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I Vardaxis, B Simovski, I Anzar, R Stratford, T Clancy, "Deep learning of antibody epitopes using positional permutation vectors." Computational and Structural Biotechnology Journal, 2024

B Malone, "An AI Platform for Designing Personalized Neoantigen Vaccines Which Induce Polyepitopic Immune Responses" 2024; The 7th International Neoantigen Summit

A. Lalanne, C. Jamet, J.-P. Delord, C. Ottensmeier, C. Le Tourneau, A. Tavernaro, G. Lacoste, B. Bastien, M. Brandely, B. Grellier, E. Quemeneur, Y. Yamashita, O. Kousuke, N. Yamagata, Y. Tanaka, K. Onoguchi, I. Pait, B. Malone, O. Baker, P. Brattas, M. Gheorghe, R. Stratford, T. Clancy, K. Bendjama, O. Lantz; "Personalized vaccine TG4050 induces polyepitopic immune responses against private neoantigens in resected HPV-negative Head and Neck cancers" AACR. 2024; LB401.

K Bendjama, "AI Empowered Infectious Disease Vaccine Development" 2024; The World Vaccine Congress Washington

K Bendjama, "Towards realization of AI drug development:Comprehensive process workflow for the Commercial Use of Personalized Cancer Vaccines" 2024; NextGen Therapies Industry Working Group Summit

Sverchkova, A., Burkholz, S., Rubsamen, R. et al. Integrative HLA typing of tumor and adjacent normal tissue can reveal insights into the tumor immune response. BMC Med Genomics 17, 37 (2024).

Gainullin M, Federico L, Røkke Osen J, Chaban V, Kared H, Alirezaylavasani A, Lund-Johansen F, Wildendahl G, Jacobsen J-A, Sarwar Anjum H, Stratford R, Tennøe S, Malone B, Clancy T, Vaage JT, Henriksen K, Wüsthoff L and Munthe LA (2024) People who use drugs show no increase in pre-existing T-cell cross-reactivity toward SARS-CoV-2 but develop a normal polyfunctional T-cell response after standard mRNA vaccination. Front. Immunol. 14:1235210. doi: 10.3389/fimmu.2023.1235210

Nielsen, M., Monberg, T., Sundvold, V., Albieri, B., Hovgaard, D., Petersen, M. M., … Svane, I. M. (2023). LTX-315 and adoptive cell therapy using tumor-infiltrating lymphocytes generate tumor specific T cells in patients with metastatic soft tissue sarcoma. OncoImmunology, 13(1).

Federico L, Malone B, Tennøe S, Chaban V, Osen JR, Gainullin M, Smorodina E, Kared H, Akbar R, Greiff V, Stratford R, Clancy T and Munthe LA (2023) Experimental validation of immunogenic SARS-CoV-2 T cell epitopes identified by artificial intelligence. Front. Immunol. 14:1265044. doi: 10.3389/fimmu.2023.1265044

Anzar I, Malone B, Samarakoon P, Vardaxis I, Simovski B, Fontenelle H, Meza-Zepeda LA, Stratford R, Keung EZ, Burgess M, Tawbi HA, Myklebost O and Clancy T (2023) The interplay between neoantigens and immune cells in sarcomas treated with checkpoint inhibition. Front. Immunol. 14:1226445. doi: 10.3389/fimmu.2023.1226445

NEC OncoImmunity to Present Developments in the Infectious Diseases at 21st Awaji International Forum on Infection and Immunity, 2023

Ellingsen EB, O'Day S, Mezheyeuski A, Gromadka A, Clancy T, Kristedja TS, Milhem M, Zakharia Y. Clinical Activity of Combined Telomerase Vaccination and Pembrolizumab in Advanced Melanoma: Results from a Phase I Trial. Clin Cancer Res. 2023 Aug 15;29(16):3026-3036. doi: 10.1158/1078-0432.CCR-23-0416. PMID: 37378632; PMCID: PMC10425723.

H Komuro, S Shinohara, Y Fukushima, A Demachi-Okamura, D Muraoka, K Masago, T Matsui, Y Sugita, Y Takahashi, R Nishida, C Takashima, T Ohki, Y Shigematsu, F Watanabe, K Adachi, T Fukuyama, H Hamana, H Kishi, D Miura, Y Tanaka, K Onoue, K Onoguchi, Y Yamashita, R Stratford, T Clancy, R Yamaguchi, H Kuroda, K Doi, H Iwata, H Matsushita, "Single-cell sequencing on CD8+ TILs revealed the nature of exhausted T cells recognizing neoantigen and cancer/testis antigen in non-small cell lung cancer." Journal for Immunotherapy of Cancer. 2023; 11(8): e007180.

Y Yamashita, "Utilization of Artificial Intelligence in vaccine development." 2023; The 39th Annual Meeting of the Japan Society of Drug Delivery System

Federico L, Tvedt THA, Gainullin M, Osen JR, Chaban V, Lund KP, Tietze L, Tran TT, Lund-Johansen F, Kared H, Lind A, Vaage JT, Stratford R, Tennøe S, Malone B, Clancy T, Myhre AEL, Gedde-Dahl T and Munthe LA (2023) Robust spike-specific CD4+ and CD8+ T cell responses in SARS-CoV-2 vaccinated hematopoietic cell transplantation recipients: a prospective, cohort study. Front. Immunol. 14:1210899. doi: 10.3389/fimmu.2023.1210899

Christian H.H. Ottensmeier, Jean-Pierre Delord, Ana Lalanne, Olivier Lantz, Camille Jamet, Annette TAVERNARO, Maud Brandely-Talbot, Benoît Grellier, Berangere Bastien, Hakim Makhloufi, Thierry Huss, Yoshiko Yamashita, Kousuke Onoue, Naoko Yamagata, Yuki Tanaka, Brandon Malone, Oliver Baker, Eric Quemeneur, Kaidre Bendjama, Christophe Le Tourneau. "Safety and immunogenicity of TG4050: A personalized cancer vaccine in head and neck carcinoma." ASCO. 2023; 6082-6082.

A Kitamura, "NEC's AI Drug Development Initiatives." 2023; 72nd SPSJ Annual Meeting

F Grazioli, P Machart, A Mösch, K Li, L V Castorina, N Pfeifer, MR Min, "Attentive variational information bottleneck for TCR–peptide interaction prediction." Bioinformatics 39.1 (2023): btac820.

Ellingsen EB, Bounova G, Kerzeli I, Anzar I, Simnica D, Aamdal E, Guren T, Clancy T, Mezheyeuski A, Inderberg EM, Mangsbo SM, Binder M, Hovig E, Gaudernack G. Characterization of the T cell receptor repertoire and melanoma tumor microenvironment upon combined treatment with ipilimumab and hTERT vaccination. J Transl Med. 2022 Sep 11;20(1):419. doi: 10.1186/s12967-022-03624-z. PMID: 36089578; PMCID: PMC9465869.

Tennøe S, Gheorghe M, Stratford R, Clancy T. The T Cell Epitope Landscape of SARS-CoV-2 Variants of Concern. Vaccines (Basel). 2022 Jul 14;10(7):1123. doi: 10.3390/vaccines10071123. PMID: 35891287; PMCID: PMC9315645.

M Block, J Delord, C Ottensmeier, C Tourneau, A Lalanne, O Lantz, K Knutson, G Lacoste, A Tavernaro, M Brandely, N Silvestre, B Grellier, Y Yamashita, K Onoue, N Yamagata, E Quemeneur, and K Bendjama, "Phase I trials of personalized cancer vaccine TG4050 in surgically treated high-risk head and neck squamous cell carcinoma (HNSCC) and relapsing ovarian cancer (OvC) patients." AACR. Cancer Research. 2022; 82(12 Suppl): CT182.

J Delord, M Block, C Ottensmeier, G Colon-Otero, C Tourneau, A Lalanne, C Jamet, O Lantz, K Knutson, G Lacoste, A Tavernaro, M Brandely-Talbot, N Silvestre, B Grellier, B Malone, Y Tanaka, K Onoue, Y Yamashita, E Quemeneur, and K Bendjama. "Phase 1 studies of personalized neoantigen vaccine TG4050 in ovarian carcinoma (OC) and head and neck squamous cell carcinoma (HNSCC)." ASCO. 2022; 2637-2637.

Anzar I, Sverchkova A, Samarakoon P, et al. Personalized HLA typing leads to the discovery of novel HLA alleles and tumor-specific HLA variants. HLA. 2022; 99(4): 313-327. doi:10.1111/tan.14562

Y Yamashita, "AI-based Neoantigen Prediction for Personalized Cancer Vaccine." 2021; The 57th Annual Meeting of Liver Cancer Study Group of Japan

Y Yamashita, "AI-based Neoantigen Prediction for Personalized Cancer Vaccine." 2021; The 13th Annual Meeting of Japanese Society of Immunotherapy for Hematological Disorders

Y Yamashita, K Bendjama, "AI-based Neoantigen Prediction for Personalized Cancer Vaccine." 2021; The 18th Annual Meeting of Japan Research Association for Immunotherapeutics

Y Yamashita, "AI-based Neoantigen Prediction for Personalized Cancer Vaccine." 2021; Bring Innovation in the Pharmaceutical Industry

Y Yamashita, "AI-based Neoantigen Prediction for Personalized Cancer Vaccine." 2021; The 4th Social Smart Dental Hospital Symposium

B Malone, B Simovski, C Moliné, J Cheng, M Gheorghe, H Fontenelle, I Vardaxis, S Tennøe, JA Malmberg, R Stratford, and T Clancy, "Artificial intelligence predicts the immunogenic landscape of SARS-CoV-2 leading to universal blueprints for vaccine designs." Scientific reports. 2020; 10(1): 1-14.

B Malone, C Tosch, B Grellier, K Onoue, T Sztyler, K Rittner, Y Yamashita, E Quemeneur, and K Bendjama, "Performance of neoantigen prediction for the design of TG4050, a patient specific neoantigen cancer vaccine." AACR. Cancer Research. 2020; 80(16 Suppl): 4566.

CLH Guerrero, Y Yamashita, M Miyara, N Imaizumi, M Kato, S Sakihama, M Hayashi, T Miyagi, K Karimata, J Uchihara, K Ohshiro, J Todoroki, S Nakachi, S Morishima, K Karube, Y Tanaka, H Masuzaki, and T Fukushima, "Proteomic profiling of HTLV-1 carriers and ATL patients reveals sTNFR2 as a novel diagnostic biomarker for acute ATL." Blood advances. 2020; 4(6): 1062-1071.

Y Yamashita, "AI-based Neoantigen Prediction for Personalized Cancer Vaccine." 2019; The 32nd Annual Meeting of the Japan Society for Biological Therapy

Sverchkova, A., Anzar, I., Stratford, R., & Clancy, T. (2019). Improved HLA typing of Class I and Class II alleles from next‐generation sequencing data. Hla, May, 1–10.

K Onoue, Y Yamashita, B Malone, Y Tanaka, B Grellier, K Bendjama, K Machida, and K Udaka, "Evaluation of HLA-peptide binding prediction method." 2019; The 23rd Annual Meeting of Japanese Association of Cancer Immunology

Anzar, I., Sverchkova, A., Stratford, R. et al. NeoMutate: an ensemble machine learning framework for the prediction of somatic mutations in cancer. BMC Med Genomics 12, 63 (2019).