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, United States, 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, edn. 1, 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, http://dx.doi.org/10.1002/9783527622672.ch14

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, edn. 1, 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, edn. 1, 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, edn. 1, Logos-Verlag, Berlin, pp. 196 - 208

Journal articles

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, vol. 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, vol. 12, pp. 2931, 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, vol. 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, vol. 92, pp. 104869, 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, vol. 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, vol. 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, vol. 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, vol. 16, pp. e0245896, http://dx.doi.org/10.1371/journal.pone.0245896

Foster S; Luciani F, 2021, 'Omics in immunology', Immunology and Cell Biology, vol. 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, vol. 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, vol. 10, pp. e1249, 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, vol. 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, vol. 11, pp. 6272, 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, vol. 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, 2020, 'Single molecule, near full-length genome sequencing of dengue virus', Scientific Reports, vol. 10, 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, vol. 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, vol. 84, pp. 104384, 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 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, vol. 13, pp. 29, http://dx.doi.org/10.1186/s12920-020-0696-z

Lee KH; Gowrishankar K; Street J; McGuire HM; Luciani F; Hughes B; Singh M; Clancy LE; Gottlieb DJ; Micklethwaite KP; Blyth E, 2020, 'Ex vivo enrichment of PRAME antigen-specific T cells for adoptive immunotherapy using CD137 activation marker selection', Clinical and Translational Immunology, vol. 9, http://dx.doi.org/10.1002/cti2.1200

McGuire HM; Rizzetto S; Withers BP; Clancy LE; Avdic S; Stern L; Patrick E; Fazekas de St Groth B; Slobedman B; Gottlieb DJ; Luciani F; Blyth E, 2020, 'Mass cytometry reveals immune signatures associated with cytomegalovirus (CMV) control in recipients of allogeneic haemopoietic stem cell transplant and CMV-specific T cells', Clinical and Translational Immunology, vol. 9, pp. e1149, http://dx.doi.org/10.1002/cti2.1149

Bagaev DV; Vroomans RMA; Samir J; Stervbo U; Rius C; Dolton G; Greenshields-Watson A; Attaf M; Egorov ES; Zvyagin IV; Babel N; Cole DK; Godkin AJ; Sewell AK; Kesmir C; Chudakov DM; Luciani F; Shugay M, 2020, 'VDJdb in 2019: Database extension, new analysis infrastructure and a T-cell receptor motif compendium', Nucleic Acids Research, vol. 48, pp. D1057 - D1062, http://dx.doi.org/10.1093/nar/gkz874

Walker MR; Leung P; Eltahla AA; Underwood A; Abayasingam A; Brasher NA; Li H; Wu BR; Maher L; Luciani F; Lloyd AR; Bull RA, 2019, 'Clearance of hepatitis C virus is associated with early and potent but narrowly-directed, Envelope-specific antibodies', Scientific Reports, vol. 9, pp. 13300, http://dx.doi.org/10.1038/s41598-019-49454-w

Singh M; Al-Eryani G; Carswell S; Ferguson JM; Blackburn J; Barton K; Roden D; Luciani F; Giang Phan T; Junankar S; Jackson K; Goodnow CC; Smith MA; Swarbrick A, 2019, 'High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes', Nature Communications, vol. 10, pp. 3120, http://dx.doi.org/10.1038/s41467-019-11049-4

Kim KW; Horton JL; Pang CNI; Jain K; Leung P; Isaacs SR; Bull RA; Luciani F; Wilkins MR; Catteau J; Lipkin WI; Rawlinson WD; Briese T; Craig ME, 2019, 'Higher abundance of enterovirus A species in the gut of children with islet autoimmunity', Scientific Reports, vol. 9, pp. 1749, http://dx.doi.org/10.1038/s41598-018-38368-8

Abayasingam A; Leung P; Eltahla A; Bull RA; Luciani F; Grebely J; Dore GJ; Applegate T; Page K; Bruneau J; Cox AL; Kim AY; Schinkel J; Shoukry NH; Lauer GM; Maher L; Hellard M; Prins M; Lloyd A; Rodrigo C, 2019, 'Genomic characterization of hepatitis C virus transmitted founder variants with deep sequencing', Infection, Genetics and Evolution, vol. 71, pp. 36 - 41, http://dx.doi.org/10.1016/j.meegid.2019.02.032

Keck ZY; Pierce BG; Lau P; Lu J; Wang Y; Underwood A; Bull RA; Prentoe J; Velázquez-Moctezuma R; Walker MR; Luciani F; Guest JD; Fauvelle C; Baumert TF; Bukh J; Lloyd AR; Foung SKH, 2019, 'Broadly neutralizing antibodies from an individual that naturally cleared multiple hepatitis c virus infections uncover molecular determinants for E2 targeting and vaccine design', PLoS Pathogens, vol. 15, pp. e1007772, http://dx.doi.org/10.1371/journal.ppat.1007772

Koutsakos M; Illing PT; Nguyen THO; Mifsud NA; Crawford JC; Rizzetto S; Eltahla AA; Clemens EB; Sant S; Chua BY; Wong CY; Allen EK; Teng D; Dash P; Boyd DF; Grzelak L; Zeng W; Hurt AC; Barr I; Rockman S; Jackson DC; Kotsimbos TC; Cheng AC; Richards M; Westall GP; Loudovaris T; Mannering SI; Elliott M; Tangye SG; Wakim LM; Rossjohn J; Vijaykrishna D; Luciani F; Thomas PG; Gras S; Purcell AW; Kedzierska K, 2019, 'Human CD8 + T cell cross-reactivity across influenza A, B and C viruses', Nature Immunology, vol. 20, pp. 613 - 625, http://dx.doi.org/10.1038/s41590-019-0320-6

Pirozyan MR; Nguyen N; Cameron B; Luciani F; Bull RA; Zekry A; Lloyd AR, 2019, 'Chemokine-Regulated Recruitment of Antigen-Specific T-Cell Subpopulations to the Liver in Acute and Chronic Hepatitis C Infection', Journal of Infectious Diseases, vol. 219, pp. 1430 - 1438, http://dx.doi.org/10.1093/infdis/jiy679

Rodrigo C; Leung P; Lloyd AR; Bull RA; Luciani F; Grebely J; Dore GJ; Applegate T; Page K; Bruneau J; Cox AL; Osburn W; Kim AY; Shoukry NH; Lauer GM; Maher L; Schinkel J; Prins M; Hellard M; Eltahla AA, 2019, 'Genomic variability of within-host hepatitis C variants in acute infection', Journal of Viral Hepatitis, vol. 26, pp. 476 - 484, http://dx.doi.org/10.1111/jvh.13051

Rodrigo C; Luciani F, 2019, 'Dynamic interactions between RNA viruses and human hosts unravelled by a decade of next generation sequencing', Biochimica et Biophysica Acta - General Subjects, vol. 1863, pp. 511 - 519, http://dx.doi.org/10.1016/j.bbagen.2018.12.003

Isaacs SR; Kim KW; Cheng JX; Bull RA; Stelzer-Braid S; Luciani F; Rawlinson WD; Craig ME, 2018, 'Amplification and next generation sequencing of near full-length human enteroviruses for identification and characterisation from clinical samples', Scientific Reports, vol. 8, http://dx.doi.org/10.1038/s41598-018-30322-y

Wang Z; Zhu L; Nguyen THO; Wan Y; Sant S; Quiñones-Parra SM; Crawford JC; Eltahla AA; Rizzetto S; Bull RA; Qiu C; Koutsakos M; Clemens EB; Loh L; Chen T; Liu L; Cao P; Ren Y; Kedzierski L; Kotsimbos T; McCaw JM; La Gruta NL; Turner SJ; Cheng AC; Luciani F; Zhang X; Doherty PC; Thomas PG; Xu J; Kedzierska K, 2018, 'Clonally diverse CD38+HLA-DR+CD8+ T cells persist during fatal H7N9 disease', Nature Communications, vol. 9, http://dx.doi.org/10.1038/s41467-018-03243-7

Moran I; Nguyen A; Khoo WH; Butt D; Bourne K; Young C; Hermes JR; Biro M; Gracie G; Ma CS; Munier CML; Luciani F; Zaunders J; Parker A; Kelleher AD; Tangye SG; Croucher PI; Brink R; Read MN; Phan TG, 2018, 'Memory B cells are reactivated in subcapsular proliferative foci of lymph nodes', Nature Communications, vol. 9, http://dx.doi.org/10.1038/s41467-018-05772-7

Underwood AP; Walker MR; Brasher NA; Eltahla AA; Maher L; Luciani F; Lloyd AR; Bull RA, 2018, 'Understanding the determinants of BnAb induction in acute HCV infection', Viruses, vol. 10, http://dx.doi.org/10.3390/v10110659

Singh M; Al-Eryani G; Carswell S; Ferguson J; Blackburn J; Barton K; Roden D; Luciani F; Phan T; Junankar S; Jackson K; Goodnow C; Smith M; Swarbrick A, 2018, 'High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes', High-throughput targeted long-read single cell sequencing reveals the clonal and transcriptional landscape of lymphocytes, http://dx.doi.org/10.1101/424945

Rizzetto S; Koppstein DNP; Samir J; Singh M; Reed JH; Cai CH; Lloyd AR; Eltahla AA; Goodnow CC; Luciani F, 2018, 'B-cell receptor reconstruction from single-cell RNA-seq with VDJPuzzle', Bioinformatics (Oxford, England), vol. 34, pp. 2846 - 2847, http://dx.doi.org/10.1093/bioinformatics/bty203

Stern L; McGuire H; Avdic S; Rizzetto S; Fazekas de St Groth B; Luciani F; Slobedman B; Blyth E, 2018, 'Mass Cytometry for the assessment of immune reconstitution after hematopoietic stem cell transplantation', Frontiers in Immunology, vol. 9, http://dx.doi.org/10.3389/fimmu.2018.01672

Cunningham EB; Hajarizadeh B; Amin J; Bretana N; Dore GJ; Degenhardt L; Larney S; Luciani F; Lloyd AR; Grebely J, 2018, 'Longitudinal injecting risk behaviours among people with a history of injecting drug use in an Australian prison setting: The HITS-p study', International Journal of Drug Policy, vol. 54, pp. 18 - 25, http://dx.doi.org/10.1016/j.drugpo.2017.12.013


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