Publications
2024
Longitudinal changes in resting state fMRI brain self-similarity of asymptomatic high school American football athletes (2024) B Fitzgerald, S Bari, N Vike, TA Lee, RJ Lycke, JD Auger, LJ Leverenz, E Nauman, J Goñi & TM Talavage. Scientific Reports 14, 1747.
Homological Landscape of Human Brain Functional Sub-Circuits. (2024) D Duong-Tran, R Kaufmann , J Chen, X Wang, S Garai, FH Xu, J Bao, E Amico, AD Kaplan, G Petri, J Goñi, Y Zhao, L Shen. Mathematics 12(3):455.
2023
Matrix-variate Regression for Sparse, Low-rank Estimation of Brain Connectivities Associated with A Clinical Outcome (2023) D Brzyski, X Hu, J Goñi, B Ances, TW Randolph, J Harezlak. IEEE Transactions on Biomedical Engineering. Accepted.
Tangent functional connectomes uncover more unique phenotypic traits (2023) K Abbas*, M Liu*, M Wang, D Duong-Tran, U Tipnis, E Amico, AD Kaplan, M Dzemidzic, D Kareken, BM Ances, J Harezlak, J Goñi. iScience 26(9), 107624. https://doi.org/10.1016/j.isci.2023.107624 Download Figure 8 code and data here. Download Figure 10 code and data here.
Intra and Inter-Individual Variability in Functional Connectomes of Patients with First Episode of Psychosis (2023) A Tepper, JV Núñez, JP Ramirez-Mahaluf, JM Aguirre, D Barbagelata, E Maldonado, CD Dellarossa, R Nachar, A Gonzalez-Valderrama, J Undurraga, J Goñi, N Crossley. NeuroImage Clinical 38, 103391
2022
A comparison of techniques for deriving clustering and switching scores from verbal fluency word lists (2022) J Bushnell, D Svaldi, MR Ayers, S Gao, F Unverzagt, J Del Gaizo, VG Wadley, RK, J Goñi, DG Clark. Front. Psychol 13, 743557.
Incorporation of spatial- and connectivity-based cortical brain region information in regularized regression: Application to Human Connectome Project data (2022) A Steiner, K Abbas, D Brzyski, K Pączek, TW Randolph, J Goñi, J Harezlak. Frontiers in Neuroscience 16
Investigating cognitive ability using action-based models of structural brain networks. V Arora, E Amico, J Goñi, M Ventresca. Journal of Complex Networks 10(4)
2021
Functional Connectome Fingerprint Gradients in Young Adults (2021) U Tipnis, K Abbas, E Tran, E Amico, L Shen, AD Kaplan, J Goñi. arXiv preprint.
A structural connectivity disruption one decade before the typical age for dementia: a study in healthy subjects with family history of Alzheimer´s disease (2021). Ramírez-Toraño, K Abbas, R Bruña, S Marcos de Pedro, N Gómez-Ruiz, A Barabash, E Pereda, A Marcos, R Lopez Higes, F Maestu*, J Goñi*. Cerebral Cortex Communications 2(4), tgab051
Connectivity‐informed adaptive regularization for generalized outcomes (2021). D Brzyski, M Karas, BM Ances, M Dzemidzic, J Goñi, TW Randolph, J Harezlak. Canadian Journal of Statistics, 49(1), 203-227.
Optimizing Differential Identifiability Improves Connectome Predictive Modeling of Cognitive Deficits in Alzheimer's Disease (2021) DO Svaldi, J Goñi, K Abbas, E Amico, DG Clark, C Muralidharan, M Dzemidzic, JD West, SL Risacher, AJ Saykin, LG Apostolova (for the Alzheimer's Disease Neuroimaging Initiative). Human Brain Mapping 42 (11) 3500-3516. Download Idiff-CPM code here
Improving functional connectome fingerprinting with degree-normalization (2021) B Chiêm, K Abbas, E Amico, DA Duong-Tran, F Crevecoeur, J Goñi. Brain Connectivity 12(2), 180-192. Download degree-normalization code here
A morphospace framework to assess configural breadth based on brain functional networks.(2021) D Duong-Tran, K Abbas, E Amico, B Corominas-Murtra, M Dzemidzic, D Kareken, M Ventresca, J Goñi. Network Neuroscience 5(3), 666-688.
Geodesic distance on optimally regularized functional connectomes uncovers individual fingerprints (2021) K Abbas, M Liu, M Venkatesh, E Amico, AD Kaplan, M Ventresca, L Pessoa, J Harezlak, J Goñi. Brain Connectivity 11(5), 333-348. Download regularization code here
Towards an information theoretical description of communication in brain networks (2021) E Amico, K Abbas, D Duong-Tran, U Tipnis, M Rajapandian, E Chumin, M Ventresca, J Harezlak, J Goñi. Network Neuroscience 5(3), 646–665.
Interactive Visualization of Deep Learning for 3D Brain Data Analysis (2021) H Li, S Fang, J Goñi, AJ Saykin, L Shen. IEEE 20th International Conference on Cognitive Informatics & Cognitive Computing pp. 85-91, Banff, AB, Canada,
2020
Identifiability of structural networks of nonlinear electronic oscillators (2020) VP Vera-Ávila, R Sevilla-Escoboza, J Goñi, RR Rivera-Durón, JM Buldú, Scientific Reports, 10(1), 1-11.
A Sparsity Inducing Nuclear-Norm Estimator (SpINNEr) for Matrix-Variate Regression in Brain Connectivity Analysis (2020) D Brzyski, X Hu, J Goñi, B Ances, TW Randolph, J Harezlak, arXiv preprint
Functional network connectivity in early-stage schizophrenia (2020). TA Hummer,, MG Yung, J Goñi, J, SK Conroy, MM Francis, NF Mehdiyoun, A Breier, Schizophrenia Research, 18, 107-115.
GEFF: Graph Embedding for Functional Fingerprinting (2020) K Abbas, E Amico, DO Svaldi, U Tipnis, DA Duong-Tran, M Liu, M Rajapandian, J Harezlak, BM Ances, J Goñi, NeuroImage 221, 117181. Download GEFF code here
Multi-timescale hybrid components of the functional brain connectome: A bimodal EEG-fMRI decomposition (2020) J Wirsich, E Amico, AL Giraud, J Goñi. S Sadaghiani. Network Neuroscience 4(3), 658-677.
Uncovering differential Identifiability in network properties of human brain functional connectomes (2020) M Rajapandian, E Amico, K Abbas, M Ventresca and J Goñi, Network Neuroscience 4(3), 698-713. Download network-properties identifiability code here
The disengaging brain: Dynamic transitions from cognitive engagement and alcoholism risk (2020) E Amico, M Dzemidzic, B Oberlin, C Carron, J Harezlak, J Goñi*, D Kareken*, NeuroImage, 116515. Article featured at: Purdue Press Release , Scientific American
Brain-wide structural connectivity alterations under the control of Alzheimer risk genes (2020). J Yan, V Raja, Z Huang, E Amico, K Nho, S Fang, O Sporns, YC Wu Y, AJ Saykin, J Goñi, L Shen. International Journal of Computational Biology and Drug Design 13(1), 58-70.
2019
Uncovering multi-site identifiability based on resting-state functional connectomes (2019) S Bari, E Amico, N Vike, TM Talavage and J Goñi, NeuroImage, Volume 202, 115967.
Centralized and distributed cognitive task processing in the human connectome (2019) E Amico, A Arenas, J Goñi.. Network Neuroscience, 3(2), 455-474. Download Jensen-Shannon FC code here
Semiparametric estimation of task-based dynamic functional connectivity on the population level (2019) MA Kudela, M Dzemidzic, BG. Oberlin, J Goñi, DA Kareken, J Harezlak. Frontiers in neuroscience, 13, 583.
Resting state network modularity along the prodromal late onset Alzheimer's disease continuum (2019) JA Contreras, A Avena-Koenigsberger, SL Risacher, JD West, E Tallman, BC McDonald, MR. Farlow, LG Apostolova, J Goñi, M Dzemidzic, YC Wu, D Kessler, L Jeub, S Fortunato, AJ. Saykin, O Sporns. NeuroImage: Clinical, 22, 101687.
Aberrations of anterior insular cortex functional connectivity in nontreatment-seeking alcoholics (2019) ME Halcomb, E Chumin, J Goñi, M Dzemidzic, KK Yoder. Psychiatry Research: Neuroimaging, 284, 21-28.
2018
Modeling communication processes in the human connectome through cooperative learning (2018) Tipnis U, Amico E, Ventresca M, Goñi J. IEEE Transactions on Network Science and Engineering, doi: 10.1109/TNSE.2018.2878487
Towards subject and diagnostic identifiability in the Alzheimer’s disease spectrum based on functional connectomes (2018) Svaldi DO, Goñi J, Sanjay A, Amico E, Risacher S, West J, Dzemidzic M, Saykin A, Apostolova L. In Stoyanov D. et al. (eds) Graphs in Biomedical Image Analysis and Integrating Medical Imaging and Non-Imaging Modalities. GRAIL 2018, Beyond MIC 2018. Lecture Notes in Computer Science, vol 11044. Springer, Cham.
Mapping higher-order relations between brain structure and function with embedded vector representations of connectomes (2018). Rosenthala G, Váša F, Griffa A, Hagmann P, Amico E, Goñi J, Avidana G, Sporns O. Nature Communications 9(1), 1-12.
The quest for identifiability in human functional connectomes (2018) Amico E, Goñi J. Nature Scientific Reports 8.1: 8254. Download Identifiability code here
Differences in White Matter Microstructure and Connectivity in Nontreatment-Seeking Individuals with Alcohol Use Disorder (2018). Chumin E, Goñi J, Halcomb M, Durazzo T, Dzemidzic M, Yoder K. Alcoholism Clinical and Experimental Research 42(5): 889-896.
Mapping hybrid Functional-structural connectivity traits in the human connectome (2018). E Amico and J Goñi. Network Neuroscience 2(3), 306-322. Download hybrid connICA code here
Positive Connectivity Predicts the Dynamic Intrinsic Topology of the Human Brain Network (2018) J Qian, I Diez, L Ortiz-Terán, C Bonadio, T Liddell, J Goñi, J Sepulcre. Frontiers in systems neuroscience, 12, 38.
Dynamic Generative Model of the Human Brain in Resting-State. (2018) D Guo, V Arora, E Amico, J Goñi, M Ventresca. (2018). In: Cherifi, C., Cherifi, H., Karsai, M., Musolesi, M. (eds) Complex Networks & Their Applications VI. COMPLEX NETWORKS 2017. Studies in Computational Intelligence, vol 689, pp 1271–1283, Springer, Cham.
2017
Brain explorer for connectomic analysis (2017). Li H, Fang S, Contreras JA, West JD, Risacher SL, Wang Y, Sporns O, Saykin AJ, Goñi J, Shen L. Alzheimer’s Disease Neuroimaging Initiative. Brain Informatics 4(4):253-269.
Brain Connectivity-Informed Regularization Methods for Regression (2017). Karas M, Brzyski D, Dzemidzic M, Goñi J, Kareken D, Randolph TW, Harezlak J. Stat Biosci s12561-017-9208-x.
Editorial: On the relation of dynamics and structure in brain networks (2017). Papo D, Goñi J, Buldu JM. Chaos 27, 047201. http://aip.scitation.org/doi/full/10.1063/1.4981391
Mapping the functional connectome traits of levels of consciousness (2017) E Amico, D Marinazzo, C Di Perri, L Heine, J Annen, C Martial, M Dzemidzic, M Kirsch, V Bonhomme, S. Laureys*, J Goñi*. NeuroImage, 148, 201-211. Download connICA code here
2016
Path ensembles and a tradeoff between communication efficiency and resilience in the human connectome (2016). A Avena-Koenigsberger, B Mišić, RX Hawkins, A Griffa, P Hagmann, J Goñi*, O Sporns*. Brain Structure and Function, 222(1), 603-618.
Generative models of the human connectome (2016). Betzel, R. F., Avena-Koenigsberger, A., Goñi, J., He, Y., de Reus, M. A., Griffa, A., ... & Sporns, O. (2016). NeuroImage, 124, 1054-1064.
2015
The Structural and Functional Connectome and Prediction of Risk for Cognitive Impairment in Older Adults (2015). JA Contreras, J Goñi, SL Risacher, O Sporns, AJ Saykin. Current Behavioral Neuroscience Reports 2 (4), 234-245.
Nodal centrality of functional network in the differentiation of schizophrenia (2015). Cheng, H., Newman, S., Goñi, J., Kent, J. S., Howell, J., Bolbecker, A., ... & Hetrick, W. P. Schizophrenia research, 168(1), 345-352.
Integrated Visualization of Human Brain Connectome Data (2015). Li, H., Fang, S., Goñi, J., Contreras, J. A., Liang, Y., Cai, C., ... & Shen, L. Brain Informatics and Health (pp. 295-305). Springer International Publishing.
Cooperative and competitive spreading dynamics on the human connectome (2015). B Misic, RF Betzel, A Nematzadeh, J Goñi, A Griffa, P Hagmann, A Flammini, YY Ahn, O Sporns. Neuron 86.6 1518-1529.
A network convergence zone in the hippocampus (2015). B Misic, J Goñi, O Sporns, AR McIntosh. Plos Comp Biol. 10(12) e1003982.
Network morphospace (2015). A Avena-Koenigsberger, J Goñi, RV Solé, O Sporns. Journal of the Royal Société-Interface 12(103) 20140881.
2014
Changes in structural and functional connectivity among resting-state networks across the human lifespan (2014). RF Betzel, L Byrge, Y He, J Goñi, XN Zuo, O Sporns. NeuroImage. 102P2:345-357.
Multiscale Integration and Predictability in Resting State Brain Activity (2014). A Kolchinsky, MP van den Heuvel, A Griffa, P Hagmann, LM Rocha, O Sporns, J Goñi. Frontiers in Neuroinformatics – Special Issue “Information-based methods for neuroimaging: analyzing structure, function and dynamics”. 8(66).
Using Pareto Optimality to Explore the Topology and Dynamics of the Human Connectome (2014). A Avena-Koenigsberger, J Goñi, RF Betzel, MP van den Heuvel, A Griffa, P Hagmann, JP Thiran, O Sporns. Phil. Trans. R. Soc. B. 369(1653).
Resting Brain Functional Connectivity Predicted by Analytic Measures of Network Communication (2014). J Goñi, MP van den Heuvel, A Avena-Koenigsberger, N Velez de Mendizabal, RF Betzel, A Griffa, P Hagmann, B Corominas-Murtra, JP Thiran, O Sporns. Proc Natl Acad Sci USA 111(2):833-8.
2013
Multi-scale community organization of the human structural connectome and its relationship with resting-state functional connectivity (2013). RF Betzel, A Griffa, A Avena-Koenigsberger, J Goñi, JP Thiran, P Hagmann, O Sporns. Network Science 1(3):353-373. arXiv: http://arxiv.org/abs/1304.0485.
Robust estimation of fractal measures for characterizing the structural complexity of the human brain: optimization and reproducibility (2013). J. Goñi, O. Sporns, H Cheng, M Aznárez-Sanado, Y Wang, S Josa, G Arrondo, VP Mathews, TA Hummer, WG Kronenberger, A Avena-Koenigsberger, AJ Saykin, MA Pastor. NeuroImage 83, 646-657.
On the origins of hierarchy in complex networks (2013) B Corominas-Murtra, J Goñi, RV Solé, C Rodríguez-Caso. Proc Natl Acad Sci USA 110(33):13316-21.
Exploring the Morphospace of Communication Efficiency in Complex Networks (2013) J Goñi, A Avena-Koenigsberger, N Velez de Mendizabal , MP van den Heuvel , R Betzel, O Sporns. PLoS ONE 8(3):e58070.
Abnormal rich club organization and functional brain dynamics in schizophrenia (2013) . MP van den Heuvel, O Sporns, G Collin, T Scheewe, RCW Mandl, W Cahn, J Goñi, HE Hulshoff Pol and RS Kahn. JAMA Psychiatry 70(8):783-92. Paper featured at: From Lichtheim to Rich Club. Brain Networks and Psychiatry (2013). E Bullmore, P. Vertes. JAMA Psychiatry.
Selective brain gray matter atrophy associated with APOE ε4 and MAPT H1 in subjects with mild cognitive impairment. (2013). J Goñi, S Cervantes, G Arrondo, P Pastor, MA Pastor. J Alzheimer Dis 33(4):1009-19.
2012
High-Cost, High-Capacity Backbone for Global Brain Communication (2012). MP van den Heuvel, RS Kahn, J Goñi, O Sporns. Proc Natl Acad Sci USA 109(28):11372-7.
2011
Measuring the hierarchy of feedforward networks (2011) B Corominas-Murtra, C Rodríguez-Caso, J Goñi, RV Solé. Chaos 21(1) 016108.
The neural substrate and functional integration of uncertainty in decision making: an information theory approach (2011). J Goñi, M Aznárez-Sanado, G Arrondo, M Fernández-Seara, FR Loayza, FH Heukamp, MA Pastor. PLoS ONE 6(3): e17408.
The semantic organization of the animal category: evidence from semantic verbal fluency and network theory (2011). J Goñi, G Arrondo, J Sepulcre, I Martincorena, N Vélez de Mendizabal, B Corominas-Murtra, B Bejarano, S Ardanza-Trevijano, H Peraita, DP Wall, P Villoslada. Cognitive Processing 12(2),183-196.
2010
Exploring the randomness of directed acyclic networks (2010). J Goñi, B Corominas-Murtra, RV Solé, C Rodríguez-Caso. Physical Review E. 82, 066115.
Topological reversibility and causality in feed-forward networks (2010). B Corominas-Murtra, C Rodríguez-Caso, J Goñi, RV Solé. New Journal of Physics 12, 113051.
Lexical access changes in patients with Multiple Sclerosis. A 2-year follow-up study (2010) J Sepulcre, H Peraita, J Goñi, B Duque, G Arrondo, I Martincorena, B Duque, N Vélez de Mendizábal, JC Masdeu, P Villoslada. J Clin Exp Neuropsyc 33(2),169.
Switcher-random-walks: a cognitive-inspired mechanism for network exploration. (2010) J Goñi, I Martincorena, B Corominas-Murtra, G Arrondo, S Ardanza-Trevijano, P Villoslada. Int J Bifurcat Chaos 20(3):913-922.
2009
Brain pathways of verbal working memory: A lesion-function correlation study. (2009) J Sepulcre, JC Masdeu, MA Pastor, J Goñi, C Barbosa, B Bejarano, P Villoslada. Neuroimage 47(2):773-8.
Fractal dimension analysis of grey matter in multiple sclerosis (2009) FJ Esteban, J Sepulcre, J Ruiz de Miras, J Navas, N Vélez de Mendizábal, J Goñi, JM Quesada, B Bejarano, P Villoslada. Journal of the Neurological Sciences 282(1-2):67-71.
Contribution of white matter lesions to gray matter atrophy in Multiple Sclerosis. Evidence from voxel-based analysis of T1 lesions in the visual pathway (2009) J Sepulcre, J Goñi, B Bejarano, N Vélez de Mendizábal, JB Toledo, JC Masdeu, P Villoslada. Archives of Neurology 66(2):173-179.
2008
Goals and pitfalls of gene network inference methods: a comparative study from virtual microarrays and network dynamics. (2008) J Goñi*, C Rodríguez-Caso*, RV Solé, P Villoslada, A Munteanu. Net-works Int Conf 2008. ISBN: 978-84-691-3819-9, pages 91-97.
Switcher random walkers: cognitive inspired strategies for an optimized random exploration of networks. (2008) J Goñi*, I Martincorena*, G Arrondo, J Sepulcre, N Vélez de Mendizabal, B Bejarano, DP Wall, S Ardanza-Trevijano, P Villoslada. Networks Int Conf 2008. ISBN: 978-84-691-3819-9, pages 83-89.
Mapping the brain pathways of declarative verbal memory. Evidence from white matter lesions in the living human brain (2008) J Sepulcre, JC Masdeu, J Sastre-Garriga, J Goñi, N Vélez de Mendizábal, B Duque, MA Pastor, B Bejarano and P Villoslada. Neuroimage 42(3):1237-43.
A computational analysis of the protein-protein interaction networks in neurodegenerative diseases (2008) J Goñi, FJ Esteban, N Velez de Mendizabal, J Sepulcre, I Agirrezabal, S Ardanza-Trevijano, P Villoslada. BMC Systems Biology 2:52.
Books
Hubs and Pathways (2014). J Sepulcre, MR Sabuncu, J Goñi. Brain Mapping: An Encyclopedic Reference. 23. Elsevier. Eds M Mesulam and S Kastner.