2-AIN-505, 2-AIN-251: Seminar in Bioinformatics (1), (3)
Winter 2022
List of papers

• Arun Das, Michael C. Schatz. Sketching and sampling approaches for fast and accurate long read classification. BMC bioinformatics, 23(1):452. 2022.
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• Yutong Qiu, Carl Kingsford. The Effect of Genome Graph Expressiveness on the Discrepancy Between Genome Graph Distance and String Set Distance. Technical Report 2022.02.18.481102, bioRxiv, 2022.
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• Jens-Uwe Ulrich, Ahmad Lutfi, Kilian Rutzen, Bernhard Y. Renard. ReadBouncer: Precise and Scalable Adaptive Sampling for Nanopore Sequencing. Technical Report 2022.02.01.478636, bioRxiv, 2022.
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• Wontack Han, Haixu Tang, Yuzhen Ye. Locality-Sensitive Hashing-Based k-Mer Clustering for Identification ofDifferential Microbial Markers Related to Host Phenotype. Journal of computational biology : a journal of computational molecular cell biology, 29(7):738-751. 2022.
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• Clément Agret, Bastien Cazaux, Antoine Limasset. Toward optimal fingerprint indexing for large scale genomics. Technical Report 2021.11.04.467355, bioRxiv,
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• Jarno N. Alanko, Simon J. Puglisi, Jaakko Vuohtoniemi. Succinct k-mer Sets Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform. Technical Report 2022.05.19.492613, bioRxiv, 2022.
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• Abhinav Dutta, David Pellow, Ron Shamir. Parameterized syncmer schemes improve long-read mapping. Technical Report 2022.01.10.475696, bioRxiv, 2022.
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• Yoshihiko Suzuki, Gene Myers. Accurate k-mer Classification Using Read Profiles. In WABI 2022, 2022.
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• Sebastian Schmidt, Jarno N. Alanko . Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time. In WABI 2022, 2022.
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• Ragnar Groot Koerkamp, Pesho Ivanov. Exact global alignment using A* with seed heuristic and match pruning. Technical Report 2022.09.19.508631, bioRxiv, 2022.
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• Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie, Christina Boucher. MONI: A Pangenomic Index for Finding Maximal Exact Matches. Journal of computational biology, 29(2):169-187. 2022.
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• Kristoffer Sahlin. Effective sequence similarity detection with strobemers. Genome research, 31(11):2080-2094. 2021.
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• Robert Edgar. Syncmers are more sensitive than minimizers for selecting conserved kmers inbiological sequences. PeerJ, 9:e10805. 2021.
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