graphs. Technical Report, bioRxiv, 2026. link |
| 2026-05-13 | |
| 2026-05-20 no seminar? |