2-AIN-505, 2-AIN-251: Seminar in Bioinformatics (1), (3)
Winter 2024
List of papers

• Jouni Siren, Parsa Eskandar, Matteo Tommaso Ungaro, Glenn Hickey, Jordan M. Eizenga, Adam M. Novak, Xian Chang, Pi-Chuan Chang, Mikhail Kolmogorov, Andrew Carroll, Jean Monlong, Benedict Paten. Personalized pangenome references. Nature methods, 2024.
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• Giovanni Quinones-Valdez, Kofi Amoah, Xinshu Xiao. Long-read RNA-seq demarcates cis- and trans-directed alternative RNA splicing. Technical Report 2024.06.14.599101, bioRxiv, 2024.
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• Michel {van Kempen}, Stephanie S. Kim, Charlotte Tumescheit, Milot Mirdita, Jeongjae Lee, Cameron L. M. Gilchrist, Johannes Soding, Martin Steinegger. Fast and accurate protein structure search with Foldseek. Nature biotechnology, 42(2):243-246. 2024.
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• Xavi Guitart, David Porubsky, DongAhn Yoo, Max L. Dougherty, Philip C. Dishuck, Katherine M. Munson, Alexandra P. Lewis, Kendra Hoekzema, Jordan Knuth, Stephen Chang, Tomi Pastinen, Evan E. Eichler. Independent expansion, selection and hypervariability of the TBC1D3 gene family in humans. bioRxiv, 2024.
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• Daria Frolova, Leandro Lima, Leah Roberts, Leonard Bohnenkämper, Roland Wittler, Jens Stoye, Zamin Iqbal. Applying rearrangement distances to enable plasmid epidemiology with pling. Technical Report 2024.06.12.598623, bioRxiv, 2024.
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• You Wu, Wenna Shao, Mengxiao Yan, Yuqin Wang, Pengfei Xu, Guoqiang Huang, Xiaofei Li, Brian D. Gregory, Jun Yang, Hongxia Wang, Xiang Yu. Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing. Nat Commun, 15(1):4049. 2024.
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• Stephen Hwang, Nathaniel K. Brown, Omar Y. Ahmed, Katharine M. Jenike, Sam Kovaka, Michael C. Schatz, Ben Langmead. MEM-based pangenome indexing for k-mer queries. Technical Report 2024-05, bioRxiv,
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• Lovro Vrček, Xavier Bresson, Thomas Laurent, Martin Schmitz, Kenji Kawaguchi, Mile Šikić. Geometric deep learning framework for de novo genome assembly. Technical Report 2024.03.11.584353, bioRxiv, 2024.
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• Dominik Stanojevic, Zhe Li, Sara Bakic, Roger Foo, Mile Sikic. Rockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing. Nat Commun, 15(1):5580. 2024.
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• Arnaud Kress, Olivier Poch, Odile Lecompte, Julie D. Thompson. Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events. Front Bioinform, 3:1178926. 2023.
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• Shuvom Sadhuka, Daniel Fridman, Bonnie Berger, Hyunghoon Cho. Assessing transcriptomic reidentification risks using discriminative sequence models. Genome Research, 33(7):1101-1112. 2023.
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