Bioinformatics

DIGEST: An online tool for designing of multiple reaction monitoring assays
prutyay gautam, Praveen Singh, Mrinal, Akash Bhaskar, Sukriti Sacher, Yashesh Dagar, Trayambak Basak, Shantanu Sengupta, Arjun Ray

bioRxiv 2023.11.27.568790; doi: https://doi.org/10.1101/2023.11.27.568790 New Results

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ProTokens: A Machine-Learned Language for Compact and Informative Encoding of Protein 3D Structures
Xiaohan Lin, Zhenyu Chen, Yanheng Li, Xingyu Lu, Chuanliu Fan, Ziqiang Cao, Shihao Feng, Yi Qin Gao, Jun Zhang

bioRxiv 2023.11.27.568722; doi: https://doi.org/10.1101/2023.11.27.568722 New Results

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A rigorous benchmarking of alignment-based HLA callers for RNA-seq data
Dottie Yu, Ram Ayyala, Sarah Hany Sadek, Likhitha Chittampalli, Hafsa Farooq, Junghyun Jung, Abdullah Al Nahid, Grigore Boldirev, Jieting Hu, Ryan Alomair, Sungmin Park, Austin D Nguyen, Alex Zelikovsky, Nicholas Mancuso, Jong Wha Joo, Reid F Thompson, Houda Alachkar, Serghei Mangul

bioRxiv 2023.05.22.541750; doi: https://doi.org/10.1101/2023.05.22.541750 New Results

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Protein domain embeddings for fast and accurate similarity search
Benjamin Giovann Iovino, Haixu Tang, Yuzhen Ye

bioRxiv 2023.11.27.567555; doi: https://doi.org/10.1101/2023.11.27.567555 New Results

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Evolution-guided large language model is a predictor of virus mutation trends
Zhiwei Nie, Xudong Liu, Jie Chen, Zhennan Wang, Yutian Liu, Haorui Si, Tianyi Dong, Fan Xu, Guoli Song, Yu Wang, Peng Zhou, Wen Gao, Yonghong Tian

bioRxiv 2023.11.27.568815; doi: https://doi.org/10.1101/2023.11.27.568815 New Results

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Variant- and Vaccination-Specific Alternative Splicing Profiles in SARS-CoV-2 Infections
Sung-Gwon Lee, Priscilla Furth, Lothar Hennighausen, Hye Kyung Lee

bioRxiv 2023.11.24.568603; doi: https://doi.org/10.1101/2023.11.24.568603 New Results

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Sequence-based drug design using transformers
Shengyu Zhang, Donghui Huo, Robert I. Horne, Yumeng Qi, Sebastian Pujalte Ojeda, Aixia Yan, Michele Vendruscolo

bioRxiv 2023.11.27.568880; doi: https://doi.org/10.1101/2023.11.27.568880 New Results

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Random forest classifiers trained on simulated data enable accurate short read-based genotyping of structural variants in the alpha globin region at Chr16p13.3
Nancy F Hansen, Xunde Wang, Mickias B. Tegegn, Zhi Liu, Mateus H. Gouveia, Gracelyn Hill, Jennifer C. Lin, Temiloluwa Okulosubo, Daniel Shriner, Swee Lay Thein, James C. Mullikin

bioRxiv 2023.11.27.568683; doi: https://doi.org/10.1101/2023.11.27.568683 New Results

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Hidden Knowledge Recovery from GAN-generated Single-cell RNA-seq Data
Xuegong Zhang, Fanhong Li, Najeeb Ullah Shah

bioRxiv 2023.11.27.568840; doi: https://doi.org/10.1101/2023.11.27.568840 New Results

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Rendering protein mutation movies with MutAmore
Konstantin Weissenow, Burkhard Rost

bioRxiv 2023.09.15.557870; doi: https://doi.org/10.1101/2023.09.15.557870 New Results

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Bioinformatics

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