General bibliography#

The references below are arranged alphabetically by first author. You can download the bib file here.

  1. Hunar Abdulrahman and Richard N Henson. Effect of trial-to-trial variability on optimal event-related fmri design: implications for beta-series correlation and multi-voxel pattern analysis. NeuroImage, 125:756–766, 2016.

  2. Alexandre Abraham, Elvis Dohmatob, Bertrand Thirion, Dimitris Samaras, and Gael Varoquaux. Region segmentation for sparse decompositions: better brain parcellations from rest fMRI. Sparsity Techniques in Medical Imaging, September 2014. URL: https://hal.inria.fr/hal-01093944.

  3. Elena Allen, Erik Erhardt, Eswar Damaraju, William Gruner, Judith Segall, Rogers Silva, Martin Havlicek, Srinivas Rachakonda, Jill Fries, Ravi Kalyanam, Andrew Michael, Arvind Caprihan, Jessica Turner, Tom Eichele, Steven Adelsheim, Angela Bryan, Juan Bustillo, Vincent Clark, Sarah Feldstein Ewing, Francesca Filbey, Corey Ford, Kent Hutchison, Rex Jung, Kent Kiehl, Piyadasa Kodituwakku, Yuko Komesu, Andrew Mayer, Godfrey Pearlson, John Phillips, Joseph Sadek, Michael Stevens, Ursina Teuscher, Robert Thoma, and Vince Calhoun. A baseline for the multivariate comparison of resting-state networks. Frontiers in Systems Neuroscience, 5:2, 2011. URL: https://www.frontiersin.org/article/10.3389/fnsys.2011.00002, doi:10.3389/fnsys.2011.00002.

  4. Katrin Amunts, Hartmut Mohlberg, Sebastian Bludau, and Karl Zilles. Julich-Brain: A 3D probabilistic atlas of the human brain’s cytoarchitecture. Science, 369(6506):988–992, August 2020. URL: https://www.science.org/doi/10.1126/science.abb4588 (visited on 2024-02-01), doi:10.1126/science.abb4588.

  5. Marti J. Anderson and John Robinson. Permutation tests for linear models. Australian & New Zealand Journal of Statistics, 43(1):75–88, 2001. URL: https://onlinelibrary.wiley.com/doi/abs/10.1111/1467-842X.00156, arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1111/1467-842X.00156, doi:https://doi.org/10.1111/1467-842X.00156.

  6. Luca Baldassarre, Janaina Mourao-Miranda, and Massimiliano Pontil. The civet image-processing environment: a fully automated comprehensive pipeline for anatomical neuroimaging research. In Proceedings of the 12th Annual Meeting of the Human Brain Mapping Organization. 2006. URL: https://www.bic.mni.mcgill.ca/users/yaddab/Yasser-HBM2006-Poster.pdf.

  7. Luca Baldassarre, Janaina Mourao-Miranda, and Massimiliano Pontil. Structured sparsity models for brain decoding from fmri data. In 2012 Second International Workshop on Pattern Recognition in NeuroImaging, volume, 5–8. 2012. URL: http://www0.cs.ucl.ac.uk/staff/M.Pontil/reading/neurosparse_prni.pdf, doi:10.1109/PRNI.2012.31.

  8. Yashar Behzadi, Khaled Restom, Joy Liau, and Thomas T. Liu. A component based noise correction method (compcor) for bold and perfusion based fmri. NeuroImage, 37(1):90–101, 2007. URL: https://www.sciencedirect.com/science/article/pii/S1053811907003837, doi:https://doi.org/10.1016/j.neuroimage.2007.04.042.

  9. Pierre Bellec. Mining the hierarchy of resting-state brain networks: selection of representative clusters in a multiscale structure. In 2013 International Workshop on Pattern Recognition in Neuroimaging, volume, 54–57. 06 2013. doi:10.1109/PRNI.2013.23.

  10. Pierre Bellec, Pedro Rosa-Neto, Oliver C. Lyttelton, Habib Benali, and Alan C. Evans. Multi-level bootstrap analysis of stable clusters in resting-state fmri. NeuroImage, 51(3):1126–1139, 2010. URL: https://www.sciencedirect.com/science/article/pii/S1053811910002697, doi:https://doi.org/10.1016/j.neuroimage.2010.02.082.

  11. Yi Chen, Praneeth Namburi, Lloyd T. Elliott, Jakob Heinzle, Chun Siong Soon, Michael W.L. Chee, and John-Dylan Haynes. Cortical surface-based searchlight decoding. NeuroImage, 56(2):582–592, 2011. Multivariate Decoding and Brain Reading. URL: https://www.sciencedirect.com/science/article/pii/S1053811910010086, doi:https://doi.org/10.1016/j.neuroimage.2010.07.035.

  12. Rastko Ciric, Daniel H. Wolf, Jonathan D. Power, David R. Roalf, Graham L. Baum, Kosha Ruparel, Russell T. Shinohara, Mark A. Elliott, Simon B. Eickhoff, Christos Davatzikos, Ruben C. Gur, Raquel E. Gur, Danielle S. Bassett, and Theodore D. Satterthwaite. Benchmarking of participant-level confound regression strategies for the control of motion artifact in studies of functional connectivity. NeuroImage, 154(1):174–187, 2017. doi:10.1016/j.neuroimage.2017.03.020.

  13. Josh M Cisler, Keith Bush, and J Scott Steele. A comparison of statistical methods for detecting context-modulated functional connectivity in fmri. Neuroimage, 84:1042–1052, 2014.

  14. Alex Clarke and Lorraine K. Tyler. Object-specific semantic coding in human perirhinal cortex. Journal of Neuroscience, 34(14):4766–4775, 2014. URL: https://www.jneurosci.org/content/34/14/4766, arXiv:https://www.jneurosci.org/content/34/14/4766.full.pdf, doi:10.1523/JNEUROSCI.2828-13.2014.

  15. D. Louis Collins and Alan C. Evans. Animal: validation and applications of nonlinear registration-based segmentation. International journal of pattern recognition and artificial intelligence, 11(08):1271–1294, 1997.

  16. D. Louis Collins, Alex P. Zijdenbos, Wim F. C. Baaré, and Alan C. Evans. Animal+insect: improved cortical structure segmentation. In Attila Kuba, Martin Šáamal, and Andrew Todd-Pokropek, editors, Information Processing in Medical Imaging, 210–223. Berlin, Heidelberg, 1999. Springer Berlin Heidelberg.

  17. D.L. Collins, A.P. Zijdenbos, V. Kollokian, J.G. Sled, N.J. Kabani, C.J. Holmes, and A.C. Evans. Design and construction of a realistic digital brain phantom. IEEE Transactions on Medical Imaging, 17(3):463–468, 1998. doi:10.1109/42.712135.

  18. R. Cameron Craddock, G.Andrew James, Paul E. Holtzheimer III, Xiaoping P. Hu, and Helen S. Mayberg. A whole brain fmri atlas generated via spatially constrained spectral clustering. Human Brain Mapping, 33(8):1914–1928, 2012. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/hbm.21333, arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/hbm.21333, doi:https://doi.org/10.1002/hbm.21333.

  19. Kamalaker Dadi, Mehdi Rahim, Alexandre Abraham, Darya Chyzhyk, Michael Milham, Bertrand Thirion, and Gaël Varoquaux. Benchmarking functional connectome-based predictive models for resting-state fmri. NeuroImage, 192:115–134, 2019. URL: https://www.sciencedirect.com/science/article/pii/S1053811919301594, doi:https://doi.org/10.1016/j.neuroimage.2019.02.062.

  20. Kamalaker Dadi, Gaël Varoquaux, Antonia Machlouzarides-Shalit, Krzysztof J. Gorgolewski, Demian Wassermann, Bertrand Thirion, and Arthur Mensch. Fine-grain atlases of functional modes for fmri analysis. NeuroImage, 221:117126, 2020. URL: https://hal.inria.fr/hal-02904869, doi:https://doi.org/10.1016/j.neuroimage.2020.117126.

  21. Anders M. Dale, Bruce Fischl, and Martin I. Sereno. Cortical surface-based analysis: i. segmentation and surface reconstruction. NeuroImage, 9(2):179–194, 1999. URL: https://www.sciencedirect.com/science/article/pii/S1053811998903950, doi:https://doi.org/10.1006/nimg.1998.0395.

  22. Russell Davidson and James G. MacKinnon. Econometric theory and methods. Oxford Univ. Press, New York, NY [u.a.], 2004. ISBN 978-0-19-512372-2. URL: http://gso.gbv.de/DB=2.1/CMD?ACT=SRCHA&SRT=YOP&IKT=1016&TRM=ppn+393847152&sourceid=fbw_bibsonomy.

  23. Ghislaine Dehaene-Lambertz, Stanislas Dehaene, Jean-Luc Anton, Aurelie Campagne, Philippe Ciuciu, Guillaume P Dehaene, Isabelle Denghien, Antoinette Jobert, Denis LeBihan, Mariano Sigman, and others. Functional segregation of cortical language areas by sentence repetition. Human brain mapping, 27(5):360–371, 2006. URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6871319/.

  24. Rahul S Desikan, Florent Ségonne, Bruce Fischl, Brian T Quinn, Bradford C Dickerson, Deborah Blacker, Randy L Buckner, Anders M Dale, R Paul Maguire, Bradley T Hyman, and others. An automated labeling system for subdividing the human cerebral cortex on mri scans into gyral based regions of interest. Neuroimage, 31(3):968–980, 2006.

  25. C Destrieux, B Fischl, AM Dale, and E Halgren. A sulcal depth-based anatomical parcellation of the cerebral cortex. NeuroImage, 47(Supplement 1):S151, 2009. doi:10.1016/S1053-8119(09)71561-7.

  26. Christophe Destrieux, Bruce Fischl, Anders Dale, and Eric Halgren. Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature. NeuroImage, 53(1):1–15, 2010. URL: https://www.sciencedirect.com/science/article/pii/S1053811910008542, doi:https://doi.org/10.1016/j.neuroimage.2010.06.010.

  27. Elvis Dohmatob, Michael Eickenberg, Bertrand Thirion, and Gaël Varoquaux. Speeding-up model-selection in GraphNet via early-stopping and univariate feature-screening. In PRNI. Stanford, United States, June 2015. URL: https://hal.inria.fr/hal-01147731.

  28. Elvis Dohmatob, Alexandre Gramfort, Bertrand Thirion, and Gaël Varoquaux. Benchmarking solvers for TV-l1 least-squares and logistic regression in brain imaging. In PRNI 2014 - 4th International Workshop on Pattern Recognition in NeuroImaging. Tübingen, Germany, June 2014. IEEE. URL: https://hal.inria.fr/hal-00991743.

  29. Nico U. F. Dosenbach, Binyam Nardos, Alexander L. Cohen, Damien A. Fair, Jonathan D. Power, Jessica A. Church, Steven M. Nelson, Gagan S. Wig, Alecia C. Vogel, Christina N. Lessov-Schlaggar, Kelly Anne Barnes, Joseph W. Dubis, Eric Feczko, Rebecca S. Coalson, John R. Pruett, Deanna M. Barch, Steven E. Petersen, and Bradley L. Schlaggar. Prediction of individual brain maturity using fmri. Science, 329(5997):1358–1361, 2010. URL: https://science.sciencemag.org/content/329/5997/1358, arXiv:https://science.sciencemag.org/content/329/5997/1358.full.pdf, doi:10.1126/science.1194144.

  30. John Duchi, Stephen Gould, and Daphne Koller. Projected subgradient methods for learning sparse gaussians. arXiv:1206.3249 [cs, stat], 06 2012. URL: https://arxiv.org/abs/1206.3249, arXiv:1206.3249.

  31. Joset A. Etzel, Jeffrey M. Zacks, and Todd S. Braver. Searchlight analysis: promise, pitfalls, and potential. NeuroImage, 78:261–269, 2013. URL: https://www.sciencedirect.com/science/article/pii/S1053811913002917, doi:https://doi.org/10.1016/j.neuroimage.2013.03.041.

  32. Nicola Filippini, Bradley J. MacIntosh, Morgan G. Hough, Guy M. Goodwin, Giovanni B. Frisoni, Stephen M. Smith, Paul M. Matthews, Christian F. Beckmann, and Clare E. Mackay. Distinct patterns of brain activity in young carriers of the apoe-ε4 allele. Proceedings of the National Academy of Sciences, 106(17):7209–7214, 2009. URL: https://www.pnas.org/content/106/17/7209, arXiv:https://www.pnas.org/content/106/17/7209.full.pdf, doi:10.1073/pnas.0811879106.

  33. Bruce Fischl, Martin I. Sereno, and Anders M. Dale. Cortical surface-based analysis: ii: inflation, flattening, and a surface-based coordinate system. NeuroImage, 9(2):195–207, 1999. URL: https://www.sciencedirect.com/science/article/pii/S1053811998903962, doi:https://doi.org/10.1006/nimg.1998.0396.

  34. Bruce Fischl, Martin I. Sereno, Roger B.H. Tootell, and Anders M. Dale. High-resolution intersubject averaging and a coordinate system for the cortical surface. Human Brain Mapping, 8(4):272–284, 1999. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/%28SICI%291097-0193%281999%298%3A4%3C272%3A%3AAID-HBM10%3E3.0.CO%3B2-4, arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/%28SICI%291097-0193%281999%298%3A4%3C272%3A%3AAID-HBM10%3E3.0.CO%3B2-4, doi:https://doi.org/10.1002/(SICI)1097-0193(1999)8:4<272::AID-HBM10>3.0.CO;2-4.

  35. Bruce Fischl, André van der Kouwe, Christophe Destrieux, Eric Halgren, Florent Ségonne, David H. Salat, Evelina Busa, Larry J. Seidman, Jill Goldstein, David Kennedy, Verne Caviness, Nikos Makris, Bruce Rosen, and Anders M. Dale. Automatically Parcellating the Human Cerebral Cortex. Cerebral Cortex, 14(1):11–22, 01 2004. URL: https://doi.org/10.1093/cercor/bhg087, arXiv:https://academic.oup.com/cercor/article-pdf/14/1/11/1193353/bhg087.pdf, doi:10.1093/cercor/bhg087.

  36. R.A. Fisher. The design of experiments. 1935. Oliver and Boyd, Edinburgh, 1935.

  37. P. Thomas Fletcher and Sarang Joshi. Riemannian geometry for the statistical analysis of diffusion tensor data. Signal Processing, 87(2):250–262, 2007. Tensor Signal Processing. URL: https://www.sciencedirect.com/science/article/pii/S0165168406001691, doi:https://doi.org/10.1016/j.sigpro.2005.12.018.

  38. Vladimir Fonov, Alan C. Evans, Kelly Botteron, C. Robert Almli, Robert C. McKinstry, and D. Louis Collins. Unbiased average age-appropriate atlases for pediatric studies. NeuroImage, 54(1):313–327, 2011. URL: https://www.sciencedirect.com/science/article/pii/S1053811910010062, doi:https://doi.org/10.1016/j.neuroimage.2010.07.033.

  39. VS Fonov, AC Evans, RC McKinstry, CR Almli, and DL Collins. Unbiased nonlinear average age-appropriate brain templates from birth to adulthood. NeuroImage, 47(Supplement 1):S102, 2009. doi:10.1016/S1053-8119(09)70884-5.

  40. Michael D. Fox, Abraham Z. Snyder, Justin L Vincent, Maurizio Corbetta, David C. Van Essen, and Marcus E. Raichle. The human brain is intrinsically organized into dynamic, anticorrelated functional networks. Proceedings of the National Academy of Sciences, 102(27):9673–9678, July 2005. doi:10.1073/pnas.0504136102.

  41. Jean A Frazier, Sufen Chiu, Janis L Breeze, Nikos Makris, Nicholas Lange, David N Kennedy, Martha R Herbert, Eileen K Bent, Vamsi K Koneru, Megan E Dieterich, and others. Structural brain magnetic resonance imaging of limbic and thalamic volumes in pediatric bipolar disorder. American Journal of Psychiatry, 162(7):1256–1265, 2005.

  42. David Freedman and David Lane. A nonstochastic interpretation of reported significance levels. Journal of Business & Economic Statistics, 1(4):292–298, 1983. URL: https://www.tandfonline.com/doi/abs/10.1080/07350015.1983.10509354, arXiv:https://www.tandfonline.com/doi/pdf/10.1080/07350015.1983.10509354, doi:10.1080/07350015.1983.10509354.

  43. J. Friedman, T. Hastie, and R. Tibshirani. Sparse inverse covariance estimation with the graphical lasso. Biostatistics, 9(3):432–441, July 2008. URL: https://academic.oup.com/biostatistics/article-lookup/doi/10.1093/biostatistics/kxm045 (visited on 2024-02-02), doi:10.1093/biostatistics/kxm045.

  44. K. J. Friston, A. P. Holmes, K. J. Worsley, J.-P. Poline, C. D. Frith, and R. S. J. Frackowiak. Statistical parametric maps in functional imaging: a general linear approach. Human Brain Mapping, 2(4):189–210, 1994. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/hbm.460020402, arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/hbm.460020402, doi:https://doi.org/10.1002/hbm.460020402.

  45. Federico Giove, Tommaso Gili, Vittorio Iacovella, Emiliano Macaluso, and Bruno Maraviglia. Images-based suppression of unwanted global signals in resting-state functional connectivity studies. Magnetic Resonance Imaging, 27(8):1058–1064, October 2009. URL: https://linkinghub.elsevier.com/retrieve/pii/S0730725X09001696 (visited on 2024-02-01), doi:10.1016/j.mri.2009.06.004.

  46. Jill M Goldstein, Larry J Seidman, Nikos Makris, Todd Ahern, Liam M O’Brien, Verne S Caviness Jr, David N Kennedy, Stephen V Faraone, and Ming T Tsuang. Hypothalamic abnormalities in schizophrenia: sex effects and genetic vulnerability. Biological psychiatry, 61(8):935–945, 2007.

  47. Krzysztof J. Gorgolewski, Gael Varoquaux, Gabriel Rivera, Yannick Schwarz, Satrajit S. Ghosh, Camille Maumet, Vanessa V. Sochat, Thomas E. Nichols, Russell A. Poldrack, Jean-Baptiste Poline, Tal Yarkoni, and Daniel S. Margulies. Neurovault.org: a web-based repository for collecting and sharing unthresholded statistical maps of the human brain. Frontiers in Neuroinformatics, 9:8, 2015. URL: https://www.frontiersin.org/article/10.3389/fninf.2015.00008, doi:10.3389/fninf.2015.00008.

  48. Alexandre Gramfort, Bertrand Thirion, and Gaël Varoquaux. Identifying predictive regions from fMRI with TV-L1 prior. In Pattern Recognition in Neuroimaging (PRNI). Philadelphia, United States, June 2013. IEEE. URL: https://hal.inria.fr/hal-00839984.

  49. William H. Greene. Econometric Analysis. Pearson Education, fifth edition, 2003. ISBN 0-13-066189-9. URL: http://pages.stern.nyu.edu/~wgreene/Text/econometricanalysis.htm.

  50. Logan Grosenick, Brad Klingenberg, Kiefer Katovich, Brian Knutson, and Jonathan E. Taylor. Interpretable whole-brain prediction analysis with graphnet. NeuroImage, 72:304–321, 2013. URL: https://www.sciencedirect.com/science/article/pii/S1053811912012487, doi:https://doi.org/10.1016/j.neuroimage.2012.12.062.

  51. James V. Haxby, M. Ida Gobbini, Maura L. Furey, Alumit Ishai, Jennifer L. Schouten, and Pietro Pietrini. Distributed and overlapping representations of faces and objects in ventral temporal cortex. Science, 293(5539):2425–2430, 2001. URL: https://science.sciencemag.org/content/293/5539/2425, arXiv:https://science.sciencemag.org/content/293/5539/2425.full.pdf, doi:10.1126/science.1063736.

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  53. Jean Honorio, Tommi Jaakkola, and Dimitris Samaras. On the statistical efficiency of $$\backslash $ell_ $\$1, p$\$ $ multi-task learning of gaussian graphical models. arXiv preprint arXiv:1207.4255, 2012. arXiv:https://arxiv.org/abs/1207.4255.

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  55. Andres Hoyos-Idrobo, Gael Varoquaux, Jonas Kahn, and Bertrand Thirion. Recursive nearest agglomeration (rena): fast clustering for approximation of structured signals. IEEE Trans. Pattern Anal. Mach. Intell., 41(3):669–681, 3 2019. URL: https://doi.org/10.1109/TPAMI.2018.2815524, doi:10.1109/TPAMI.2018.2815524.

  56. Andrés Hoyos-Idrobo, Gaël Varoquaux, Yannick Schwartz, and Bertrand Thirion. Frem – scalable and stable decoding with fast regularized ensemble of models. NeuroImage, 180:160–172, 2018. New advances in encoding and decoding of brain signals. URL: https://www.sciencedirect.com/science/article/pii/S1053811917308182, doi:https://doi.org/10.1016/j.neuroimage.2017.10.005.

  57. Koji Jimura and Russell A. Poldrack. Analyses of regional-average activation and multivoxel pattern information tell complementary stories. Neuropsychologia, 50(4):544–552, 2012. Multivoxel pattern analysis and cognitive theories. URL: https://www.sciencedirect.com/science/article/pii/S0028393211005070, doi:https://doi.org/10.1016/j.neuropsychologia.2011.11.007.

  58. Thorsten Kahnt, Marcus Grueschow, Oliver Speck, and John-Dylan Haynes. Perceptual learning and decision-making in human medial frontal cortex. Neuron, 70(3):549–559, 2011. URL: https://www.sciencedirect.com/science/article/pii/S0896627311002960, doi:https://doi.org/10.1016/j.neuron.2011.02.054.

  59. André Knops, Bertrand Thirion, Edward M. Hubbard, Vincent Michel, and Stanislas Dehaene. Recruitment of an Area Involved in Eye Movements During Mental Arithmetic. Science, 324(5934):1583–1585, June 2009. URL: https://www.science.org/doi/10.1126/science.1171599 (visited on 2024-02-02), doi:10.1126/science.1171599.

  60. Nikolaus Kriegeskorte, Rainer Goebel, and Peter Bandettini. Information-based functional brain mapping. Proceedings of the National Academy of Sciences, 103(10):3863–3868, 2006. URL: https://www.pnas.org/content/103/10/3863, doi:10.1073/pnas.0600244103.

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  63. Jack L. Lancaster, Marty G. Woldorff, Lawrence M. Parsons, Mario Liotti, Catarina S. Freitas, Lacy Rainey, Peter V. Kochunov, Dan Nickerson, Shawn A. Mikiten, and Peter T. Fox. Automated talairach atlas labels for functional brain mapping. Human Brain Mapping, 10(3):120–131, 2000. URL: https://onlinelibrary.wiley.com/doi/abs/10.1002/1097-0193%28200007%2910%3A3%3C120%3A%3AAID-HBM30%3E3.0.CO%3B2-8, arXiv:https://onlinelibrary.wiley.com/doi/pdf/10.1002/1097-0193%28200007%2910%3A3%3C120%3A%3AAID-HBM30%3E3.0.CO%3B2-8, doi:https://doi.org/10.1002/1097-0193(200007)10:3<120::AID-HBM30>3.0.CO;2-8.

  64. Martin A. Lindquist, Stephan Geuter, Tor D. Wager, and Brian S. Caffo. Modular preprocessing pipelines can reintroduce artifacts into fmri data. bioRxiv, 2018. URL: https://www.biorxiv.org/content/early/2018/09/04/407676, arXiv:https://www.biorxiv.org/content/early/2018/09/04/407676.full.pdf, doi:10.1101/407676.

  65. Hesheng Liu, Steven M. Stufflebeam, Jorge Sepulcre, Trey Hedden, and Randy L. Buckner. Evidence from intrinsic activity that asymmetry of the human brain is controlled by multiple factors. Proceedings of the National Academy of Sciences, 106(48):20499–20503, December 2009. URL: https://pnas.org/doi/full/10.1073/pnas.0908073106 (visited on 2024-02-01), doi:10.1073/pnas.0908073106.

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