By Professor David Thomas

Conference Abstracts

Barnet M; Jackson K; Gao B; Nagrial A; Boyer M; Cooper W; Hui R; Linton A; Tattersall M; Russell A; Gibson G; Cebon J; Long G; Menzies A; Scolyer R; Lacaze P; Brink R; Peters T; Cowley M; Gayevskiy V; Thomas D; Pinese M; Blinman P; Kao S; Goodnow C, 2018, 'P1.04-11 Exploring the Germ-Line Contribution to Exceptional Response to PD-1/PD-L1 Inhibition in Patients with NSCLC by Whole Genome Sequencing', in Journal of Thoracic Oncology, Elsevier, Vol. 13, pp. s529, http://dx.doi.org/10.1016/j.jtho.2018.08.726

Tyrrell V; Lau L; Arndt G; Barahona P; Cowley M; Ekert P; Failes T; Fletcher J; Gifford A; Haber M; Kamili A; Kumar A; Lock R; Marshall G; Mayoh C; Mead S; Mould E; O'Brien T; Pinese M; Khuong-Quang DA; Thomas D; Trahair T; Tsoli M; Tucker K; Wharby M; Wong M; Xie J; Ziegler D, 2018, 'Zero childhood cancer – Accelerating translation of experimental oncology: Better matching drug to target', in Pathology, Elsevier, Vol. 50, pp. s31, http://dx.doi.org/10.1016/j.pathol.2017.12.072

Jones RM; Melton PE; Rea A; Ingley E; Ballinger ML; Wood DJ; Thomas DM; Moses EK, 2016, 'Whole Exome Sequencing in Multigenerational Mixed Cancer Families Identifies a Putative Risk Variant in the PDIA2 Gene', in GENETIC EPIDEMIOLOGY, WILEY-BLACKWELL, CANADA, Toronto, Vol. 40, pp. 644 - 644, presented at Annual Meeting of the International-Genetic-Epidemiology-Society, CANADA, Toronto, 24 October 2016 - 26 October 2016, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000386034800102&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Thomas DM, 2015, 'MANAGING SARCOMA FROM A MEDICAL ONCOLOGIST PERSPECTIVE', in Asia-Pacific Journal of Clinical Oncology, WILEY-BLACKWELL, Vol. 11, pp. 75 - 75, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000364320800041&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Chantrill L; Nagrial A; Watson C; Johns A; Martyn-Smith M; Simpson S; Mead S; Jones M; Samra J; Gill A; Watson N; Chin V; Humphris J; Chou A; Brown B; Morey A; Thomas D; Sebastian L; Sjoquist K; Yip S; Pavlakis N; Asghari R; Harvey S; Grimison P; Simes J; Biankin A, 2015, 'Precision medicine for advanced pancreas cancer: the individualised molecular pancreatic cancer therapy (IMPACT) trial', in Asia-Pacific Journal of Clinical Oncology, WILEY-BLACKWELL, Vol. 11, pp. 147 - 148

McBride KA; Young M-A; Schlub TE; Kirk J; Tattersall MHN; Ballinger M; Thomas D; Mitchell G, 2015, 'THE PSYCHOSOCIAL EFFECTS OF A WHOLE BODY MRI SCREENING TRIAL IN SARCOMA PATIENTS WITH A GERMLINE TP53 MUTATION', in Asia-Pacific Journal of Clinical Oncology, WILEY-BLACKWELL, Vol. 11, pp. 178 - 178, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000364320800325&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Thomas D, 2015, 'RANKL and giant cell tumor of bone: the growing problem of benign tumours', in CLINICAL ENDOCRINOLOGY, WILEY, AUSTRALIA, Adelaide, Vol. 84, pp. 3 - 4, presented at Annual Scientific Meeting of the Endocrine-Society-of-Australia, AUSTRALIA, Adelaide, 23 August 2015 - 26 August 2015, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000372310400010&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Peng G; Bojadzieva J; Ballinger ML; Thomas DM; Strong L; Wang W, 2015, 'LFSpro: A risk assessment tool to estimate TP53 mutation status in families with Li-Fraumeni syndrome', in CANCER RESEARCH, AMER ASSOC CANCER RESEARCH, PA, Philadelphia, Vol. 75, presented at 106th Annual Meeting of the American-Association-for-Cancer-Research (AACR), PA, Philadelphia, 18 April 2015 - 22 April 2015, http://dx.doi.org/10.1158/1538-7445.AM2015-2762

Preprints

Tran M; Chan JC; Huang ML; Kansara M; Grady JP; Napier CE; Thavaneswaran S; Ballinger ML; Thomas DM; Lin FP, 2025, A Robust BERT-Based Deep Learning Model for Automated Cancer Type Extraction from Unstructured Pathology Reports, http://dx.doi.org/10.48550/arxiv.2508.15149

Gianferante DM; Moore A; Spector L; Wheeler W; Yang T; Hubbard A; Gorlick R; Patiño-García A; Lecanda F; Flanagan A; Amary F; Andrulis IL; Wunder JS; Thomas DM; Ballinger ML; Serra M; Hattinger C; Demerath E; Johnson W; Birmann B; De Vivo I; Giles G; Teras L; Arslan A; Vermeulen RCH; Sample J; Freedman ND; Huang W-Y; Chanock SJ; Savage SA; Berndt SI; Mirabello L, 2023, Genetically Inferred Birthweight, Height, and Puberty Timing and Risk of Osteosarcoma, http://dx.doi.org/10.2139/ssrn.4441724

Shin SJ; Dodd E; Peng G; Bojadzieva J; Chen J; Amos C; Mai P; Savage S; Ballinger M; Thomas D; Yuan Y; Strong L; Wang W, 2019, Risk of differential cancer types over age in families with Li-Fraumeni syndrome: a validation study using multi-center cohorts, http://dx.doi.org/10.1101/567727

Pinese M; Lacaze P; Rath E; Stone A; Brion M-J; Ameur A; Nagpal S; Puttick C; Husson S; Degrave D; Navin Cristina T; Silva Kahl V; Statham A; Woods R; McNeil J; Riaz M; Barr M; Nelson M; Reid C; Murray A; Shah R; Wolfe R; Atkins J; Fitzsimmons C; Cairns H; Green M; Carr V; Cowley M; Pickett H; James P; Powell J; Kaplan W; Gibson G; Gyllensten U; Cairns M; McNamara M; Dinger M; Thomas D, 2018, The Medical Genome Reference Bank: Whole genomes and phenotype of 2,570 healthy elderly, http://dx.doi.org/10.1101/473348

Pattnaik S; Vacher C; Lee HC; Kaplan W; Thomas D; Wu J; Pinese M, 2018, Network-aware mutation clustering of cancer, http://dx.doi.org/10.1101/432872

Wood MA; Thomas DM; Simpson JC, 2009, SPH Simulations of Negative (Nodal) Superhumps: A Parametric Study, http://dx.doi.org/10.48550/arxiv.0906.2713

Thavaneswaran S; Lin FP; Kansara M; Grady JP; Espinoza D; Joshua AM; Grimison P; Craft P; Cosman R; Lee C; Harwood K; Chinchen S; Corpuz T; Ballinger M; Sebastian L; Simes J; Thomas D, A signal-seeking Phase II trial of Durvalumab and Tremelimumab Focused on Advanced, Rare and Less Common Cancers, http://dx.doi.org/10.1101/2022.06.30.22277092

Thavaneswaran S; Sebastian L; Kansara M; Ballinger M; Espinoza D; Lin F; Lee C; Sjoquist K; Grady J; Cowley M; Joshua A; Qiu M; Oakes S; Simes J; Thomas D, A Signal-seeking Phase Iia Trial of Palbociclib in Advanced Cancers With Cell Cycle Pathway Alterations – A Substudy of the Molecular Screening and Therapeutics (Most) Program, http://dx.doi.org/10.21203/rs.3.rs-254137/v1

Minoche AE; Lundie B; Peters GB; Ohnesorg T; Pinese M; Thomas DM; Zankl A; Roscioli T; Schonrock N; Kummerfeld S; Burnett L; Dinger ME; Cowley MJ, ClinSV: Clinical grade structural and copy number variant detection from whole genome sequencing data, http://dx.doi.org/10.1101/2020.06.30.20143453

Walpole I; Zaman FY; Zhao P; Marshall VM; Lin F; Thomas DM; Shackleton M; Antolin AA; Ameratunga M, Computational repurposing of oncology drugs through off-target drug binding interactions from pharmacological databases, http://dx.doi.org/10.1101/2023.07.01.547311

Collet L; Telouk P; Albarede F; Girodet M; Maqua C; Rogasik M; Ducimetière F; Tabone-Eglinger S; Brahmi M; Dufresne A; Thomas DM; Ballinger ML; Blay J-Y; Ray-Coquard I, Connecting the changing metallomic spectrum and survival in sarcoma: a pilot study, http://dx.doi.org/10.21203/rs.3.rs-3291225/v1

Lin FP; Thavaneswaran S; Grady JP; Ballinger M; Kansara M; Oakes SR; Desai J; Lee CK; Simes J; Thomas DM, Criteria-based curation of a therapy-focused compendium to support treatment recommendations in precision oncology, http://dx.doi.org/10.1101/2020.12.18.20248521

Jung M; Poltavets V; Skhinas JN; Tax G; Kamili A; Xie A; Ghamrawi S; Graber P; Mao J; Wong-Erasmus M; Cui L; Kimpton K; Venkat P; Mayoh C; Fleuren EDG; Fordham AM; Barger Z; Grady J; Thomas DM; Du EY; Cowley MJ; Gifford AJ; Fletcher JI; Lau LMS; Dolman MEM; Gooding JJ; Kavallaris M, Engineered paediatric tumours retain maintains tumour genotype and phenotype for precision medicine, http://dx.doi.org/10.1101/2024.11.17.619539

Cai Z; Boys EL; Noor Z; Aref A; Xavier D; Lucas N; Williams SG; Koh JMS; Poulos RC; Wu Y; Dausmann M; MacKenzie KL; Aguilar-Mahecha A; Armengol C; Barranco MM; Basik M; Bowman ED; Clifton-Bligh RJ; Connolly EA; Cooper WA; Dalal B; DeFazio A; Filipits M; Flynn PJ; Graham JD; George J; Gill AJ; Gnant M; Habib R; Harris CC; Harvey K; Horvath LG; Jackson C; Kohonen-Corish MRJ; Lim E; Liu J; Long G; Lord RV; Mann GJ; McCaughan GW; Morgan L; Murphy LC; Nagabushan S; Nagrial AM; Navinés J; Panizza BJ; Samra JS; Scolyer RA; Souglakos I; Swarbrick A; Thomas DM; Balleine RL; Hains PG; Robinson PJ; Zhong Q; Reddel RR, Federated deep learning enables cancer subtyping by proteomics, http://dx.doi.org/10.1101/2024.10.16.618763

Puttick C; Kumar KR; Davis RL; Pinese M; Thomas DM; Dinger ME; Sue CM; Cowley MJ, mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data, http://dx.doi.org/10.1101/852210

Best M; Bartley N; Napier C; Fisher A; Ballinger M; Thomas D; Goldstein D; Tucker K; Biesecker B; Butow P, Return of comprehensive tumour genomic profiling results to advanced cancer patients: a qualitative study, http://dx.doi.org/10.21203/rs.3.rs-1190781/v1

Kaur S; Sikta N; Schafferhans A; Bordin N; Cowley MJ; Thomas DM; Ballinger ML; O’Donoghue SI, Streamlined use of protein structures in variant analysis, http://dx.doi.org/10.1101/2021.09.10.459756

Lacaze P; Pinese M; Kaplan W; Stone A; Brion M-J; Woods RL; McNamara M; McNeil JJ; Dinger ME; Thomas DM, The Medical Genome Reference Bank: a whole-genome data resource of 4,000 healthy elderly individuals. Rationale and cohort design, http://dx.doi.org/10.1101/274019

Jadhao S; Davison C; Roulis EV; Lee S; Lacaze P; Riaz M; McNeil JJ; Thomas DM; Pecheniuk NM; Hyland CA; Flower RL; Nagaraj SH, Using Whole Genome Sequencing to Characterize Clinically Significant Blood Groups Among Healthy Older Australians, http://dx.doi.org/10.1101/2021.04.18.21255241

Chan EKF; Petersen DC; Lyons RJ; Baldi BF; Papenfuss AT; Thomas DM; Hayes VM, Whole genome optical mapping reveals multiple fusion events chained by large novel sequences in cancer, http://dx.doi.org/10.1101/166173

Other

Nagrial A; Carlino MS; Gunjur A; Brown MP; Harris S; Underhill C; Zielinski R; Kee D; Lam W-S; Chan H; Harrup R; So J; Collins IM; Michael M; Chionh F; Uy C; Mariadason J; Torres J; Ballinger ML; Grady JP; Tavancheh E; Palmer J; Thomas DM; Wilkie K; Cebon J; Klein O, 2026, Data from Nivolumab and Ipilimumab Combination Treatment in Patients with Advanced Intrahepatic Cholangiocarcinoma and Gallbladder Cancer: Results from the Phase II MoST-CIRCUIT Trial, http://dx.doi.org/10.1158/1078-0432.c.8630732

Nagrial A; Carlino MS; Gunjur A; Brown MP; Harris S; Underhill C; Zielinski R; Kee D; Lam W-S; Chan H; Harrup R; So J; Collins IM; Michael M; Chionh F; Uy C; Mariadason J; Torres J; Ballinger ML; Grady JP; Tavancheh E; Palmer J; Thomas DM; Wilkie K; Cebon J; Klein O, 2026, Supplementary Table S1 from Nivolumab and Ipilimumab Combination Treatment in Patients with Advanced Intrahepatic Cholangiocarcinoma and Gallbladder Cancer: Results from the Phase II MoST-CIRCUIT Trial, http://dx.doi.org/10.1158/1078-0432.33143048

Cote GM; Aberoumand M; Choy E; Sebastian L; Mazzola E; Grimison P; Merriam P; Ballinger M; Thavaneswaran S; Lin F; Grady JP; Millward M; Brown MP; Harrup R; Espinoza D; Demetri G; Littlefield BA; Simes RJ; George S; Thomas D, 2026, Data from A Phase 2 Study of Eribulin in Patients with Metastatic Angiosarcoma and Epithelioid Hemangioendothelioma, http://dx.doi.org/10.1158/1078-0432.c.8509442

Cote GM; Aberoumand M; Choy E; Sebastian L; Mazzola E; Grimison P; Merriam P; Ballinger M; Thavaneswaran S; Lin F; Grady JP; Millward M; Brown MP; Harrup R; Espinoza D; Demetri G; Littlefield BA; Simes RJ; George S; Thomas D, 2026, Supplementary Tables 1-3 from A Phase 2 Study of Eribulin in Patients with Metastatic Angiosarcoma and Epithelioid Hemangioendothelioma, http://dx.doi.org/10.1158/1078-0432.32530688

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Data from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.c.8353092

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Figure 1 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744587

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Figure 2 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744584

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Supplementary Figure S1 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744581

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Supplementary Figure S2 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744578

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Supplementary Methods S1 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744575

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Supplementary Table S1 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744572

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Supplementary Table S2 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744569

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Supplementary Table S3 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744566

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Supplementary Table S4 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744563

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Supplementary Table S5 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744560

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Supplementary Table S6 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744557

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Table 1 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744554

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Table 2 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744548

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Table 3 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744545

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Table 4 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744539

Thomas DM; Kim JE; Barlesi F; Martens UM; Krzakowski M; Dziadziuszko R; Jeong JH; Daniele G; Wilson TR; Wu F; Simmons BP; Patel S; Sbirnac M; Kaul M; Gadgeel SM, 2026, Table 5 from TAPISTRY: A Phase II Study of Atezolizumab in Patients with Tumor Mutational Burden–High Tumors, http://dx.doi.org/10.1158/1078-0432.31744536

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