Publications

[Journals] | [In proceedings] | [Book Chapters] | [Pre Prints] | [Thesis]

^† means that the authors contributed equally to the work
^‡ means that the authors jointly supervised the work

Journals

• Visconti A.^†, Rossi N.^†, Bondt A., Hipgrave Ederveen A., Thareja G., Koeleman C.A.M., Stephan N., Halama A., Lomax-Browne H.J., Pickering M.C., Zhou X., Wuhrer M.^‡, Suhre K.^‡, and Falchi M.^‡, The genetics and epidemiology of N- and O- Immunoglobin A glycomics, Genome Medicine, 2024, doi:10.1186/s13073-024-01369-6

• Valdes A.M.^†, Louca P.^†, Visconti A., Asnicar F., Bermingham6 K., Nogal A., Wong K., Wolf J., Michelotti G., Segata N., Spector T.D., Berry S.E., Falchi M., Menni C., Vitamin A carotenoids, but not retinoids, mediate the impact of a healthy diet on gut microbial diversity, BMC Medicine, 2024, doi:10.1186/s12916-024-03543-4

• Rossi N., Syed N., Visconti A., Aliyev E., Berry S., Bourbon M., Spector T.D., Hysi P.G.^‡, Fakhro K.A.^‡, Falchi M.^‡, Rare variants at KCNJ2 are associated with LDL-cholesterol levels in a cross-population study, npj genomic medicine, 2024, doi:10.1038/s41525-024-00417-9

• Attaye I.^†, Beynon-Cobb B.^†, Louca P., Nogal A., Visconti A., Tettamanzi F., Wong K., Michellotti G., Spector T.D., Falchi M., Bell J.T., and Menni C., Cross-sectional analyses of metabolites across biological samples mediating dietary acid load and chronic kidney disease, iScience, 2024, doi:10.1016/j.isci.2024.109132

• Danckert N.P.^†,, Freidin M.B.^†,, Granville Smith I., Wells P.M., Naeini M.K., Visconti A., Compte R., MacGregor A., and Williams F.M.K, Treatment response in rheumatoid arthritis is predicted by the microbiome: a large observational study in UK DMARD-naïve patients, Rheumatology, 2024, doi:10.1093/rheumatology/keae045

• Kirk D., Costeira R., Visconti A., Mirzaei M.K., Deng L., Valdes A.M., and Menni C., Bacteriophages, gut bacteria, and microbial pathways interplay in cardiometabolic health, Cell Reports, 2024, doi:10.1016/j.celrep.2024.113728

• Budu-Aggrey A., Kilanowski A., Sobczyk M.K., Shringarpure S.S., Mitchell R., …, Visconti A., …, Holloway J.W., Min J., Brown S.J., Standl M., and Paternoster L., European and multi-ancestry genome-wide association meta-analysis of atopic dermatitis highlights importance of systemic immune regulation, Nature Communications, 2023, doi:10.1038/s41467-023-41180-2

• Nogal, A.^†, Tettamanzi F.^†, Dong Q., Louca P., Visconti, A., …, Spector T.D., Bell J.T., Gieger C., Valdes A.M.^‡, and Menni C.^‡ A faecal metabolite signature of impaired fasting glucose: results from two independent population-based cohorts, Diabetes, 2023, doi:/10.2337/db23-0170

• Nogal, A., Asnicar, F., Vijay, A., Kouraki, A., Visconti, A., …, Spector T.D., Valdes A.M.^‡, and Menni C.^‡, Genetic and gut microbiome determinants of SCFA circulating and faecal levels, postprandial responses and links to chronic and acute inflammation, Gut Microbes, 2023, doi:0.1080/19490976.2023.2240050

• Louca P., Meijnikman A., Nogal MacHo A., Asnicar F., Attaye I., Vijay A., Kouraki A., Visconti A., …, Bulsiewicz W., Nieuwdorp M., Valdes A., Menni C., The secondary bile acid isoursodeoxycholate is associated with postprandial lipaemia inflammation and appetite and changes post bariatric surgery, Cell Reports Medicine, 2023, doi:10.1016/j.xcrm.2023.100993

• Zito A., Roberts A.L.^†, Visconti A.^†, Rossi N., Andres-Ejarque R., Nardone S., El-Sayed Moustafa J.S., Falchi M., and Small K.S., Escape from X-inactivation in twins exhibits intra- and inter-individual variability across tissues and is heritable, PLoS Genetics, 2023, doi:10.1371/journal.pgen.1010556

• Visconti A., Rossi N., Deriš H., Lee K.A., …, Sasieni P., Bataille V.^‡, Lauc G.^‡, and Falchi M.^‡, Total serum N‐glycans associate with response to immune checkpoint inhibition therapy and survival in patients with advanced melanoma, BMC Cancer, 2023 doi:10.1186/s12885-023-10511-3

• Valles-Colomer M., Blanco-Míguez A., Manghi P., Asnicar F., …, Visconti A., …, Spector T.D., Domenici E., Collado M.C., and Segata N., The person-to-person transmission landscape of the gut and oral microbiomes, Nature, 2023 doi:10.1038/s41586-022-05620-1

• Zhang X., Adebayo A.S., Wang D., Raza Y., Tomlinson M., Dooley H., Bowyer R.C.E., Small K., Steves C.J., Spector T.D., Duncan E.L., Visconti A.^‡, and Falchi M.^‡, PPI-induced changes in plasma metabolite levels influence total hip bone mineral density in a UK cohort, Journal of Bone and Mineral Research, 2022 doi:10.1002/jbmr.4754

• Rossi N.^†, Lee K. A.^†, Bermudez M.V., Visconti A., Thomas A.M., Bolte L.A., …, Weersma R.K., Hospers G.A.P., Fehrmann R.S.N, Bataille V.^‡, and Falchi M.^‡, Circulating inflammatory proteins associate with response to immune checkpoint inhibition therapy in patients with advanced melanoma, EBioMedicine, 2022 doi:10.1016/j.ebiom.2022.104235

• Visconti A.^†, Murray B.^†, Rossi N., Wolf J., Ourselin S., Spector T.D., Freeman E.E., Bataille V.^‡, and Falchi M.^‡ Cutaneous Manifestations of SARS-CoV-2 infection during the Delta and Omicron waves in 348,691 UK users of the UK ZOE COVID Study App, British Journal of Dermatology, 2022, doi:10.1111/bjd.21784

• Le Roy C.I., Kurilshikov A., Leeming E.R., Visconti A., Bowyer R.C.E, Menni C., Falchi M., Koutnikova H., Veiga P., Zhernakova A., Derrien M., and Spector T.D. Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome, BMC Microbiology, 2022, doi:10.1186/s12866-021-02364-2

• Murray B., Kerfoot E., Chen L., Deng J., Graham M.S., Sudre C.H., Molteni E., Canas L.S., Antonelli M., Klaser K., Visconti A., Hammers A., Chan A.T., Franks P.W., Davies R., Wolf J., Spector T.D., Steves C.J., Modat M., and Ourselin S. Accessible data curation and analytics for international-scale citizen science datasets, Scientific Data, 2021, doi:10.1038/s41597-021-01071-x

• Grosche S.^†, Marenholz I.^†, Esparza-Gordillo J.^†, Arnau-Sole A.^†, …, Visconti A., …, Worth CL, Xu CJ, and Lee YA, Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4, Nature Communications, 2021, doi:10.1038/s41467-021-26783-x

• Dotz V.^†, Visconti A.^†, Lomax-Browne H.^†, Florent C.^†, Ederveen A.H., Medjeral-Thomas N., Cook H.T., Pickering M., Wuhrer M.^‡, and Falchi M.^‡, O- and N-Glycosylation of Serum Immunoglobulin A is Associated with IgA Nephropathy and Glomerular Function, Journal of the American Society of Nephrology, 2021, doi:10.1681/ASN.2020081208

• Sudre C.H.^†, Lee K.A.^†, Lochlainn M.N.^†, Varsavsky T, Murray B., …, Visconti A., …, Spector T.D., Steves C.J.^‡, and Ourselin S.^‡, Symptom clusters in COVID-19: A potential clinical prediction tool from the COVID Symptom Study app, Science Advances, 2021, doi:10.1126/sciadv.abd4177

• Piaggeschi G., Rolla S., Rossi N., Brusa D., Naccarati A., Couvreur S., Spector T.D., Roederer M., Mangino M., Cordero F., Falchi M.^‡, and Visconti A.^‡, Immune trait shifts in association with tobacco smoking: a study in healthy women, Frontiers in immunology, 2021, doi:10.3389/fimmu.2021.637974

• Rossi N.^†, Aliyev E.^†, Visconti A., Akil A.S.A., Syed N., Aamer W., Padmajeya S.S., Falchi M.^‡, and Fakhro K.A.^‡, Ethnic-specific association of amylase gene copy number with adiposity traits in a large Middle Eastern biobank, Genomic Medicine, 2021, doi:10.1038/s41525-021-00170-3

• Williams F.M.K., Freidin M.B., Mangino M., Couvreur S., Visconti A., Bowyer R.C.E., Le Roy C.I., Falchi M., Mompeó O., Sudre C., Davies R., Hammond C., Menni C., Steves C.J., and Spector T.D., Self-Reported Symptoms of COVID-19, Including Symptoms Most Predictive of SARS-CoV-2 Infection, Are Heritable, Twin Research and Human Genetics, 2021, doi:10.1017/thg.2020.85

• Visconti A.^†, Bataille V.^†, Rossi N., Kluk J., Murphy R., Puig S., Nambi R., Bowyer R.C.E., Murray B., Bournot A., Wolf J., Ourselin S., Steves C., Spector T.D.^‡, and Falchi M.^‡, Diagnostic value of cutaneous manifestation of SARS-CoV-2 infection, British Journals of Dermatology, 2021, doi:10.1111/bjd.19807

• Hopkinson N.S.^†, Rossi N.^†, El-Sayed_Moustafa J., Laverty A.A., Quint J.K., Freidin M., Visconti A., Murray B., Modat M., Ourselin S., Small K., Davies R., Wolf J., Spector T.D., Steves C.J.^‡, and Falchi M.^‡, Current smoking and COVID-19 risk: results from a population symptom app in over 2.4 million people, Thorax, 2021, doi:10.1136/thoraxjnl-2020-216422

• Bar N.^†, Korem T.^†, Weissbrod O., Zeevi D., Rothschild D., Leviatan S., Kosower N., Lotan-Pompan M., Weinberger A., Le Roy C.I., Menni C., Visconti A., Falchi M., Spector T.D., The IMI DIRECT consortium, Adamski J., Franks P.W., Pedersen O. and Segal E., A reference map of potential determinants for the human serum metabolome, Nature, 2020, doi:10.1038/s41586-020-2896-2

• Zazzara M.B.^†, Penfold R.S.^†, Roberts A.L.^†, Lee, K.A., Dooley H., Sudre C.H., Welch C., Bowyer R.C.E, Visconti A., …, Martin F.C., Steves C.J.^‡, and Lochlainn M.N.^‡, Probable delirium is a presenting symptom of COVID-19 in frail, older adults: a cohort study of 322 hospitalised and 535 community-based older adults, Age and Ageing, 2020, doi:10.1093/ageing/afaa223

• Sanna M.^†, Li X.^†, Visconti A., Freidin M. B., Sacco C., Ribero S., Hysi P., Bataille V., Han J.^‡, and Falchi M.^‡, Looking for Sunshine: Genetic Predisposition to Sun-Seeking in 265,000 Individuals of European Ancestry, Journal of Investigative Dermatology, 2020, doi:10.1016/j.jid.2020.08.014

• Lee K.A.^†, Ma W.^†, Sikavi D.R., …, Visconti A., …, Ourselin S., Spector T.D., and Chan A.T., COPE consortium, Cancer and Risk of COVID-19 Through a General Community Survey, Oncologist, 2020, doi:10.1634/theoncologist.2020-0572

• Scarfi F., Orozco A.P., Visconti A., and Bataille V., An Aggressive Clinical Presentation of Familial Leiomyomatosis Associated with a Fumarate Hydratase Gene Variant of Uncertain Clinical Significance, Acta Dermato-venereologica, 2020, doi:10.2340/00015555-3573

• Menni C.^†, Valdes A. M.^†, Freidin M.B., Sudre C.H., Nguyen L.H., Drew D.A., Ganesh S., Varsavsky T., Cardoso M.J., El-Sayed Moustafa J.S., Visconti A., Hysi P., Bowyer R.C.E., Mangino M., Falchi M., Wolf J., Ourselin S., Chan A.T., Steves C.J.^‡, and Spector T.D.^‡, Real-time tracking of self-reported symptoms to predict potential COVID-19, Nature Medicine, 2020, doi:10.1038/s41591-020-0916-2

• Landi M.T., Bishop D.T., MacGregor S., …, Visconti A., …, Shi J., Iles M.M. and Law M.H., Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility, Nature Genetics, 2020, doi:10.1038/s41588-020-0611-8

• Visconti A., Sanna M., Bataille V., and Mario F., Genetics plays a role in nevi distribution in women, Melanoma Management, 2020, doi:10.2217/mmt-2019-0019 [Invited editorial]

• Martin T.C., Illieva K.M., Visconti A., Beaumont M., Kiddle S.J., Dobson R.J.B., Mangino M., Lim E.M., Pezer M., Steves C.J., Bell J.T., Wilson S.G., Lauc G., Roederer M., Walsh J.P., Spector T.D.^‡, Karagiannis S.N.^‡, Dysregulated Antibody, Natural Killer Cell and Immune Mediator Profiles in Autoimmune Thyroid Diseases, MDPI Cells, 2020, doi:10.3390/cells9030665

• Visconti A.^†, Le Roy C.I.^†, Rosa F., Rossi N., Martin T.C., Mohney R.P., Li W., de Rinaldis E., Bell J.T., Venter J.C., Nelson K.E., Spector T.D.^‡, and Falchi M.^‡, Interplay between the human gut microbiome and host metabolism, Nature Communications, 2019, doi:10.1038/s41467-019-12476-z

• Visconti A., Ribero S., Sanna M., Spector T.D. Bataille V., and Falchi M., Body site‐specific genetic effects influence naevus count distribution in women, Pigment Cell & Melanoma Research, 2019, doi:10.1111/pcmr.12820

• Cullen H., Krishnan M.L., Selzam S., Ball G., Visconti A, Saxena A., Counsell S.J., Hajnal J., Breen G., Plomin R. & Edwards A.D., Polygenic risk for neuropsychiatric disease and vulnerability to abnormal deep grey matter development, Scientific Reports, 2019, doi:10.1038/s41598-019-38957-1

• Duffy D., Zhu G., Li X., …, Visconti A., … Falchi M., Han J.^‡, Martin N.G.^‡, Melanoma GWAS Consortium Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways, Nature Communications, 2018, doi:10.1038/s41467-018-06649-5

• Martin T.C.^†, Visconti A^†, Spector T.D., and Falchi M., Conducting metagenomic studies in microbiology and clinical research, Applied Microbiology and Biotechnology, 2018, doi:10.1007/s00253-018-9209-9

• Visconti A., Martin T.C., and Falchi M., YAMP: a containerised workflow enabling reproducibility in metagenomics research, GigaScience, 2018, doi:10.1093/gigascience/giy072

• Visconti A., Duffy D., Liu F., Zhu G., …, Han J., Bataille V., and Falchi M., Genome-wide association study in 176,678 Europeans reveals genetic loci for tanning response to sun exposure, Nature Communications, 2018, doi:10.1038/s41467-018-04086-y

• Hysi P.G.^†, Valdes A.M.^†, Liu F.^†, Furlotte N.A., Evans D.M., Bataille V., Visconti A., …, Kayser M.^‡, and Spector T.D.^‡, Genome-wide association meta-analysis of individuals of European ancestry identifies new loci explaining a substantial fraction of hair color variation and heritability, Nature Genetics, 2018, doi:10.1038/s41588-018-0100-5

• Zaghlool S.B., Mook-Kanamori D.O., Kader S., Stephan N., Halama A., Engelke R., Sarwath H., Al-Dous E. K., Mohamoud Y. A., Roemisch-Margl W., Adamski J., Kastenmüller G., Friedrich N., Visconti A., …, Malek J.A., and Suhre K, Deep molecular phenotypes link complex disorders and physiological insult to CpG methylation, Human Molecular Genetics, 2018, doi:10.1093/hmg/ddy006

• Visconti A., Al-Shafai M., Al Muftah W.A., Zaghlool S.B., Mangino M., Suhre K., and Falchi M., PopPAnTe: population and pedigree association testing for quantitative data, BMC Genomics, 2017, doi:10.1186/s12864-017-3527-7

• Puig-Butille J.A., Gimenez-Xavier P., Visconti A., Nsengimana J., Garcia-Garcia F., Tell-Marti G., Escamez M.J., Newton-Bishop J.A., Bataille V., Del Rio M., Dopazo J., Falchi M, and Puig S., Genomic expression differences between cutaneous cells from red hair colour individuals and black hair colour individuals based on bioinformatic analysis, Oncotarget, 2016, doi:10.18632/oncotarget.14140

• Ribero S.^†, Sanna M.^†, Visconti A., Navarini A., Aviv A.,Glass D., Spector T.D., Smith C., Simpson M., Barker J., Mangino M., Falchi M.^‡, and Bataille V.^‡, Acne and telomere length. A new spectrum between senescence and apoptosis pathways, The Journal of Investigative Dermatology, 2016, doi:10.1016/j.jid.2016.09.014

• Lomax-Browne H.J.^†, Visconti A.^†, Pusey C.D., Cook H.T., Spector T.D., Pickering M.C^‡, and Falchi M^‡, IgA1 Glycosylation is Heritable in Healthy Twins, Journal of the American Society of Nephrology, 2016, doi:10.1681/ASN.2016020184

• Gialluisi A., Visconti A., Willcutt E.G., Smith S.D., Pennington B.F. Falchi M., DeFries J.C., Olson R.K., Francks C., and Fisher S.E., Investigating the effects of copy number variants on reading and language performance, Journal of Neurodevelopmental Disorders, 2016, doi:10.1186/s11689-016-9147-8

• Al Muftah W.A.^†, Al-Shafai M.^†, Zaghlool S.B., Visconti A., Tsai P.C., Kumar P., Spector T., Bell J.T., Falchi M.^‡, and Suhre K.^‡, Epigenetic associations of type 2 diabetes and BMI in an Arab population, Clinical Epigenetics, 2016, doi:10.1186/s13148-016-0177-6

• Johnson M.R., Shkura K., Langley S.R., …, Visconti A., …, Kaminski R.M., Deary I.J., and Petretto E., Systems genetics identifies a convergent gene network for cognition and neurodevelopmental disease, Nature Neuroscience, 2015 doi:10.1038/nn.4205

• Visconti A., Ermondi G., Caron G., and Esposito R., Prediction and Interpretation of the Lipophilicity of Small Peptides, Journal of Computer-Aided Molecular Design, 2015, doi:10.1007/s10822-015-9829-4

• Visconti A., Cordero F., and Pensa R.G., Leveraging additional knowledge to support coherent bicluster discovery in gene expression data, Intelligent Data Analysis, 2014, doi:10.3233/IDA-140671

• Ermondi G., Visconti A., Esposito R., and Caron G., The Block Relevance (BR) analysis supports the dominating effect of solutes hydrogen bond acidity on D(logP_oct-tol), European Journal of Pharmaceutical Sciences, 2014, doi:10.1016/j.ejps.2013.12.007

• Marbach D., Costello J.C., Kuffner R., Vega N., Prill R.J., Camacho D., Allison K.R., …, Visconti A., …, Kellis M., Collins J.J., and Stolovitzky G., Wisdom of crowds for robust gene network inference, Nature Methods, 2012, doi:10.1038/nmeth.2016

• Visconti A., Esposito R., and Cordero F., Restructuring the Gene Ontology to Emphasize Regulative Pathways and to Improve Gene Similarity Queries, Int. J. Computational Biology and Drug Design, 2011, doi:10.1504/IJCBDD.2011.041411

• Bonfante P., Cordero F., Ghignone S., Ienco D., Lanfranco L., Leonardi G., Meo R., Montani S., Roversi L., and Visconti A., A Modular Database Architecture Enabled to Comparative Sequence Analysis, LNCS Transactions on Large-Scale Data- and Knowledge-Centered Systems - TLDKS IV, LNCS 6990, 2011, doi:10.1007/978-3-642-23740-9_6

In proceedings

• Contaldo S.G., Pietropaolo E., Bosio L., Pernice S., Terrone I., Baccega D., Wang Y., Sahoo R.K., Rizzo G., Visconti A., Berchialla P., and Beccuti M., PHeP: TrustAlert Open-Source Platform for Enhancing Predictive Healthcare with Deep Learning, 19th conference on Computational Intelligence methods for Bioinformatics and Biostatistics, Benevento, Italia, September 4-6, 2024

• Esposito R, Radicioni D.P., and Visconti A., CDoT: optimizing MAP queries on trees, In proceedings of AI*IA 2013: Advances in Artificial Intelligence, XIIIth Int. Conf. of the Italian Association for Artificial Intelligence, Turin, December 4-6, 2013, LNAI 8249, doi:10.1007/978-3-319-03524-6_41

• Visconti A., Esposito R., and Cordero F., Tackling the DREAM Challenge for Gene Regulatory Networks Reverse Engineering, In Proceedings of AI*IA 2011: Artificial Intelligence Around Man and Beyond, XIIth Int. Conf. of the Italian Association for Artificial Intelligence - Palermo, September 15-17, 2011, LNAI 6934, doi:10.1007/978-3-642-23954-0_34

• Visconti A., Cordero F., Botta M., Calogero R.A., Gene Ontology rewritten for computing gene functional similarity, In Proceedings of the Fourth International Conferences on Complex, Intelligent and Software Intensive Systems, February 15-18, 2010, doi:10.1109/CISIS.2010.30

• Cordero F., Pensa R.G, Visconti A., Ienco D. and Botta M., Ontology-driven Co-clustering of Gene Expression Data, In proceedings of AI*IA 2009: Emergent Perspectives in Artificial Intelligence, XI Int. Conf. of the Italian Association for Artificial Intelligence - Reggio Emilia, December 9-12, 2009, LNAI 5883, doi:10.1007/978-3-642-10291-2_43

• Cordero F., Visconti A., and Botta M., A new protein motif extraction framework based on constrained co-clustering, In Proceedings of the 24th Annual ACM Symposium on Applied Computing - March 8-12, 2009, doi:10.1145/1529282.1529445

Book Chapters

• Visconti A., Cordero F., Ienco D., and Pensa R.G., Coclustering under Gene Ontology Derived Constraints for Pathway Identification, Biological Knowledge Discovery Handbook: Preprocessing, Mining and Postprocessing of Biological Data, Mourad Elloumi and Albert Y. Zomaya (Eds.), 2014, doi:10.1002/9781118617151.ch27

Pre Prints

• Ometto S.^†, Chatterjee S.^†, Vergani A.M., Landini A., Sharapov S,, Giacopuzzi E., Visconti A., Bianchi E., Santonastaso F., Soda E.M., Cisternino F., Ieva F., Di Angelantonio E., Pirastu N., Glastonbury G.A., \emph{Unsupervised cardiac MRI phenotyping with 3D diffusion autoencoders reveals novel genetic insights}, medRxiv, 2024, doi:10.1101/2024.11.04.24316700

• Zolfo M., Silverj A., Blanco-Míguez A., Manghi P., Rota-Stabelli O., …, Visconti A., …, Asnicar F., Kitano H., Yamada T., Segata N., Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples, bioRxiv, 2024, doi:10.1101/2024.02.19.580813

Thesis

• Visconti A., Systems Biology: Knowledge Discovery and Reverse Engineering, PhD Thesis, Department of Computer Science, University of Turin, 2012

• Visconti A., SPOT: an algorithm for the extraction and the analysis of biological patterns, Master Thesis, Department of Computer Science, University of Turin, 2008

• Visconti A., The Haskell language, Bachelor Thesis, Department of Computer Science, University of Turin, 2006