Bioinformatics

HiCDiff: single-cell Hi-C data denoising with diffusion models
yanli wang, Jianlin Cheng

bioRxiv 2023.12.01.569684; doi: https://doi.org/10.1101/2023.12.01.569684 New Results

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Contrasting Sequence with Structure: Pre-training Graph Representations with PLMs
Louis Callum Butler Robinson, Timothy Atkinson, Liviu Copoiu, Patrick Bordes, Thomas Pierrot, Thomas Barrett

bioRxiv 2023.12.01.569611; doi: https://doi.org/10.1101/2023.12.01.569611 New Results

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Democratizing computational pathology: optimized Whole Slide Image representations for The Cancer Genome Atlas
Tristan Lazard, marvin Lerousseau, Sophie Gardrat, Anne Vincent-Salomon, Marc-Henri Stern, Manuel Rodrigues, Etienne Decenciere, Thomas Walter

bioRxiv 2023.12.04.569894; doi: https://doi.org/10.1101/2023.12.04.569894 Confirmatory Results

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Balanced Permeability Index: a multi-parameter index for improved in-vitro permeability
Dahlia R. Weiss, Javier L. Baylon, Ethan D. Evans, Anthony Paiva, Gerry Everlof, Jingfang Cutrone, Fabio Broccatelli

bioRxiv 2023.12.01.569478; doi: https://doi.org/10.1101/2023.12.01.569478 New Results

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Reprogramming of cardiac phosphoproteome, proteome and transcriptome confers resilience to chronic adenylyl cyclase-driven stress
Jia-Hua Qu, Khalid Chakir, Kirill V. Tarasov, Daniel R. Riordon, Maria Grazia Perino, Allwin Jennifa Silvester, Edward G. Lakatta

bioRxiv 2022.04.29.488779; doi: https://doi.org/10.1101/2022.04.29.488779 Confirmatory Results

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Benchmarking computational methods to identify spatially variable genes and peaks
Zhijian Li, Zain M. Patel, Dongyuan Song, Guanao Yan, Jingyi Jessica Li, Luca Pinello

bioRxiv 2023.12.02.569717; doi: https://doi.org/10.1101/2023.12.02.569717 New Results

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Kinetics-based Inference of Environment-Dependent Microbial Interactions and Their Dynamic Variation
Hyun-Seob Song, Na-Rae Lee, Aimee K. Kessell, Hugh C. McCullough, Seo-Young Park, Kang Zhou, Dong-Yup Lee

bioRxiv 2022.08.27.505268; doi: https://doi.org/10.1101/2022.08.27.505268 New Results

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Molecular dynamics simulations provide insights into ULK-101 potency and selectivity toward autophagic kinases ULK1/2
Robert M Vaughan, Bradley M Dickson, Katie R Martin, Jeffery P Mackeigan

bioRxiv 2023.12.01.569261; doi: https://doi.org/10.1101/2023.12.01.569261 New Results

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Comparison and benchmark of deep learning methods for non-coding RNA classification
Constance Creux, Farida Zehraoui, Francois Radvanyi, Fariza Tahi

bioRxiv 2023.11.24.568536; doi: https://doi.org/10.1101/2023.11.24.568536 New Results

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Pathformer: a biological pathway informed Transformer integrating multi-omics data for disease diagnosis and prognosis
Xiaofan Liu, Yuhuan Tao, Zilin Cai, Pengfei Bao, Hongli Ma, Kexing Li, Mengtao Li, Yunping Zhu, Zhi John Lu

bioRxiv 2023.05.23.541554; doi: https://doi.org/10.1101/2023.05.23.541554 New Results

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Bioinformatics

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