Select Publications

Book Chapters

Van Der Byl W; Rizzetto S; Samir J; Cai C; Eltahla AA; Luciani F, 2019, 'Single-Cell Transcriptome Analysis of T Cells', in Methods in Molecular Biology, pp. 155 - 205, http://dx.doi.org/10.1007/978-1-4939-9728-2_16

Bull RA; Luciani F, 2016, 'Next-Generation Sequencing, What Has It Told Us So Far?', in Foodborne Viral Pathogens, CRC Press

Mishto M; Luciani F; Holzhutter H; Bellavista E; Santoro A; Textoris-Taube K; Kloetzel P; Zaikin A; Franceschi C, 2008, 'ProteaMAlg: a Proteasome Modelling Algorithm to address the complexity of intracellular protein degradation kinetics.', in Gastone C; Lamberti E; Fortunati V; Franceschi C (ed.), Biocomplexity at the cutting edge of Physics, System Biology and Humanities, Bononia University Press, Bononia

Zaikin A; Luciani F; Kurths J, 2007, 'Constructing a virtual proteasome', in Bertau M; Mosekilde E; Westerhoff HV (ed.), Biosimulation in Drug Development, Wiley-VCH Verlag GmbH & Co, Germany, pp. 373 - 402

Luciani F; Nielsen M; Kesmir C; Di napoli M, 2007, 'Theoretical models for proteasome function: predictive methods to understand the ubiquitin protein system in neurodegenerative diseases. [Chapter on modelling proteasome degradation and of potential mechanisms behind the accumulation of proteins leading to neurodegenerative diseases, such as Huntington disease or Amyotrophic Lateral Sclerosis.]', in Napoli MD; Wojcik C (ed.), The Ubiquitin Proteasome System in the Central Nervous System: From Physiology to Pathology, Nova Biomedical Books

Luciani F; Zaikin A, 2006, 'Mathematical models of the proteasome product size', in Schimansky Geier L; Malchow H; Poeschel T (ed.), Irreversible Prozesse und Selbstorganisation, Logos-Verlag, Berlin, pp. 279 - 292

Luciani F; Zaikin A, 2006, 'Mathematical models of the proteasome product size distribution', in Schimansky-Geier L; Malchow H; Poeschel T (ed.), Irreversible Prozesse und Selbstorganisation, Logos-Verlag, Berlin, pp. 196 - 208

Journal articles

Van Der Byl W; Nüssing S; Peters TJ; Ahn A; Li H; Ledergor G; David E; Koh AS; Wagle MV; Deguit CDT; de Menezes MN; Travers A; Sampurno S; Ramsbottom KM; Li R; Kallies A; Beavis PA; Jungmann R; Bastings MMC; Belz GT; Goel S; Trapani JA; Crabtree GR; Chang HY; Amit I; Goodnow CC; Luciani F; Parish IA, 2024, 'The CD8+ T cell tolerance checkpoint triggers a distinct differentiation state defined by protein translation defects', Immunity, 57, pp. 1324 - 1344.e8, http://dx.doi.org/10.1016/j.immuni.2024.04.026

Underwood AP; Gupta M; Wu B-R; Eltahla AA; Boo I; Wang JJ; Agapiou D; Abayasingam A; Reynaldi A; Keoshkerian E; Zhao Y; Brasher N; Walker MR; Bukh J; Maher L; Gordon T; Davenport MP; Luciani F; Drummer HE; Lloyd AR; Bull RA, 2024, 'B cell characteristics define HCV reinfection outcome.', J Hepatol, http://dx.doi.org/10.1016/j.jhep.2024.04.004

Louie RY; Samir J; Cai C; McGuire H; Amos T; Fergsuson J; Deveson I; Adikari T; Bonomi M; Bishop D; Mason CE; Balderas R; Ruella M; Singh M; Gottlieb D; Blyth E; Micklethwaite K; Luciani F, 2024, 'Abstract 882: Harnessing single cell multi-omics data to identify predictors of clinical outcome in CD19 CAR T cell therapy', Cancer Research, 84, pp. 882 - 882, http://dx.doi.org/10.1158/1538-7445.am2024-882

Pham VVH; Jue TR; Bell JL; Luciani F; Michniewicz F; Cirillo G; Vahdat L; Mayoh C; Vittorio O, 2024, 'A novel network-based method identifies a cuproplasia-related pan-cancer gene signature to predict patient outcome', Human Genetics, http://dx.doi.org/10.1007/s00439-024-02673-2

Louie RHY; Cai C; Samir J; Singh M; Deveson IW; Ferguson JM; Amos TG; McGuire HM; Gowrishankar K; Adikari T; Balderas R; Bonomi M; Ruella M; Bishop D; Gottlieb D; Blyth E; Micklethwaite K; Luciani F, 2023, 'CAR+ and CAR T cells share a differentiation trajectory into an NK-like subset after CD19 CAR T cell infusion in patients with B cell malignancies', Nature Communications, 14, http://dx.doi.org/10.1038/s41467-023-43656-7

Yang Y; Louie R; Puc J; Vedvyas Y; Alcaina Y; Min IM; Britz M; Luciani F; Jin MM, 2023, 'Chimeric Antigen Receptor T Cell Therapy Targeting Epithelial Cell Adhesion Molecule in Gastric Cancer: Mechanisms of Tumor Resistance', Cancers, 15, http://dx.doi.org/10.3390/cancers15235552

Ghita L; Yao Z; Xie Y; Duran V; Cagirici HB; Samir J; Osman I; Rebellón-Sánchez DE; Agudelo-Rojas OL; Sanz AM; Sahoo MK; Robinson ML; Gelvez-Ramirez RM; Bueno N; Luciani F; Pinsky BA; Montoya JG; Estupiñan-Cardenas MI; Villar-Centeno LA; Rojas-Garrido EM; Rosso F; Quake SR; Zanini F; Einav S, 2023, 'Global and cell type-specific immunological hallmarks of severe dengue progression identified via a systems immunology approach', Nature Immunology, 24, pp. 2150 - 2163, http://dx.doi.org/10.1038/s41590-023-01654-3

Melén E; Lambrecht BN; Lloyd CM; Rothenberg ME; Kabashima K; Luciani F; Coquet JM; Ober C; Nawijn MC; Platts-Mills T; von Mutius E, 2023, 'A conversation on allergy: recognizing the past and looking to the future', Immunology and Cell Biology, 101, pp. 936 - 946, http://dx.doi.org/10.1111/imcb.12688

van de Sandt CE; Nguyen THO; Gherardin NA; Crawford JC; Samir J; Minervina AA; Pogorelyy MV; Rizzetto S; Szeto C; Kaur J; Ranson N; Sonda S; Harper A; Redmond SJ; McQuilten HA; Menon T; Sant S; Jia X; Pedrina K; Karapanagiotidis T; Cain N; Nicholson S; Chen Z; Lim R; Clemens EB; Eltahla A; La Gruta NL; Crowe J; Lappas M; Rossjohn J; Godfrey DI; Thomas PG; Gras S; Flanagan KL; Luciani F; Kedzierska K, 2023, 'Newborn and child-like molecular signatures in older adults stem from TCR shifts across human lifespan', Nature Immunology, 24, pp. 1890 - 1907, http://dx.doi.org/10.1038/s41590-023-01633-8

Luciani F; Louie RY; Cai C; Singh M; Deveson I; Ferguson J; Amos T; McGuire H; Samir J; Gowrishankar K; Adikari T; Balderas R; Bishop D; Gottileb D; Blyth E; Micklethwaite K, 2023, 'CAR +and CAR −T cells differentiate into an NK-like subset that is associated with increased inflammatory cytokines following infusion', The Journal of Immunology, 210, pp. 159.15 - 159.15, http://dx.doi.org/10.4049/jimmunol.210.supp.159.15

Yang Y; Louie R; Puc J; Vedvyas Y; Alcaina Y; Min IM; Britz M; Luciani F; Jin MM, 2023, 'Abstract 912: Single cell analysis reveals tumor evolution and CAR T cell dysfunction associated with tumor resistance', Cancer Research, 83, pp. 912 - 912, http://dx.doi.org/10.1158/1538-7445.am2023-912

Gupta M; Balachandran H; Louie RHY; Li H; Agapiou D; Keoshkerian E; Christ D; Rawlinson W; Mina MM; Post JJ; Hudson B; Gilroy N; Konecny P; Bartlett AW; Sasson SC; Ahlenstiel G; Dwyer D; Lloyd AR; Martinello M; Luciani F; Bull RA, 2023, 'High activation levels maintained in receptor-binding domain–specific memory B cells in people with severe coronavirus disease 2019', Immunology and Cell Biology, 101, pp. 142 - 155, http://dx.doi.org/10.1111/imcb.12607

Luciani F; Papa E; Leggeri A; Condò R; Giovannetti F; Calabrese L, 2023, 'Peripheral ameloblastoma: case report and our experience 20 years', Acta Biomedica, 94, http://dx.doi.org/10.23750/abm.v94iS1.13527

Underwood AP; Gupta M; Wu B-R; Eltahla AA; Boo I; Wang JJ; Agapiou D; Abayasingam A; Reynaldi A; Keoshkerian E; Zhao Y; Brasher N; Walker MR; Bukh J; Maher L; Gordon T; Davenport M; Luciani F; Drummer HE; Lloyd AR; Bull RA, 2023, 'B Cell Signatures and Antibody Imprinting Define HCV Reinfection Outcome', , http://dx.doi.org/10.2139/ssrn.4418620

Shek D; Gao B; Mahajan H; Nagrial A; Carlino MS; Luciani F; Read SA; Ahlenstiel G, 2023, 'In-depth profiling of tumor tissue derived from malignant pleural mesothelioma patients identifies potential biomarkers predicting response to immune-checkpoint inhibitor therapy', Genes & Diseases, pp. 101189 - 101189, http://dx.doi.org/10.1016/j.gendis.2023.101189

Cai C; Samir J; Pirozyan MR; Adikari TN; Gupta M; Leung P; Hughes B; Van der Byl W; Rizzetto S; Elthala A; Keoshkerian E; Palgen JL; Peters T; Nguyen THO; Louie R; Kedzierska K; Gaudieri S; Bull RA; Lloyd AR; Luciani F, 2022, 'Identification of human progenitors of exhausted CD8+ T cells associated with elevated IFN-γ response in early phase of viral infection', Nature Communications, 13, http://dx.doi.org/10.1038/s41467-022-35281-7

Cai C; Samir J; Adikari T; Peters T; Luciani F, 2022, 'The functional and molecular determinants of HCV-specific CD8 T cell responses during early infection', The Journal of Immunology, 208, pp. 169.12 - 169.12, http://dx.doi.org/10.4049/jimmunol.208.supp.169.12

Massey J; Jackson K; Singh M; Hughes B; Withers B; Ford C; Khoo M; Hendrawan K; Zaunders J; Charmeteau-De Muylder B; Cheynier R; Luciani F; Ma D; Moore J; Sutton I, 2022, 'Haematopoietic Stem Cell Transplantation Results in Extensive Remodelling of the Clonal T Cell Repertoire in Multiple Sclerosis', Frontiers in Immunology, 13, http://dx.doi.org/10.3389/fimmu.2022.798300

Luciani F; Papa E; Leggeri A; Calabrese C; Coniglione F; Calabrese L, 2022, 'DIAGNOSIS AND TREATMENT PLANNING IN ORAL SURGERY USING CONE BEAM COMPUTED TOMOGRAPHY (CBCT): A NARRATIVE REVIEW', International Journal of Clinical Dentistry, 15, pp. 795 - 820

Goncharov M; Bagaev D; Shcherbinin D; Zvyagin I; Bolotin D; Thomas PG; Minervina AA; Pogorelyy MV; Ladell K; McLaren JE; Price DA; Nguyen THO; Rowntree LC; Clemens EB; Kedzierska K; Dolton G; Rius CR; Sewell A; Samir J; Luciani F; Zornikova KV; Khmelevskaya AA; Sheetikov SA; Efimov GA; Chudakov D; Shugay M, 2022, 'VDJdb in the pandemic era: a compendium of T cell receptors specific for SARS-CoV-2', Nature Methods, http://dx.doi.org/10.1038/s41592-022-01578-0

Wagle MV; Vervoort SJ; Kelly MJ; Van Der Byl W; Peters TJ; Martin BP; Martelotto LG; Nüssing S; Ramsbottom KM; Torpy JR; Knight D; Reading S; Thia K; Miosge LA; Howard DR; Gloury R; Gabriel SS; Utzschneider DT; Oliaro J; Powell JD; Luciani F; Trapani JA; Johnstone RW; Kallies A; Goodnow CC; Parish IA, 2021, 'Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance', Nature Communications, 12, pp. 2782, http://dx.doi.org/10.1038/s41467-021-23044-9

Hensen L; Illing PT; Bridie Clemens E; Nguyen THO; Koutsakos M; van de Sandt CE; Mifsud NA; Nguyen AT; Szeto C; Chua BY; Halim H; Rizzetto S; Luciani F; Loh L; Grant EJ; Saunders PM; Brooks AG; Rockman S; Kotsimbos TC; Cheng AC; Richards M; Westall GP; Wakim LM; Loudovaris T; Mannering SI; Elliott M; Tangye SG; Jackson DC; Flanagan KL; Rossjohn J; Gras S; Davies J; Miller A; Tong SYC; Purcell AW; Kedzierska K, 2021, 'CD8+ T cell landscape in Indigenous and non-Indigenous people restricted by influenza mortality-associated HLA-A*24:02 allomorph', Nature Communications, 12, http://dx.doi.org/10.1038/s41467-021-23212-x

Micklethwaite KP; Gowrishankar K; Gloss BS; Li Z; Street JA; Moezzi L; Mach MA; Sutrave G; Clancy LE; Bishop DC; Louie RHY; Cai C; Foox J; MacKay M; Sedlazeck FJ; Blombery P; Mason CE; Luciani F; Gottlieb DJ; Blyth E, 2021, 'Investigation of product-derived lymphoma following infusion of piggyBac-modified CD19 chimeric antigen receptor T cells', Blood, 138, pp. 1391 - 1405, http://dx.doi.org/10.1182/blood.2021010858

González-Candelas F; Shaw MA; Phan T; Kulkarni-Kale U; Paraskevis D; Luciani F; Kimura H; Sironi M, 2021, 'One year into the pandemic: Short-term evolution of SARS-CoV-2 and emergence of new lineages', Infection, Genetics and Evolution, 92, http://dx.doi.org/10.1016/j.meegid.2021.104869

Zhao Y; Cai C; Samir J; Palgen JL; Keoshkerian E; Li H; Bull RA; Luciani F; An H; Lloyd AR, 2021, 'Human CD8 T-stem cell memory subsets phenotypic and functional characterization are defined by expression of CD122 or CXCR3', European Journal of Immunology, 51, pp. 1732 - 1747, http://dx.doi.org/10.1002/eji.202049057

Sullivan LC; Nguyen THO; Harpur CM; Stankovic S; Kanagarajah AR; Koutsakos M; Saunders PM; Cai Z; Gray JA; Widjaja JML; Lin J; Pietra G; Mingari MC; Moretta L; Samir J; Luciani F; Westall GP; Malmberg KJ; Kedzierska K; Brooks AG, 2021, 'Natural killer cell receptors regulate responses of HLA-E-restricted T cells', Science Immunology, 6, http://dx.doi.org/10.1126/sciimmunol.abe9057

Sutton HJ; Aye R; Idris AH; Vistein R; Nduati E; Kai O; Mwacharo J; Li X; Gao X; Andrews TD; Koutsakos M; Nguyen THO; Nekrasov M; Milburn P; Eltahla A; Berry AA; KC N; Chakravarty S; Sim BKL; Wheatley AK; Kent SJ; Hoffman SL; Lyke KE; Bejon P; Luciani F; Kedzierska K; Seder RA; Ndungu FM; Cockburn IA, 2021, 'Atypical B cells are part of an alternative lineage of B cells that participates in responses to vaccination and infection in humans', Cell Reports, 34, http://dx.doi.org/10.1016/j.celrep.2020.108684

Kwon JA; Chambers GM; Luciani F; Zhang L; Kinathil S; Kim D; Thein HH; Botha W; Thompson S; Lloyd A; Yap L; Gray RT; Butler T, 2021, 'Hepatitis C treatment strategies in prisons: A cost-effectiveness analysis', PLoS ONE, 16, pp. e0245896, http://dx.doi.org/10.1371/journal.pone.0245896

Foster S; Luciani F, 2021, 'Omics in immunology', Immunology and Cell Biology, 99, pp. 133 - 134, http://dx.doi.org/10.1111/imcb.12435

Louie RHY; Luciani F, 2021, 'Recent advances in single-cell multimodal analysis to study immune cells', Immunology and Cell Biology, 99, pp. 157 - 167, http://dx.doi.org/10.1111/imcb.12432

Gottlieb DJ; Clancy LE; Withers B; McGuire HM; Luciani F; Singh M; Hughes B; Gloss B; Kliman D; Ma CKK; Panicker S; Bishop D; Dubosq MC; Li Z; Avdic S; Micklethwaite K; Blyth E, 2021, 'Prophylactic antigen-specific T-cells targeting seven viral and fungal pathogens after allogeneic haemopoietic stem cell transplant', Clinical and Translational Immunology, 10, http://dx.doi.org/10.1002/cti2.1249

Lim CS; Sozzi V; Littlejohn M; Yuen LKW; Warner N; Betz-Stablein B; Luciani F; Revill PA; Brown CM, 2021, 'Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes', Microbial Genomics, 7, pp. 1 - 13, http://dx.doi.org/10.1099/mgen.0.000492

Bull RA; Adikari TN; Ferguson JM; Hammond JM; Stevanovski I; Beukers AG; Naing Z; Yeang M; Verich A; Gamaarachchi H; Kim KW; Luciani F; Stelzer-Braid S; Eden JS; Rawlinson WD; van Hal SJ; Deveson IW, 2020, 'Analytical validity of nanopore sequencing for rapid SARS-CoV-2 genome analysis', Nature Communications, 11, http://dx.doi.org/10.1038/s41467-020-20075-6

Adikari TN; Di Giallonardo F; Leung P; Grifoni A; Sette A; Weiskopf D; Bull RA; Luciani F, 2020, 'Conserved epitopes with high HLA-I population coverage are targets of CD8+ T cells associated with high IFN-γ responses against all dengue virus serotypes', Scientific Reports, 10, http://dx.doi.org/10.1038/s41598-020-77565-2

Adikari TN; Riaz N; Sigera C; Leung P; Valencia BM; Barton K; Smith MA; Bull RA; Li H; Luciani F; Weeratunga P; Thein TL; Lim VWX; Leo YS; Rajapakse S; Fink K; Lloyd AR; Fernando D; Rodrigo C; Valencia Arroyo BM, 2020, 'Single molecule, near full-length genome sequencing of dengue virus', Scientific Reports, 10, pp. 18196, http://dx.doi.org/10.1038/s41598-020-75374-1

Niño JLG; Pageon SV; Tay SS; Colakoglu F; Kempe D; Hywood J; Mazalo JK; Cremasco J; Govendir MA; Dagley LF; Hsu K; Rizzetto S; Zieba J; Rice G; Prior V; O’neill G; Williams RJ; Nisbet DR; Kramer B; Webb AI; Luciani F; Read MN; Biro M, 2020, 'Cytotoxic T cells swarm by homotypic chemokine signalling', eLife, 9, pp. 1 - 71, http://dx.doi.org/10.7554/eLife.56554

Sironi M; Hasnain SE; Rosenthal B; Phan T; Luciani F; Shaw MA; Sallum MA; Mirhashemi ME; Morand S; González-Candelas F, 2020, 'SARS-CoV-2 and COVID-19: A genetic, epidemiological, and evolutionary perspective', Infection, Genetics and Evolution, 84, http://dx.doi.org/10.1016/j.meegid.2020.104384

Castellano-González G; McGuire HM; Luciani F; Clancy LE; Li Z; Avdic S; Hughes B; Singh M; De St Groth BF; Renga G; Pariano M; Bellet MM; Romani L; Gottlieb DJ, 2020, 'Rapidly expanded partially HLA DRB1-matched fungus-specific T cells mediate in vitro and in vivo antifungal activity', Blood Advances, 4, pp. 3443 - 3456, http://dx.doi.org/10.1182/bloodadvances.2020001565

Bretaña NA; Gray RR; Cunningham EB; Betz-Stablein B; Ribeiro R; Graw F; Luciani F; Lloyd AR, 2020, 'Combined treatment and prevention strategies for hepatitis C virus elimination in the prisons in New South Wales: a modelling study', Addiction, 115, pp. 901 - 913, http://dx.doi.org/10.1111/add.14830

Li H; Cameron B; Douglas D; Stapleton S; Cheguelman G; Butler T; Luciani F; Lloyd AR, 2020, 'Incident hepatitis B virus infection and immunisation uptake in Australian prison inmates', Vaccine, 38, pp. 3255 - 3260, http://dx.doi.org/10.1016/j.vaccine.2020.02.076

Brasher NA; Eltahla AA; Underwood A; Boo I; Rizzetto S; Walker MR; Rodrigo C; Luciani F; Maher L; Drummer HE; Tedla N; Lloyd AR; Bull RA, 2020, 'B cell immunodominance in primary hepatitis C virus infection', Journal of Hepatology, 72, pp. 670 - 679, http://dx.doi.org/10.1016/j.jhep.2019.11.011

Singh M; Jackson KJL; Wang JJ; Schofield P; Field MA; Koppstein D; Peters TJ; Burnett DL; Rizzetto S; Nevoltris D; Masle-Farquhar E; Faulks ML; Russell A; Gokal D; Hanioka A; Horikawa K; Colella AD; Chataway TK; Blackburn J; Mercer TR; Langley DB; Goodall DM; Jefferis R; Gangadharan Komala M; Kelleher AD; Suan D; Rischmueller M; Christ D; Brink R; Luciani F; Gordon TP; Goodnow CC; Reed JH, 2020, 'Lymphoma Driver Mutations in the Pathogenic Evolution of an Iconic Human Autoantibody', Cell, 180, pp. 878 - 894.e19, http://dx.doi.org/10.1016/j.cell.2020.01.029

Samir J; Rizzetto S; Gupta M; Luciani F, 2020, 'Exploring and analysing single cell multi-omics data with VDJView', BMC Medical Genomics, 13, http://dx.doi.org/10.1186/s12920-020-0696-z


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