2-AIN-506, 2-AIN-252: Seminar in Bioinformatics (2), (4)
Summer 2026
List of papers
- 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.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Sumit Walia, Harsh Motwani, Yu-Hsiang Tseng, Kyle Smith, Russell Corbett-Detig, Yatish Turakhia.
Compressive pangenomics using mutation-annotated networks.
Nature genetics,
58(2):445-453.
2026.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Karina Ilchenko, Remy A. Bonnin, Eduardo P. C. Rocha, Eugen Pfeifer.
Efficient detection and typing of phage-plasmids.
mBio,
:e0300025.
2026.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- 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.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- 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,
16(1):2921.
2025.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- 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,
57(10):2589-2602.
2025.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- 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,
20(8):1187-1195.
2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- 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,
13(1):1131.
2022.
[ Abstract ] [ BibTeX ] [ PubMed ]
- 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,
6(10).
2020.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- James Robertson, John H. E. Nash.
MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies.
Microb Genom,
4(8).
2018.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
