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Articles published in
PLoS Comput Biol
    September 2023
  1. BORST JP, Aubin S, Stewart TC
    A whole-task brain model of associative recognition that accounts for human behavior and neuroimaging data.
    PLoS Comput Biol. 2023;19:e1011427.
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    August 2023
  2. CABRERA-ALVAREZ J, Doorn N, Maestu F, Susi G, et al
    Modeling the role of the thalamus in resting-state functional connectivity: Nature or structure.
    PLoS Comput Biol. 2023;19:e1011007.
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  3. LI J, Rentzeperis I, van Leeuwen C
    Functional and spatial rewiring principles jointly regulate context-sensitive computation.
    PLoS Comput Biol. 2023;19:e1011325.
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  4. MACKAY M, Huo S, Kaiser M
    Spatial organisation of the mesoscale connectome: A feature influencing synchrony and metastability of network dynamics.
    PLoS Comput Biol. 2023;19:e1011349.
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  5. KOYAMA H, Okumura H, Ito AM, Nakamura K, et al
    Effective mechanical potential of cell-cell interaction explains three-dimensional morphologies during early embryogenesis.
    PLoS Comput Biol. 2023;19:e1011306.
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    July 2023
  6. HARRISON PJ, Gupta A, Rietdijk J, Wieslander H, et al
    Evaluating the utility of brightfield image data for mechanism of action prediction.
    PLoS Comput Biol. 2023;19:e1011323.
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    May 2023
  7. WEISER SC, Mullen BR, Ascencio D, Ackman JB, et al
    Data-driven segmentation of cortical calcium dynamics.
    PLoS Comput Biol. 2023;19:e1011085.
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  8. HE H, Hong L, Sajda P
    Pupillary response is associated with the reset and switching of functional brain networks during salience processing.
    PLoS Comput Biol. 2023;19:e1011081.
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  9. ZHENG Y, Tang S, Zheng H, Wang X, et al
    Noise improves the association between effects of local stimulation and structural degree of brain networks.
    PLoS Comput Biol. 2023;19:e1010866.
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  10. MILLER KJ, Muller KR, Valencia GO, Huang H, et al
    Canonical Response Parameterization: Quantifying the structure of responses to single-pulse intracranial electrical brain stimulation.
    PLoS Comput Biol. 2023;19:e1011105.
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    April 2023
  11. CLUSELLA P, Deco G, Kringelbach ML, Ruffini G, et al
    Complex spatiotemporal oscillations emerge from transverse instabilities in large-scale brain networks.
    PLoS Comput Biol. 2023;19:e1010781.
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  12. SHINDE A, Mohapatra S, Schlaug G
    Identifying the engagement of a brain network during a targeted tDCS-fMRI experiment using a machine learning approach.
    PLoS Comput Biol. 2023;19:e1011012.
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  13. BRACCI S, Mraz J, Zeman A, Leys G, et al
    The representational hierarchy in human and artificial visual systems in the presence of object-scene regularities.
    PLoS Comput Biol. 2023;19:e1011086.
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  14. WANG Z, Natekar P, Tea C, Tamir S, et al
    MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data.
    PLoS Comput Biol. 2023;19:e1011060.
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    March 2023
  15. PLASZCZYNSKI S, Grammaticos B, Pallud J, Campagne JE, et al
    Predicting regrowth of low-grade gliomas after radiotherapy.
    PLoS Comput Biol. 2023;19:e1011002.
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  16. MULLER PM, Meisel C
    Spatial and temporal correlations in human cortex are inherently linked and predicted by functional hierarchy, vigilance state as well as antiepileptic drug load.
    PLoS Comput Biol. 2023;19:e1010919.
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    February 2023
  17. LIAO C, Sawayama M, Xiao B
    Unsupervised learning reveals interpretable latent representations for translucency perception.
    PLoS Comput Biol. 2023;19:e1010878.
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  18. RUFFINI G, Damiani G, Lozano-Soldevilla D, Deco N, et al
    LSD-induced increase of Ising temperature and algorithmic complexity of brain dynamics.
    PLoS Comput Biol. 2023;19:e1010811.
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  19. LUNDSTROM BN, Richner TJ
    Neural adaptation and fractional dynamics as a window to underlying neural excitability.
    PLoS Comput Biol. 2023;19:e1010527.
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  20. FEY P, Weber DL, Stebani J, Morchel P, et al
    Non-destructive classification of unlabeled cells: Combining an automated benchtop magnetic resonance scanner and artificial intelligence.
    PLoS Comput Biol. 2023;19:e1010842.
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    January 2023
  21. STEN S, Podeus H, Sundqvist N, Elinder F, et al
    A quantitative model for human neurovascular coupling with translated mechanisms from animals.
    PLoS Comput Biol. 2023;19:e1010818.
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  22. PHILLIPS CM, Lima EABF, Gadde M, Jarrett AM, et al
    Towards integration of time-resolved confocal microscopy of a 3D in vitro microfluidic platform with a hybrid multiscale model of tumor angiogenesis.
    PLoS Comput Biol. 2023;19:e1009499.
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  23. SOTO FA, Narasiwodeyar S
    Improving the validity of neuroimaging decoding tests of invariant and configural neural representation.
    PLoS Comput Biol. 2023;19:e1010819.
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    December 2022
  24. OGANE T, Noshiro D, Ando T, Yamashita A, et al
    Development of hidden Markov modeling method for molecular orientations and structure estimation from high-speed atomic force microscopy time-series images.
    PLoS Comput Biol. 2022;18:e1010384.
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  25. VAN DE STEEN F, Pinotsis D, Devos W, Colenbier N, et al
    Dynamic causal modelling shows a prominent role of local inhibition in alpha power modulation in higher visual cortex.
    PLoS Comput Biol. 2022;18:e1009988.
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  26. SUNDQVIST N, Sten S, Thompson P, Andersson BJ, et al
    Mechanistic model for human brain metabolism and its connection to the neurovascular coupling.
    PLoS Comput Biol. 2022;18:e1010798.
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  27. JIANG X, Isogai T, Chi J, Danuser G, et al
    Fine-grained, nonlinear registration of live cell movies reveals spatiotemporal organization of diffuse molecular processes.
    PLoS Comput Biol. 2022;18:e1009667.
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    November 2022
  28. SANZ PERL Y, Escrichs A, Tagliazucchi E, Kringelbach ML, et al
    Strength-dependent perturbation of whole-brain model working in different regimes reveals the role of fluctuations in brain dynamics.
    PLoS Comput Biol. 2022;18:e1010662.
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  29. DAMICELLI F, Hilgetag CC, Goulas A
    Brain connectivity meets reservoir computing.
    PLoS Comput Biol. 2022;18:e1010639.
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  30. NIETO-CASTANON A
    Brain-wide connectome inferences using functional connectivity MultiVariate Pattern Analyses (fc-MVPA).
    PLoS Comput Biol. 2022;18:e1010634.
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  31. BISWAS R, Shlizerman E
    Statistical perspective on functional and causal neural connectomics: The Time-Aware PC algorithm.
    PLoS Comput Biol. 2022;18:e1010653.
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    October 2022
  32. YIP A, Smith-Roberge J, Khorasani SH, Aucoin MG, et al
    Calibrating spatiotemporal models of microbial communities to microscopy data: A review.
    PLoS Comput Biol. 2022;18:e1010533.
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  33. SCHACH S, Lindner A, Braun DA
    Bounded rational decision-making models suggest capacity-limited concurrent motor planning in human posterior parietal and frontal cortex.
    PLoS Comput Biol. 2022;18:e1010585.
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  34. BERENS SC, Bird CM
    Hippocampal and medial prefrontal cortices encode structural task representations following progressive and interleaved training schedules.
    PLoS Comput Biol. 2022;18:e1010566.
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  35. SCHMITT O, Nitzsche C, Eipert P, Prathapan V, et al
    Reaction-diffusion models in weighted and directed connectomes.
    PLoS Comput Biol. 2022;18:e1010507.
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    September 2022
  36. SOLER-TOSCANO F, Galadi JA, Escrichs A, Sanz Perl Y, et al
    What lies underneath: Precise classification of brain states using time-dependent topological structure of dynamics.
    PLoS Comput Biol. 2022;18:e1010412.
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  37. YAMAMOTO T, Cockburn K, Greco V, Kawaguchi K, et al
    Probing the rules of cell coordination in live tissues by interpretable machine learning based on graph neural networks.
    PLoS Comput Biol. 2022;18:e1010477.
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  38. GATICA M, E Rosas F, A M Mediano P, Diez I, et al
    High-order functional redundancy in ageing explained via alterations in the connectome in a whole-brain model.
    PLoS Comput Biol. 2022;18:e1010431.
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    August 2022
  39. ALASFOUR A, Gabriel P, Jiang X, Shamie I, et al
    Spatiotemporal dynamics of human high gamma discriminate naturalistic behavioral states.
    PLoS Comput Biol. 2022;18:e1010401.
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  40. KERSTJENS S, Michel G, Douglas RJ
    Constructive connectomics: How neuronal axons get from here to there using gene-expression maps derived from their family trees.
    PLoS Comput Biol. 2022;18:e1010382.
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    July 2022
  41. SHERMAN MT, Fountas Z, Seth AK, Roseboom W, et al
    Trial-by-trial predictions of subjective time from human brain activity.
    PLoS Comput Biol. 2022;18:e1010223.
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  42. TEN OEVER S, Kaushik K, Martin AE
    Inferring the nature of linguistic computations in the brain.
    PLoS Comput Biol. 2022;18:e1010269.
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    June 2022
  43. SMITH E, Peters J
    Motor response vigour and visual fixation patterns reflect subjective valuation during intertemporal choice.
    PLoS Comput Biol. 2022;18:e1010096.
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  44. 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.
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  45. 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.
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  46. WAN Q, Menendez JA, Postle BR
    Priority-based transformations of stimulus representation in visual working memory.
    PLoS Comput Biol. 2022;18:e1009062.
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    April 2022
  47. 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.
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  48. 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.
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  49. 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.
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  50. 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.
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    March 2022
  51. MATSUDA T, Homae F, Watanabe H, Taga G, et al
    Oscillator decomposition of infant fNIRS data.
    PLoS Comput Biol. 2022;18:e1009985.
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  52. 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.
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    February 2022
  53. KAISER D, Jacobs AM, Cichy RM
    Modelling brain representations of abstract concepts.
    PLoS Comput Biol. 2022;18:e1009837.
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    January 2022
  54. 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.
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  55. YANG Y, Turci F, Kague E, Hammond CL, et al
    Dominating lengthscales of zebrafish collective behaviour.
    PLoS Comput Biol. 2022;18:e1009394.
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    December 2021
  56. XIAO ZC, Lin KK, Young LS
    A data-informed mean-field approach to mapping of cortical parameter landscapes.
    PLoS Comput Biol. 2021;17:e1009718.
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  57. 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.
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    November 2021
  58. 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.
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  59. 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.
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  60. 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.
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  61. 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.
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  62. ITO S, Si Y, Litke AM, Feldheim DA, et al
    Nonlinear visuoauditory integration in the mouse superior colliculus.
    PLoS Comput Biol. 2021;17:e1009181.
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  63. 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.
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    October 2021
  64. 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.
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  65. MIHELIC SA, Sikora WA, Hassan AM, Williamson MR, et al
    Segmentation-Less, Automated, Vascular Vectorization.
    PLoS Comput Biol. 2021;17:e1009451.
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  66. DOMINEY PF
    Narrative event segmentation in the cortical reservoir.
    PLoS Comput Biol. 2021;17:e1008993.
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  67. 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.
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    September 2021
  68. 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.
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  69. 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.
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  70. 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.
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  71. 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.
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    August 2021
  72. 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.
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  73. 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.
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  74. 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.
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  75. SCHAWORONKOW N, Voytek B
    Enhancing oscillations in intracranial electrophysiological recordings with data-driven spatial filters.
    PLoS Comput Biol. 2021;17:e1009298.
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  76. 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.
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  77. TU Y, Ta D, Lu ZL, Wang Y, et al
    Topology-preserving smoothing of retinotopic maps.
    PLoS Comput Biol. 2021;17:e1009216.
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    July 2021
  78. 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.
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  79. 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.
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  80. 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.
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  81. 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.
    >> Share

  82. 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.
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  83. 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.
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  84. 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.
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  85. 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.
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    June 2021
  86. 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.
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  87. 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.
    >> Share

  88. 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.
    >> Share

  89. 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.
    >> Share


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