2-AIN-506, 2-AIN-252: Seminar in Bioinformatics (2), (4)
Summer 2024
List of papers

• Genomic data in the All of Us Research Program. Nature, 2024.
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• Vikram S. Shivakumar, Omar Y. Ahmed, Sam Kovaka, Mohsen Zakeri, Ben Langmead. Sigmoni: classification of nanopore signal with a compressed pangenome index. bioRxiv, 2023.
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• Can Firtina, Nika Mansouri Ghiasi, Joel Lindegger, Gagandeep Singh, Meryem Banu Cavlak, Haiyu Mao, Onur Mutlu. RawHash: enabling fast and accurate real-time analysis of raw nanopore signals for large genomes. Bioinformatics, 39(39 Suppl 1):i297-i307. 2023.
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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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• Jonas A. Sibbesen, Jordan M. Eizenga, Adam M. Novak, Jouni Siren, Xian Chang, Erik Garrison, Benedict Paten. Haplotype-aware pantranscriptome analyses using spliced pangenome graphs. Nature methods, 20(2):239-247. 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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• Xiaojing An, Priyanka Ghosh, Patrick Keppler, Sureyya Emre Kurt, Sriram Krishnamoorthy, Ponnuswamy Sadayappan, Aravind Sukumaran Rajam, Umit V. Catalyurek, Ananth Kalyanaraman. BOA: A partitioned view of genome assembly. iScience, 25(11):105273. 2022.
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• Teshome Tilahun Bizuayehu, Kornel Labun, Martin Jakubec, Kirill Jefimov, Adnan Muhammad Niazi, Eivind Valen. Long-read single-molecule RNA structure sequencing using nanopore. Nucleic acids research, 50(20):e120. 2022.
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• Jennifer Klunk, Tauras P. Vilgalys, Christian E. Demeure, Xiaoheng Cheng, Mari Shiratori, Julien Madej, Remi Beau, Derek Elli, Maria I. Patino, Rebecca Redfern, Sharon N. DeWitte, Julia A. Gamble, Jesper L. Boldsen, Ann Carmichael, Nukhet Varlik, Katherine Eaton, Jean-Christophe Grenier, G. Brian Golding, Alison Devault, Jean-Marie Rouillard, Vania Yotova, Renata Sindeaux, Chun Jimmie Ye, Matin Bikaran, Anne Dumaine, Jessica F. Brinkworth, Dominique Missiakas, Guy A. Rouleau, Matthias Steinrucken, Javier Pizarro-Cerda, Hendrik N. Poinar, Luis B. Barreiro. Evolution of immune genes is associated with the Black Death. Nature, 611(7935):312-319. 2022. See also follow-up discussion Barton A. R. et al. .
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• Hussein A. Hejase, Ziyi Mo, Leonardo Campagna, Adam Siepel. A Deep-Learning Approach for Inference of Selective Sweeps from the Ancestral Recombination Graph. Molecular biology and evolution, 39(1). 2022.
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