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Articles published in PLoS Comput Biol

Retrieve available abstracts of 93 articles:
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Single Articles

    June 2022
  1. SMITH E, Peters J
    Motor response vigour and visual fixation patterns reflect subjective valuation during intertemporal choice.
    PLoS Comput Biol. 2022;18:e1010096.
    PubMed     Abstract available

  2. GAGL B, Richlan F, Ludersdorfer P, Sassenhagen J, et al
    The lexical categorization model: A computational model of left ventral occipito-temporal cortex activation in visual word recognition.
    PLoS Comput Biol. 2022;18:e1009995.
    PubMed     Abstract available

  3. KIM H, Min C, Jeong B, Lee KJ, et al
    Deciphering clock cell network morphology within the biological master clock, suprachiasmatic nucleus: From the perspective of circadian wave dynamics.
    PLoS Comput Biol. 2022;18:e1010213.
    PubMed     Abstract available

  4. WAN Q, Menendez JA, Postle BR
    Priority-based transformations of stimulus representation in visual working memory.
    PLoS Comput Biol. 2022;18:e1009062.
    PubMed     Abstract available

    April 2022
  5. KAR A, Petit M, Refahi Y, Cerutti G, et al
    Benchmarking of deep learning algorithms for 3D instance segmentation of confocal image datasets.
    PLoS Comput Biol. 2022;18:e1009879.
    PubMed     Abstract available

  6. CHEN S, Loper J, Zhou P, Paninski L, et al
    Blind demixing methods for recovering dense neuronal morphology from barcode imaging data.
    PLoS Comput Biol. 2022;18:e1009991.
    PubMed     Abstract available

  7. SCHELLEKENS W, Bakker C, Ramsey NF, Petridou N, et al
    Moving in on human motor cortex. Characterizing the relationship between body parts with non-rigid population response fields.
    PLoS Comput Biol. 2022;18:e1009955.
    PubMed     Abstract available

  8. MUNGLANI G, Vogler H, Grossniklaus U
    Fast and flexible processing of large FRET image stacks using the FRET-IBRA toolkit.
    PLoS Comput Biol. 2022;18:e1009242.
    PubMed     Abstract available

    March 2022
  9. MATSUDA T, Homae F, Watanabe H, Taga G, et al
    Oscillator decomposition of infant fNIRS data.
    PLoS Comput Biol. 2022;18:e1009985.
    PubMed     Abstract available

  10. AMYOT R, Marchesi A, Franz CM, Casuso I, et al
    Simulation atomic force microscopy for atomic reconstruction of biomolecular structures from resolution-limited experimental images.
    PLoS Comput Biol. 2022;18:e1009970.
    PubMed     Abstract available

    February 2022
  11. KAISER D, Jacobs AM, Cichy RM
    Modelling brain representations of abstract concepts.
    PLoS Comput Biol. 2022;18:e1009837.
    PubMed     Abstract available

    January 2022
  12. DONOVAN-MAIYE RM, Brown JM, Chan CK, Ding L, et al
    A deep generative model of 3D single-cell organization.
    PLoS Comput Biol. 2022;18:e1009155.
    PubMed     Abstract available

  13. YANG Y, Turci F, Kague E, Hammond CL, et al
    Dominating lengthscales of zebrafish collective behaviour.
    PLoS Comput Biol. 2022;18:e1009394.
    PubMed     Abstract available

    December 2021
  14. XIAO ZC, Lin KK, Young LS
    A data-informed mean-field approach to mapping of cortical parameter landscapes.
    PLoS Comput Biol. 2021;17:e1009718.
    PubMed     Abstract available

  15. RUBIO-TEVES M, Diez-Hermano S, Porrero C, Sanchez-Jimenez A, et al
    Benchmarking of tools for axon length measurement in individually-labeled projection neurons.
    PLoS Comput Biol. 2021;17:e1009051.
    PubMed     Abstract available

    November 2021
  16. ALTAN E, Solla SA, Miller LE, Perreault EJ, et al
    Estimating the dimensionality of the manifold underlying multi-electrode neural recordings.
    PLoS Comput Biol. 2021;17:e1008591.
    PubMed     Abstract available

  17. PRALJAK N, Iram S, Goreke U, Singh G, et al
    Integrating deep learning with microfluidics for biophysical classification of sickle red blood cells adhered to laminin.
    PLoS Comput Biol. 2021;17:e1008946.
    PubMed     Abstract available

  18. BOZHANOVA NG, Harp JM, Bender BJ, Gavrikov AS, et al
    Computational redesign of a fluorogen activating protein with Rosetta.
    PLoS Comput Biol. 2021;17:e1009555.
    PubMed     Abstract available

  19. MENDONCA T, Jones AA, Pozo JM, Baxendale S, et al
    Origami: Single-cell 3D shape dynamics oriented along the apico-basal axis of folding epithelia from fluorescence microscopy data.
    PLoS Comput Biol. 2021;17:e1009063.
    PubMed     Abstract available

  20. ITO S, Si Y, Litke AM, Feldheim DA, et al
    Nonlinear visuoauditory integration in the mouse superior colliculus.
    PLoS Comput Biol. 2021;17:e1009181.
    PubMed     Abstract available

  21. KIM J, Lee SW, Yoon S, Park H, et al
    Neurocomputational mechanism of controllability inference under a multi-agent setting.
    PLoS Comput Biol. 2021;17:e1009549.
    PubMed     Abstract available

    October 2021
  22. LAGACHE T, Hanson A, Perez-Ortega JE, Fairhall A, et al
    Tracking calcium dynamics from individual neurons in behaving animals.
    PLoS Comput Biol. 2021;17:e1009432.
    PubMed     Abstract available

  23. MIHELIC SA, Sikora WA, Hassan AM, Williamson MR, et al
    Segmentation-Less, Automated, Vascular Vectorization.
    PLoS Comput Biol. 2021;17:e1009451.
    PubMed     Abstract available

    Narrative event segmentation in the cortical reservoir.
    PLoS Comput Biol. 2021;17:e1008993.
    PubMed     Abstract available

  25. ARORA Y, Walia P, Hayashibe M, Muthalib M, et al
    Grey-box modeling and hypothesis testing of functional near-infrared spectroscopy-based cerebrovascular reactivity to anodal high-definition tDCS in healthy humans.
    PLoS Comput Biol. 2021;17:e1009386.
    PubMed     Abstract available

    September 2021
  26. HANSEN BC, Greene MR, Field DJ
    Dynamic Electrode-to-Image (DETI) mapping reveals the human brain's spatiotemporal code of visual information.
    PLoS Comput Biol. 2021;17:e1009456.
    PubMed     Abstract available

  27. BRIDGEFORD EW, Wang S, Wang Z, Xu T, et al
    Eliminating accidental deviations to minimize generalization error and maximize replicability: Applications in connectomics and genomics.
    PLoS Comput Biol. 2021;17:e1009279.
    PubMed     Abstract available

  28. MISRA J, Surampudi SG, Venkatesh M, Limbachia C, et al
    Learning brain dynamics for decoding and predicting individual differences.
    PLoS Comput Biol. 2021;17:e1008943.
    PubMed     Abstract available

  29. MILLER KJ, Muller KR, Hermes D
    Basis profile curve identification to understand electrical stimulation effects in human brain networks.
    PLoS Comput Biol. 2021;17:e1008710.
    PubMed     Abstract available

    August 2021
  30. LEBEL P, Dial R, Vemuri VNP, Garcia V, et al
    Label-free imaging and classification of live P. falciparum enables high performance parasitemia quantification without fixation or staining.
    PLoS Comput Biol. 2021;17:e1009257.
    PubMed     Abstract available

  31. DWIVEDI K, Bonner MF, Cichy RM, Roig G, et al
    Unveiling functions of the visual cortex using task-specific deep neural networks.
    PLoS Comput Biol. 2021;17:e1009267.
    PubMed     Abstract available

  32. SCHINDLER D, Moldenhawer T, Stange M, Lepro V, et al
    Analysis of protrusion dynamics in amoeboid cell motility by means of regularized contour flows.
    PLoS Comput Biol. 2021;17:e1009268.
    PubMed     Abstract available

  33. SCHAWORONKOW N, Voytek B
    Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters.
    PLoS Comput Biol. 2021;17:e1009298.
    PubMed     Abstract available

  34. CHIZHOV AV, Graham LJ
    A strategy for mapping biophysical to abstract neuronal network models applied to primary visual cortex.
    PLoS Comput Biol. 2021;17:e1009007.
    PubMed     Abstract available

  35. TU Y, Ta D, Lu ZL, Wang Y, et al
    Topology-preserving smoothing of retinotopic maps.
    PLoS Comput Biol. 2021;17:e1009216.
    PubMed     Abstract available

    July 2021
  36. HASHEMI M, Vattikonda AN, Sip V, Diaz-Pier S, et al
    On the influence of prior information evaluated by fully Bayesian criteria in a personalized whole-brain model of epilepsy spread.
    PLoS Comput Biol. 2021;17:e1009129.
    PubMed     Abstract available

  37. KOIDE H, Kodera N, Bisht S, Takada S, et al
    Modeling of DNA binding to the condensin hinge domain using molecular dynamics simulations guided by atomic force microscopy.
    PLoS Comput Biol. 2021;17:e1009265.
    PubMed     Abstract available

  38. KINGSLEY JL, Costello JR, Raghunand N, Rejniak KA, et al
    Bridging cell-scale simulations and radiologic images to explain short-time intratumoral oxygen fluctuations.
    PLoS Comput Biol. 2021;17:e1009206.
    PubMed     Abstract available

  39. NIINA T, Matsunaga Y, Takada S
    Rigid-body fitting to atomic force microscopy images for inferring probe shape and biomolecular structure.
    PLoS Comput Biol. 2021;17:e1009215.
    PubMed     Abstract available

  40. HANUSSEK M, Bartusch F, Kruger J
    Performance and scaling behavior of bioinformatic applications in virtualization environments to create awareness for the efficient use of compute resources.
    PLoS Comput Biol. 2021;17:e1009244.
    PubMed     Abstract available

  41. WANG Z, Ding Y, Satta S, Roustaei M, et al
    A hybrid of light-field and light-sheet imaging to study myocardial function and intracardiac blood flow during zebrafish development.
    PLoS Comput Biol. 2021;17:e1009175.
    PubMed     Abstract available

  42. SANZ PERL Y, Pallavicini C, Perez Ipina I, Demertzi A, et al
    Perturbations in dynamical models of whole-brain activity dissociate between the level and stability of consciousness.
    PLoS Comput Biol. 2021;17:e1009139.
    PubMed     Abstract available

  43. WEINSTEIN BG, Graves SJ, Marconi S, Singh A, et al
    A benchmark dataset for canopy crown detection and delineation in co-registered airborne RGB, LiDAR and hyperspectral imagery from the National Ecological Observation Network.
    PLoS Comput Biol. 2021;17:e1009180.
    PubMed     Abstract available

    June 2021
  44. BAUER A, Prechova M, Fischer L, Thievessen I, et al
    pyTFM: A tool for traction force and monolayer stress microscopy.
    PLoS Comput Biol. 2021;17:e1008364.
    PubMed     Abstract available

  45. TRENTHAM-DIETZ A, Alagoz O, Chapman C, Huang X, et al
    Reflecting on 20 years of breast cancer modeling in CISNET: Recommendations for future cancer systems modeling efforts.
    PLoS Comput Biol. 2021;17:e1009020.
    PubMed     Abstract available

  46. RICHIE-HALFORD A, Yeatman JD, Simon N, Rokem A, et al
    Multidimensional analysis and detection of informative features in human brain white matter.
    PLoS Comput Biol. 2021;17:e1009136.
    PubMed     Abstract available

  47. NISHIDA S, Blanc A, Maeda N, Kado M, et al
    Behavioral correlates of cortical semantic representations modeled by word vectors.
    PLoS Comput Biol. 2021;17:e1009138.
    PubMed     Abstract available

    May 2021
  48. KALM K, Norris D
    Sequence learning recodes cortical representations instead of strengthening initial ones.
    PLoS Comput Biol. 2021;17:e1008969.
    PubMed     Abstract available

  49. ARTHURS CJ, Khlebnikov R, Melville A, Marcan M, et al
    CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation.
    PLoS Comput Biol. 2021;17:e1008881.
    PubMed     Abstract available

  50. MENSCH A, Mairal J, Thirion B, Varoquaux G, et al
    Extracting representations of cognition across neuroimaging studies improves brain decoding.
    PLoS Comput Biol. 2021;17:e1008795.
    PubMed     Abstract available

  51. SIMIONATO G, Hinkelmann K, Chachanidze R, Bianchi P, et al
    Red blood cell phenotyping from 3D confocal images using artificial neural networks.
    PLoS Comput Biol. 2021;17:e1008934.
    PubMed     Abstract available

  52. PEDERSEN ML, Ironside M, Amemori KI, McGrath CL, et al
    Computational phenotyping of brain-behavior dynamics underlying approach-avoidance conflict in major depressive disorder.
    PLoS Comput Biol. 2021;17:e1008955.
    PubMed     Abstract available

    April 2021
  53. PARIZ A, Fischer I, Valizadeh A, Mirasso C, et al
    Transmission delays and frequency detuning can regulate information flow between brain regions.
    PLoS Comput Biol. 2021;17:e1008129.
    PubMed     Abstract available

  54. CAI C, Friedrich J, Singh A, Eybposh MH, et al
    VolPy: Automated and scalable analysis pipelines for voltage imaging datasets.
    PLoS Comput Biol. 2021;17:e1008806.
    PubMed     Abstract available

  55. KAJIWARA M, Nomura R, Goetze F, Kawabata M, et al
    Inhibitory neurons exhibit high controlling ability in the cortical microconnectome.
    PLoS Comput Biol. 2021;17:e1008846.
    PubMed     Abstract available

    March 2021
  56. VEITH I, Mencattini A, Picant V, Serra M, et al
    Apoptosis mapping in space and time of 3D tumor ecosystems reveals transmissibility of cytotoxic cancer death.
    PLoS Comput Biol. 2021;17:e1008870.
    PubMed     Abstract available

  57. LIN YE, Shnitzer T, Talmon R, Villarroel-Espindola F, et al
    Graph of graphs analysis for multiplexed data with application to imaging mass cytometry.
    PLoS Comput Biol. 2021;17:e1008741.
    PubMed     Abstract available

  58. AL-TAHAN H, Mohsenzadeh Y
    Reconstructing feedback representations in the ventral visual pathway with a generative adversarial autoencoder.
    PLoS Comput Biol. 2021;17:e1008775.
    PubMed     Abstract available

  59. RASERO J, Sentis AI, Yeh FC, Verstynen T, et al
    Integrating across neuroimaging modalities boosts prediction accuracy of cognitive ability.
    PLoS Comput Biol. 2021;17:e1008347.
    PubMed     Abstract available

    February 2021
  60. SIP V, Hashemi M, Vattikonda AN, Woodman MM, et al
    Data-driven method to infer the seizure propagation patterns in an epileptic brain from intracranial electroencephalography.
    PLoS Comput Biol. 2021;17:e1008689.
    PubMed     Abstract available

  61. CORONEL-OLIVEROS C, Cofre R, Orio P
    Cholinergic neuromodulation of inhibitory interneurons facilitates functional integration in whole-brain models.
    PLoS Comput Biol. 2021;17:e1008737.
    PubMed     Abstract available

  62. MERGENTHALER P, Hariharan S, Pemberton JM, Lourenco C, et al
    Rapid 3D phenotypic analysis of neurons and organoids using data-driven cell segmentation-free machine learning.
    PLoS Comput Biol. 2021;17:e1008630.
    PubMed     Abstract available

  63. GALLOIS B, Candelier R
    FastTrack: An open-source software for tracking varying numbers of deformable objects.
    PLoS Comput Biol. 2021;17:e1008697.
    PubMed     Abstract available

  64. GERSHMAN SJ, Guitart-Masip M, Cavanagh JF
    Neural signatures of arbitration between Pavlovian and instrumental action selection.
    PLoS Comput Biol. 2021;17:e1008553.
    PubMed     Abstract available

  65. KATAHIRA K, Toyama A
    Revisiting the importance of model fitting for model-based fMRI: It does matter in computational psychiatry.
    PLoS Comput Biol. 2021;17:e1008738.
    PubMed     Abstract available

  66. NOTERMANS T, Tanska P, Korhonen RK, Khayyeri H, et al
    A numerical framework for mechano-regulated tendon healing-Simulation of early regeneration of the Achilles tendon.
    PLoS Comput Biol. 2021;17:e1008636.
    PubMed     Abstract available

  67. SEELIGER K, Ambrogioni L, Gucluturk Y, van den Bulk LM, et al
    End-to-end neural system identification with neural information flow.
    PLoS Comput Biol. 2021;17:e1008558.
    PubMed     Abstract available

  68. KUMAR MG, Hu M, Ramanujan A, Sur M, et al
    Functional parcellation of mouse visual cortex using statistical techniques reveals response-dependent clustering of cortical processing areas.
    PLoS Comput Biol. 2021;17:e1008548.
    PubMed     Abstract available

  69. SCHNECKENREITHER G, Tschandl P, Rippinger C, Sinz C, et al
    Reproduction of patterns in melanocytic proliferations by agent-based simulation and geometric modeling.
    PLoS Comput Biol. 2021;17:e1008660.
    PubMed     Abstract available

    January 2021
  70. HARTUNG G, Badr S, Moeini M, Lesage F, et al
    Voxelized simulation of cerebral oxygen perfusion elucidates hypoxia in aged mouse cortex.
    PLoS Comput Biol. 2021;17:e1008584.
    PubMed     Abstract available

  71. FRIEDRICH J, Giovannucci A, Pnevmatikakis EA
    Online analysis of microendoscopic 1-photon calcium imaging data streams.
    PLoS Comput Biol. 2021;17:e1008565.
    PubMed     Abstract available

  72. AQIL M, Atasoy S, Kringelbach ML, Hindriks R, et al
    Graph neural fields: A framework for spatiotemporal dynamical models on the human connectome.
    PLoS Comput Biol. 2021;17:e1008310.
    PubMed     Abstract available

    December 2020
  73. LACHANCE J, Cohen DJ
    Practical fluorescence reconstruction microscopy for large samples and low-magnification imaging.
    PLoS Comput Biol. 2020;16:e1008443.
    PubMed     Abstract available

  74. FENYVES BG, Szilagyi GS, Vassy Z, Soti C, et al
    Synaptic polarity and sign-balance prediction using gene expression data in the Caenorhabditis elegans chemical synapse neuronal connectome network.
    PLoS Comput Biol. 2020;16:e1007974.
    PubMed     Abstract available

  75. NINO DF, Djayakarsana D, Milstein JN
    FOCAL3D: A 3-dimensional clustering package for single-molecule localization microscopy.
    PLoS Comput Biol. 2020;16:e1008479.
    PubMed     Abstract available

  76. KUMAR S, Ellis CT, O'Connell TP, Chun MM, et al
    Searching through functional space reveals distributed visual, auditory, and semantic coding in the human brain.
    PLoS Comput Biol. 2020;16:e1008457.
    PubMed     Abstract available

  77. FAGERHOLM ED, Tangwiriyasakul C, Friston KJ, Violante IR, et al
    Neural diffusivity and pre-emptive epileptic seizure intervention.
    PLoS Comput Biol. 2020;16:e1008448.
    PubMed     Abstract available

    November 2020
  78. LI B, Yang YT, Capra JA, Gerstein MB, et al
    Predicting changes in protein thermodynamic stability upon point mutation with deep 3D convolutional neural networks.
    PLoS Comput Biol. 2020;16:e1008291.
    PubMed     Abstract available

  79. DAI K, Gratiy SL, Billeh YN, Xu R, et al
    Brain Modeling ToolKit: An open source software suite for multiscale modeling of brain circuits.
    PLoS Comput Biol. 2020;16:e1008386.
    PubMed     Abstract available

  80. AMYOT R, Flechsig H
    BioAFMviewer: An interactive interface for simulated AFM scanning of biomolecular structures and dynamics.
    PLoS Comput Biol. 2020;16:e1008444.
    PubMed     Abstract available

  81. MA J, Do M, Le Gros MA, Peskin CS, et al
    Strong intracellular signal inactivation produces sharper and more robust signaling from cell membrane to nucleus.
    PLoS Comput Biol. 2020;16:e1008356.
    PubMed     Abstract available

    October 2020
  82. CORDIDO A, Cernadas E, Fernandez-Delgado M, Garcia-Gonzalez MA, et al
    CystAnalyser: A new software tool for the automatic detection and quantification of cysts in Polycystic Kidney and Liver Disease, and other cystic disorders.
    PLoS Comput Biol. 2020;16:e1008337.
    PubMed     Abstract available

  83. MUNOZ-AGUIRRE M, Ntasis VF, Rojas S, Guigo R, et al
    PyHIST: A Histological Image Segmentation Tool.
    PLoS Comput Biol. 2020;16:e1008349.
    PubMed     Abstract available

  84. BEUL SF, Hilgetag CC
    Systematic modelling of the development of laminar projection origins in the cerebral cortex: Interactions of spatio-temporal patterns of neurogenesis and cellular heterogeneity.
    PLoS Comput Biol. 2020;16:e1007991.
    PubMed     Abstract available

    September 2020
  85. XU M, Wang Z, Zhang H, Pantazis D, et al
    A new Graph Gaussian embedding method for analyzing the effects of cognitive training.
    PLoS Comput Biol. 2020;16:e1008186.
    PubMed     Abstract available

  86. WEI Z, Lin BJ, Chen TW, Daie K, et al
    A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology.
    PLoS Comput Biol. 2020;16:e1008198.
    PubMed     Abstract available

  87. YANG L, Ghosh RP, Franklin JM, Chen S, et al
    NuSeT: A deep learning tool for reliably separating and analyzing crowded cells.
    PLoS Comput Biol. 2020;16:e1008193.
    PubMed     Abstract available

  88. KORFHAGE N, Muhling M, Ringshandl S, Becker A, et al
    Detection and segmentation of morphologically complex eukaryotic cells in fluorescence microscopy images via feature pyramid fusion.
    PLoS Comput Biol. 2020;16:e1008179.
    PubMed     Abstract available

  89. ROY A, Varela M, Chubb H, MacLeod R, et al
    Identifying locations of re-entrant drivers from patient-specific distribution of fibrosis in the left atrium.
    PLoS Comput Biol. 2020;16:e1008086.
    PubMed     Abstract available

  90. PAPADOPOULOS L, Lynn CW, Battaglia D, Bassett DS, et al
    Relations between large-scale brain connectivity and effects of regional stimulation depend on collective dynamical state.
    PLoS Comput Biol. 2020;16:e1008144.
    PubMed     Abstract available

    June 2020
  91. MAYR S, Hauser F, Puthukodan S, Axmann M, et al
    Statistical analysis of 3D localisation microscopy images for quantification of membrane protein distributions in a platelet clot model.
    PLoS Comput Biol. 2020;16:e1007902.
    PubMed     Abstract available

  92. KONRATH F, Mittermeier A, Cristiano E, Wolf J, et al
    A systematic approach to decipher crosstalk in the p53 signaling pathway using single cell dynamics.
    PLoS Comput Biol. 2020;16:e1007901.
    PubMed     Abstract available

  93. LERMA-USABIAGA G, Benson N, Winawer J, Wandell BA, et al
    A validation framework for neuroimaging software: The case of population receptive fields.
    PLoS Comput Biol. 2020;16:e1007924.
    PubMed     Abstract available

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