Computational Systems Oncology

Selected Publications
All Publications

Lab members are in bold, ^* Co-first authors, Co-corresponding authors

Varrone M., Tavernari D., Santamaria-Martinez A., Walsh L.A., and Ciriello G. (2024) CellCharter: a scalable framework to chart and compare cell niches across multiple samples and spatial -omics technologies . Nat. Genetics, 56(1), 74-84
Highlights:

Ciriello G. , Magnani L. et al. (2024) Cancer Evolution: A Multifaceted Affair . Cancer Discovery, (review) 14(1), 36-48

Lambuta R.A.*, Nanni L. *, Liu Y. , Diaz-Miyar J., Iyer A. , Tavernari D. , Katanayeva N., Ciriello G., Oricchio E. (2023) Whole-genome doubling drives oncogenic loss of chromatin segregation . Nature,
Highlights:

Mina M. , Iyer A. , and Ciriello G. (2022) Epistasis and evolutionary dependencies in human cancers . Curr Opin Genet Dev., 77, (Review),

Liu Y. , Nanni L. , Sungalee Y., Zufferey M. , Tavernari D. , Mina M. , Ceri S., Oricchio E., and Ciriello G. (2021) Systematic inference and comparison of multi-scale chromatin sub-compartments connects spatial organization to cell phenotypes . Nature Communications, 12 (1), 1-11

Sungalee S.^*, Liu Y. ^*, Lambuta R.A., Katanayeva N., Collier M.D., Tavernari D. , Roulland S., Ciriello G. , and Oricchio E. (2021) Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci . Nature Genetics, 53 (5), 650-662

Tavernari D. , Battistello E. , Dheilly E., Petruzzella A.S., Mina M. , Sordet-Dessimoz J., Peters S., Krueger T., Gfeller D., Riggi N., Oricchio E., Letovanec I.
and Ciriello G. (2021) Non-genetic evolution drives lung adenocarcinoma spatial heterogeneity and progression . Cancer Discovery, 11, 1490-1507

Zufferey M. , Liu Y. , Tavernari D., Mina M., and Ciriello G. (2021) Systematic assessment of gene co-regulation within chromatin domains determines differentially active domains across human cancers . Genome Biology, 22 (1), 1-24

Ciriello G. and Magnani L. (2021) The many faces of cancer evolution . iScience , 24 (5)

Mina M., Iyer A., Tavernari D., Raynaud F. and Ciriello G. (2020) Discovering functional evolutionary dependencies in human cancers . Nature Genetics, 52, 1198-1207
Highlights:

Dheily, E.^*, Battistello E.^*, Katanayeva N., Sungalee S., Michaux, J., Duns G., Wehrle S., Sordet-Dessimoz J., Mina M., Racle J., Farinha P., Coukos G., Gfeller D., Mottok A., Kridel E., Correia B.E., Steidl C., Bassani-Stenberg M., Ciriello G., Zoete V., Oricchio E. (2020) Cathepsin S Regulates Antigen Processing and T Cell Activity in Non-Hodgkin Lymphoma . Cancer Cell, 5, 674-689
Highlights:

Raynaud F., Mina M., Ciriello G. (2019) Dynamic Emergence of Observed and Hidden Intra-tumor Heterogeneity . iScience, 21, 157-167

Donaldson-Collier M.C.^*, Sungalee S.^*, Zufferey M.^*, Tavernari D.^*, Katanayeva N., Battistello E., Mina M., Douglass K., Rey T., Raynaud F., Manley S.,
Ciriello G., Oricchio E. (2019) EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within topologically associating domains.
Nature Genetics, https://doi.org/10.1038/s41588-018-0338-y
Check out the Video Abstract:

Highlights:

Zeng Q., Michael I.P, Zhang P., Saghafinia S., Knott G., Jiao W., McCabe B.D., Galván J.A., Robinson H.P.C., Zlobec I., Ciriello G., Hanahan D. (2019) Synaptic proximity enables NMDAR signalling to promote brain metastasis . Nature, 573, 526-531

Cheng W-C., Tsui Y-C., Ragusa S., Koelzer V.H., Mina M., Franco F., Läubli H., Tschumi B., Speiser D., Romero P., Zippelius A., Petrova T.V., Mertz K., Ciriello G., Ho P-C. (2019) Uncoupling protein 2 reprograms the tumor microenvironment to support the anti-tumor immune cycle . Nat. Immunology, 20, 206-217

Zufferey M.^*, Tavernari D.^*, Oricchio E., Ciriello G. (2018) Comparison of computational methods for the identification of topologically associating domains. Genome Biology, 19:217

Saghafinia S.^*, Mina M.^*, Riggi N., Hanahan D., Ciriello G. (2018) Pan-cancer landscape of aberrant DNA methylation across human tumors . Cell Reports, 25(4), 1066-1080

Raynaud F., Mina M., Tavernari D., Ciriello G. (2018) Pan-cancer inference of intra-tumor heterogeneity reveals associations with different forms of genomic instability . PLoS Genetics, 14(9), e1007669. https://doi.org/10.1371/journal.pgen.1007669

Sanchez-Vega F.^*, Mina M.^*, Armenia J.^*, Chatila W.K., Luna A., La K.C., Dimitriadoy S., Liu D.L., Kantheti H.S., Saghafinia S., Chakravarty D., Daian F., Gao Q., Bailey M.H., Liang W., Foltz S.M., Shmulevich I., Ding I., Heins Z., Ochoa A., Gross B., Gao J., Zhang H., Kundra R., Kandoth C., Bahceci I., Dervishi L., Dogrusoz U., Zhou W., Shen H., Laird P.W., Way G.P., Greene C.S., Liang H., Xiao Y., Wang C., Iavarone A., Berger A.H., Bivona T.G., Lazar A.J., Hammer G.D., Giordano T., Kwong L.N., McArthur G., Huang C., Tward A.D., Frederick M.J., McCormick F., Meyerson M., The Cancer Genome Atlas Research Network, Van Allen E.M., Cherniack A.D.,
Ciriello G., Sander C., Schultz N. (2018) Oncogenic Signaling Pathways in The Cancer Genome Atlas . Cell, 173(2), 321-337

Battistello E., Katanayeva N., Dheilly E., Tavernari D., Donaldson M.C., Bonsignore L., Thome-Miazza M., Christie A.L., Murakami M.A., Michielin O., Ciriello G., Zoete V., Oricchio E. (2018) Pan-SRC kinase inhibition blocks B-cell receptor oncogenic signaling in non-Hodgkin lymphoma . Blood, 131(21), 2345-2356
Highlights:

Mina M., Raynaud F., Tavernari D., Battistello E., Sungalee S. , Saghafinia S., Laessle T., Sanchez-Vega F., Schultz N., Oricchio E., Ciriello G. (2017) Conditional Selection of Genomic Alterations Dictates Cancer Evolution and Oncogenic Dependencies. Cancer Cell, 32(2), 155-168
Highlights:

Oricchio E., Katanayeva N., Donaldson M.C., Sungalee S., Pasion J.P., Béguelin W., Battistello E., Sanghvi V.R., Jiang M., Jiang Y., Teater M., Parmigiani A., Budanov A.V., Chan F.C., Shah S.P., Kridel R., Melnick A.M., Ciriello G. and Wendel H-G. (2017) Genetic and epigenetic inactivation of SESTRIN1 controls mTORC1 and response to EZH2 inhibition in follicular lymphoma, Science Trans. Med., 9, 396

Ciriello G.^*, Gatza M.L.^*, Bexk A.H., Wilkerson M.D., Rhie S.K., Pastore A., Zhang H., McLellan M., Yau C., Kandoth C., Bowlby R., Shen H., Hayat S., Fieldhouse R., Lester S.C., Tse G.M.K., Factor R.E., Collins L.C., Allison K.H., Chen Y.Y., Jensen K., Johnson N.B., Oesterreich S., Mills G.B., Cherniack A., Robertson G., Benz C., Sander, C., Laird P.W., Hoadley K.A., King T.A., TCGA Research Network, Perou C.M., (2015) Comprehensive molecular portraits of invasive lobular breast cancer, Cell, 163, 2 506-519

Oricchio E., Ciriello G., Jiang M., Boyce M.H., Schatz. J.H., Heguy A., Viale A., de Stanchina E., Teruya-Feldstein J., Bouska A., McKeithan T., Sander C., Tam W., Seshan V.E., Chan J., Chaganti R.S.K & Wendel H.G. (2014) Frequent disruption of the RB pathway in indolent follicular lymphoma suggests a new combination therapy. J. Exp. Medicine, 211, 7, 1379-91

Ciriello G., Miller L.M., Aksoy B.A., Senbabaoglu Y., Schultz N. & Sander C. (2013) Emerging landscape of oncogenic signatures across human cancers. Nat. Genetics, 45, 10, 1127-1133

Ciriello G., Sinha R., Hoadley K.A., Jacobsen A.S., Reva B., Perou C.M., Sander C. & Schultz N. (2013), The molecular diversity of Luminal A breast tumors. Breast Cancer Res. Treat., 141, 3, 409-420

Ciriello G., Cerami E.G., Sander C. & Schultz N. (2012), Mutual Exclusivity Analysis Identifies Oncogenic Network Modules. Genome Res., 22, 398-406

The complete list of publications can be found here

Publications