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PLOS Computational Biology  
A computational analysis of the oncogenic and anti-tumor immunity role of P4HA3 in human cancers

Hong Yan Huang, Fu Wei Zhang, Jie Yu, Yan Hong Xiao, Di Zhu, XiaoLin Yi, XiaoHua Lin, Ming Jin, Hai Yun Jin, Yong Sheng Huang, Shu Wei Ren

Research Article | published 06 Nov 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012284

Views: 592Citations: 0Saves: 0 • Shares: 0

Quantitative evaluation of DNA damage repair dynamics to elucidate predictors of autism vs. cancer in individuals with germline PTEN variants

Ruipeng Wei, Masahiro Hitomi, Tammy Sadler, Lamis Yehia, Daniela Calvetti, Jacob Scott, Charis Eng

Research Article | published 02 Oct 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012449

Views: 785Citations: 0Saves: 8 • Shares: 1

COPS: A novel platform for multi-omic disease subtype discovery via robust multi-objective evaluation of clustering algorithms

Teemu J. Rintala, Vittorio Fortino

Research Article | published 05 Aug 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012275

Views: 883Citations: 0Saves: 0 • Shares: 0

A variational autoencoder trained with priors from canonical pathways increases the interpretability of transcriptome data

Bin Liu, Bodo Rosenhahn, Thomas Illig, David S. DeLuca

Research Article | published 03 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011198

Views: 932Citations: 1Saves: 0 • Shares: 0

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

Views: 1477Citations: 1Saves: 7 • Shares: 2

DBDNMF: A Dual Branch Deep Neural Matrix Factorization method for drug response prediction

Hui Liu, Feng Wang, Jian Yu, Yong Pan, Chaoju Gong, Liang Zhang, Lin Zhang

Research Article | published 04 Apr 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012012

Views: 1005Citations: 1Saves: 0 • Shares: 0

Tissue-adjusted pathway analysis of cancer (TPAC): A novel approach for quantifying tumor-specific gene set dysregulation relative to normal tissue

H. Robert Frost

Research Article | published 11 Jan 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011717

Views: 921Citations: 0Saves: 0 • Shares: 0

Recurrence risk stratification of hepatocellular carcinomas based on immune gene expression and features extracted from pathological images

Tao Ding, Xiao Li, Jiu Mo, Gregory Alexander, Jialu Li

Research Article | published 29 Dec 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011716

Views: 780Citations: 0Saves: 0 • Shares: 0

Predicting lncRNA-disease associations based on heterogeneous graph convolutional generative adversarial network

Zhonghao Lu, Hua Zhong, Lin Tang, Jing Luo, Wei Zhou, Lin Liu

Research Article | published 29 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011634

Views: 1540Citations: 6Saves: 0 • Shares: 0

Addressing erroneous scale assumptions in microbe and gene set enrichment analysis

Kyle C. McGovern, Michelle Pistner Nixon, Justin D. Silverman

Research Article | published 20 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011659

Views: 934Citations: 5Saves: 3 • Shares: 1

XA4C: eXplainable representation learning via Autoencoders revealing Critical genes

Qing Li, Yang Yu, Pathum Kossinna, Theodore Lun, Wenyuan Liao, Qingrun Zhang

Research Article | published 02 Oct 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011476

Views: 1787Citations: 2Saves: 0 • Shares: 0

Identifying a developmental transition in honey bees using gene expression data

Bryan C. Daniels, Ying Wang, Robert E. Page Jr, Gro V. Amdam

Research Article | published 21 Sep 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010704

Views: 978Citations: 1Saves: 6 • Shares: 2

Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression

Bayarbaatar Amgalan, Chi-Ping Day, Teresa M. Przytycka

Research Article | published 18 Sep 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011472

Views: 911Citations: 0Saves: 3 • Shares: 6

iPiDA-SWGCN: Identification of piRNA-disease associations based on Supplementarily Weighted Graph Convolutional Network

Jialu Hou, Hang Wei, Bin Liu

Research Article | published 20 Jun 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011242

Views: 1512Citations: 8Saves: 10 • Shares: 1

Structure learning for gene regulatory networks

Anthony Federico, Joseph Kern, Xaralabos Varelas, Stefano Monti

Research Article | published 18 May 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011118

Views: 2282Citations: 1Saves: 14 • Shares: 12

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