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

    • "Charting multicellular tissue structure cell-to-cell" News & View, Nat. Genetics

  • 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,

    • "Whole-genome doubling perturbs the 3D genome" Research Highlight, Nat. Genetics
    • "Genome Doubling Weakens DNA Organization and Supports Tumorigenesis" Research Watch, Cancer Discovery
    • "Genome doubling perturbs DNA packing and promotes cancer development" Research Briefings, Nature

  • 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

    • "Evolutionary dependencies show paths to cancer development" Martin S. Taylor, Nat. Genetics
    • Featured in Nature Cancer Milestones

  • 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

    • "Genetic Alterations Impact Immune Microenvironment Interactions in Follicular Lymphoma" Riether C. & Ochsenbein A.F., Cancer Cell
    • "Cathepsin S protease mediates T-cell response in Non-Hodgkin Lymphoma" Research Watch Cancer Discovery

  • 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,

    Check out the Video Abstract:

    • "The 3D Genome: EZH2 Comes into the Fold" Gerard L. Brien & Adrian P. Bracken, Trends in Molecular Medicine
    • Elisa's Interview at the Radio Television Suisse (French)
    • Also highlighted in:

  • 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.

  • 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

    • "The future of kinase inhibitors for DLBCL?"   Sarah E. M. Herman Blood

  • 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

    • "Cliques and Schisms of Cancer Genes"   Peter J. Campbell. Cancer Cell
    • "Conditional selection determines the pathways of cancer evolution"   David Killock.
      Nature Review Clinical Oncology

  • 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

  • Supplemental Data
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    This article has been also highlighted in: EurekaAlert Economist HuffingtonPost ScienceDaily

  • 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

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  • The complete list of publications can be found here

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