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PLOS Computational Biology  
Integration of unpaired single cell omics data by deep transfer graph convolutional network

Yulong Kan, Yunjing Qi, Zhongxiao Zhang, Xikeng Liang, Weihao Wang, Shuilin Jin

Research Article | published 16 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012625

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The role of chromatin state in intron retention: A case study in leveraging large scale deep learning models

Ahmed Daoud, Asa Ben-Hur

Research Article | published 10 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012755

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Integrative analysis of ATAC-seq and RNA-seq for cells infected by human T-cell leukemia virus type 1

Azusa Tanaka, Yasuhiro Ishitsuka, Hiroki Ohta, Norihiro Takenouchi, Masanori Nakagawa, Ki-Ryang Koh, Chiho Onishi, Hiromitsu Tanaka, Akihiro Fujimoto, Jun-ichirou Yasunaga, Masao Matsuoka

Research Article | published 02 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012690

Views: 489Citations: 0Saves: 9 • Shares: 3

Cancer molecular subtyping using limited multi-omics data with missingness

Yongqi Bu, Jiaxuan Liang, Zhen Li, Jianbo Wang, Jun Wang, Guoxian Yu

Research Article | published 26 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012710

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Predicting lung aging using scRNA-Seq data

Qi Song, Alex Singh, John E. McDonough, Taylor S. Adams, Robin Vos, Ruben De Man, Greg Myers, Laurens J. Ceulemans, Bart M. Vanaudenaerde, Wim A. Wuyts, Xiting Yan, Jonas Schupp, James S. Hagood, Naftali Kaminski, Ziv Bar-Joseph

Research Article | published 19 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012632

Views: 1032Citations: 0Saves: 1 • Shares: 19

scMoMtF: An interpretable multitask learning framework for single-cell multi-omics data analysis

Wei Lan, Tongsheng Ling, Qingfeng Chen, Ruiqing Zheng, Min Li, Yi Pan

Research Article | published 18 Dec 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012679

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Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation

Jørgen Ankill, Zhi Zhao, Xavier Tekpli, Elin H. Kure, Vessela N. Kristensen, Anthony Mathelier, Thomas Fleischer

Research Article | published 18 Nov 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012565

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IMI-driver: Integrating multi-level gene networks and multi-omics for cancer driver gene identification

Peiting Shi, Junmin Han, Yinghao Zhang, Guanpu Li, Xionghui Zhou

Methods | published 26 Aug 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012389

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Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer’s disease

Easwaran Ramamurthy, Snigdha Agarwal, Noelle Toong, Heather Sestili, Irene M. Kaplow, Ziheng Chen, BaDoi Phan, Andreas R. Pfenning

Research Article | published 26 Aug 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012356

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scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data

Fengdi Zhao, Xin Ma, Bing Yao, Qing Lu, Li Chen

Methods | published 02 Aug 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011854

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Identifying topologically associating domains using differential kernels

Luka Maisuradze, Megan C. King, Ivan V. Surovtsev, Simon G. J. Mochrie, Mark D. Shattuck, Corey S. O’Hern

Research Article | published 15 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012221

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Role of diffusion and reaction of the constituents in spreading of histone modification marks

Vinoth Manivannan, Mandar M. Inamdar, Ranjith Padinhateeri

Research Article | published 11 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012235

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Learning Micro-C from Hi-C with diffusion models

Tong Liu, Hao Zhu, Zheng Wang

Research Article | published 17 May 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012136

Views: 1381Citations: 0Saves: 1 • Shares: 2

Interpretable online network dictionary learning for inferring long-range chromatin interactions

Vishal Rana, Jianhao Peng, Chao Pan, Hanbaek Lyu, Albert Cheng, Minji Kim, Olgica Milenkovic

Research Article | published 16 May 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012095

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Machine learning and multi-omics data reveal driver gene-based molecular subtypes in hepatocellular carcinoma for precision treatment

Meng Wang, Xinyue Yan, Yanan Dong, Xiaoqin Li, Bin Gao

Research Article | published 10 May 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012113

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