Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Review Article
  • Published:

Network models to enhance the translational impact of cross-species studies

Abstract

Neuroscience studies are often carried out in animal models for the purpose of understanding specific aspects of the human condition. However, the translation of findings across species remains a substantial challenge. Network science approaches can enhance the translational impact of cross-species studies by providing a means of mapping small-scale cellular processes identified in animal model studies to larger-scale inter-regional circuits observed in humans. In this Review, we highlight the contributions of network science approaches to the development of cross-species translational research in neuroscience. We lay the foundation for our discussion by exploring the objectives of cross-species translational models. We then discuss how the development of new tools that enable the acquisition of whole-brain data in animal models with cellular resolution provides unprecedented opportunity for cross-species applications of network science approaches for understanding large-scale brain networks. We describe how these tools may support the translation of findings across species and imaging modalities and highlight future opportunities. Our overarching goal is to illustrate how the application of network science tools across human and animal model studies could deepen insight into the neurobiology that underlies phenomena observed with non-invasive neuroimaging methods and could simultaneously further our ability to translate findings across species.

This is a preview of subscription content, access via your institution

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Cross-species translational research workflow.
Fig. 2: Measuring large-scale neural activity across species and scales.
Fig. 3: Translational models in the areas of neurodevelopment, neuromodulation and neurodegeneration.
Fig. 4: A multilayer network conception of neural signals across modalities in the mouse brain.

References

  1. C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012–2018 (1998).

    Article  Google Scholar 

  2. Mouse Genome Sequencing Consortium et al. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562 (2002).

    Article  Google Scholar 

  3. Howe, K. et al. The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498–503 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Bakken, T. E. et al. Comparative cellular analysis of motor cortex in human, marmoset and mouse. Nature 598, 111–119 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Jackson, B. J., Fatima, G. L., Oh, S. & Gire, D. H. Many paths to the same goal: balancing exploration and exploitation during probabilistic route planning. eNeuro 7, ENEURO.0536-19.2020 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  6. Calhoun, A. J., Chalasani, S. H. & Sharpee, T. O. Maximally informative foraging by Caenorhabditis elegans. eLife 3, e04220 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  7. Kidd, C. & Hayden, B. Y. The psychology and neuroscience of curiosity. Neuron 88, 449–460 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. de Bono, M. & Maricq, A. V. Neuronal substrates of complex behaviors in C. elegans. Annu. Rev. Neurosci. 28, 451–501 (2005).

    Article  PubMed  Google Scholar 

  9. Kalueff, A. V., Stewart, A. M. & Gerlai, R. Zebrafish as an emerging model for studying complex brain disorders. Trends Pharmacol. Sci. 35, 63–75 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Fornito, A., Zalesky, A. & Bullmore, E. Fundamentals of Brain Network Analysis (Elsevier, 2016).

  11. Betzel, R. F. & Bassett, D. S. Multi-scale brain networks. Neuroimage 160, 73–83 (2017).

    Article  PubMed  Google Scholar 

  12. Bassett, D. S., Zurn, P. & Gold, J. I. On the nature and use of models in network neuroscience. Nat. Rev. Neurosci. 19, 566–578 (2018). This review provides an introduction to network models and their utility for studying the brain across scales.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Friston, K. J. Functional and effective connectivity in neuroimaging: a synthesis. Hum. Brain Mapp. 2, 56–78 (1994).

    Article  Google Scholar 

  14. Rubinov, M. & Sporns, O. Complex network measures of brain connectivity: uses and interpretations. Neuroimage 52, 1059–1069 (2010).

    Article  PubMed  Google Scholar 

  15. Sporns, O. Graph theory methods: applications in brain networks. Dialogues Clin. Neurosci. 20, 111–121 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  16. Gu, S. et al. Controllability of structural brain networks. Nat. Commun. 6, 8414–10 (2015).

    Article  CAS  PubMed  Google Scholar 

  17. Muldoon, S. F. et al. Stimulation-based control of dynamic brain networks. PLoS Comput. Biol. 12, e1005076 (2016).

    Article  PubMed  PubMed Central  Google Scholar 

  18. Karrer, T. M. et al. A practical guide to methodological considerations in the controllability of structural brain networks. J. Neural Eng. 17, 026031 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  19. Ito, T., Yang, G. R., Laurent, P., Schultz, D. H. & Cole, M. W. Constructing neural network models from brain data reveals representational transformations linked to adaptive behavior. Nat. Commun. 13, 673–16 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Perich, M. G. & Rajan, K. Rethinking brain-wide interactions through multi-region ‘network of networks’ models. Curr. Opin. Neurobiol. 65, 146–151 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Srivastava, P., Fotiadis, P., Parkes, L. & Bassett, D. S. The expanding horizons of network neuroscience: from description to prediction and control. Neuroimage 258, 119250 (2022).

    Article  PubMed  Google Scholar 

  22. Sporns, O. Contributions and challenges for network models in cognitive neuroscience. Nat. Neurosci. 17, 652–660 (2014).

    Article  CAS  PubMed  Google Scholar 

  23. Medaglia, J. D., Lynall, M.-E. & Bassett, D. S. Cognitive network neuroscience. J. Cogn. Neurosci. 27, 1471–1491 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  24. Wang, Z., Dai, Z., Gong, G., Zhou, C. & He, Y. Understanding structural–functional relationships in the human brain: a large-scale network perspective. Neuroscientist 21, 290–305 (2015).

    Article  PubMed  Google Scholar 

  25. Deco, G. & Kringelbach, M. L. Great expectations: using whole-brain computational connectomics for understanding neuropsychiatric disorders. Neuron 84, 892–905 (2014).

    Article  CAS  PubMed  Google Scholar 

  26. Woo, C.-W., Chang, L. J., Lindquist, M. A. & Wager, T. D. Building better biomarkers: brain models in translational neuroimaging. Nat. Neurosci. 20, 365–377 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Scannell, J. W. & Young, M. P. The connectional organization of neural systems in the cat cerebral cortex. Curr. Biol. 3, 191–200 (1993).

    Article  CAS  PubMed  Google Scholar 

  28. Mars, R. B. et al. Comparing brains by matching connectivity profiles. Neurosci. Biobehav. Rev. 60, 90–97 (2016).

    Article  PubMed  Google Scholar 

  29. van den Heuvel, M. P., Bullmore, E. T. & Sporns, O. Comparative connectomics. Trends Cogn. Sci. 20, 345–361 (2016). This review highlights the utility of network approaches for excavating similarities and differences in the organization of the brain across species.

    Article  PubMed  Google Scholar 

  30. Liu, Z.-Q., Zheng, Y.-Q. & Misic, B. Network topology of the marmoset connectome. Netw. Neurosci. 4, 1181–1196 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  31. Ardesch, D. J. et al. Scaling principles of white matter connectivity in the human and nonhuman primate brain. Cereb. Cortex 32, 2831–2842 (2022).

    Article  PubMed  Google Scholar 

  32. Eccles, J. C. The synapse: from electrical to chemical transmission. Annu. Rev. Neurosci. 5, 325–339 (1982).

    Article  CAS  PubMed  Google Scholar 

  33. Fox, P. T. et al. Mapping human visual cortex with positron emission tomography. Nature 323, 806–809 (1986).

    Article  CAS  PubMed  Google Scholar 

  34. Belliveau, J. W. et al. Functional mapping of the human visual cortex by magnetic resonance imaging. Science 254, 716–719 (1991).

    Article  CAS  PubMed  Google Scholar 

  35. Kwong, K. K. et al. Dynamic magnetic resonance imaging of human brain activity during primary sensory stimulation. Proc. Natl Acad. Sci. USA 89, 5675–5679 (1992).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Fox, P. T. & Raichle, M. E. Focal physiological uncoupling of cerebral blood flow and oxidative metabolism during somatosensory stimulation in human subjects. Proc. Natl Acad. Sci. USA 83, 1140–1144 (1986).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Raichle, M. E. A brief history of human brain mapping. Trends Neurosci. 32, 118–126 (2009).

    Article  CAS  PubMed  Google Scholar 

  38. Calhoun, V. D., Pearlson, G. D. & Sui, J. Data-driven approaches to neuroimaging biomarkers for neurological and psychiatric disorders: emerging approaches and examples. Curr. Opin. Neurol. 34, 469–479 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  39. Büchel, C., Coull, J. T. & Friston, K. J. The predictive value of changes in effective connectivity for human learning. Science 283, 1538–1541 (1999).

    Article  PubMed  Google Scholar 

  40. Averbeck, B. B. & Lee, D. Neural noise and movement-related codes in the macaque supplementary motor area. J. Neurosci. 23, 7630–7641 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Romo, R., Hernández, A., Zainos, A. & Salinas, E. Correlated neuronal discharges that increase coding efficiency during perceptual discrimination. Neuron 38, 649–657 (2003).

    Article  CAS  PubMed  Google Scholar 

  42. Rilling, J. K. & van den Heuvel, M. P. Comparative primate connectomics. Brain Behav. Evol. 91, 170–179 (2018).

    Article  PubMed  Google Scholar 

  43. Watts, D. J. & Strogatz, S. H. Collective dynamics of ‘small-world’ networks. Nature 393, 440–442 (1998).

    Article  CAS  PubMed  Google Scholar 

  44. Hilgetag, C. C., Burns, G. A., O’Neill, M. A., Scannell, J. W. & Young, M. P. Anatomical connectivity defines the organization of clusters of cortical areas in the macaque monkey and the cat. Philos. Trans. R. Soc. Lond. B Biol. Sci. 355, 91–110 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Whitesell, J. D. et al. Regional, layer, and cell-type-specific connectivity of the mouse default mode network. Neuron 109, 545–559.e8 (2021). This study identifies neurons within specific layers of the cortex that preferentially project to other regions within the DMN.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Lu, H. et al. Rat brains also have a default mode network. Proc. Natl Acad. Sci. USA 109, 3979–3984 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Hsu, L.-M. et al. Constituents and functional implications of the rat default mode network. Proc. Natl Acad. Sci. USA 113, E4541–E4547 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Belcher, A. M. et al. Large-scale brain networks in the awake, truly resting marmoset monkey. J. Neurosci. 33, 16796–16804 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  49. Mantini, D. et al. Default mode of brain function in monkeys. J. Neurosci. 31, 12954–12962 (2011).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Garin, C. M. et al. An evolutionary gap in primate default mode network organization. Cell Rep. 39, 110669 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Toi, P. T. et al. In vivo direct imaging of neuronal activity at high temporospatial resolution. Science 378, 160–168 (2022).

    Article  CAS  PubMed  Google Scholar 

  52. Renier, N. et al. Mapping of brain activity by automated volume analysis of immediate early genes. Cell 165, 1789–1802 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Liebmann, T. et al. Three-dimensional study of Alzheimer’s disease hallmarks using the iDISCO clearing method. Cell Rep. 16, 1138–1152 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Kirst, C. et al. Mapping the fine-scale organization and plasticity of the brain vasculature. Cell 180, 780–795.e25 (2020).

    Article  CAS  PubMed  Google Scholar 

  55. Seiriki, K. et al. High-speed and scalable whole-brain imaging in rodents and primates. Neuron 94, 1085–1100.e6 (2017).

    Article  CAS  PubMed  Google Scholar 

  56. Seiriki, K. et al. Whole-brain block-face serial microscopy tomography at subcellular resolution using FAST. Nat. Protoc. 14, 1509–1529 (2019).

    Article  CAS  PubMed  Google Scholar 

  57. Maric, D. et al. Whole-brain tissue mapping toolkit using large-scale highly multiplexed immunofluorescence imaging and deep neural networks. Nat. Commun. 12, 1550 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Nguyen, J. P. et al. Whole-brain calcium imaging with cellular resolution in freely behaving Caenorhabditis elegans. Proc. Natl Acad. Sci. USA 113, E1074–E1081 (2016).

    Article  CAS  PubMed  Google Scholar 

  59. Cong, L. et al. Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio). eLife 6, e28158 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  60. Barson, D. et al. Simultaneous mesoscopic and two-photon imaging of neuronal activity in cortical circuits. Nat. Methods 17, 107–113 (2020).

    Article  CAS  PubMed  Google Scholar 

  61. Zerbi, V. et al. Rapid reconfiguration of the functional connectome after chemogenetic locus coeruleus activation. Neuron 103, 702–718.e5 (2019). This study demonstrates that stimulating norepinephrine release in the brain causes increased functional connectivity between regions involved in salience processing.

    Article  CAS  PubMed  Google Scholar 

  62. Tu, W., Ma, Z. & Zhang, N. Brain network reorganization after targeted attack at a hub region. Neuroimage 237, 118219 (2021).

    Article  PubMed  Google Scholar 

  63. Rocchi, F. et al. Increased fMRI connectivity upon chemogenetic inhibition of the mouse prefrontal cortex. Nat. Commun. 13, 1056 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Tu, W., Ma, Z., Ma, Y., Dopfel, D. & Zhang, N. Suppressing anterior cingulate cortex modulates default mode network and behavior in awake rats. Cereb. Cortex 31, 312–323 (2021).

    Article  PubMed  Google Scholar 

  65. Oyarzabal, E. A. et al. Chemogenetic stimulation of tonic locus coeruleus activity strengthens the default mode network. Sci. Adv. 8, eabm9898 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  66. Oh, S. W. et al. A mesoscale connectome of the mouse brain. Nature 508, 207–214 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Schmitt, O. & Eipert, P. neuroVIISAS: approaching multiscale simulation of the rat connectome. Neuroinformatics 10, 243–267 (2012).

    Article  PubMed  Google Scholar 

  68. Scannell, J. W., Blakemore, C. & Young, M. P. Analysis of connectivity in the cat cerebral cortex. J. Neurosci. 15, 1463–1483 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Markov, N. T. et al. A weighted and directed interareal connectivity matrix for macaque cerebral cortex. Cereb. Cortex 24, 17–36 (2014).

    Article  CAS  PubMed  Google Scholar 

  70. Xu, F. et al. High-throughput mapping of a whole rhesus monkey brain at micrometer resolution. Nat. Biotechnol. 39, 1521–1528 (2021).

    Article  CAS  PubMed  Google Scholar 

  71. Saleeba, C., Dempsey, B., Le, S., Goodchild, A. & McMullan, S. A student’s guide to neural circuit tracing. Front. Neurosci. 13, 897 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  72. Wu, H., Williams, J. & Nathans, J. Complete morphologies of basal forebrain cholinergic neurons in the mouse. eLife 3, e02444 (2014).

    Article  PubMed  PubMed Central  Google Scholar 

  73. Wang, Q. et al. The Allen mouse brain common coordinate framework: a 3D reference atlas. Cell 181, 936–953.e20 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Winnubst, J. et al. Reconstruction of 1000 projection neurons reveals new cell types and organization of long-range connectivity in the mouse brain. Cell 179, 268–281.e13 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Gao, L. et al. Single-neuron projectome of mouse prefrontal cortex. Nat. Neurosci. 25, 515–529 (2022).

    Article  CAS  PubMed  Google Scholar 

  76. Mars, R. B. et al. Whole brain comparative anatomy using connectivity blueprints. eLife 7, e35237 (2018). This study provides a framework for comparing and translating cortical atlases across primate species.

    Article  PubMed  PubMed Central  Google Scholar 

  77. Richiardi, J. et al. BRAIN NETWORKS. Correlated gene expression supports synchronous activity in brain networks. Science 348, 1241–1244 (2015). This study identifies a set of genes that are associated with functional connectivity in the human brain and structural connectivity in the mouse brain.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Mechling, A. E. et al. Deletion of the mu opioid receptor gene in mice reshapes the reward–aversion connectome. Proc. Natl Acad. Sci. USA 113, 11603–11608 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  79. Mills, B. D. et al. Correlated gene expression and anatomical communication support synchronized brain activity in the mouse functional connectome. J. Neurosci. 38, 5774–5787 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  80. Arnatkeviciute, A., Fulcher, B. D., Bellgrove, M. A. & Fornito, A. Where the genome meets the connectome: understanding how genes shape human brain connectivity. Neuroimage 244, 118570 (2021).

    Article  CAS  PubMed  Google Scholar 

  81. Beauchamp, A. et al. Whole-brain comparison of rodent and human brains using spatial transcriptomics. eLife 11, e79418 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  82. Cui, Z. et al. Optimization of energy state transition trajectory supports the development of executive function during youth. eLife 9, 17 (2020).

    Article  Google Scholar 

  83. Scheid, B. H. et al. Time-evolving controllability of effective connectivity networks during seizure progression. Proc. Natl Acad. Sci. USA 118, e2006436118 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Braun, U. et al. Brain network dynamics during working memory are modulated by dopamine and diminished in schizophrenia. Nat. Commun. 12, 3478 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Parkes, L. et al. Network controllability in transmodal cortex predicts positive psychosis spectrum symptoms. Biol. Psychiatry 90, 409–418 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  86. Liu, Y.-Y. & Barabási, A.-L. Control principles of complex systems. Rev. Mod. Phys. 88, 035006 (2016).

    Article  Google Scholar 

  87. Yan, G. et al. Network control principles predict neuron function in the Caenorhabditis elegans connectome. Nature 550, 519–523 (2017). This study experimentally validates NCT predictions about the role of specific neurons in motor function.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Semple, B. D., Blomgren, K., Gimlin, K., Ferriero, D. M. & Noble-Haeusslein, L. J. Brain development in rodents and humans: identifying benchmarks of maturation and vulnerability to injury across species. Prog. Neurobiol. 106–107, 1–16 (2013).

    Article  PubMed  Google Scholar 

  89. Iwata, R. Temporal differences of neurodevelopment processes between species. Neurosci. Res. 177, 8–15 (2022).

    Article  PubMed  Google Scholar 

  90. Huttenlocher, P. R. Synaptic density in human frontal cortex — developmental changes and effects of aging. Brain Res. 163, 195–205 (1979).

    Article  CAS  PubMed  Google Scholar 

  91. Power, J. D., Fair, D. A., Schlaggar, B. L. & Petersen, S. E. The development of human functional brain networks. Neuron 67, 735–748 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Uddin, L. Q., Supekar, K. & Menon, V. Typical and atypical development of functional human brain networks: insights from resting-state FMRI. Front. Syst. Neurosci. 4, 21 (2010).

    Article  PubMed  PubMed Central  Google Scholar 

  93. Levitt, P. & Veenstra-VanderWeele, J. Neurodevelopment and the origins of brain disorders. Neuropsychopharmacology 40, 1–3 (2015).

    Article  PubMed  Google Scholar 

  94. Grayson, D. S. & Fair, D. A. Development of large-scale functional networks from birth to adulthood: a guide to the neuroimaging literature. Neuroimage 160, 15–31 (2017).

    Article  PubMed  Google Scholar 

  95. Graham, A. M., Marr, M., Buss, C., Sullivan, E. L. & Fair, D. A. Understanding vulnerability and adaptation in early brain development using network neuroscience. Trends Neurosci. 44, 276–288 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Grayson, D. S., Kroenke, C. D., Neuringer, M. & Fair, D. A. Dietary omega-3 fatty acids modulate large-scale systems organization in the rhesus macaque brain. J. Neurosci. 34, 2065–2074 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Kovacs-Balint, Z. et al. Early developmental trajectories of functional connectivity along the visual pathways in rhesus monkeys. Cereb. Cortex 29, 3514–3526 (2019).

    Article  CAS  PubMed  Google Scholar 

  98. Miranda-Dominguez, O. et al. Carotenoids improve the development of cerebral cortical networks in formula-fed infant macaques. Sci. Rep. 12, 15220 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Witvliet, D. et al. Connectomes across development reveal principles of brain maturation. Nature 596, 257–261 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Batalle, D. et al. Long-term reorganization of structural brain networks in a rabbit model of intrauterine growth restriction. Neuroimage 100, 24–38 (2014).

    Article  PubMed  Google Scholar 

  101. Batalle, D. et al. Altered small-world topology of structural brain networks in infants with intrauterine growth restriction and its association with later neurodevelopmental outcome. Neuroimage 60, 1352–1366 (2012).

    Article  PubMed  Google Scholar 

  102. Lee, S.-H. & Dan, Y. Neuromodulation of brain states. Neuron 76, 209–222 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  103. Tolomeo, S. & Yu, R. Brain network dysfunctions in addiction: a meta-analysis of resting-state functional connectivity. Transl. Psychiatry 12, 41 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  104. Joutsa, J. et al. Brain lesions disrupting addiction map to a common human brain circuit. Nat. Med. 28, 1249–1255 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  105. Hsu, L.-M. et al. Intrinsic insular–frontal networks predict future nicotine dependence severity. J. Neurosci. 39, 5028–5037 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  106. Keeley, R. J. et al. Intrinsic differences in insular circuits moderate the negative association between nicotine dependence and cingulate–striatal connectivity strength. Neuropsychopharmacology 45, 1042–1049 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  107. Hong, L. E. et al. Association of nicotine addiction and nicotine’s actions with separate cingulate cortex functional circuits. Arch. Gen. Psychiatry 66, 431–441 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  108. Hong, L. E. et al. A genetically modulated, intrinsic cingulate circuit supports human nicotine addiction. Proc. Natl Acad. Sci. USA 107, 13509–13514 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Cruces-Solis, H., Nissen, W., Ferger, B. & Arban, R. Whole-brain signatures of functional connectivity after bidirectional modulation of the dopaminergic system in mice. Neuropharmacology 178, 108246 (2020).

    Article  CAS  PubMed  Google Scholar 

  110. Kimbrough, A. et al. Brain-wide functional architecture remodeling by alcohol dependence and abstinence. Proc. Natl Acad. Sci. USA 117, 2149–2159 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Kimbrough, A. et al. Characterization of the brain functional architecture of psychostimulant withdrawal using single-cell whole-brain imaging. eNeuro 8, ENEURO.0208-19.2021 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  112. Brynildsen, J. K. et al. Gene coexpression patterns predict opiate-induced brain-state transitions. Proc. Natl Acad. Sci. USA 117, 19556–19565 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  113. Li, B.-J. et al. A brain network model for depression: from symptom understanding to disease intervention. CNS Neurosci. Ther. 24, 1004–1019 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  114. Hultman, R. et al. Brain-wide electrical spatiotemporal dynamics encode depression vulnerability. Cell 173, 166–180.e14 (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  115. Andalman, A. S. et al. Neuronal dynamics regulating brain and behavioral state transitions. Cell 177, 970–985.e20 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  116. Grossman, Y. & Dzirasa, K. Is depression a disorder of electrical brain networks? Neuropsychopharmacology 45, 230–231 (2020).

    Article  PubMed  Google Scholar 

  117. Drysdale, A. T. et al. Resting-state connectivity biomarkers define neurophysiological subtypes of depression. Nat. Med. 23, 28–38 (2017).

    Article  CAS  PubMed  Google Scholar 

  118. Xia, C. H. et al. Linked dimensions of psychopathology and connectivity in functional brain networks. Nat. Commun. 9, 3003–3014 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  119. Zhang, Y. et al. Identification of psychiatric disorder subtypes from functional connectivity patterns in resting-state electroencephalography. Nat. Biomed. Eng. 5, 309–323 (2021).

    Article  PubMed  Google Scholar 

  120. Brettschneider, J., Del Tredici, K., Lee, V. M. Y. & Trojanowski, J. Q. Spreading of pathology in neurodegenerative diseases: a focus on human studies. Nat. Rev. Neurosci. 16, 109–120 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  121. Braak, H. & Braak, E. Neuropathological stageing of Alzheimer-related changes. Acta Neuropathol. 82, 239–259 (1991).

    Article  CAS  PubMed  Google Scholar 

  122. Del Tredici, K., Rüb, U., de Vos, R. A. I., Bohl, J. R. E. & Braak, H. Where does Parkinson disease pathology begin in the brain? J. Neuropathol. Exp. Neurol. 61, 413–426 (2002).

    Article  PubMed  Google Scholar 

  123. Braak, H. et al. Staging of brain pathology related to sporadic Parkinson’s disease. Neurobiol. Aging 24, 197–211 (2003).

    Article  PubMed  Google Scholar 

  124. Braak, H., Ghebremedhin, E., Rüb, U., Bratzke, H. & Del Tredici, K. Stages in the development of Parkinson’s disease-related pathology. Cell Tissue Res. 318, 121–134 (2004).

    Article  PubMed  Google Scholar 

  125. Braak, H., Alafuzoff, I., Arzberger, T., Kretzschmar, H. & Del Tredici, K. Staging of Alzheimer disease-associated neurofibrillary pathology using paraffin sections and immunocytochemistry. Acta Neuropathol. 112, 389–404 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  126. Bloom, G. S. Amyloid-β and Tau: the trigger and bullet in Alzheimer disease pathogenesis. JAMA Neurol. 71, 505–508 (2014).

    Article  PubMed  Google Scholar 

  127. Irwin, D. J., Lee, V. M. Y. & Trojanowski, J. Q. Parkinson’s disease dementia: convergence of α-synuclein, tau and amyloid-β pathologies. Nat. Rev. Neurosci. 14, 626–636 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  128. van der Kant, R., Goldstein, L. S. B. & Ossenkoppele, R. Amyloid-β-independent regulators of tau pathology in Alzheimer disease. Nat. Rev. Neurosci. 21, 21–35 (2020).

    Article  PubMed  Google Scholar 

  129. Calabresi, P. et al. α-Synuclein in Parkinson’s disease and other synucleinopathies: from overt neurodegeneration back to early synaptic dysfunction. Cell Death Dis. 14, 176 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  130. Keating, S. S., San Gil, R., Swanson, M. E. V., Scotter, E. L. & Walker, A. K. TDP-43 pathology: from noxious assembly to therapeutic removal. Prog. Neurobiol. 211, 102229 (2022).

    Article  CAS  PubMed  Google Scholar 

  131. Robert, A., Schöll, M. & Vogels, T. Tau seeding mouse models with patient brain-derived aggregates. Int. J. Mol. Sci. 22, 6132 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  132. Clavaguera, F. et al. Transmission and spreading of tauopathy in transgenic mouse brain. Nat. Cell Biol. 11, 909–913 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  133. Mezias, C., LoCastro, E., Xia, C. & Raj, A. Connectivity, not region-intrinsic properties, predicts regional vulnerability to progressive tau pathology in mouse models of disease. Acta Neuropathol. Commun. 5, 61 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  134. Henderson, M. X. et al. Spread of α-synuclein pathology through the brain connectome is modulated by selective vulnerability and predicted by network analysis. Nat. Neurosci. 22, 1248–1257 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  135. Henderson, M. X. et al. Glucocerebrosidase activity modulates neuronal susceptibility to pathological α-synuclein insult. Neuron 105, 822–836.e7 (2020).

    Article  CAS  PubMed  Google Scholar 

  136. Mezias, C., Rey, N., Brundin, P. & Raj, A. Neural connectivity predicts spreading of α-synuclein pathology in fibril-injected mouse models: involvement of retrograde and anterograde axonal propagation. Neurobiol. Dis. 134, 104623 (2020).

    Article  CAS  PubMed  Google Scholar 

  137. Cornblath, E. J. et al. Computational modeling of tau pathology spread reveals patterns of regional vulnerability and the impact of a genetic risk factor. Sci. Adv. 7, eabg6677 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  138. Rahayel, S. et al. Differentially targeted seeding reveals unique pathological alpha-synuclein propagation patterns. Brain 145, 1743–1756 (2022).

    Article  PubMed  Google Scholar 

  139. Anand, C., Maia, P. D., Torok, J., Mezias, C. & Raj, A. The effects of microglia on tauopathy progression can be quantified using Nexopathy in silico (Nexis) models. Sci. Rep. 12, 21170 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  140. Raj, A., Kuceyeski, A. & Weiner, M. A network diffusion model of disease progression in dementia. Neuron 73, 1204–1215 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  141. Dagher, A. & Zeighami, Y. Testing the protein propagation hypothesis of Parkinson disease. J. Exp. Neurosci. 12, 1179069518786715 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  142. Brown, J. A. et al. Patient-tailored, connectivity-based forecasts of spreading brain atrophy. Neuron 104, 856–868.e5 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  143. Pandya, S. et al. Predictive model of spread of Parkinson’s pathology using network diffusion. Neuroimage 192, 178–194 (2019).

    Article  CAS  PubMed  Google Scholar 

  144. Zheng, Y.-Q. et al. Local vulnerability and global connectivity jointly shape neurodegenerative disease propagation. PLoS Biol. 17, e3000495 (2019).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  145. Ossenkoppele, R. et al. Tau covariance patterns in Alzheimer’s disease patients match intrinsic connectivity networks in the healthy brain. Neuroimage Clin. 23, 101848 (2019).

    Article  PubMed  PubMed Central  Google Scholar 

  146. Warren, J. D. et al. Molecular nexopathies: a new paradigm of neurodegenerative disease. Trends Neurosci. 36, 561–569 (2013).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  147. Asai, H. et al. Depletion of microglia and inhibition of exosome synthesis halt tau propagation. Nat. Neurosci. 18, 1584–1593 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  148. Maphis, N. et al. Reactive microglia drive tau pathology and contribute to the spreading of pathological tau in the brain. Brain 138, 1738–1755 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  149. Leyns, C. E. G. et al. TREM2 deficiency attenuates neuroinflammation and protects against neurodegeneration in a mouse model of tauopathy. Proc. Natl Acad. Sci. USA 114, 11524–11529 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  150. Gratuze, M. et al. TREM2-independent microgliosis promotes tau-mediated neurodegeneration in the presence of ApoE4. Neuron 111, 202–219.e7 (2023).

    Article  CAS  PubMed  Google Scholar 

  151. Nestler, E. J. & Hyman, S. E. Animal models of neuropsychiatric disorders. Nat. Neurosci. 13, 1161–1169 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  152. Xu, T. et al. Cross-species functional alignment reveals evolutionary hierarchy within the connectome. Neuroimage 223, 117346 (2020).

    Article  PubMed  Google Scholar 

  153. Jaime, S. et al. Delta rhythm orchestrates the neural activity underlying the resting state BOLD signal via phase–amplitude coupling. Cereb. Cortex 29, 119–133 (2019).

    Article  PubMed  Google Scholar 

  154. Liang, Z., Ma, Y., Watson, G. D. R. & Zhang, N. Simultaneous GCaMP6-based fiber photometry and fMRI in rats. J. Neurosci. Methods 289, 31–38 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  155. Lake, E. M. R. et al. Simultaneous cortex-wide fluorescence Ca2+ imaging and whole-brain fMRI. Nat. Methods 17, 1262–1271 (2020). This study identifies region-specific differences in functional connectivity networks derived from calcium and haemodynamic signals acquired simultaneously.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  156. Wei, Z. et al. A comparison of neuronal population dynamics measured with calcium imaging and electrophysiology. PLoS Comput. Biol. 16, e1008198 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  157. Jewell, S. W., Hocking, T. D., Fearnhead, P. & Witten, D. M. Fast nonconvex deconvolution of calcium imaging data. Biostatistics 21, 709–726 (2020).

    Article  PubMed  Google Scholar 

  158. Fleming, W., Jewell, S., Engelhard, B., Witten, D. M. & Witten, I. B. Inferring spikes from calcium imaging in dopamine neurons. PLoS ONE 16, e0252345 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  159. Bessadok, A., Mahjoub, M. A. & Rekik, I. Graph neural networks in network neuroscience. IEEE Trans. Pattern Anal. Mach. Intell. 45, 5833–5848 (2023).

    Article  PubMed  Google Scholar 

  160. Wang, P. Y., Sapra, S., George, V. K. & Silva, G. A. Generalizable machine learning in neuroscience using graph neural networks. Front. Artif. Intell. 4, 618372 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  161. Wein, S. et al. Forecasting brain activity based on models of spatiotemporal brain dynamics: a comparison of graph neural network architectures. Netw. Neurosci. 6, 665–701 (2022).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  162. Cochran, K. et al. Domain-adaptive neural networks improve cross-species prediction of transcription factor binding. Genome Res. 32, 512–523 (2022). This study demonstrates the utility of a neural network model for translating transcription factor binding sites from mouse to human.

    Article  PubMed  PubMed Central  Google Scholar 

  163. Sanz Leon, P. et al. The Virtual Brain: a simulator of primate brain network dynamics. Front. Neuroinform. 7, 10 (2013).

    Article  PubMed  PubMed Central  Google Scholar 

  164. Melozzi, F., Woodman, M. M., Jirsa, V. K. & Bernard, C. The Virtual Mouse Brain: a computational neuroinformatics platform to study whole mouse brain dynamics. eNeuro 4, ENEURO.0111-17.2017 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  165. Kumar, V. G., Dutta, S., Talwar, S., Roy, D. & Banerjee, A. Biophysical mechanisms governing large-scale brain network dynamics underlying individual-specific variability of perception. Eur. J. Neurosci. 52, 3746–3762 (2020).

    Article  PubMed  Google Scholar 

  166. McClements, M. E., Staurenghi, F., MacLaren, R. E. & Cehajic-Kapetanovic, J. Optogenetic gene therapy for the degenerate retina: recent advances. Front. Neurosci. 14, 570909 (2020).

    Article  PubMed  PubMed Central  Google Scholar 

  167. Shen, Y., Campbell, R. E., Côté, D. C. & Paquet, M.-E. Challenges for therapeutic applications of opsin-based optogenetic tools in humans. Front. Neural Circuits 14, 41 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  168. Andersson, M. et al. Optogenetic control of human neurons in organotypic brain cultures. Sci. Rep. 6, 24818 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  169. Mitchell, S. M., Lange, S. & Brus, H. Gendered citation patterns in international relations journals. Int. Stud. Perspect. 14, 485–492 (2013).

    Article  Google Scholar 

  170. Dion, M. L., Sumner, J. L. & Mitchell, S. M. Gendered citation patterns across political science and social science methodology fields. Political Anal. 26, 312–327 (2018).

    Article  Google Scholar 

  171. Caplar, N., Tacchella, S. & Birrer, S. Quantitative evaluation of gender bias in astronomical publications from citation counts. Nat. Astron. 1, 0141 (2017).

    Article  Google Scholar 

  172. Maliniak, D., Powers, R. & Walter, B. F. The gender citation gap in international relations. Int. Organ. 67, 889–922 (2013).

    Article  Google Scholar 

  173. Dworkin, J. D. et al. The extent and drivers of gender imbalance in neuroscience reference lists. Nat. Neurosci. 23, 918–926 (2020).

    Article  CAS  PubMed  Google Scholar 

  174. Bertolero, M. A. et al. Racial and ethnic imbalance in neuroscience reference lists and intersections with gender. Preprint at bioRxiv https://doi.org/10.1101/2020.10.12.336230 (2020).

    Article  Google Scholar 

  175. Wang, X. et al. Gendered citation practices in the field of communication. Ann. Int. Commun. Assoc. 45, 134–153 (2021).

    CAS  PubMed  PubMed Central  Google Scholar 

  176. Chatterjee, P. & Werner, R. M. Gender disparity in citations in high-impact journal articles. JAMA Netw. Open. 4, e2114509 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  177. Fulvio, J. M., Akinnola, I. & Postle, B. R. Gender (im)balance in citation practices in cognitive neuroscience. J. Cogn. Neurosci. 33, 3–7 (2021).

    Article  PubMed  Google Scholar 

  178. Zhou, D. et al. dalejn/cleanBib: v1.1.2. Zenodo https://doi.org/10.5281/zenodo.4104748 (2022).

  179. Ambekar, A., Ward, C., Mohammed, J., Male, S. & Skiena, S. Name-ethnicity classification from open sources. In Proc. 15th ACM SIGKDD Int. Conf. Knowledge Discovery and Data Mining (eds Elder, J. F., IV, Fogelman-Soulie, F., Flach, P. & Zaki, M.) 49–58 (ACM, 2009).

  180. Sood, G. & Laohaprapanon, S. Predicting race and ethnicity from the sequence of characters in a name. Preprint at https://doi.org/10.48550/arXiv.1805.02109 (2018).

  181. Jun, J. J. et al. Fully integrated silicon probes for high-density recording of neural activity. Nature 551, 232–236 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  182. Bakker, R., Tiesinga, P. & Kötter, R. The Scalable Brain Atlas: instant web-based access to public brain atlases and related content. Neuroinformatics 13, 353–366 (2015).

    Article  PubMed  PubMed Central  Google Scholar 

  183. Calabrese, E. et al. A diffusion tensor MRI atlas of the postmortem rhesus macaque brain. Neuroimage 117, 408–416 (2015).

    Article  PubMed  Google Scholar 

  184. Lein, E. S. et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature 445, 168–176 (2007).

    Article  CAS  PubMed  Google Scholar 

  185. Betzel, R. F., Gu, S., Medaglia, J. D., Pasqualetti, F. & Bassett, D. S. Optimally controlling the human connectome: the role of network topology. Sci. Rep. 6, 30770 (2016).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  186. Bassett, D. S. & Sporns, O. Network neuroscience. Nat. Neurosci. 20, 353–364 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  187. Wu, Z. et al. A comprehensive survey on graph neural networks. IEEE Trans. Neural Netw. Learn. Syst. 32, 4–24 (2021).

    Article  PubMed  Google Scholar 

  188. Wein, S. et al. A graph neural network framework for causal inference in brain networks. Sci. Rep. 11, 8061 (2021).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  189. Li, X. et al. BrainGNN: interpretable brain graph neural network for fMRI analysis. Med. Image Anal. 74, 102233 (2021).

    Article  PubMed  PubMed Central  Google Scholar 

  190. Liu, X., Shen, Q. & Zhang, S. Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network. Genome Res. 33, 96–111 (2023).

    Article  PubMed  PubMed Central  Google Scholar 

  191. Makris, N. et al. Decreased volume of left and total anterior insular lobule in schizophrenia. Schizophr. Res. 83, 155–171 (2006).

    Article  PubMed  Google Scholar 

  192. Frazier, J. A. et al. Structural brain magnetic resonance imaging of limbic and thalamic volumes in pediatric bipolar disorder. Am. J. Psychiatry 162, 1256–1265 (2005).

    Article  PubMed  Google Scholar 

  193. Desikan, R. S. et al. An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest. Neuroimage 31, 968–980 (2006).

    Article  PubMed  Google Scholar 

  194. Goldstein, J. M. et al. Hypothalamic abnormalities in schizophrenia: sex effects and genetic vulnerability. Biol. Psychiatry 61, 935–945 (2007).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This work was supported by National Institutes of Health (NIH) grant F32AA030475-01A1 to J.K.B.

Author information

Authors and Affiliations

Authors

Contributions

J.K.B., M.X.H. and D.S.B. researched data for the article, provided substantial contributions to discussion of its content, wrote the article, and reviewed and edited the manuscript before submission. K.R. provided a substantial contribution to discussion of the article’s content, and reviewed and edited the manuscript before submission.

Corresponding author

Correspondence to Dani S. Bassett.

Ethics declarations

Competing interests

The authors declare no competing interests.

Peer review

Peer review information

Nature Reviews Neuroscience thanks D. Batalle, who co-reviewed with G. De Alteriis; A. Raj; and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Glossary

Average path lengths

The average number of edges that connects each pair of nodes in a network.

Control energy

The magnitude of input required to drive the brain from one activity state to another while accounting for its structural topology, time and the number of nodes into which input is given.

Degree

The sum of connections to a given node.

Global efficiency

A measure of the efficiency of long-range communication in a network.

Modularity

A measure of how readily a network can be partitioned into subgroups of nodes that are more strongly connected to one another than to the rest of the network.

Multilayer network

A graph structure in which nodes are organized into multiple layers; intra-layer edges represent relations between nodes within a layer, and inter-layer edges represent relations between nodes in different layers.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Brynildsen, J.K., Rajan, K., Henderson, M.X. et al. Network models to enhance the translational impact of cross-species studies. Nat. Rev. Neurosci. 24, 575–588 (2023). https://doi.org/10.1038/s41583-023-00720-x

Download citation

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41583-023-00720-x

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing