Vavouraki, N. ORCID: https://orcid.org/0000-0003-2581-4935, Tomkins, J. E. ORCID: https://orcid.org/0000-0003-3010-6634, Kara, E. ORCID: https://orcid.org/0000-0001-5428-6743, Houlden, H., Hardy, J., Tindall, M. J., Lewis, P. A. ORCID: https://orcid.org/0000-0003-4537-0489 and Manzoni, C. (2021) Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias. iScience, 24 (5). 102484. ISSN 2589-0042 doi: https://doi.org/10.1016/j.isci.2021.102484

Kluss, J. H., Mazza, M. C., Li, Y., Manzoni, C., Lewis, P. A., Cookson, M. R. ORCID: https://orcid.org/0000-0002-1058-3831 and Mamais, A. (2021) Preclinical modeling of chronic inhibition of the Parkinson’s disease associated kinase LRRK2 reveals altered function of the endolysosomal system in vivo. Molecular Neurodegeneration, 16 (1). 17. ISSN 1750-1326 doi: https://doi.org/10.1186/s13024-021-00441-8

Manzoni, C. and Ferrari, R. (2021) Mendelian and sporadic FTD: disease risk and avenues from genetics to disease pathways through in silico modelling. In: Ghetti, B., Buratti, E., Boeve, B. and Rademakers, R. (eds.) Frontotemporal Dementias. Advances in Experimental Medicine and Biology, 1281. Springer, pp. 283-296. ISBN 9783030511395 doi: https://doi.org/10.1007/978-3-030-51140-1_17

Costa, B., Manzoni, C. ORCID: https://orcid.org/0000-0001-5367-4023, Bernal-Quiros, M., Kia, D. A., Aguilar, M., Alvarez, I., Alvarez, V., Andreassen, O. ORCID: https://orcid.org/0000-0002-4461-3568, Anfossi, M., Bagnoli, S., Benussi, L., Bernardi, L., Binetti, G., Blackburn, D., Boada, M., Borroni, B., Bowns, L., Bråthen, G. ORCID: https://orcid.org/0000-0003-3224-7983, Bruni, A. C., Chiang, H.-H., Clarimon, J., Colville, S., Conidi, M. E., Cope, T. E., Cruchaga, C., Cupidi, C., Di Battista, M. E., Diehl-Schmid, J., Diez-Fairen, M., Dols-Icardo, O., Durante, E., Flisar, D., Frangipane, F., Galimberti, D. ORCID: https://orcid.org/0000-0002-9284-5953, Gallo, M., Gallucci, M., Ghidoni, R. ORCID: https://orcid.org/0000-0002-7691-1957, Graff, C., Grafman, J. H., Grossman, M., Hardy, J., Hernández, I., Holloway, G. J. T., Huey, E. D., Illán-Gala, I. ORCID: https://orcid.org/0000-0002-5418-2052, Karydas, A., Khoshnood, B., Kramberger, M. G., Kristiansen, M., Lewis, P. A., Lleó, A., Madhan, G. K., Maletta, R., Maver, A., Menendez-Gonzalez, M., Milan, G., Miller, B., Mol, M. O. ORCID: https://orcid.org/0000-0003-2533-2530, Momeni, P., Moreno-Grau, S., Morris, C. M. ORCID: https://orcid.org/0000-0002-3749-0993, Nacmias, B. ORCID: https://orcid.org/0000-0001-9338-9040, Nilsson, C., Novelli, V., Öijerstedt, L., Padovani, A., Pal, S., Panchbhaya, Y., Pastor, P. ORCID: https://orcid.org/0000-0002-7493-8777, Peterlin, B., Piaceri, I., Pickering-Brown, S., Pijnenburg, Y. A. L. ORCID: https://orcid.org/0000-0003-2464-1905, Puca, A. A., Rainero, I., Rendina, A. ORCID: https://orcid.org/0000-0001-5331-2807, Richardson, A. M. T., Rogaeva, E., Rogelj, B. ORCID: https://orcid.org/0000-0003-3898-1943, Rollinson, S. ORCID: https://orcid.org/0000-0002-0921-4318, Rossi, G., Rossmeier, C., Rowe, J. B., Rubino, E. ORCID: https://orcid.org/0000-0002-7553-7553, Ruiz, A., Sanchez-Valle, R., Sando, S. B., Santillo, A. F., Saxon, J., Scarpini, E. ORCID: https://orcid.org/0000-0002-6395-2119, Serpente, M., Smirne, N., Sorbi, S., Suh, E., Tagliavini, F., Thompson, J. C., Trojanowski, J. Q., Van Deerlin, V. M., Van der Zee, J. ORCID: https://orcid.org/0000-0003-4381-8040, Van Broeckhoven, C. ORCID: https://orcid.org/0000-0003-0183-7665, van Rooij, J., Van Swieten, J. C., Veronesi, A., Vitale, E. ORCID: https://orcid.org/0000-0003-4651-3875, Waldö, M. L., Woodward, C., Yokoyama, J., Escott-Price, V., Polke, J. M. and Ferrari, R. (2020) C9orf72, age at onset, and ancestry help discriminate behavioral from language variants in FTLD cohorts. Neurology, 95 (24). e3288-e3302. ISSN 0028-3878 doi: https://doi.org/10.1212/WNL.0000000000010914

Cogo, S., Manzoni, C., Lewis, P. A. and Greggio, E. (2020) Leucine‐rich repeat kinase 2 and lysosomal dyshomeostasis in Parkinson disease. Journal of Neurochemistry, 152 (3). pp. 273-283. ISSN 1471-4159 doi: https://doi.org/10.1111/jnc.14908

Manzoni, C., Lewis, P. A. and Ferrari, R. (2020) Network analysis for complex neurodegenerative diseases. Current Genetic Medicine Reports, 8 (1). pp. 17-25. ISSN 2167-4876 doi: https://doi.org/10.1007/s40142-020-00181-z

Tomkins, J. E., Ferrari, R., Vavouraki, N., Hardy, J., Lovering, R. C., Lewis, P. A., McGuffin, L. J. ORCID: https://orcid.org/0000-0003-4501-4767 and Manzoni, C. (2020) PINOT: an intuitive resource for integrating protein-protein interactions. Cell Communication and Signaling, 18 (92). ISSN 1478-811X doi: https://doi.org/10.1186/s12964-020-00554-5

Bonham, L. W., Steele, N. Z. R., Karch, C. M., Broce, I., Geier, E. G., Wen, N. L., Momeni, P., Hardy, J., Miller, Z. A., Gorno-Tempini, M. L., Hess, C. P., Lewis, P., Miller, B. L., Seeley, W. W., Manzoni, C., Desikan, R. S., Baranzini, S. E., Ferrari, R. and Yokoyama, J. S. (2019) Genetic variation across RNA metabolism and cell death gene networks is implicated in the semantic variant of primary progressive aphasia. Scientific Reports, 9 (1). 10854. ISSN 2045-2322 doi: https://doi.org/10.1038/s41598-019-46415-1

Mamais, A., Manzoni, C., Nazish, I., Arber, C., Sonustun, B., Wray, S., Warner, T. T., Cookson, M. R., Lewis, P. A. and Bandopadhyay, R. (2018) Analysis of macroautophagy related proteins in G2019S LRRK2 Parkinson's disease brains with Lewy body pathology. Brain Research, 1701. pp. 75-84. ISSN 0006-8993 doi: https://doi.org/10.1016/j.brainres.2018.07.023

Price, A., Manzoni, C., Cookson, M. R. and Lewis, P. A. (2018) The LRRK2 signalling system. Cell and Tissue Research, 373 (1). pp. 39-50. ISSN 0302-766X doi: https://doi.org/10.1007/s00441-017-2759-9

Leksmono, C., Manzoni, C., Tomkins, J., Lucchesi, W., Cottrell, G. ORCID: https://orcid.org/0000-0001-9098-7627 and Lewis, P. A. (2018) Measuring lactase enzymatic activity in the teaching lab. Journal of Visualized Experiments (138). e54377. ISSN 1940-087X doi: https://doi.org/10.3791/54377

Ferrari, R., Kia, D. A., Tomkins, J. E., Hardy, J., Wood, N. W., Lovering, R. C., Lewis, P. A. and Manzoni, C. (2018) Stratification of candidate genes for Parkinson’s disease using weighted protein interaction network analysis. BMC Genomics, 19. 452. ISSN 1471-2164 doi: https://doi.org/10.1186/s12864-018-4804-9

Tomkins, J. E., Dihanich, S., Beilina, A., Ferrari, R., Ilacqua, N., Cookson, M. R., Lewis, P. A. and Manzoni, C. (2018) Comparative protein interaction network analysis identifies shared and distinct functions for the human ROCO proteins. Proteomics, 18 (10). 1700444. ISSN 1615-9853 doi: https://doi.org/10.1002/pmic.201700444

Manzoni, C., Mamais, A., Dihanich, S., Soutar, M. P. M., Plun-Favreau, H., Bandopadhyay, R., Abeti, R., Giunti, P., Hardy, J., Cookson, M. R., Tooze, S. A. and Lewis, P. A. (2018) mTOR independent alteration in ULK1 Ser758 phosphorylation following chronic LRRK2 kinase inhibition. Bioscience Reports, 38 (2). BSR20171669. ISSN 0144-8463 doi: https://doi.org/10.1042/BSR20171669

Manzoni, C., Kia, D. A., Vandrovcova, J., Hardy, J., Wood, N. W., Lewis, P. A. and Ferrari, R. (2018) Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences. Briefings In Bioinformatics, 19 (2). pp. 286-302. ISSN 1467-5463 doi: https://doi.org/10.1093/bib/bbw114

Giacomina, R., Redaelli, V., Contiero, P., Fabiano, S., Tagliabue, G., Perego, P., Benussi, L., Bruni, A., Filippini, G., Farinotti, M., Giaccone, G., Buitatiotis, S., Manzoni, C., Ferrari, R. and Tagliavini, F. (2018) Tau mutations serve as a novel risk factor for cancer. Cancer Research, 78 (13). pp. 3731-3739. ISSN 0008-5472 doi: https://doi.org/10.1158/0008-5472.CAN-17-3175

Manzoni, C. and Lewis, P. A. (2017) LRRK2 and autophagy. In: Rideout, H. J. (ed.) Leucine-Rich Repeat Kinase 2 (LRRK2). Advances in Neurobiology (ISSN:2190-5215), 14. Springer International Publishing, Cham, Switzerland, pp. 89-105. ISBN 9783319499673 doi: https://doi.org/10.1007/978-3-319-49969-7_5

Ferrari, R., Lovering, R. C., Hardy, J., Lewis, P. A. and Manzoni, C. (2017) Weighted protein interaction network analysis of frontotemporal dementia. Journal of Proteome Research, 16 (2). pp. 999-1013. ISSN 1535-3907 doi: https://doi.org/10.1021/acs.jproteome.6b00934

Manzoni, C. (2017) The LRRK2-macroautophagy axis and its relevance to Parkinson's Disease. Biochemical Society Transactions, 45 (1). pp. 155-162. ISSN 1470-8752 doi: https://doi.org/10.1042/bst20160265

Manzoni, C., Mamais, A., Roosen, D. A., Dihanich, S., Soutar, M. P. M., Plun-Favreau, H., Bandopadhyay, R., Hardy, J., Tooze, S. A., Cookson, M. R. and Lewis, P. A. (2016) mTOR independent regulation of macroautophagy by Leucine Rich Repeat Kinase 2 via Beclin-1. Scientific Reports, 6. 35106. ISSN 2045-2322 doi: https://doi.org/10.1038/srep35106

Kara, E., Tucci, A., Manzoni, C., Lynch, D. S., Elpidorou, M., Bettencourt, C., Chelban, V., Manole, A., Hamed, S., Haridy, N., Federoff, M., Preza, E., Hughes, D., Pittman, A., Jaunmuktane, Z., Brandner, S., Xiromerisiou, G., Wiethoff, S., Schottlaender, L., Proukakis, C., Morris, H., Warner, T., Bhatia, K., Korlipara, P., Singleton, A., Hardy, J., Wood, N., Lewis, P. and Houlden, H. (2016) Genetic and phenotypic characterization of complex hereditary spastic paraplegia. Brain : A Journal of Neurology, 139 (7). pp. 1904-1918. ISSN 1460-2156 doi: https://doi.org/10.1093/brain/aww111

Manzoni, C., Denny, P., Lovering, R. C. and Lewis, P. A. (2015) Computational analysis of the LRRK2 interactome. PeerJ, 3. 778. ISSN 2167-8359 doi: https://doi.org/10.7717/peerj.778

Dihanich, S., Civiero, L., Manzoni, C., Mamais, A., Bandopadhyay, R., Greggio, E. and Lewis, P. A. (2014) GTP binding controls complex formation by the human ROCO protein MASL1. FEBS Journal, 281 (1). pp. 261-274. ISSN 1742-464X doi: https://doi.org/10.1111/febs.12593

Schulte, E. C., Ellwanger, D. C., Dihanich, S., Manzoni, C., Stangl, K., Schormair, B., Graf, E., Eck, S., Mollenhauer, B., Haubenberger, D., Pirker, W., Zimprich, A., Brücke, T., Lichtner, P., Peters, A., Gieger, C., Trenkwalder, C., Mewes, H.-W., Meitinger, T., Lewis, P. A., Klünemann, H. H. and Winkelmann, J. (2014) Rare variants in LRRK1 and Parkinson's disease. Neurogenetics, 15 (1). pp. 49-57. ISSN 1364-6745 doi: https://doi.org/10.1007/s10048-013-0383-8

Manzoni, C., Mamais, A., Dihanich, S., McGoldrick, P., Devine, M. J., Zerle, J., Kara, E., Taanman, J.-W., Healy, D. G., Marti-Masso, J.-F., Schapira, A. H., Plun-Favreau, H., Tooze, S., Hardy, J., Bandopadhyay, R. and Lewis, P. A. (2013) Pathogenic Parkinson’s disease mutations across the functional domains of LRRK2 alter the autophagic/lysosomal response to starvation. Biochemical and Biophysical Research Communications, 441 (4). pp. 862-866. ISSN 0006-291X doi: https://doi.org/10.1016/j.bbrc.2013.10.159

Jebelli, J. D., Dihanich, S., Civiero, L., Manzoni, C., Greggio, E. and Lewis, P. A. (2012) GTP binding and intramolecular regulation by the ROC domain of Death Associated Protein Kinase 1. Scientific Reports, 2. 695. ISSN 2045-2322 doi: https://doi.org/10.1038/srep00695