2-AIN-506, 2-AIN-252: Seminar in Bioinformatics (2), (4)
Summer 2025
List of papers

• You Wu, Li Xu, Xiaohong Cong, Hanxiao Li, Yanli Li. Scmaskgan: masked multi-scale CNN and attention-enhanced GAN for scRNA-seq dropout imputation. BMC bioinformatics, 26(1):130. 2025.
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• Jim Shaw, Yun William Yu. Rapid species-level metagenome profiling and containment estimation with sylph. Nature biotechnology, 43(8):1348-1359. 2025.
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• Megan K. Le, Qian Qin, Heng Li. colorSV: Long-range Somatic Structural Variation Calling from Matched Tumor-normal Co-assembly Graphs. Genomics, proteomics & bioinformatics, 2025.
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• Líndez PP, Danielsen LS, Kovačić I, Avellí MP, Nesme J, Jensen LJ, Nissen JN, Sørensen SJ, Rasmussen S.. Accurate plasmid reconstruction from metagenomics data using assembly-alignment graphs and contrastive learning. Technical Report, bioRxiv, 2025.
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• Suraj Rajendran, Eeshaan Rehani, William Phu, Qiansheng Zhan, Jonas E. Malmsten, Marcos Meseguer, Kathleen A. Miller, Zev Rosenwaks, Olivier Elemento, Nikica Zaninovic, Iman Hajirasouliha. A foundational model for in vitro fertilization trained on 18 million time-lapse images. Nat Commun, 16(1):6235. 2025.
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• Walfred Ma, Mark Jp Chaisson. Genotyping sequence-resolved copy number variation using pangenomes reveals paralog-specific global diversity and expression divergence of duplicated genes. bioRxiv, 2025.
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• Renmao Tian, Jizhong Zhou, Behzad Imanian. PlasmidHunter: accurate and fast prediction of plasmid sequences using gene content profile and machine learning. Briefings in bioinformatics, 25(4). 2024.
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• Gaetan Benoit, Sebastien Raguideau, Robert James, Adam M. Phillippy, Rayan Chikhi, Christopher Quince. High-quality metagenome assembly from long accurate reads with metaMDBG. Nature biotechnology, 42(9):1378-1383. 2024.
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• Qianhui Zhu, Shenghan Gao, Binghan Xiao, Zilong He, Songnian Hu. Plasmer: an Accurate and Sensitive Bacterial Plasmid Prediction Tool Based on Machine Learning of Shared k-mers and Genomic Features. Microbiol Spectr, 11(3):e0464522. 2023.
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• 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.
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