2-AIN-505, 2-AIN-251: Seminar in Bioinformatics (1), (3)
Winter 2021
List of papers

  • Dhaivat Joshi, Shunfu Mao, Sreeram Kannan, Suhas Diggavi. QAlign: aligning nanopore reads accurately using current-level modeling. Bioinformatics, 37(5):625-633. 2021.
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  • Thomas Buchler, Caroline Rather, Pascal Weber, Enno Ohlebusch. Coordinate Systems for Pangenome Graphs based on the Level Function and Minimum Path Covers. In Proceedings of the 14th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2021) - Volume 3: BIOINFORMATICS, pages 21-29, pp. 21-29, 2021.
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  • Jouni Sirén et al.. Genotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit. Technical Report 2020.12.04.412486, bioRxiv, 2021.
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  • Peter Peresini, Vladimir Boza, Brona Brejova, Tomas Vinar. Nanopore Base Calling on the Edge. Bioinformatics, 2021.
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  • Vladimír Boža, Peter Perešíni, Broňa Brejová, Tomáš Vinař. Dynamic Pooling Improves Nanopore Base Calling Accuracy. Technical Report https://arxiv.org/abs/2105.07520, arXiv,
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  • Omar Ahmed, Massimiliano Rossi, Sam Kovaka, Michael C. Schatz, Travis Gagie, Christina Boucher, Ben Langmead. Pan-genomic matching statistics for targeted nanopore sequencing. iScience, 24(6):102696. 2021.
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  • Paola Bonizzoni, Clelia De Felice, Alessia Petescia, Yuri Pirola, Raffaella Rizzi, Jens Stoye, Rocco Zaccagnino, Rosalba Zizza. Can We Replace Reads by Numeric Signatures? Lyndon Fingerprints as Representations of Sequencing Reads for Machine Learning. In AlCoB 2021: Algorithms for Computational Biology, 2021.
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  • Pay Giesselmann, Bjorn Brandl, Etienne Raimondeau, Rebecca Bowen, Christian Rohrandt, Rashmi Tandon, Helene Kretzmer, Gunter Assum, Christina Galonska, Reiner Siebert, Ole Ammerpohl, Andrew Heron, Susanne A. Schneider, Julia Ladewig, Philipp Koch, Bernhard M. Schuldt, James E. Graham, Alexander Meissner, Franz-Josef Muller. Analysis of short tandem repeat expansions and their methylation state withnanopore sequencing. Nature biotechnology, 37(12):1478-1481. 2019.
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  • Xuran Wang, Jihwan Park, Katalin Susztak, Nancy R. Zhang, Mingyao Li. Bulk tissue cell type deconvolution with multi-subject single-cell expressionreference. Nat Commun, 10(1):380. 2019.
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  • Nicholas Eriksson, Lior Pachter, Yumi Mitsuya, Soo-Yon Rhee, Chunlin Wang, Baback Gharizadeh, Mostafa Ronaghi, Robert W. Shafer, Niko Beerenwinkel. Viral population estimation using pyrosequencing. PLoS Comput Biol, 4(4):e1000074. 2008.
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