Dr Frank Lin

Dr Frank Lin

Senior Research Fellow

2022 - FAIDH, Fellowship of the Australasian Institute of Digital Health
2019 - FRACP, Internal Medicine (Medical Oncology), Fellowship of the Royal Australasian College of Physicians
2009 - PhD, University of New South Wales (Medical informatics) - Australia
2003 - MB ChB, University of Otago - New Zealand

Medicine & Health
School of Clinical Medicine

Frank is a medical oncologist and clinical  informatician based in Sydney, Australia. Frank holds conjoint research appointments at the NHMRC Clinical Trial Centre, University of Sydney and the Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research. Frank completed specialist training in medical oncology in both New Zealand (Waikato Hospital) and Australia (The Kinghorn Cancer Centre and St Vincent’s Hospital, Sydney).

Frank’s research expertise is in evidence-based precision medicine and application of digital health in oncology. His research focuses on empowering genomic decision-making, multidisciplinary care, and biomarker development in oncology through artificial intelligence and machine learning. He is co-investigator of several clinical trials in early drug development as part of Australian Genomic Cancer Medicine Program. He leads the development and maintains the TOPOGRAPH precision oncology knowledgebase, as well as the development of open source resources for treatment decision-support and electronic medical record analytics. He is chief investigator and co-investigator on several grants. Frank is also an Associate Editor of JCO Clinical Cancer Informatics.

Location
Level 11, Kinghorn Centre for Clinical Genomics Garvan Institute of Medical Research 370 Victorial Street Darlinghurst, NSW 2010
  • Book Chapters | 2012
    Gallego B; Concha ÓP; Lin FPY; Coiera EW, 2012, 'Exploring the role of pathology test results in the prediction of remaining days of hospitalisation.', in Maeder AJ; Martin Sanchez FJ (ed.), Studies in Health Technology and Informatics, Health Informatics: Building a Healthcare Future Through Trusted Information, IOS Press, Amsterdam, pp. 45 - 50, http://dx.doi.org/10.3233/978-1-61499-078-9-45
  • Journal articles | 2023
    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
    Journal articles | 2023
    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, pp. e0284327, http://dx.doi.org/10.1371/journal.pone.0284327
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2023
    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
    Journal articles | 2022
    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
    Journal articles | 2022
    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
    Journal articles | 2021
    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
    Journal articles | 2021
    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, http://dx.doi.org/10.1038/s41698-021-00194-z
    Journal articles | 2021
    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
    Journal articles | 2020
    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
    Journal articles | 2019
    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
    Journal articles | 2018
    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
    Journal articles | 2017
    Epstein RJ; Lin FP, 2017, 'Cancer and the omics revolution', Australian Family Physician, 46, pp. 189 - 193
    Journal articles | 2017
    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, http://dx.doi.org/10.1038/s41598-017-07111-0
    Journal articles | 2016
    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, http://dx.doi.org/10.1186/s12885-016-2972-z
    Journal articles | 2016
    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
    Journal articles | 2015
    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
    Journal articles | 2014
    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
    Journal articles | 2013
    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
    Journal articles | 2011
    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
    Journal articles | 2011
    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
    Journal articles | 2009
    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
    Journal articles | 2009
    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, http://dx.doi.org/10.1080/00313020903071447
  • Conference Abstracts | 2022
    Lin FP-Y; Thavaneswaran S; Grady JP; Napier CE; Kansara M; Sebastian L; Kee D; Oakes SR; Blackburn J; Scott HS; Glover A; Fox SB; Goldstein D; Leo P; Amanuel B; Desai J; Lee CK; Ballinger ML; Simes J; Thomas DM, 2022, 'Molecular therapy selection in treatment-refractory advanced cancers: A retrospective cohort study determining the utility of TOPOGRAPH knowledge base.', in Journal of Clinical Oncology, American Society of Clinical Oncology (ASCO), Vol. 40, pp. 3073 - 3073, http://dx.doi.org/10.1200/jco.2022.40.16_suppl.3073
    Preprints | 2022
    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, 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
    Preprints | 2021
    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
    Preprints | 2020
    Lin FPY; Salih OSM; Scott N; Jameson MB; Epstein RJ, 2020, Repurposing digitised clinical narratives to discover prognostic factors and predict survival in patients with advanced cancer, , http://dx.doi.org/10.1101/2020.10.28.20214627
    Preprints | 2020
    Lin FPY, 2020, Design and implementation of an intelligent framework for supporting evidence-based treatment recommendations in precision oncology, , http://dx.doi.org/10.1101/2020.11.15.383448
    Conference Abstracts | 2018
    Lin FP; Salih OSM; Epstein RJ, 2018, 'EXPLORATORY ANALYSIS OF CLINICAL PROGNOSTIC FACTORS IN PATIENTS WITH ADVANCED CANCER USING COMPUTATIONAL TEXT MINING OF ROUTINE DIGITISED ONCOLOGY CORRESPONDENCE', in INTERNAL MEDICINE JOURNAL, WILEY, Vol. 48, pp. 8 - 8, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000431995500009&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Conference Papers | 2018
    Lin FPY; Tan ABT, 2018, 'A Signal-Seeking Text Mining Analysis for Identifying Clinical Factors Associated with Treatment Benefit from Pazopanib or Sunitinib in Metastatic Clear Cell Renal Cell Carcinoma', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY, pp. 38 - 38, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000437670700033&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Conference Abstracts | 2017
    Lin FP-Y; Groza T; Kocbek S; Antezana E; Epstein RJ, 2017, 'The Cancer Care Treatment Outcomes Ontology (CCTO): A computable ontology for profiling treatment outcomes of patients with solid tumors.', in JOURNAL OF CLINICAL ONCOLOGY, AMER SOC CLINICAL ONCOLOGY, IL, Chicago, Vol. 35, presented at 53rd Annual Clinical Science Meeting of the American-Society-of-Clinical-Oncology (ASCO) / Symposium on Old Targets, New Drugs - Her2 and MET, IL, Chicago, 02 June 2017 - 07 June 2017, http://dx.doi.org/10.1200/JCO.2017.35.15_suppl.e18137
    Conference Abstracts | 2017
    Lin FP-Y; Martin C; Kocbek S; Joshua AM; Dear RF-G; Lim E; Chantrill LA; Chin VT; Epstein RJ, 2017, 'Identifying determinants of quality of life in patients undergoing systemic therapy for solid tumors.', in JOURNAL OF CLINICAL ONCOLOGY, AMER SOC CLINICAL ONCOLOGY, IL, Chicago, Vol. 35, presented at 53rd Annual Clinical Science Meeting of the American-Society-of-Clinical-Oncology (ASCO) / Symposium on Old Targets, New Drugs - Her2 and MET, IL, Chicago, 02 June 2017 - 07 June 2017, http://dx.doi.org/10.1200/JCO.2017.35.15_suppl.6596
    Conference Abstracts | 2016
    Lin FPY; Pokorny A; Teng C; Dear R; Epstein RJ, 2016, 'AN ALTERNATING DECISION TREE MODEL FOR PREDICTING MULTIDISCIPLINARY TEAM MEETING DECISION ABOUT ADJUVANT CHEMOTHERAPY IN EARLY BREAST CANCER PATIENTS', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY-BLACKWELL, Vol. 12, pp. 59 - 59, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000380005100043&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Conference Papers | 2016
    Teng C; Shahid N; Lin FPY; Moylan E, 2016, 'FEASIBILITY OF A RESEARCH PROTOCOL FOR STUDYING PATTERNS OF INVESTIGATION AND TREATMENT FOR BONE COMPLICATIONS IN PATIENTS TREATED WITH AROMATASE INHIBITORS FOR EARLY BREAST CANCER', in ASIA-PACIFIC JOURNAL OF CLINICAL ONCOLOGY, WILEY-BLACKWELL, pp. 132 - 132, https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000387769900207&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=891bb5ab6ba270e68a29b250adbe88d1
    Conference Posters | 2011
    Lin FP, 2011, 'Uncovering genes associated with human infections in pathogenic bacteria: a novel integrative analysis linking genome, bibliome, and diseasome', San Francisco, pp. 131, presented at AMIA Translational Bioinformatics Summit, San Francisco, 07 March 2011 - 09 March 2011
    Conference Papers | 2010
    Lin FP; Coiera E, 2010, 'A clinical workflow model for facilitating the design and evaluation of computerised clinical decision support systems', in 18th Annual Health Informatics Conference, Health Informatics Society of Australia, Mebourne, pp. 61 - 65, presented at HIC2010: Informing the business of healthcare, Melbourne, 24 August 2010 - 26 August 2010, http://search.informit.com.au/documentSummary;dn=429770463684403;res=IELHEA
    Conference Papers | 2010
    Lin FP; Polasek TM; Stephen A; Tsafnat G; Doogue MP, 2010, 'BICEPP: a computational text mining method for predicting binary characteristics of drugs', in BMC Bioinformatics, Melbourne, Australia, pp. 40 - 40, presented at ASCEPT Annual Scientific meeting, Melbourne, Australia, 28 November 2010 - 01 December 2010, http://dx.doi.org/10.1186/1471-2105-12-112
    Conference Papers | 2009
    Lin FP, 2009, 'Towards Personalised Pharmacotherapy: A Perspective from Biomedical Informatics', in HIC 2009: Proceedings; Frontiers of Health Informatics - Redefining Healthcare, National Convention Centre Canberra, 19-21 August 2009., Informit (RMIT Publishing), Melbourne, Australia, pp. 57 - 62, presented at HIC2009 Frontiers of Health Informatics - Redefining Healthcare, Canberra, 19 August 2009 - 21 August 2009, http://search.informit.com.au/documentSummary;dn=497482681236702;res=IELHSS
    Conference Papers | 2007
    Lin FP, 2007, 'The role of data mining in clinical predictive medicine: a narrative review.', in HIC 2006 Bridging the Digital Divide: Clinician, consumer and computer, HIC 2006 Bridging the Digital Divide: Clinician, consumer and computer, Melbourne, pp. 169 - 174, presented at HIC 2006 Bridging the Digital Divide: Clinician, consumer and computer, Melbourne, 31 July 2007 - 02 August 2007, http://training.informit.com.au/documentSummary;dn=951771578616360;res=IELHSS