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Articles published in PLoS Comput Biol

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    March 2021
  1. 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

  2. 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

    February 2021
  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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
  13. 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

  14. 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

  15. 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
  16. LACHANCE J, Cohen DJ
    Practical fluorescence reconstruction microscopy for large samples and low-magnification imaging.
    PLoS Comput Biol. 2020;16:e1008443.
    PubMed     Abstract available

  17. 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

  18. 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

  19. 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

  20. 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
  21. 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

  22. 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

  23. 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

  24. 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
  25. 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

  26. 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

  27. 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
  28. 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

  29. 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

  30. 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

  31. 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

  32. 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

  33. 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

    August 2020
  34. STERN T, Shvartsman SY, Wieschaus EF
    Template-based mapping of dynamic motifs in tissue morphogenesis.
    PLoS Comput Biol. 2020;16:e1008049.
    PubMed     Abstract available

  35. ZHANG RY, Wei XX, Kay K
    Understanding multivariate brain activity: Evaluating the effect of voxelwise noise correlations on population codes in functional magnetic resonance imaging.
    PLoS Comput Biol. 2020;16:e1008153.
    PubMed     Abstract available

  36. PASCUCCI D, Rubega M, Plomp G
    Modeling time-varying brain networks with a self-tuning optimized Kalman filter.
    PLoS Comput Biol. 2020;16:e1007566.
    PubMed     Abstract available

  37. ITO T, Brincat SL, Siegel M, Mill RD, et al
    Task-evoked activity quenches neural correlations and variability across cortical areas.
    PLoS Comput Biol. 2020;16:e1007983.
    PubMed     Abstract available

    July 2020
  38. LE TTT, Adler FR
    Is mammography screening beneficial: An individual-based stochastic model for breast cancer incidence and mortality.
    PLoS Comput Biol. 2020;16:e1008036.
    PubMed     Abstract available

  39. CASTRO S, El-Deredy W, Battaglia D, Orio P, et al
    Cortical ignition dynamics is tightly linked to the core organisation of the human connectome.
    PLoS Comput Biol. 2020;16:e1007686.
    PubMed     Abstract available

  40. HASELDEN WD, Kedarasetti RT, Drew PJ
    Spatial and temporal patterns of nitric oxide diffusion and degradation drive emergent cerebrovascular dynamics.
    PLoS Comput Biol. 2020;16:e1008069.
    PubMed     Abstract available

  41. VERBIST C, Muller MG, Mansvelder HD, Legenstein R, et al
    The location of the axon initial segment affects the bandwidth of spike initiation dynamics.
    PLoS Comput Biol. 2020;16:e1008087.
    PubMed     Abstract available

  42. BUTENKO K, Bahls C, Schroder M, Kohling R, et al
    OSS-DBS: Open-source simulation platform for deep brain stimulation with a comprehensive automated modeling.
    PLoS Comput Biol. 2020;16:e1008023.
    PubMed     Abstract available

  43. BEREZUTSKAYA J, Freudenburg ZV, Guclu U, van Gerven MAJ, et al
    Brain-optimized extraction of complex sound features that drive continuous auditory perception.
    PLoS Comput Biol. 2020;16:e1007992.
    PubMed     Abstract available

    June 2020
  44. KHATAMI F, Escabi MA
    Spiking network optimized for word recognition in noise predicts auditory system hierarchy.
    PLoS Comput Biol. 2020;16:e1007558.
    PubMed     Abstract available

  45. LI X, Ni Q, He X, Kong J, et al
    Tensile force-induced cytoskeletal remodeling: Mechanics before chemistry.
    PLoS Comput Biol. 2020;16:e1007693.
    PubMed     Abstract available

  46. SHAO Y, Zhang J, Tao L
    Dimensional reduction of emergent spatiotemporal cortical dynamics via a maximum entropy moment closure.
    PLoS Comput Biol. 2020;16:e1007265.
    PubMed     Abstract available

  47. 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

  48. 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

  49. 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

    May 2020
  50. ALIMOHAMADI H, Smith AS, Nowak RB, Fowler VM, et al
    Non-uniform distribution of myosin-mediated forces governs red blood cell membrane curvature through tension modulation.
    PLoS Comput Biol. 2020;16:e1007890.
    PubMed     Abstract available

  51. FAGERHOLM ED, Foulkes WMC, Gallero-Salas Y, Helmchen F, et al
    Conservation laws by virtue of scale symmetries in neural systems.
    PLoS Comput Biol. 2020;16:e1007865.
    PubMed     Abstract available

    April 2020
  52. LEE CT, Laughlin JG, Angliviel de La Beaumelle N, Amaro RE, et al
    3D mesh processing using GAMer 2 to enable reaction-diffusion simulations in realistic cellular geometries.
    PLoS Comput Biol. 2020;16:e1007756.
    PubMed     Abstract available

  53. HARTOYO A, Cadusch PJ, Liley DTJ, Hicks DG, et al
    Inferring a simple mechanism for alpha-blocking by fitting a neural population model to EEG spectra.
    PLoS Comput Biol. 2020;16:e1007662.
    PubMed     Abstract available

  54. BARTOLO R, Saunders RC, Mitz AR, Averbeck BB, et al
    Dimensionality, information and learning in prefrontal cortex.
    PLoS Comput Biol. 2020;16:e1007514.
    PubMed     Abstract available

  55. PONZI A, Barton SJ, Bunner KD, Rangel-Barajas C, et al
    Striatal network modeling in Huntington's Disease.
    PLoS Comput Biol. 2020;16:e1007648.
    PubMed     Abstract available

  56. SAXENA S, Kinsella I, Musall S, Kim SH, et al
    Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data.
    PLoS Comput Biol. 2020;16:e1007791.
    PubMed     Abstract available

  57. LUGAGNE JB, Lin H, Dunlop MJ
    DeLTA: Automated cell segmentation, tracking, and lineage reconstruction using deep learning.
    PLoS Comput Biol. 2020;16:e1007673.
    PubMed     Abstract available

  58. HADDAD Y, Adam V, Heger Z
    Ten quick tips for homology modeling of high-resolution protein 3D structures.
    PLoS Comput Biol. 2020;16:e1007449.
    PubMed     Abstract available

    March 2020
    Seven quick tips for analysis scripts in neuroimaging.
    PLoS Comput Biol. 2020;16:e1007358.

  60. BERNASEK SM, Pelaez N, Carthew RW, Bagheri N, et al
    Fly-QMA: Automated analysis of mosaic imaginal discs in Drosophila.
    PLoS Comput Biol. 2020;16:e1007406.
    PubMed     Abstract available

  61. CASSIDY KC, Sefcik J, Raghav Y, Chang A, et al
    ProteinVR: Web-based molecular visualization in virtual reality.
    PLoS Comput Biol. 2020;16:e1007747.
    PubMed     Abstract available

  62. CZAJA B, Gutierrez M, Zavodszky G, de Kanter D, et al
    The influence of red blood cell deformability on hematocrit profiles and platelet margination.
    PLoS Comput Biol. 2020;16:e1007716.
    PubMed     Abstract available

  63. ELDRED KC, Avelis C, Johnston RJ Jr, Roberts E, et al
    Modeling binary and graded cone cell fate patterning in the mouse retina.
    PLoS Comput Biol. 2020;16:e1007691.
    PubMed     Abstract available

  64. MORRIS TA, Naik J, Fibben KS, Kong X, et al
    Striated myocyte structural integrity: Automated analysis of sarcomeric z-discs.
    PLoS Comput Biol. 2020;16:e1007676.
    PubMed     Abstract available

    February 2020
  65. GALLAHER JA, Massey SC, Hawkins-Daarud A, Noticewala SS, et al
    From cells to tissue: How cell scale heterogeneity impacts glioblastoma growth and treatment response.
    PLoS Comput Biol. 2020;16:e1007672.
    PubMed     Abstract available

  66. DAI K, Hernando J, Billeh YN, Gratiy SL, et al
    The SONATA data format for efficient description of large-scale network models.
    PLoS Comput Biol. 2020;16:e1007696.
    PubMed     Abstract available

  67. TANG QY, Kaneko K
    Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis.
    PLoS Comput Biol. 2020;16:e1007670.
    PubMed     Abstract available

  68. SABRIN KM, Wei Y, van den Heuvel MP, Dovrolis C, et al
    The hourglass organization of the Caenorhabditis elegans connectome.
    PLoS Comput Biol. 2020;16:e1007526.
    PubMed     Abstract available

  69. ALLARD A, Serrano MA
    Navigable maps of structural brain networks across species.
    PLoS Comput Biol. 2020;16:e1007584.
    PubMed     Abstract available

    January 2020
  70. HANNIG J, Schafer H, Ackermann J, Hebel M, et al
    Bioinformatics analysis of whole slide images reveals significant neighborhood preferences of tumor cells in Hodgkin lymphoma.
    PLoS Comput Biol. 2020;16:e1007516.
    PubMed     Abstract available

  71. PETERSEN RS, Colins Rodriguez A, Evans MH, Campagner D, et al
    A system for tracking whisker kinematics and whisker shape in three dimensions.
    PLoS Comput Biol. 2020;16:e1007402.
    PubMed     Abstract available

  72. KUMAR M, Ellis CT, Lu Q, Zhang H, et al
    BrainIAK tutorials: User-friendly learning materials for advanced fMRI analysis.
    PLoS Comput Biol. 2020;16:e1007549.
    PubMed     Abstract available

    December 2019
  73. REISCHL M, Jouda M, MacKinnon N, Fuhrer E, et al
    Motion prediction enables simulated MR-imaging of freely moving model organisms.
    PLoS Comput Biol. 2019;15:e1006997.
    PubMed     Abstract available

  74. LI B, Taniguchi D, Gedara JP, Gogulancea V, et al
    NUFEB: A massively parallel simulator for individual-based modelling of microbial communities.
    PLoS Comput Biol. 2019;15:e1007125.
    PubMed     Abstract available

  75. BOONMAN A, Fenton B, Yovel Y
    The benefits of insect-swarm hunting to echolocating bats, and its influence on the evolution of bat echolocation signals.
    PLoS Comput Biol. 2019;15:e1006873.
    PubMed     Abstract available

  76. BETZEL RF, Wood KC, Angeloni C, Neimark Geffen M, et al
    Stability of spontaneous, correlated activity in mouse auditory cortex.
    PLoS Comput Biol. 2019;15:e1007360.
    PubMed     Abstract available

  77. FINGER H, Gast R, Gerloff C, Engel AK, et al
    Probing neural networks for dynamic switches of communication pathways.
    PLoS Comput Biol. 2019;15:e1007551.
    PubMed     Abstract available

    November 2019
  78. ZHOU J, Benson NC, Kay K, Winawer J, et al
    Predicting neuronal dynamics with a delayed gain control model.
    PLoS Comput Biol. 2019;15:e1007484.
    PubMed     Abstract available

  79. ALEXANDER DM, Ball T, Schulze-Bonhage A, van Leeuwen C, et al
    Large-scale cortical travelling waves predict localized future cortical signals.
    PLoS Comput Biol. 2019;15:e1007316.
    PubMed     Abstract available

  80. GROSSKURTH ED, Bach DR, Economides M, Huys QJM, et al
    No substantial change in the balance between model-free and model-based control via training on the two-step task.
    PLoS Comput Biol. 2019;15:e1007443.
    PubMed     Abstract available

  81. RULE ME, Schnoerr D, Hennig MH, Sanguinetti G, et al
    Neural field models for latent state inference: Application to large-scale neuronal recordings.
    PLoS Comput Biol. 2019;15:e1007442.
    PubMed     Abstract available

  82. MENEZES DE OLIVEIRA M, Pang JC, Robinson PA, Liu X, et al
    Feasibility of functional magnetic resonance imaging of ocular dominance and orientation preference in primary visual cortex.
    PLoS Comput Biol. 2019;15:e1007418.
    PubMed     Abstract available

    October 2019
  83. BALABAN G, Halliday BP, Bai W, Porter B, et al
    Scar shape analysis and simulated electrical instabilities in a non-ischemic dilated cardiomyopathy patient cohort.
    PLoS Comput Biol. 2019;15:e1007421.
    PubMed     Abstract available

  84. SCHMIDT H, Knosche TR
    Action potential propagation and synchronisation in myelinated axons.
    PLoS Comput Biol. 2019;15:e1007004.
    PubMed     Abstract available

  85. AGUILERA LU, Raymond W, Fox ZR, May M, et al
    Computational design and interpretation of single-RNA translation experiments.
    PLoS Comput Biol. 2019;15:e1007425.
    PubMed     Abstract available

  86. LI M, Han Y, Aburn MJ, Breakspear M, et al
    Transitions in information processing dynamics at the whole-brain network level are driven by alterations in neural gain.
    PLoS Comput Biol. 2019;15:e1006957.
    PubMed     Abstract available

    September 2019
  87. LU AX, Kraus OZ, Cooper S, Moses AM, et al
    Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting.
    PLoS Comput Biol. 2019;15:e1007348.
    PubMed     Abstract available

    August 2019
  88. PEREIRA BOTELHO D, Curran K, Lowery MM
    Anatomically accurate model of EMG during index finger flexion and abduction derived from diffusion tensor imaging.
    PLoS Comput Biol. 2019;15:e1007267.
    PubMed     Abstract available

  89. KOPPE G, Toutounji H, Kirsch P, Lis S, et al
    Identifying nonlinear dynamical systems via generative recurrent neural networks with applications to fMRI.
    PLoS Comput Biol. 2019;15:e1007263.
    PubMed     Abstract available

    Arrhythmia mechanisms and spontaneous calcium release: Bi-directional coupling between re-entrant and focal excitation.
    PLoS Comput Biol. 2019;15:e1007260.
    PubMed     Abstract available

  91. ROGERSON LE, Zhao Z, Franke K, Euler T, et al
    Bayesian hypothesis testing and experimental design for two-photon imaging data.
    PLoS Comput Biol. 2019;15:e1007205.
    PubMed     Abstract available

    July 2019
  92. RUDRARAJU S, Moulton DE, Chirat R, Goriely A, et al
    A computational framework for the morpho-elastic development of molluskan shells by surface and volume growth.
    PLoS Comput Biol. 2019;15:e1007213.
    PubMed     Abstract available

  93. KAROLAK A, Poonja S, Rejniak KA
    Morphophenotypic classification of tumor organoids as an indicator of drug exposure and penetration potential.
    PLoS Comput Biol. 2019;15:e1007214.
    PubMed     Abstract available

  94. WILSON ED, Anderson SR, Dean P, Porrill J, et al
    Sensorimotor maps can be dynamically calibrated using an adaptive-filter model of the cerebellum.
    PLoS Comput Biol. 2019;15:e1007187.
    PubMed     Abstract available

    June 2019
  95. HODNELAND E, Hanson E, Saevareid O, Naevdal G, et al
    A new framework for assessing subject-specific whole brain circulation and perfusion using MRI-based measurements and a multi-scale continuous flow model.
    PLoS Comput Biol. 2019;15:e1007073.
    PubMed     Abstract available

  96. FORSGREN MF, Karlsson M, Dahlqvist Leinhard O, Dahlstrom N, et al
    Model-inferred mechanisms of liver function from magnetic resonance imaging data: Validation and variation across a clinically relevant cohort.
    PLoS Comput Biol. 2019;15:e1007157.
    PubMed     Abstract available

    May 2019
  97. STIGLIANI A, Jeska B, Grill-Spector K
    Differential sustained and transient temporal processing across visual streams.
    PLoS Comput Biol. 2019;15:e1007011.
    PubMed     Abstract available

  98. HAKKINEN TJ, Sova SS, Corfe IJ, Tjaderhane L, et al
    Modeling enamel matrix secretion in mammalian teeth.
    PLoS Comput Biol. 2019;15:e1007058.
    PubMed     Abstract available

  99. CAI MB, Schuck NW, Pillow JW, Niv Y, et al
    Representational structure or task structure? Bias in neural representational similarity analysis and a Bayesian method for reducing bias.
    PLoS Comput Biol. 2019;15:e1006299.
    PubMed     Abstract available

  100. SCHAWORONKOW N, Nikulin VV
    Spatial neuronal synchronization and the waveform of oscillations: Implications for EEG and MEG.
    PLoS Comput Biol. 2019;15:e1007055.
    PubMed     Abstract available

  101. KULIKOV V, Guo SM, Stone M, Goodman A, et al
    DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images.
    PLoS Comput Biol. 2019;15:e1007012.
    PubMed     Abstract available

    April 2019
  102. MALANDRINO A, Trepat X, Kamm RD, Mak M, et al
    Dynamic filopodial forces induce accumulation, damage, and plastic remodeling of 3D extracellular matrices.
    PLoS Comput Biol. 2019;15:e1006684.
    PubMed     Abstract available

  103. CHOI H, Mihalas S
    Synchronization dependent on spatial structures of a mesoscopic whole-brain network.
    PLoS Comput Biol. 2019;15:e1006978.
    PubMed     Abstract available

    March 2019
  104. AVENA-KOENIGSBERGER A, Yan X, Kolchinsky A, van den Heuvel MP, et al
    A spectrum of routing strategies for brain networks.
    PLoS Comput Biol. 2019;15:e1006833.
    PubMed     Abstract available

  105. LAGE-CASTELLANOS A, Valente G, Formisano E, De Martino F, et al
    Methods for computing the maximum performance of computational models of fMRI responses.
    PLoS Comput Biol. 2019;15:e1006397.
    PubMed     Abstract available

  106. BIZZEGO A, Bussola N, Chierici M, Maggio V, et al
    Evaluating reproducibility of AI algorithms in digital pathology with DAPPER.
    PLoS Comput Biol. 2019;15:e1006269.
    PubMed     Abstract available

    February 2019
  107. TABAS A, Andermann M, Schuberth V, Riedel H, et al
    Modeling and MEG evidence of early consonance processing in auditory cortex.
    PLoS Comput Biol. 2019;15:e1006820.
    PubMed     Abstract available

  108. OLMI S, Petkoski S, Guye M, Bartolomei F, et al
    Controlling seizure propagation in large-scale brain networks.
    PLoS Comput Biol. 2019;15:e1006805.
    PubMed     Abstract available

    January 2019
  109. MARKOVIC D, Reiter AMF, Kiebel SJ
    Predicting change: Approximate inference under explicit representation of temporal structure in changing environments.
    PLoS Comput Biol. 2019;15:e1006707.
    PubMed     Abstract available

  110. ALQUEZAR-BAETA C, Gimeno-Martos S, Miguel-Jimenez S, Santolaria P, et al
    OpenCASA: A new open-source and scalable tool for sperm quality analysis.
    PLoS Comput Biol. 2019;15:e1006691.
    PubMed     Abstract available

  111. FOX ZR, Munsky B
    The finite state projection based Fisher information matrix approach to estimate information and optimize single-cell experiments.
    PLoS Comput Biol. 2019;15:e1006365.
    PubMed     Abstract available

  112. SHEN G, Horikawa T, Majima K, Kamitani Y, et al
    Deep image reconstruction from human brain activity.
    PLoS Comput Biol. 2019;15:e1006633.
    PubMed     Abstract available

    December 2018
  113. GROEN IIA, Jahfari S, Seijdel N, Ghebreab S, et al
    Scene complexity modulates degree of feedback activity during object detection in natural scenes.
    PLoS Comput Biol. 2018;14:e1006690.
    PubMed     Abstract available

  114. LEE BC, Tward DJ, Mitra PP, Miller MI, et al
    On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model.
    PLoS Comput Biol. 2018;14:e1006610.
    PubMed     Abstract available

  115. VANDERSICKEL N, Watanabe M, Tao Q, Fostier J, et al
    Dynamical anchoring of distant arrhythmia sources by fibrotic regions via restructuring of the activation pattern.
    PLoS Comput Biol. 2018;14:e1006637.
    PubMed     Abstract available

  116. HAY EA, Parthasarathy R
    Performance of convolutional neural networks for identification of bacteria in 3D microscopy datasets.
    PLoS Comput Biol. 2018;14:e1006628.
    PubMed     Abstract available

  117. RAZETTI A, Medioni C, Malandain G, Besse F, et al
    A stochastic framework to model axon interactions within growing neuronal populations.
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  118. TOWNSEND RG, Gong P
    Detection and analysis of spatiotemporal patterns in brain activity.
    PLoS Comput Biol. 2018;14:e1006643.
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    November 2018
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    Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs.
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  120. VAROQUAUX G, Schwartz Y, Poldrack RA, Gauthier B, et al
    Atlases of cognition with large-scale human brain mapping.
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  121. KLUGHAMMER N, Bischof J, Schnellbacher ND, Callegari A, et al
    Cytoplasmic flows in starfish oocytes are fully determined by cortical contractions.
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  122. ANTON-SANCHEZ L, Effenberger F, Bielza C, Larranaga P, et al
    A regularity index for dendrites - local statistics of a neuron's input space.
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  123. JIMENEZ-CARRETERO D, Abrishami V, Fernandez-de-Manuel L, Palacios I, et al
    Tox_(R)CNN: Deep learning-based nuclei profiling tool for drug toxicity screening.
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  124. BEUL SF, Goulas A, Hilgetag CC
    Comprehensive computational modelling of the development of mammalian cortical connectivity underlying an architectonic type principle.
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  125. HARTUNG G, Vesel C, Morley R, Alaraj A, et al
    Simulations of blood as a suspension predicts a depth dependent hematocrit in the circulation throughout the cerebral cortex.
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    October 2018
  126. KALFAS I, Vinken K, Vogels R
    Representations of regular and irregular shapes by deep Convolutional Neural Networks, monkey inferotemporal neurons and human judgments.
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  127. XU S, Kim S, Chen ISY, Chou T, et al
    Modeling large fluctuations of thousands of clones during hematopoiesis: The role of stem cell self-renewal and bursty progenitor dynamics in rhesus macaque.
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  128. SOTO FA, Vucovich LE, Ashby FG
    Linking signal detection theory and encoding models to reveal independent neural representations from neuroimaging data.
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    September 2018
  129. JAMALABADI H, Alizadeh S, Schonauer M, Leibold C, et al
    Multivariate classification of neuroimaging data with nested subclasses: Biased accuracy and implications for hypothesis testing.
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  130. FUKUSHIMA M, Sporns O
    Comparison of fluctuations in global network topology of modeled and empirical brain functional connectivity.
    PLoS Comput Biol. 2018;14:e1006497.
    PubMed     Abstract available

  131. BABICHEV A, Morozov D, Dabaghian Y
    Robust spatial memory maps encoded by networks with transient connections.
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  132. STOIANOV IP, Pennartz CMA, Lansink CS, Pezzulo G, et al
    Model-based spatial navigation in the hippocampus-ventral striatum circuit: A computational analysis.
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  133. BHAGWAT N, Viviano JD, Voineskos AN, Chakravarty MM, et al
    Modeling and prediction of clinical symptom trajectories in Alzheimer's disease using longitudinal data.
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    August 2018
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    Calcium imaging and dynamic causal modelling reveal brain-wide changes in effective connectivity and synaptic dynamics during epileptic seizures.
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  135. KATTHAGEN T, Mathys C, Deserno L, Walter H, et al
    Modeling subjective relevance in schizophrenia and its relation to aberrant salience.
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  136. KIM H, Moon JY, Mashour GA, Lee U, et al
    Mechanisms of hysteresis in human brain networks during transitions of consciousness and unconsciousness: Theoretical principles and empirical evidence.
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  137. PASTORE VP, Massobrio P, Godjoski A, Martinoia S, et al
    Identification of excitatory-inhibitory links and network topology in large-scale neuronal assemblies from multi-electrode recordings.
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    Dorsal anterior cingulate-brainstem ensemble as a reinforcement meta-learner.
    PLoS Comput Biol. 2018;14:e1006370.
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    July 2018
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    Shared spatiotemporal category representations in biological and artificial deep neural networks.
    PLoS Comput Biol. 2018;14:e1006327.
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  140. PETKOSKI S, Palva JM, Jirsa VK
    Phase-lags in large scale brain synchronization: Methodological considerations and in-silico analysis.
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    Subgraphs of functional brain networks identify dynamical constraints of cognitive control.
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    June 2018
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    Thalamocortical and intracortical laminar connectivity determines sleep spindle properties.
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  143. LUENGO-SANCHEZ S, Fernaud-Espinosa I, Bielza C, Benavides-Piccione R, et al
    3D morphology-based clustering and simulation of human pyramidal cell dendritic spines.
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    May 2018
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    The complex ecosystem in non small cell lung cancer invasion.
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  145. SANCHEZ-RODRIGUEZ LM, Iturria-Medina Y, Baines EA, Mallo SC, et al
    Design of optimal nonlinear network controllers for Alzheimer's disease.
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    Porcupine: A visual pipeline tool for neuroimaging analysis.
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    Simulations to benchmark time-varying connectivity methods for fMRI.
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    Community-based benchmarking improves spike rate inference from two-photon calcium imaging data.
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    April 2018
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    A probabilistic, distributed, recursive mechanism for decision-making in the brain.
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    Mechanical unfolding reveals stable 3-helix intermediates in talin and alpha-catenin.
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    Organization of the core respiratory network: Insights from optogenetic and modeling studies.
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    Computational mechanisms underlying cortical responses to the affordance properties of visual scenes.
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  153. SCHOTT B, Traub M, Schlagenhauf C, Takamiya M, et al
    EmbryoMiner: A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos.
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    A computational model of shared fine-scale structure in the human connectome.
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    March 2018
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    An open source tool for automatic spatiotemporal assessment of calcium transients and local 'signal-close-to-noise' activity in calcium imaging data.
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  156. SCHIEFER J, Niederbuhl A, Pernice V, Lennartz C, et al
    From correlation to causation: Estimating effective connectivity from zero-lag covariances of brain signals.
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  157. VIEJO G, Cortier T, Peyrache A
    Brain-state invariant thalamo-cortical coordination revealed by non-linear encoders.
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  158. IRASTORZA-AZCARATE I, Acemel RD, Tena JJ, Maeso I, et al
    4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data.
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    ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy.
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    speaq 2.0: A complete workflow for high-throughput 1D NMR spectra processing and quantification.
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  161. KONDO Y, Aoki K, Ishii S
    Inverse tissue mechanics of cell monolayer expansion.
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    February 2018
  162. DU H, Wang Y, Haensel D, Lee B, et al
    Multiscale modeling of layer formation in epidermis.
    PLoS Comput Biol. 2018;14:e1006006.
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  163. SPALDING C, Keen E, Smith DJ, Krachler AM, et al
    Mathematical modelling of the antibiotic-induced morphological transition of Pseudomonas aeruginosa.
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    A biophysical model of dynamic balancing of excitation and inhibition in fast oscillatory large-scale networks.
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    Hub connectivity, neuronal diversity, and gene expression in the Caenorhabditis elegans connectome.
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  166. DONHAUSER PW, Florin E, Baillet S
    Imaging of neural oscillations with embedded inferential and group prevalence statistics.
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  167. CHAKRABORTTY B, Blilou I, Scheres B, Mulder BM, et al
    A computational framework for cortical microtubule dynamics in realistically shaped plant cells.
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    January 2018
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    Static length changes of cochlear outer hair cells can tune low-frequency hearing.
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    A neural network model for the orbitofrontal cortex and task space acquisition during reinforcement learning.
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    November 2017
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    Choose, rate or squeeze: Comparison of economic value functions elicited by different behavioral tasks.
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    Optimal synaptic signaling connectome for locomotory behavior in Caenorhabditis elegans: Design minimizing energy cost.
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    October 2017
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    Dynamics and heterogeneity of brain damage in multiple sclerosis.
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    A deep convolutional neural network for classification of red blood cells in sickle cell anemia.
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    A method to quantify mechanobiologic forces during zebrafish cardiac development using 4-D light sheet imaging and computational modeling.
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    Decoding brain activity using a large-scale probabilistic functional-anatomical atlas of human cognition.
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    September 2017
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    Synthesizing developmental trajectories.
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    Altering neuronal excitability to preserve network connectivity in a computational model of Alzheimer's disease.
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    Features of spatial and functional segregation and integration of the primate connectome revealed by trade-off between wiring cost and efficiency.
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    Correlated receptor transport processes buffer single-cell heterogeneity.
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    August 2017
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    Noise correlations in the human brain and their impact on pattern classification.
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    From homeostasis to behavior: Balanced activity in an exploration of embodied dynamic environmental-neural interaction.
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