By Dr Frank Po-Yen Lin

Journal articles

Thavaneswaran S; Lin F; Grady JP; Espinoza D; Huang ML; Chinchen S; Sebastian L; Kansara M; Mersiades T; Lee CK; Desai J; Grimison P; Brown M; Millward M; Harrup R; O’Byrne K; Nagrial A; Craft P; Simes J; Joshua AM; Thomas DM, 2024, 'A signal-seeking phase 2 study of Trastuzumab emtansine in tumours harbouring HER2 amplification or mutation', npj Precision Oncology, 8, http://dx.doi.org/10.1038/s41698-024-00698-4

Deng F; Li Y; Yang B; Sang R; Deng W; Kansara M; Lin F; Thavaneswaran S; Thomas DM; Goldys EM, 2024, 'Topological barrier to Cas12a activation by circular DNA nanostructures facilitates autocatalysis and transforms DNA/RNA sensing', Nature Communications, 15, pp. 1818, http://dx.doi.org/10.1038/s41467-024-46001-8

Zaheed M; Grady JP; Murrow B; Douglas B; Carpenter E; Mckay S; Liang S; Taylor N; Lin FP-Y; Goldstein D; Tucker K; Thomas DM; Ballinger ML, 2024, 'Translating potential germline findings from tumour profiling into routine clinical care.', Journal of Clinical Oncology, 42, pp. 105 - 105, http://dx.doi.org/10.1200/jco.2024.42.23_suppl.105

Lin FP-Y; Grady JP; Napier CE; Callow M; Thavaneswaran S; Huang ML; Zaheed M; Kansara M; Sebastian L; Ballinger ML; Simes J; Thomas DM, 2024, 'Impact of artificial intelligence (AI) decision support on clinical trial participation: A before-after implementation study on a nationwide molecular tumor board.', Journal of Clinical Oncology, 42, pp. 1557 - 1557, http://dx.doi.org/10.1200/jco.2024.42.16_suppl.1557

Tan E; Tran M; Rademaker M; Lin FPY, 2024, 'Bridging AI development with clinical relevance—A scoping review of skin cancer models since CLEAR Derm. Where to next?', Australasian Journal of Dermatology, 65, pp. e56 - e58, http://dx.doi.org/10.1111/ajd.14207

Nakajima EC; Simpson A; Bogaerts J; de Vries EGE; Do R; Garalda E; Goldmacher G; Kinahan PE; Lambin P; LeStage B; Li Q; Lin F; Litière S; Perez-Lopez R; Petrick N; Schwartz L; Seymour L; Shankar L; Laurie SA, 2024, 'Tumor Size Is Not Everything: Advancing Radiomics as a Precision Medicine Biomarker in Oncology Drug Development and Clinical Care. A Report of a Multidisciplinary Workshop Coordinated by the RECIST Working Group', JCO Precision Oncology, 8, http://dx.doi.org/10.1200/PO.23.00687

Tan E; Lim S; Lamont D; Epstein R; Lim D; Lin FPY, 2024, 'Development and validation of a deep learning model for improving detection of nonmelanoma skin cancers treated with Mohs micrographic surgery', JAAD International, 14, pp. 39 - 47, http://dx.doi.org/10.1016/j.jdin.2023.10.007

Kang J; Lafata K; Kim E; Yao C; Lin F; Rattay T; Nori H; Katsoulakis E; Lee CI, 2024, 'Artificial intelligence across oncology specialties: Current applications and emerging tools', BMJ Oncology, 3, http://dx.doi.org/10.1136/bmjonc-2023-000134

Siu DHW; Lin FPY; Cho D; Lord SJ; Heller GZ; Simes RJ; Lee CK, 2024, 'Framework for the Use of External Controls to Evaluate Treatment Outcomes in Precision Oncology Trials', JCO Precision Oncology, 8, http://dx.doi.org/10.1200/PO.23.00317

Novis E; Glover A; Grady JP; Silvestri A; Thavaneswaran S; Lin F; Ballinger ML; Thomas DM, 2024, 'Oncogenic mutations in the TP53 and PI-3 kinase/AKT pathway are independent predictors of survival for advanced thyroid cancer: Analysis from the Molecular Screening and Therapeutics (MoST) program', Surgery (United States), http://dx.doi.org/10.1016/j.surg.2024.05.058

Lin FP; Mersiades A; Lee J; Xu W; Chinchen S; Charakidis M; Thavaneswaran S; Hughes BGM; Underhill CR; Takhar HS; Harrup R; Nagrial A; Millward M; Desai J; Espinoza D; Lee CK; Solomon BJ; Simes J; Pavlakis N; Thomas D, 2024, '623P Phase II trial of vemurafenib (VEM) and cobimetinib (COB) in BRAF V600-mutated solid tumours and first-line (1L) non-small cell lung cancer (NSCLC): Australian molecular screening and therapeutics (MoST) substudy 12', Annals of Oncology, 35, pp. S498 - S498, http://dx.doi.org/10.1016/j.annonc.2024.08.690

Kong BY; Lin FP-Y; Espinoza D; Thavaneswaran S; Meniawy T; Desai J; Harrup R; Selva-Nayagam S; Charakidis M; Cuff K; Sebastian L; Lee CK; Chinchen S; Thomas DM; Ballinger ML; Simes J; Goldstein D, 2024, '636P Tucatinib and trastuzumab in advanced cancers with HER2 mutations or amplification: A molecular screening and therapeutics (MoST) program substudy', Annals of Oncology, 35, pp. S505 - S505, http://dx.doi.org/10.1016/j.annonc.2024.08.703

McNamee N; Lin F; Sim H-W; Napier C; Thomas D; Simes J; Thavaneswaran S, 2023, 'PATH-25. EXPLORING THE PROGNOSTIC IMPLICATIONS OF MOLECULAR ALTERATIONS IN ASTROCYTOMAS USING COMPREHENSIVE GENOMIC PROFILING (CGP)', Neuro-Oncology, 25, pp. v173 - v173, http://dx.doi.org/10.1093/neuonc/noad179.0655

Zeverijn LJ; Looze EJ; Thavaneswaran S; van Berge Henegouwen JM; Simes RJ; Hoes LR; Sjoquist KM; van der Wijngaart H; Sebastian L; Geurts BS; Lee CK; de Wit GF; Espinoza D; Roepman P; Lin FP; Jansen AML; de Leng WWJ; van der Noort V; Leek LVM; de Vos FYFL; van Herpen CML; Gelderblom H; Verheul HMW; Thomas DM; Voest EE, 2023, 'Limited clinical activity of palbociclib and ribociclib monotherapy in advanced cancers with cyclin D-CDK4/6 pathway alterations in the Dutch DRUP and Australian MoST trials', International Journal of Cancer, 153, pp. 1413 - 1422, http://dx.doi.org/10.1002/ijc.34649

Lin FP, 2023, 'Delivering Data-Driven Precision and Equitable Artificial Intelligence Decision Tools in Oncology: Exploring the Informarker Concept', JCO clinical cancer informatics, 7, pp. e2300142, http://dx.doi.org/10.1200/CCI.23.00142

Thavaneswaran S; Kansara M; Lin F; Espinoza D; Grady JP; Lee CK; Ballinger ML; Sebastian L; Corpuz T; Qiu MR; Mundra P; Bailey CG; Schmitz U; Simes J; Joshua AM; Thomas DM, 2023, 'A signal-seeking Phase 2 study of olaparib and durvalumab in advanced solid cancers with homologous recombination repair gene alterations', British Journal of Cancer, 129, pp. 475 - 485, http://dx.doi.org/10.1038/s41416-023-02311-0

Tan E; Lim D; Lin F, 2023, 'Response to Felmingham C. et al's “Improving Skin cancer Management with ARTificial intelligence (SMARTI): A pre-post intervention trial of an artificial intelligence system used as a diagnostic aid for skin cancer management in a real-world specialist dermatology setting”', Journal of the American Academy of Dermatology, 89, pp. e107, http://dx.doi.org/10.1016/j.jaad.2023.03.062

Zeverijn LJ; Looze E; Thavaneswaran S; van Berge Henegouwen JM; Simes J; Hoes LR; Geurts B; Sebastian L; Roepman P; Lin FP-Y; Jansen AML; de Leng WWJ; van der Noort V; Leek LVM; De Vos FYFL; Verheul HMW; Gelderblom H; Thomas DM; Voest EE; Sjoquist KM, 2023, 'Clinical activity of palbociclib and ribociclib monotherapy in advanced cancers with cyclin D-CDK4/6 pathway alterations in the Dutch DRUP and Australian MoST trials.', Journal of Clinical Oncology, 41, pp. 3101 - 3101, http://dx.doi.org/10.1200/jco.2023.41.16_suppl.3101

Kansara M; Lin FP-Y; Thavaneswaran S; Napier CE; Grady JP; Ballinger ML; Simes J; Thomas DM, 2023, 'Genomic alterations associated with response to immune checkpoint inhibitors in rare cancers: A biomarker exploration study from the Australian Molecular Screening and Therapeutics (MoST) Program.', Journal of Clinical Oncology, 41, pp. 2594 - 2594, http://dx.doi.org/10.1200/jco.2023.41.16_suppl.2594

Thavaneswaran S; Lin FP-Y; Napier CE; Grady JP; Ballinger ML; Kansara M; Grimison PS; Pavlakis N; Wong MK; Sjoquist KM; Goldstein D; Chantrill LA; Simes J; Thomas DM, 2023, 'Genomic targetability and survival outcomes of biliary tract cancers (BTC): A retrospective cohort study of the Australian Molecular Screening and Therapeutics (MoST) program.', Journal of Clinical Oncology, 41, pp. 4093 - 4093, http://dx.doi.org/10.1200/jco.2023.41.16_suppl.4093

Lin FP-Y; Thavaneswaran S; Napier CE; Grady JP; Kansara M; Sebastian L; Kee D; Zaheed M; Millward M; Brown MP; Charakidis M; Craft PS; Grimison PS; Harrup RA; O'Byrne KJ; Desai J; Lee CK; Ballinger ML; Simes J; Thomas DM, 2023, 'Genomic therapy matching in rare and refractory cancers: Updated results from a retrospective cohort study in the Molecular Screening and Therapeutic (MoST) program.', Journal of Clinical Oncology, 41, pp. 1540 - 1540, http://dx.doi.org/10.1200/jco.2023.41.16_suppl.1540

Lin FP-Y; Joshua AM; Epstein RJ, 2023, 'Machine learning prediction of patient-reported outcomes associated with systemic therapy from medical records.', Journal of Clinical Oncology, 41, pp. e13564 - e13564, http://dx.doi.org/10.1200/jco.2023.41.16_suppl.e13564

Kee D; Lin FP-Y; Thavaneswaran S; Napier CE; Harrison ML; Beale PJ; Lynch J; Davis AJ; Ananda S; Lombard JM; Friedlander M; Kansara M; Sebastian L; Lee CK; Ballinger ML; Simes J; Thomas DM, 2023, 'Molecular tumor profiling and therapy selection in advanced gynecological cancers: A retrospective cohort analysis from the Australian Molecular Screening and Therapeutics (MoST) Program.', Journal of Clinical Oncology, 41, pp. 5526 - 5526, http://dx.doi.org/10.1200/jco.2023.41.16_suppl.5526

Thavaneswaran S; Mersiades A; Lin FP-Y; Espinoza D; Grady JP; Lee CK; Desai J; Brown MP; Grimison PS; O'Byrne KJ; Harrup RA; Nagrial A; Sebastian L; Chinchen S; Kansara M; Craft PS; Millward M; Simes J; Joshua AM; Thomas DM, 2023, 'Trastuzumab emtansine (T-DM1) in advanced cancers with HER2 mutations or amplification: Results from the Molecular Screening and Therapeutics (MoST) Program substudy.', Journal of Clinical Oncology, 41, pp. 3127 - 3127, http://dx.doi.org/10.1200/jco.2023.41.16_suppl.3127

Yam AO; Bailey J; Lin F; Jakovija A; Youlten SE; Counoupas C; Gunzer M; Bald T; Woodruff TM; Triccas JA; Goldstein LD; Gallego-Ortega D; Grey ST; Chtanova T, 2023, 'Neutrophil Conversion to a Tumor-Killing Phenotype Underpins Effective Microbial Therapy', Cancer Research, 83, pp. 1315 - 1328, http://dx.doi.org/10.1158/0008-5472.CAN-21-4025

Epstein RJ; Lin FPY; Brink RA; Blackburn J, 2023, 'Synonymous alterations of cancer-associated Trp53 CpG mutational hotspots cause fatal developmental jaw malocclusions but no tumors in knock-in mice', PLoS ONE, 18, http://dx.doi.org/10.1371/journal.pone.0284327

Kansara M; Bhardwaj N; Thavaneswaran S; Xu C; Lee JK; Chang LB; Madison RW; Lin F; Hsu E; Patel VK; Aleshin A; Oxnard GR; Simes J; Nimeiri H; Thomas DM, 2023, 'Early circulating tumor DNA dynamics as a pan-tumor biomarker for long-term clinical outcome in patients treated with durvalumab and tremelimumab', Molecular Oncology, 17, pp. 298 - 311, http://dx.doi.org/10.1002/1878-0261.13349

Epstein RJ; Gu Y; Lin FPY, 2023, 'Can cancer go green? It’s up to us', Frontiers in Oncology, 13, http://dx.doi.org/10.3389/fonc.2023.1074091

Po-Yen Lin F; Salih OSM; Scott N; Jameson MB; Epstein RJ, 2022, 'Development and Validation of a Machine Learning Approach Leveraging Real-World Clinical Narratives as a Predictor of Survival in Advanced Cancer', JCO clinical cancer informatics, 6, pp. e2200064, http://dx.doi.org/10.1200/CCI.22.00064

Bartonicek N; Rouet R; Warren J; Loetsch C; Rodriguez GS; Walters S; Lin F; Zahra D; Blackburn J; Hammond JM; Reis ALM; Deveson IW; Zammit N; Zeraati M; Grey S; Christ D; Mattick JS; Chtanova T; Brink R; Dinger ME; Weatheritt RJ; Sprent J; King C, 2022, 'The retroelement Lx9 puts a brake on the immune response to virus infection', Nature, 608, pp. 757 - 765, http://dx.doi.org/10.1038/s41586-022-05054-9

Lin FP; Thavaneswaran S; Grady JP; Ballinger M; Kansara M; Oakes SR; Desai J; Lee CK; Simes J; Thomas DM, 2021, 'Criteria-based curation of a therapy-focused compendium to support treatment recommendations in precision oncology', npj Precision Oncology, 5, pp. 58, http://dx.doi.org/10.1038/s41698-021-00194-z

Thavaneswaran S; Ballinger M; Butow P; Meiser B; Goldstein D; Lin F; Napier C; Thomas D; Best M, 2021, 'The experiences and needs of australian medical oncologists in integrating comprehensive genomic profiling into clinical care: A nation-wide survey', Oncotarget, 12, pp. 2169 - 2176, http://dx.doi.org/10.18632/ONCOTARGET.28076

Geary RL; Yasin NABHM; Lin F; Whalley D; Thotathil Z; DeGroot C, 2021, 'Stereotactic ablative radiotherapy for early stage lung cancer and lung metastases in a New Zealand population', New Zealand Medical Journal, 134, pp. 45 - 56

Gu YF; Lin FP; Epstein RJ, 2021, 'How aging of the global population is changing oncology', ecancermedicalscience, 15, http://dx.doi.org/10.3332/ecancer.2021.ed119

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

Lin FP-Y; Jameson MB; Epstein RJ, 2019, 'Predicting survival in advanced cancers by applying machine learning to clinical narratives.', Journal of Global Oncology, 5, pp. 32 - 32, http://dx.doi.org/10.1200/jgo.2019.5.suppl.32

Lin FP; Epstein RJ; Groza T; Kocbek S; Antezana E, 2018, 'Cancer care treatment outcome ontology: A novel computable ontology for profiling treatment outcomes in patients with solid tumors', JCO Clinical Cancer Informatics, 2018, pp. 1 - 14, http://dx.doi.org/10.1200/CCI.18.00026

Lin FPY; Pokorny A; Teng C; Epstein RJ, 2017, 'TEPAPA: A novel in silico feature learning pipeline for mining prognostic and associative factors from text-based electronic medical records', Scientific Reports, 7, pp. 6918, http://dx.doi.org/10.1038/s41598-017-07111-0

Epstein RJ; Lin FP, 2017, 'Cancer and the omics revolution', Australian Family Physician, 46, pp. 189 - 193

Lin FPY; Pokorny A; Teng C; Dear R; Epstein RJ, 2016, 'Computational prediction of multidisciplinary team decision-making for adjuvant breast cancer drug therapies: A machine learning approach', BMC Cancer, 16, pp. 929, http://dx.doi.org/10.1186/s12885-016-2972-z

Tan E; Lin F; Sheck L; Salmon P; Ng S, 2016, 'A practical decision-tree model to predict complexity of reconstructive surgery after periocular basal cell carcinoma excision', Journal of the European Academy of Dermatology and Venereology, http://dx.doi.org/10.1111/jdv.14012

Tan E; Lin FPY; Sheck LHN; Salmon PJ; Ng SGJ, 2015, 'Growth of periocular basal cell carcinomas', British Journal of Dermatology, 172, pp. 1002 - 1007, http://dx.doi.org/10.1111/bjd.13470

Tsafnat G; Jasch D; Misra A; Choong MK; Lin FY-P; Coiera E, 2014, 'Gene–disease association with literature based enrichment', Journal of Biomedical Informatics, 49, pp. 221 - 226, http://dx.doi.org/10.1016/j.jbi.2014.03.007

Sheck LHN; Tan E; Lin FPY; Mortimer NJ; Salmon PJ; Ng SGJ, 2013, 'THE IMPACT OF WAITING TIME FOR ELECTIVE SURGERY ON THE GROWTH OF PERIOCULAR BASAL CELL CARCINOMAS', CLINICAL AND EXPERIMENTAL OPHTHALMOLOGY, 41, pp. 22 - 22, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000329507100032&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1

Polasek TM; Lin FP; Doogue MP, 2011, 'Clinically relevant information on pharmacokinetic drug-drug interactions', Journal of Pharmacy Practice and Research, 41, pp. 77 - 78

Lin FP; Stephen A; Polasek TM; Tsafnat G; Doogue MP, 2011, 'BICEPP: an example-based statistical text mining method for predicting the binary characteristics of drugs', BMC bioinformatics, 12, pp. 112

Lin FP; Sintchenko V; Kong F; Gilbert GL; Coiera E, 2009, 'Commonly used molecular epidemiology markers of Streptococcus agalactiae do not appear to predict virulence', Pathology, 41, pp. 576 - 581

Lin FP; Coiera E; Lan R; Sintchenko V, 2009, 'In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles.', BMC bioinformatics, 10, pp. 86 - 86, http://dx.doi.org/10.1186/1471-2105-10-86

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