By Professor David Thomas

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

Collet L; Telouk P; Albarede F; Girodet M; Maqua C; Rogasik M; Ducimetière F; Tabone-Eglinger S; Brahmi M; Dufresne A; Thomas D; Ballinger M; Blay J-Y; Ray-Coquard I, 2023, Connecting the changing metallomic spectrum and survival in sarcoma: a pilot study, http://dx.doi.org/10.21203/rs.3.rs-3291225/v1

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

Best M; Bartley N; Napier C; Fisher A; Ballinger M; Thomas D; Goldstein D; Tucker K; Biesecker B; Butow P, 2022, 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

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

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

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

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