Cancer immunogenomics and bioinformatics

1. Vensko SP II, Bortone D, Vincent BG. Predicting tumor antigens using the LENS workflow through RAFT. Methods Mol Biol. 2025;2932:319–342. PubMed
2. Patel SA, Whang Y, Medley C, Chen K, Jordan J, Bortone D, et al. Tarlatamab for large cell neuroendocrine carcinoma in a young adult: a case report. JTO Clin Res Rep. 2024;5(10):100712. PubMed
3. Di Modugno F, Di Carlo A, Spada S, Palermo B, … Bortone DS, et al. Tumoral and stromal hMENA isoforms impact tertiary lymphoid structure localization in lung cancer and predict immune checkpoint blockade response in patients with cancer. EBioMedicine. 2024;101:105003. PubMed
4. Vensko SP, Olsen K, Bortone D, Smith CC, Chai S, Beckabir W, et al. LENS: Landscape of Effective Neoantigens Software. Bioinformatics. 2023;39(6):btad322. PubMed
5. Olsen KS, Jadi O, Dexheimer S, Bortone DS, Vensko SP, et al. Shared graft-versus-leukemia minor histocompatibility antigens in DISCOVeRY-BMT. Blood Adv. 2023;7(9):1635–1649. PubMed
6. Anders CK, Woodcock MG, Van Swearingen AED, Moore DT, … Bortone D, et al. Evaluating the efficacy of a priming dose of cyclophosphamide prior to pembrolizumab to treat metastatic triple negative breast cancer. J Immunother Cancer. 2022;10(2):e003427. PubMed
7. Bortone DS, Woodcock MG, Parker JS, Vincent BG. Improved T-cell receptor diversity estimates associate with survival and response to anti-PD-1 therapy. Cancer Immunol Res. 2021;9(1):103–112. PubMed
8. Wood CG, Ferguson JE 3rd, Parker JS, Moore DT, … Bortone DS, et al. Neoadjuvant pazopanib and molecular analysis of tissue response in renal cell carcinoma. JCI Insight. 2020;5(22):e132852. PubMed
9. Smith CC, Bixby LM, Miller KL, Selitsky SR, Bortone DS, Hoadley KA, et al. Using RNA sequencing to characterize the tumor microenvironment. Methods Mol Biol. 2020;2055:245–272. PubMed
10. Free ME, Stember KG, Hess JJ, McInnis EA, … Bortone DS, et al. Restricted myeloperoxidase epitopes drive the adaptive immune response in MPO-ANCA vasculitis. J Autoimmun. 2020;106:102306. PubMed
11. Thorsson V, Gibbs DL, Brown SD, Wolf D, Bortone DS, et al. The immune landscape of cancer. Immunity. 2018;48(4):812–830.e14. PubMed
12. Smith CC, Beckermann KE, Bortone DS, De Cubas AA, Bixby LM, et al. Endogenous retroviral signatures predict immunotherapy response in clear cell renal cell carcinoma. J Clin Invest. 2018;128(11):4804–4820. PubMed
13. Lansford JL, Dharmasiri U, Chai S, Hunsucker SA, Bortone DS, et al. Computational modeling and confirmation of leukemia-associated minor histocompatibility antigens. Blood Adv. 2018;2(16):2052–2062. PubMed
14. Nishijima TF, Kardos J, Chai S, Smith CC, Bortone DS, et al. Molecular and clinical characterization of a claudin-low subtype of gastric cancer. JCO Precis Oncol. 2017;1:1–10. PubMed

Neuroscience and methods

1. Zang N, Issa JB, Ditri TB, Bortone DS, Touve MA, et al. Multicolor polymeric nanoparticle neuronal tracers. ACS Cent Sci. 2020;6(3):436–445. PubMed
2. Bortone DS, Olsen SR, Scanziani M. Translaminar inhibitory cells recruited by layer 6 corticothalamic neurons suppress visual cortex. Neuron. 2014;82(2):474–485. PubMed Video abstract
3. Henderson L, Bortone DS, Lim C, Zambon AC. Classic “broken cell” techniques and newer live cell methods for cell cycle assessment. Am J Physiol Cell Physiol. 2013;304(10):C927–C938. PubMed
4. Olsen SR, Bortone DS, Adesnik H, Scanziani M. Gain control by layer six in cortical circuits of vision. Nature. 2012;483(7387):47–52. Co-first author. PubMed
5. Bortone D, Polleux F. KCC2 expression promotes the termination of cortical interneuron migration in a voltage-sensitive calcium-dependent manner. Neuron. 2009;62(1):53–71. PubMed
6. Bortone DS, Mitchell K, Manis PB. Developmental time course of potassium channel expression in the rat cochlear nucleus. Hear Res. 2006;211(1–2):114–125. PubMed
7. Hand R, Bortone D, Mattar P, Nguyen L, Heng JI, et al. Phosphorylation of Neurogenin2 specifies the migration properties and the dendritic morphology of pyramidal neurons in the neocortex. Neuron. 2005;48(1):45–62. PubMed

Patents and applications

1. Overhead tensile-actuated solar tracking system and method. US 12,348,180 B1. Issued 1 July 2025. Sole inventor. Google Patents
2. Gianneschi NC, Zang N, Scanziani M, Bortone DS, Ditri TB, Rush AM. Retrograde neuronal tracers detectable by fluorescence and other imaging methods. US patent application 17/797,181 (US 2023/0203369 A1); WO 2021/163498 A1. Filed 12 February 2021, priority 14 February 2020. Assigned to Howard Hughes Medical Institute, Northwestern University and the University of California, San Diego. Published 29 June 2023. Google Patents