2-AIN-506, 2-AIN-252: Seminar in Bioinformatics (2), (4)
Summer 2025
List of papers
- Roman Sarrazin-Gendron, Parham {Ghasemloo Gheidari}, Alexander Butyaev, Timothy Keding, Eddie Cai, Jiayue Zheng, Renata Mutalova, Julien Mounthanyvong, Yuxue Zhu, Elena Nazarova, Chrisostomos Drogaris, Kornel Erhart, Amelie Brouillette, Gabriel Richard, Randy Pitchford, Sebastien Caisse, Mathieu Blanchette, Daniel McDonald, Rob Knight, Attila Szantner, Jerome Waldispuhl.
Improving microbial phylogeny with citizen science within a mass-market video game.
Nature biotechnology,
43(1):76-84.
2025.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Qiong Chen, Boliang Zhang, Chen Peng, Jiajun Huang, Xiaotao Shen, Chao Jiang.
Kun-peng: an ultra-memory-efficient, fast, and accurate pan-domain taxonomic classifier for all.
bioRxiv,
2024.12.19.629356.
2024.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Davide Bolognini, Alma Halgren, Runyang Nicolas Lou, Alessandro Raveane, Joana L. Rocha, Andrea Guarracino, Nicole Soranzo, Chen-Shan Chin, Erik Garrison, Peter H. Sudmant.
Recurrent evolution and selection shape structural diversity at the amylase locus.
Nature,
634(8034):617-625.
2024.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- AJ Petri, K Sahlin.
De novo clustering of extensive long-read transcriptome datasets with isONclust3.
bioRxiv,
3:2024-10.
2024.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
- Yanglan Gan, Yuhan Chen, Guangwei Xu, Wenjing Guo, Guobing Zou.
Deep enhanced constraint clustering based on contrastive learning for scRNA-seq data.
Briefings in bioinformatics,
24(4).
2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Chen-Shan Chin, Sairam Behera, Asif Khalak, Fritz J. Sedlazeck, Peter H. Sudmant, Justin Wagner, Justin M. Zook.
Multiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes.
Nature methods,
20(8):1213-1221.
2023.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Endre Neparaczki, Luca Kis, Zoltan Maroti, Bence Kovacs, Gergely I. B. Varga, Miklos Makoldi, Pamjav Horolma, Eva Teiszler, Balazs Tihanyi, Peter L. Nagy, Kitti Maar, Attila Gyenesei, Oszkar Schutz, Eszter Dudas, Tibor Torok, Vesna Pascuttini-Juraga, Ivancica Peharda, Laszlo Tamas Vizi, Gabor Horvath-Lugossy, Miklos Kasler.
The genetic legacy of the Hunyadi descendants.
Heliyon,
8(11):e11731.
2022.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Rob Patro, Geet Duggal, Michael I. Love, Rafael A. Irizarry, Carl Kingsford.
Salmon provides fast and bias-aware quantification of transcript expression.
Nature methods,
14(4):417-419.
2017.
[ Abstract ] [ Download from publisher ] [ BibTeX ] [ PubMed ]
- Petar Veličković, Guillem Cucurull, Arantxa Casanova, Adriana Romero, Pietro Lio, Yoshua Bengio.
Graph Attention Networks.
arXiv,
1710.10903.
2017.
[ Abstract ] [ Download from publisher ] [ BibTeX ]
