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

Jung M; Poltavets V; Skhinas J; Tax G; Kamili A; Xie AJ; Ghamrawi S; Graber P; Mao J; Wong-Erasmus M; Cui L; Kimpton K; Venkat P; Mayoh C; Fleuren E; Fordham A; Barger Z; Grady J; Thomas D; Du EY; Cowley M; Gifford A; Fletcher J; Lau L; Dolman E; Gooding J; Kavallaris M, 2024, 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 E; Noor Z; Aref A; Xavier D; Lucas N; Williams S; Koh J; Poulos R; Wu Y; Dausmann M; MacKenzie K; Aguilar-Mahecha A; Armengol C; Barranco M; Basik M; Bowman E; Clifton-Bligh R; Connolly E; Cooper W; Dalal B; DeFazio A; Filipits M; Flynn P; Graham D; George J; Gill A; Gnant M; Habib R; Harris C; Harvey K; Horvath L; Jackson C; Kohonen-Corish M; Lim E; Liu J; Long G; Lord R; Mann G; McCaughan G; Morgan L; Murphy L; Nagabushan S; Nagrial A; Navinés J; Panizza B; Samra J; Scolyer R; Souglakos I; Swarbrick A; Thomas D; Balleine R; Hains P; Robinson P; Zhong Q; Reddel R, 2024, Federated deep learning enables cancer subtyping by proteomics, http://dx.doi.org/10.1101/2024.10.16.618763

Walpole I; Zaman F; Zhao P; Marshall V; Lin F; Thomas D; Shackleton M; Antolin A; Ameratunga M, 2023, 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 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

Thavaneswaran S; Lin F; Kansara M; Grady J; Espinoza D; Joshua A; Grimison P; Craft P; Cosman R; Lee C; Harwood K; Chinchen S; Corpuz T; Ballinger M; Sebastian L; Simes J; Thomas D, 2022, 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

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

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, 2021, 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

Kaur S; Sikta N; Schafferhans A; Bordin N; Cowley M; Thomas D; Ballinger M; O’Donoghue S, 2021, Streamlined use of protein structures in variant analysis, http://dx.doi.org/10.1101/2021.09.10.459756

Jadhao S; Davison C; Roulis E; Lee S; Lacaze P; Riaz M; McNeil J; Thomas D; Pecheniuk N; Hyland C; Flower R; Nagaraj S, 2021, Using Whole Genome Sequencing to Characterize Clinically Significant Blood Groups Among Healthy Older Australians, http://dx.doi.org/10.1101/2021.04.18.21255241

Minoche A; Lundie B; Peters G; Ohnesorg T; Pinese M; Thomas D; Zankl A; Roscioli T; Schonrock N; Kummerfeld S; Burnett L; Dinger M; Cowley M, 2020, ClinSV: Clinical grade structural and copy number variant detection from whole genome sequencing data, http://dx.doi.org/10.1101/2020.06.30.20143453

Lin F; Thavaneswaran S; Grady J; Ballinger M; Kansara M; Oakes S; Desai J; Lee CK; Simes J; Thomas D, 2020, 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

Puttick C; Kumar K; Davis R; Pinese M; Thomas D; Dinger M; Sue C; Cowley M, 2019, mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data, http://dx.doi.org/10.1101/852210

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

Lacaze P; Pinese M; Kaplan W; Stone A; Brion M-J; Woods R; McNamara M; McNeil J; Dinger M; Thomas D, 2018, 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

Chan EKF; Petersen D; Lyons R; Baldi B; Papenfuss A; Thomas D; Hayes V, 2017, Whole genome optical mapping reveals multiple fusion events chained by large novel sequences in cancer, http://dx.doi.org/10.1101/166173

Thomas DM; Wood MA, 2016, The Emergence of Negative Superhumps in Cataclysmic Variables: Smoothed Particle Hydrodynamics Simulations, http://dx.doi.org/10.48550/arxiv.1602.06314

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

Back to profile page