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Articles published in
PLoS Comput Biol
    February 2026
  1. SHAFER-SKELTON A, Brady TF, Serences JT
    A 2D Gabor-wavelet baseline model out-performs a 3D surface model in scene-responsive cortex.
    PLoS Comput Biol. 2026;22:e1013888.
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  2. HART D, Cashwell K, Bhandari A, Premasinghe J, et al
    A framework for evaluating predicted sperm trajectories in crowded microscopy videos.
    PLoS Comput Biol. 2026;22:e1013955.
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    January 2026
  3. LIN M, Li K, Wang X, Sun J, et al
    Peak strain dispersion as a nonlinear mediator in HFpEF: Unraveling subtype-specific pathways via SHAP-augmented ensemble modeling.
    PLoS Comput Biol. 2026;22:e1013891.
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  4. SANCERE L, Lorenz C, Helbig D, Persa OD, et al
    Histo-Miner: Deep learning based tissue features extraction pipeline from H&E whole slide images of cutaneous squamous cell carcinoma.
    PLoS Comput Biol. 2026;22:e1013907.
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  5. BOKOR BLEILE Y, Yadav P, Koehl P, Rehfeldt F, et al
    Persistence diagrams as morphological signatures of cells: A method to measure and compare cells within a population.
    PLoS Comput Biol. 2026;22:e1013890.
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  6. VETTER SD, Schurman CA, Alliston T, Slabaugh G, et al
    Deep learning models to map osteocyte networks from confocal microscopy can successfully distinguish between young and aged bone.
    PLoS Comput Biol. 2026;22:e1013914.
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    December 2025
  7. LISOWSKI CM, King GM, Kosztin I
    Automated registration and clustering for enhanced localization atomic force microscopy of flexible membrane proteins.
    PLoS Comput Biol. 2025;21:e1013277.
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  8. YANG L, Lu J, Wu X, Zhang X, et al
    Stable individualized brain computing model informed by spatiotemporal co-activity patterns.
    PLoS Comput Biol. 2025;21:e1013817.
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  9. ZHANG L, Shi W, Zhao Z, Wang Z, et al
    Lysergic acid diethylamide-derived excitatory/inhibitory ratio change enhances global synchrony in functional brain dynamics.
    PLoS Comput Biol. 2025;21:e1013822.
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  10. BONTE T, Pourcelot O, Safieddine A, Slimani F, et al
    A deep learning approach for time-consistent cell cycle phase prediction from microscopy data.
    PLoS Comput Biol. 2025;21:e1013800.
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  11. MARRAZZO G, De Martino F, Mukovskiy A, Giese MA, et al
    Neural encoding of biomechanically (im)possible human movements in occipitotemporal cortex.
    PLoS Comput Biol. 2025;21:e1013694.
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  12. BOHRER CH, Larson DR
    A methodology to reduce the localization error in multi-loci microscopy provides new insights into enhancer biology.
    PLoS Comput Biol. 2025;21:e1013796.
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  13. MORRISON M, Young LS
    A data-driven biology-based network model reproduces C. elegans premotor neural dynamics.
    PLoS Comput Biol. 2025;21:e1013818.
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  14. MOUTAKANNI T, Couprie C, Yi S, Doron M, et al
    Cell-DINO: Self-supervised image-based embeddings for cell fluorescent microscopy.
    PLoS Comput Biol. 2025;21:e1013828.
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    November 2025
  15. LIARDI A, Rosas FE, Carhart-Harris RL, Blackburne G, et al
    Null models for comparing information decomposition across complex systems.
    PLoS Comput Biol. 2025;21:e1013629.
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  16. GAUTHAMAN RM, Menard B, Bonner MF
    Universal scale-free representations in human visual cortex.
    PLoS Comput Biol. 2025;21:e1013714.
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  17. VARLEY TF, Mediano PAM, Patania A, Bongard J, et al
    The topology of synergy: Linking topological and information-theoretic approaches to higher-order interactions in complex systems.
    PLoS Comput Biol. 2025;21:e1013649.
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    October 2025
  18. GATICA M, Atkinson-Clement C, Coronel-Oliveros C, Alkhawashki M, et al
    Understanding the high-order network plasticity mechanisms of ultrasound neuromodulation.
    PLoS Comput Biol. 2025;21:e1013514.
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  19. LACHUER H, Moebel E, Mace AS, Masson A, et al
    Deep learning detection of dynamic exocytosis events in fluorescence TIRF microscopy.
    PLoS Comput Biol. 2025;21:e1013556.
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  20. RAIOLA M, Esteban I, Ivanovitch K, Sendra M, et al
    A method for analysing tissue motion and deformation during mammalian organogenesis.
    PLoS Comput Biol. 2025;21:e1013275.
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  21. CHANG J, Yang Z, Zhou C
    Simultaneously determining regional heterogeneity and connection directionality from neural activity and symmetric connection.
    PLoS Comput Biol. 2025;21:e1013612.
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  22. LEHUE F, Coronel-Oliveros C, Medel V, Liebe T, et al
    Noradrenaline and acetylcholine shape functional connectivity organization of NREM substages: An empirical and simulation study.
    PLoS Comput Biol. 2025;21:e1012852.
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  23. HIMMELBERG MM, Kwak Y, Carrasco M, Winawer J, et al
    Unpacking the V1 map: Differential covariation of preferred spatial frequency and cortical magnification across spatial dimensions.
    PLoS Comput Biol. 2025;21:e1013599.
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  24. TIROUMALECHETTY A, Frankel EB, Kurshan PT
    WormSNAP: A software for fast, accurate, and unbiased detection of fluorescent puncta in C. elegans.
    PLoS Comput Biol. 2025;21:e1013643.
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    September 2025
  25. PATTON A, Davidsen J
    Changing cognitive chimera states in human brain networks with age: Variations in cognitive integration and segregation.
    PLoS Comput Biol. 2025;21:e1013093.
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  26. CALKA M, Badin P, Nazari MA, Rochette M, et al
    The G-OBIM tongue model: An accurate open-source biomechanical model of a male human tongue.
    PLoS Comput Biol. 2025;21:e1013378.
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  27. ST-YVES G, Kay K, Naselaris T
    Variation in the geometry of concept manifolds across human visual cortex.
    PLoS Comput Biol. 2025;21:e1013416.
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  28. XU Y, Prat CS, Sense F, van Rijn H, et al
    Default mode network connectivity predicts individual differences in long-term forgetting: Evidence for storage degradation, not retrieval failure.
    PLoS Comput Biol. 2025;21:e1013485.
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  29. JACOB LPL, Bailes SM, Williams SD, Stringer C, et al
    Brainwide hemodynamics predict EEG neural rhythms across sleep and wakefulness in humans.
    PLoS Comput Biol. 2025;21:e1013497.
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  30. PRADELLI F, Minervini G, Venkatesh P, Azad S, et al
    Mathematical modeling and simulation of tumor-induced angiogenesis in retinal hemangioblastoma.
    PLoS Comput Biol. 2025;21:e1012799.
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    August 2025
  31. KRUPER J, Richie-Halford A, Qiao J, Gilmore A, et al
    A software ecosystem for brain tractometry processing, analysis, and insight.
    PLoS Comput Biol. 2025;21:e1013323.
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  32. LI L, Uriyanghai U, Wai C, Yuan H, et al
    Temporal evolution of hemodynamics in murine arteriovenous fistula: A micro-CT based CFD study.
    PLoS Comput Biol. 2025;21:e1012985.
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    July 2025
  33. KAYYALI M, Minchole A, Qian S, Young A, et al
    Anatomical-electrical coupling of cardiac axes: Definitions and population variability for advancing personalised ECG interpretation.
    PLoS Comput Biol. 2025;21:e1013161.
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  34. KAY K, Prince JS, Gebhart T, Tuckute G, et al
    Disentangling signal and noise in neural responses through generative modeling.
    PLoS Comput Biol. 2025;21:e1012092.
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  35. XIAO J, Yin Q, Li L, Meng Y, et al
    Tracking causal pathways in TMS-evoked brain responses.
    PLoS Comput Biol. 2025;21:e1013316.
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  36. THEIS S, Mendieta-Serrano MA, Chapa-Y-Lazo B, Chen J, et al
    CellMet: Extracting 3D shape and topology metrics from confluent cells within tissues.
    PLoS Comput Biol. 2025;21:e1013260.
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    June 2025
  37. STIKVOORT W, Perez-Ordoyo E, Mindlin I, Escrichs A, et al
    Nonequilibrium brain dynamics elicited as the origin of perturbative complexity.
    PLoS Comput Biol. 2025;21:e1013150.
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  38. BAKER MR, Klassen BT, Jensen MA, Ojeda Valencia G, et al
    Parameterization of intraoperative human microelectrode recordings: Linking action potential morphology to brain anatomy.
    PLoS Comput Biol. 2025;21:e1013184.
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  39. KANDASAMY A, Yeh YT, Serrano R, Mercola M, et al
    Uncertainty-aware traction force microscopy.
    PLoS Comput Biol. 2025;21:e1013079.
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    May 2025
  40. BOTVINIK-NEZER R, Geuter S, Lindquist MA, Wager TD, et al
    Expectation generation and its effect on subsequent pain and visual perception.
    PLoS Comput Biol. 2025;21:e1013053.
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  41. O'CONNOR OM, Dunlop MJ
    Cell-TRACTR: A transformer-based model for end-to-end segmentation and tracking of cells.
    PLoS Comput Biol. 2025;21:e1013071.
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  42. VILLANUEVA-BAXARIAS I, Pellise-Tintore A, Perez-Rodriguez M, Nogue L, et al
    Understanding the hemodynamic changes in fetuses with coarctation of the aorta using a lumped model of fetal circulation.
    PLoS Comput Biol. 2025;21:e1013096.
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  43. ZHAN Y, Musella F, Alber F
    MaxComp: Predicting single-cell chromatin compartments from 3D chromosome structures.
    PLoS Comput Biol. 2025;21:e1013114.
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  44. YAMANE Y, Li Y, Matsumoto K, Kanai R, et al
    Optical Neuroimage Studio (OptiNiSt): Intuitive, scalable, extendable framework for optical neuroimage data analysis.
    PLoS Comput Biol. 2025;21:e1013087.
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  45. SCHNITZERLEIN M, Greto E, Wegner A, Moller A, et al
    Cellular morphodynamics as quantifiers for functional states of resident tissue macrophages in vivo.
    PLoS Comput Biol. 2025;21:e1011859.
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    April 2025
  46. HICKL V, Khan A, Rossi RM, Silva BFB, et al
    Segmentation of dense and multi-species bacterial colonies using models trained on synthetic microscopy images.
    PLoS Comput Biol. 2025;21:e1012874.
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  47. BARJUAN L, Zheng M, Serrano MA
    The multiscale self-similarity of the weighted human brain connectome.
    PLoS Comput Biol. 2025;21:e1012848.
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  48. LEIBOVICH N, Goyal S
    Limitations and optimizations of cellular lineages tracking.
    PLoS Comput Biol. 2025;21:e1012880.
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  49. GRABOT L, Merholz G, Winawer J, Heeger DJ, et al
    Traveling waves in the human visual cortex: An MEG-EEG model-based approach.
    PLoS Comput Biol. 2025;21:e1013007.
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  50. VRIENS T, Vassena E, Pezzulo G, Baldassarre G, et al
    Meta-Reinforcement Learning reconciles surprise, value, and control in the anterior cingulate cortex.
    PLoS Comput Biol. 2025;21:e1013025.
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  51. KE J, Song H, Bai Z, Rosenberg MD, et al
    Dynamic brain connectivity predicts emotional arousal during naturalistic movie-watching.
    PLoS Comput Biol. 2025;21:e1012994.
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    March 2025
  52. ALTERIIS G, Sherwood O, Ciaramella A, Leech R, et al
    DySCo: A general framework for dynamic functional connectivity.
    PLoS Comput Biol. 2025;21:e1012795.
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  53. SIGALAS E, Libedinsky C
    Mixed recurrent connectivity in primate prefrontal cortex.
    PLoS Comput Biol. 2025;21:e1012867.
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  54. WANG Z, Yang Y, Huang Z, Zhao W, et al
    Exploring the transmission of cognitive task information through optimal brain pathways.
    PLoS Comput Biol. 2025;21:e1012870.
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  55. DINNAGE R, Kleineberg M
    Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills.
    PLoS Comput Biol. 2025;21:e1012887.
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  56. WANG T, Quast C, Bonner F, Kelm M, et al
    Investigation of hemodynamic bulk flow patterns caused by aortic stenosis using a combined 4D Flow MRI-CFD framework.
    PLoS Comput Biol. 2025;21:e1012467.
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    January 2025
  57. BEN MESSAOUD R, Le Du V, Bousfiha C, Corsi MC, et al
    Low-dimensional controllability of brain networks.
    PLoS Comput Biol. 2025;21:e1012691.
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  58. BADROU A, Mariano CA, Ramirez GO, Shankel M, et al
    Towards constructing a generalized structural 3D breathing human lung model based on experimental volumes, pressures, and strains.
    PLoS Comput Biol. 2025;21:e1012680.
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  59. REN P, Cui X, Liang X
    Connectome-based biophysical models of pathological protein spreading in neurodegenerative diseases.
    PLoS Comput Biol. 2025;21:e1012743.
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  60. GROS O, Passmore JB, Borst NO, Kutra D, et al
    Spherical harmonics texture extraction for versatile analysis of biological objects.
    PLoS Comput Biol. 2025;21:e1012349.
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    December 2024
  61. FORRESTER M, Petros S, Cattell O, Lai YM, et al
    Whole brain functional connectivity: Insights from next generation neural mass modelling incorporating electrical synapses.
    PLoS Comput Biol. 2024;20:e1012647.
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  62. VANSLAMBROUCK M, Thiels W, Vangheel J, van Bavel C, et al
    Image-based force inference by biomechanical simulation.
    PLoS Comput Biol. 2024;20:e1012629.
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  63. YUAN M, Goovaerts S, Vanneste M, Matthews H, et al
    Mapping genes for human face shape: Exploration of univariate phenotyping strategies.
    PLoS Comput Biol. 2024;20:e1012617.
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  64. STASINSKI J, Taher H, Meier JM, Schirner M, et al
    Homeodynamic feedback inhibition control in whole-brain simulations.
    PLoS Comput Biol. 2024;20:e1012595.
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  65. CELIKER E, Woodrow C, Guadayol O, Davranoglou LR, et al
    Mechanical network equivalence between the katydid and mammalian inner ears.
    PLoS Comput Biol. 2024;20:e1012641.
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  66. KANG J, Park HJ
    Integration of partially observed multimodal and multiscale neural signals for estimating a neural circuit using dynamic causal modeling.
    PLoS Comput Biol. 2024;20:e1012655.
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  67. BRYANT AG, Aquino K, Parkes L, Fornito A, et al
    Extracting interpretable signatures of whole-brain dynamics through systematic comparison.
    PLoS Comput Biol. 2024;20:e1012692.
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    October 2024
  68. CHEN L, Huang ZH, Sun Y, Domaratzki M, et al
    Conditional probabilistic diffusion model driven synthetic radiogenomic applications in breast cancer.
    PLoS Comput Biol. 2024;20:e1012490.
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  69. ISHAR J, Tam YM, Mages S, Klughammer J, et al
    BoReMi: Bokeh-based jupyter-interface for registering spatio-molecular data to related microscopy images.
    PLoS Comput Biol. 2024;20:e1012504.
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  70. RANJAN A, Swain JK, Ahluwalia BS, Melandso F, et al
    3-D Visualization of Atlantic salmon skin through Ultrasound and Photoacoustic Microscopy.
    PLoS Comput Biol. 2024;20:e1011709.
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  71. YU S, Wu J, Shao Y, Qiu D, et al
    A novel classification framework for genome-wide association study of whole brain MRI images using deep learning.
    PLoS Comput Biol. 2024;20:e1012527.
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  72. COCUZZA CV, Sanchez-Romero R, Ito T, Mill RD, et al
    Distributed network flows generate localized category selectivity in human visual cortex.
    PLoS Comput Biol. 2024;20:e1012507.
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    September 2024
  73. FRANCO JP, Bossaerts P, Murawski C
    The neural dynamics associated with computational complexity.
    PLoS Comput Biol. 2024;20:e1012447.
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    August 2024
  74. RAMOS JDS, Vieira IHP, Rocha WS, Esquerdo RP, et al
    A transfer learning approach to identify Plasmodium in microscopic images.
    PLoS Comput Biol. 2024;20:e1012327.
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  75. GUNNARSSON EB, Kim S, Choi B, Schmid JK, et al
    Understanding patient-derived tumor organoid growth through an integrated imaging and mathematical modeling framework.
    PLoS Comput Biol. 2024;20:e1012256.
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  76. DEAN WF, Nawara TJ, Albert RM, Mattheyses AL, et al
    OOPS: Object-Oriented Polarization Software for analysis of fluorescence polarization microscopy images.
    PLoS Comput Biol. 2024;20:e1011723.
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  77. MAHJOORY K, Bahmer A, Henry MJ
    Convolutional neural networks can identify brain interactions involved in decoding spatial auditory attention.
    PLoS Comput Biol. 2024;20:e1012376.
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  78. SEELER D, Grdseloff N, Rodel CJ, Kloft C, et al
    Novel mathematical approach to accurately quantify 3D endothelial cell morphology and vessel geometry based on fluorescently marked endothelial cell contours: Application to the dorsal aorta of wild-type and Endoglin-deficient zebrafish embryos.
    PLoS Comput Biol. 2024;20:e1011924.
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    July 2024
  79. CHEN AA, Clark K, Dewey BE, DuVal A, et al
    PARE: A framework for removal of confounding effects from any distance-based dimension reduction method.
    PLoS Comput Biol. 2024;20:e1012241.
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    June 2024
  80. SANDA P, Hlinka J, van den Berg M, Skoch A, et al
    Cholinergic modulation supports dynamic switching of resting state networks through selective DMN suppression.
    PLoS Comput Biol. 2024;20:e1012099.
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  81. YAO T, Pajaziti E, Quail M, Schievano S, et al
    Image2Flow: A proof-of-concept hybrid image and graph convolutional neural network for rapid patient-specific pulmonary artery segmentation and CFD flow field calculation from 3D cardiac MRI data.
    PLoS Comput Biol. 2024;20:e1012231.
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    May 2024
  82. DAGNINO PC, Escrichs A, Lopez-Gonzalez A, Gosseries O, et al
    Re-awakening the brain: Forcing transitions in disorders of consciousness by external in silico perturbation.
    PLoS Comput Biol. 2024;20:e1011350.
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  83. CHUNG MK, Huang SG, Carroll IC, Calhoun VD, et al
    Topological state-space estimation of functional human brain networks.
    PLoS Comput Biol. 2024;20:e1011869.
    >> Share

  84. RYU J, Nejatbakhsh A, Torkashvand M, Gangadharan S, et al
    Versatile multiple object tracking in sparse 2D/3D videos via deformable image registration.
    PLoS Comput Biol. 2024;20:e1012075.
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  85. CONTE M, Woodall RT, Gutova M, Chen BT, et al
    Structural and practical identifiability of contrast transport models for DCE-MRI.
    PLoS Comput Biol. 2024;20:e1012106.
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    March 2024
  86. TOYOSHIMA Y, Sato H, Nagata D, Kanamori M, et al
    Ensemble dynamics and information flow deduction from whole-brain imaging data.
    PLoS Comput Biol. 2024;20:e1011848.
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  87. LIU P, Bo K, Ding M, Fang R, et al
    Emergence of Emotion Selectivity in Deep Neural Networks Trained to Recognize Visual Objects.
    PLoS Comput Biol. 2024;20:e1011943.
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  88. WANG HT, Meisler SL, Sharmarke H, Clarke N, et al
    Continuous evaluation of denoising strategies in resting-state fMRI connectivity using fMRIPrep and Nilearn.
    PLoS Comput Biol. 2024;20:e1011942.
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    February 2024
  89. CHEN LD, Caprio MA, Chen DM, Kouba AJ, et al
    Enhancing predictive performance for spectroscopic studies in wildlife science through a multi-model approach: A case study for species classification of live amphibians.
    PLoS Comput Biol. 2024;20:e1011876.
    >> Share

  90. ESCHWEILER D, Yilmaz R, Baumann M, Laube I, et al
    Denoising diffusion probabilistic models for generation of realistic fully-annotated microscopy image datasets.
    PLoS Comput Biol. 2024;20:e1011890.
    >> Share

  91. SOULOS P, Isik L
    Disentangled deep generative models reveal coding principles of the human face processing network.
    PLoS Comput Biol. 2024;20:e1011887.
    >> Share


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