Eight quick tips for biologically and medically informed machine learning

Luca Oneto, Davide Chicco

PLOS Computational Biology: published January 9, 2025 | https://doi.org/10.1371/journal.pcbi.1012711

Ten simple rules for good model-sharing practices

Ismael Kherroubi Garcia, Christopher Erdmann, Sandra Gesing, Michael Barton, Lauren Cadwallader, Geerten Hengeveld, Christine R. Kirkpatrick, Kathryn Knight, Carsten Lemmen, Rebecca Ringuette, Qing Zhan, Melissa Harrison, Feilim Mac Gabhann, Natalie Meyers, Cailean Osborne, Charlotte Till, Paul Brenner, Matt Buys, Min Chen, Allen Lee, Jason Papin, Yuhan Rao

PLOS Computational Biology: published January 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012702

The tumour histopathology “glossary” for AI developers

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

PLOS Computational Biology: published January 23, 2025 | https://doi.org/10.1371/journal.pcbi.1012708

Exploiting the similarity of dissimilarities for biomedical applications and enhanced machine learning

Mohammad Neamul Kabir, Li Rong Wang, Wilson Wen Bin Goh

PLOS Computational Biology: published January 24, 2025 | https://doi.org/10.1371/journal.pcbi.1012716

Ten simple rules to complete successfully a computational MSc thesis project

Edoardo Saccenti, Cristina Furlan

PLOS Computational Biology: published January 28, 2025 | https://doi.org/10.1371/journal.pcbi.1012756

Connectome-based biophysical models of pathological protein spreading in neurodegenerative diseases

Peng Ren, Xuehua Cui, Xia Liang

PLOS Computational Biology: published January 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012743

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

PLOS Computational Biology: published January 2, 2025 | https://doi.org/10.1371/journal.pcbi.1012690

Sparse high-dimensional decomposition of non-primary auditory cortical receptive fields

Shoutik Mukherjee, Behtash Babadi, Shihab Shamma

PLOS Computational Biology: published January 2, 2025 | https://doi.org/10.1371/journal.pcbi.1012721

Biomathematical enzyme kinetics model of prebiotic autocatalytic RNA networks: degenerating parasite-specific hyperparasite catalysts confer parasite resistance and herald the birth of molecular immunity

Magnus Pirovino, Christian Iseli, Joseph A. Curran, Bernard Conrad

PLOS Computational Biology: published January 3, 2025 | https://doi.org/10.1371/journal.pcbi.1012162

Role and modulation of various spinal pathways for human upper limb control in different gravity conditions

Alice Bruel, Lina Bacha, Emma Boehly, Constance De Trogoff, Luca Represa, Gregoire Courtine, Auke Ijspeert

PLOS Computational Biology: published January 6, 2025 | https://doi.org/10.1371/journal.pcbi.1012069

Excitatory-inhibitory homeostasis and bifurcation control in the Wilson-Cowan model of cortical dynamics

Francisco Páscoa dos Santos, Paul F. M. J. Verschure

PLOS Computational Biology: published January 6, 2025 | https://doi.org/10.1371/journal.pcbi.1012723

Ensemble learning-based predictor for driver synonymous mutation with sequence representation

Chuanmei Bi, Yong Shi, Junfeng Xia, Zhen Liang, Zhiqiang Wu, Kai Xu, Na Cheng

PLOS Computational Biology: published January 6, 2025 | https://doi.org/10.1371/journal.pcbi.1012744

Learning predictive signatures of HLA type from T-cell repertoires

María Ruiz Ortega, Mikhail V. Pogorelyy, Anastasia A. Minervina, Paul G. Thomas, Thierry Mora, Aleksandra M. Walczak

PLOS Computational Biology: published January 6, 2025 | https://doi.org/10.1371/journal.pcbi.1012724

Low-dimensional controllability of brain networks

Remy Ben Messaoud, Vincent Le Du, Camile Bousfiha, Marie-Constance Corsi, Juliana Gonzalez-Astudillo, Brigitte Charlotte Kaufmann, Tristan Venot, Baptiste Couvy-Duchesne, Lara Migliaccio, Charlotte Rosso, Paolo Bartolomeo, Mario Chavez, Fabrizio De Vico Fallani

PLOS Computational Biology: published January 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012691

Aggregating multiple test results to improve medical decision-making

Lucas Böttcher, Maria R. D’Orsogna, Tom Chou

PLOS Computational Biology: published January 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012749

Intraneuronal binding of amyloid beta with reelin—Implications for the onset of Alzheimer’s disease

Asgeir Kobro-Flatmoen, Stig W. Omholt

PLOS Computational Biology: published January 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012709

Benchmarking uncertainty quantification for protein engineering

Kevin P. Greenman, Ava P. Amini, Kevin K. Yang

PLOS Computational Biology: published January 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012639

Bayesian active sound localisation: To what extent do humans perform like an ideal-observer?

Glen McLachlan, Piotr Majdak, Jonas Reijniers, Michael Mihocic, Herbert Peremans

PLOS Computational Biology: published January 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012108

Prioritization of causal genes from genome-wide association studies by Bayesian data integration across loci

Zeinab Mousavi, Marios Arvanitis, ThuyVy Duong, Jennifer A. Brody, Alexis Battle, Nona Sotoodehnia, Ali Shojaie, Dan E. Arking, Joel S. Bader

PLOS Computational Biology: published January 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012725

A genome-scale metabolic model for the denitrifying bacterium Thauera sp. MZ1T accurately predicts degradation of pollutants and production of polymers

Diego Tec-Campos, Juan D. Tibocha-Bonilla, Celina Jiang, Anurag Passi, Deepan Thiruppathy, Cristal Zuñiga, Camila Posadas, Alejandro Zepeda, Karsten Zengler

PLOS Computational Biology: published January 7, 2025 | https://doi.org/10.1371/journal.pcbi.1012736

Fast yet force-effective mode of supracellular collective cell migration due to extracellular force transmission

Amrit Bagchi, Bapi Sarker, Jialiang Zhang, Marcus Foston, Amit Pathak

PLOS Computational Biology: published January 9, 2025 | https://doi.org/10.1371/journal.pcbi.1012664

Multi-region infectious disease prediction modeling based on spatio-temporal graph neural network and the dynamic model

Xiaoyi Wang, Zhen Jin

PLOS Computational Biology: published January 9, 2025 | https://doi.org/10.1371/journal.pcbi.1012738

Prediction of cccDNA dynamics in hepatitis B patients by a combination of serum surrogate markers

Kwang Su Kim, Masashi Iwamoto, Kosaku Kitagawa, Hyeongki Park, Sanae Hayashi, Senko Tsukuda, Takeshi Matsui, Masanori Atsukawa, Kentaro Matsuura, Natthaya Chuaypen, Pisit Tangkijvanich, Lena Allweiss, Takara Nishiyama, Naotoshi Nakamura, Yasuhisa Fujita, Eiryo Kawakami, Shinji Nakaoka, Masamichi Muramatsu, Kazuyuki Aihara, Takaji Wakita, Alan S. Perelson, Maura Dandri, Koichi Watashi, Shingo Iwami, Yasuhito Tanaka

PLOS Computational Biology: published January 9, 2025 | https://doi.org/10.1371/journal.pcbi.1012615

Deciphering the interplay between biology and physics with a finite element method-implemented vertex organoid model: A tool for the mechanical analysis of cell behavior on a spherical organoid shell

Julien Laussu, Deborah Michel, Léa Magne, Stephane Segonds, Steven Marguet, Dimitri Hamel, Muriel Quaranta-Nicaise, Frederick Barreau, Emmanuel Mas, Vincent Velay, Florian Bugarin, Audrey Ferrand

PLOS Computational Biology: published January 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012681

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

Ahmed Daoud, Asa Ben-Hur

PLOS Computational Biology: published January 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012755

A robust transfer learning approach for high-dimensional linear regression to support integration of multi-source gene expression data

Lulu Pan, Qian Gao, Kecheng Wei, Yongfu Yu, Guoyou Qin, Tong Wang

PLOS Computational Biology: published January 10, 2025 | https://doi.org/10.1371/journal.pcbi.1012739

Benchmarking residue-resolution protein coarse-grained models for simulations of biomolecular condensates

Alejandro Feito, Ignacio Sanchez-Burgos, Ignacio Tejero, Eduardo Sanz, Antonio Rey, Rosana Collepardo-Guevara, Andrés R. Tejedor, Jorge R. Espinosa

PLOS Computational Biology: published January 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012737

Dialogue mechanisms between astrocytic and neuronal networks: A whole-brain modelling approach

Obaï Bin Ka’b Ali, Alexandre Vidal, Christophe Grova, Habib Benali

PLOS Computational Biology: published January 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012683

HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data

Evan Gorstein, Rosa Aghdam, Claudia Solís-Lemus

PLOS Computational Biology: published January 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012143

Towards constructing a generalized structural 3D breathing human lung model based on experimental volumes, pressures, and strains

Arif Badrou, Crystal A. Mariano, Gustavo O. Ramirez, Matthew Shankel, Nuno Rebelo, Mona Eskandari

PLOS Computational Biology: published January 13, 2025 | https://doi.org/10.1371/journal.pcbi.1012680

Mechanisms for dysregulation of excitatory-inhibitory balance underlying allodynia in dorsal horn neural subcircuits

Alexander G. Ginsberg, Scott F. Lempka, Bo Duan, Victoria Booth, Jennifer Crodelle

PLOS Computational Biology: published January 14, 2025 | https://doi.org/10.1371/journal.pcbi.1012234

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

PLOS Computational Biology: published January 16, 2025 | https://doi.org/10.1371/journal.pcbi.1012625

Adaptation optimizes sensory encoding for future stimuli

Jiang Mao, Constantin A Rothkopf, Alan A Stocker

PLOS Computational Biology: published January 17, 2025 | https://doi.org/10.1371/journal.pcbi.1012746

Extracting the fingerprints of sequences of random rhythmic auditory stimuli from electrophysiological data

Fernando A. Najman, Antonio Galves, Marcela Svarc, Claudia D. Vargas

PLOS Computational Biology: published January 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012765

Data-driven model discovery and model selection for noisy biological systems

Xiaojun Wu, MeiLu McDermott, Adam L MacLean

PLOS Computational Biology: published January 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012762

A Structural Model of Truncated Gaussia princeps Luciferase Elucidating the Crucial Catalytic Function of No.76 Arginine towards Coelenterazine Oxidation

Nan Wu, Zhi-Chao Xu, Kai-Dong Du, Shen Huang, Naohiro Kobayashi, Yutaka Kuroda, Yan-Hong Bai

PLOS Computational Biology: published January 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012722

Trajectory inference from single-cell genomics data with a process time model

Meichen Fang, Gennady Gorin, Lior Pachter

PLOS Computational Biology: published January 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012752

Balancing central control and sensory feedback produces adaptable and robust locomotor patterns in a spiking, neuromechanical model of the salamander spinal cord

Alessandro Pazzaglia, Andrej Bicanski, Andrea Ferrario, Jonathan Arreguit, Dimitri Ryczko, Auke Ijspeert

PLOS Computational Biology: published January 21, 2025 | https://doi.org/10.1371/journal.pcbi.1012101

Physiology-informed regularisation enables training of universal differential equation systems for biological applications

Max de Rooij, Balázs Erdős, Natal A. W. van Riel, Shauna D. O’Donovan

PLOS Computational Biology: published January 23, 2025 | https://doi.org/10.1371/journal.pcbi.1012198

Data-driven discovery and parameter estimation of mathematical models in biological pattern formation

Hidekazu Hishinuma, Hisako Takigawa-Imamura, Takashi Miura

PLOS Computational Biology: published January 23, 2025 | https://doi.org/10.1371/journal.pcbi.1012689

Social mates dynamically coordinate aggressive behavior to produce strategic territorial defense

Nicole M. Moody, Cole M. Williams, Sohini Ramachandran, Matthew J. Fuxjager

PLOS Computational Biology: published January 24, 2025 | https://doi.org/10.1371/journal.pcbi.1012740

Specificity and tunability of efflux pumps: A new role for the proton gradient?

Matthew Gerry, Duncan Kirby, Boian S. Alexandrov, Dvira Segal, Anton Zilman

PLOS Computational Biology: published January 27, 2025 | https://doi.org/10.1371/journal.pcbi.1012772

Biophysical modeling and experimental analysis of the dynamics of C. elegans body-wall muscle cells

Xuexing Du, Jennifer Crodelle, Victor James Barranca, Songting Li, Yunzhu Shi, Shangbang Gao, Douglas Zhou

PLOS Computational Biology: published January 27, 2025 | https://doi.org/10.1371/journal.pcbi.1012318

Human-like face pareidolia emerges in deep neural networks optimized for face and object recognition

Pranjul Gupta, Katharina Dobs

PLOS Computational Biology: published January 27, 2025 | https://doi.org/10.1371/journal.pcbi.1012751

DNA spontaneously wrapping around a histone core prefers negative supercoiling: A Brownian dynamics study

Chunhong Long, Hongqiong Liang, Biao Wan

PLOS Computational Biology: published January 28, 2025 | https://doi.org/10.1371/journal.pcbi.1012362

The calcitron: A simple neuron model that implements many learning rules via the calcium control hypothesis

Toviah Moldwin, Li Shay Azran, Idan Segev

PLOS Computational Biology: published January 29, 2025 | https://doi.org/10.1371/journal.pcbi.1012754

The role of oscillations in grid cells’ toroidal topology

Giovanni di Sarra, Siddharth Jha, Yasser Roudi

PLOS Computational Biology: published January 29, 2025 | https://doi.org/10.1371/journal.pcbi.1012776

ASGCL: Adaptive Sparse Mapping-based graph contrastive learning network for cancer drug response prediction

Yunyun Dong, Yuanrong Zhang, Yuhua Qian, Yiming Zhao, Ziting Yang, Xiufang Feng

PLOS Computational Biology: published January 30, 2025 | https://doi.org/10.1371/journal.pcbi.1012748

Correction: Epidemiological and health economic implications of symptom propagation in respiratory pathogens: A mathematical modelling investigation

Phoebe Asplin, Matt J. Keeling, Rebecca Mancy, Edward M. Hill

PLOS Computational Biology: published January 29, 2025 | https://doi.org/10.1371/journal.pcbi.1012791

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