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PLOS Computational Biology  
The tumour histopathology “glossary” for AI developers

Soham Mandal, Ann-Marie Baker, Trevor A. Graham, Konstantin Bräutigam

Education | published 23 Jan 2025 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012708

Views: 1221Citations: 0Saves: 0 • Shares: 0

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

Kernel Bayesian logistic tensor decomposition with automatic rank determination for predicting multiple types of miRNA-disease associations

Yingjun Ma, Yuanyuan Ma

Research Article | published 08 Jul 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012287

Views: 662Citations: 0Saves: 0 • Shares: 0

Threshold-awareness in adaptive cancer therapy

MingYi Wang, Jacob G. Scott, Alexander Vladimirsky

Research Article | published 14 Jun 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012165

Views: 760Citations: 0Saves: 0 • Shares: 0

Mathematical modeling of the evolution of resistance and aggressiveness of high-grade serous ovarian cancer from patient CA-125 time series

Kanyarat Jitmana, Jason I. Griffiths, Sian Fereday, Anna DeFazio, David Bowtell, for Australian Ovarian Cancer Study , Frederick R. Adler

Research Article | published 29 May 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1012073

Views: 1012Citations: 1Saves: 0 • Shares: 0

Benchmarking multi-ancestry prostate cancer polygenic risk scores in a real-world cohort

Yajas Shah, Scott Kulm, Jones T. Nauseef, Zhengming Chen, Olivier Elemento, Kevin H. Kensler, Ravi N. Sharaf

Research Article | published 10 Apr 2024 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011990

Views: 1095Citations: 0Saves: 2 • Shares: 6

A zero-agnostic model for copy number evolution in cancer

Henri Schmidt, Palash Sashittal, Benjamin J. Raphael

Research Article | published 09 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011590

Views: 1274Citations: 4Saves: 7 • Shares: 4

A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing

Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, Nicola Calonaci, Alberto D’Onofrio, Fabio Anselmi, Marco Antoniotti, Alex Graudenzi, Giulio Caravagna

Research Article | published 02 Nov 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011557

Views: 2675Citations: 2Saves: 7 • Shares: 34

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

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

Explainable multi-task learning improves the parallel estimation of polygenic risk scores for many diseases through shared genetic basis

Adrien Badré, Chongle Pan

Research Article | published 07 Jul 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011211

Views: 1787Citations: 3Saves: 17 • Shares: 1

A combined experimental-computational approach uncovers a role for the Golgi matrix protein Giantin in breast cancer progression

Salim Ghannoum, Damiano Fantini, Muhammad Zahoor, Veronika Reiterer, Santosh Phuyal, Waldir Leoncio Netto, Øystein Sørensen, Arvind Iyer, Debarka Sengupta, Lina Prasmickaite, Gunhild Mari Mælandsmo, Alvaro Köhn-Luque, Hesso Farhan

Research Article | published 17 Apr 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010995

Views: 1559Citations: 3Saves: 12 • Shares: 10

Predicting regrowth of low-grade gliomas after radiotherapy

Stéphane Plaszczynski, Basile Grammaticos, Johan Pallud, Jean-Eric Campagne, Mathilde Badoual

Research Article | published 31 Mar 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1011002

Views: 1378Citations: 4Saves: 10 • Shares: 1

Quantification of spatial and phenotypic heterogeneity in an agent-based model of tumour-macrophage interactions

Joshua A. Bull, Helen M. Byrne

Research Article | published 27 Mar 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010994

Views: 2633Citations: 17Saves: 35 • Shares: 16

OSCAR: Optimal subset cardinality regression using the L0-pseudonorm with applications to prognostic modelling of prostate cancer

Anni S. Halkola, Kaisa Joki, Tuomas Mirtti, Marko M. Mäkelä, Tero Aittokallio, Teemu D. Laajala

Research Article | published 10 Mar 2023 PLOS Computational Biology

https://doi.org/10.1371/journal.pcbi.1010333

Views: 1400Citations: 3Saves: 4 • Shares: 7

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