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Dinler Amaral Antunes

TitleAssistant Professor
InstitutionUniversity of Houston
DepartmentBiology and Biochemistry
Address4800 Calhoun Rd
Houston TX 77004
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Alves CC, Lewis J, Antunes DA, Donadi EA. The Role of Vimentin Peptide Citrullination in the Structure and Dynamics of HLA-DRB1 Rheumatoid Arthritis Risk-Associated Alleles. Int J Mol Sci. 2024 Dec 24; 26(1). PMID: 39795892; PMCID: PMC11719467.
      Citations:    Fields:    Translation:HumansCells
    2. Le HN, de Freitas MV, Antunes DA. Strengths and limitations of web servers for the modeling of TCRpMHC complexes. Comput Struct Biotechnol J. 2024 Dec; 23:2938-2948. PMID: 39104710; PMCID: PMC11298609.
      Citations:    
    3. Wang B, Reville PK, Yassouf MY, Jelloul FZ, Ly C, Desai PN, Wang Z, Borges P, Veletic I, Dasdemir E, Burks JK, Tang G, Guo S, Garza AI, Nasnas C, Vaughn NR, Baran N, Deng Q, Matthews J, Gunaratne PH, Antunes DA, Ekmekcioglu S, Sasaki K, Garcia MB, Cuglievan B, Hao D, Daver N, Green MR, Konopleva M, Futreal A, Post SM, Abbas HA. Comprehensive characterization of IFN? signaling in acute myeloid leukemia reveals prognostic and therapeutic strategies. Nat Commun. 2024 Feb 28; 15(1):1821. PMID: 38418901; PMCID: PMC10902356.
      Citations: 8     Fields:    Translation:Humans
    4. Fasoulis R, Rigo MM, Liz?e G, Antunes DA, Kavraki LE. APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries. J Chem Inf Model. 2024 03 11; 64(5):1730-1750. PMID: 38415656; PMCID: PMC10936522.
      Citations: 2     Fields:    Translation:AnimalsCells
    5. Antunes DA, Baker BM, Cornberg M, Selin LK. Editorial: Quantification and prediction of T-cell cross-reactivity through experimental and computational methods. Front Immunol. 2024; 15:1377259. PMID: 38444853; PMCID: PMC10912571.
      Citations:    Fields:    Translation:Cells
    6. Fasoulis R, Rigo MM, Antunes DA, Paliouras G, Kavraki LE. Transfer learning improves pMHC kinetic stability and immunogenicity predictions. Immunoinformatics (Amst). 2024 Mar; 13. PMID: 38577265; PMCID: PMC10994007.
      Citations: 3     
    7. Bebis G, Kato M, Kohandel M, Wilkie K, Antunes DA, Chen K, Dou J. Editorial: Advances in mathematical and computational oncology, volume III. Front Oncol. 2023; 13:1282882. PMID: 37817766; PMCID: PMC10561312.
      Citations:    
    8. Antunes DA, Schoeder CT, Baek M, Donadi EA. Editorial: Structural modeling and computational analyses of immune system molecules. Front Immunol. 2023; 14:1274670. PMID: 37731492; PMCID: PMC10508985.
      Citations:    Fields:    
    9. Conev A, Rigo MM, Devaurs D, Fonseca AF, Kalavadwala H, de Freitas MV, Clementi C, Zanatta G, Antunes DA, Kavraki LE. EnGens: a computational framework for generation and analysis of representative protein conformational ensembles. Brief Bioinform. 2023 07 20; 24(4). PMID: 37418278; PMCID: PMC10359083.
      Citations: 7     Fields:    Translation:Cells
    10. Fonseca AF, Antunes DA. CrossDome: an interactive R package to predict cross-reactivity risk using immunopeptidomics databases. Front Immunol. 2023; 14:1142573. PMID: 37377956; PMCID: PMC10291144.
      Citations: 4     Fields:    Translation:HumansCells
    11. Desai PN, Wang B, Fonseca A, Borges P, Jelloul FZ, Reville PK, Lee E, Ly C, Basi A, Root J, Baran N, Post SM, Deng Q, Sun H, Harmanci AO, Burks JK, Gomez JA, DiNardo CD, Daver NG, Alatrash G, Konopleva M, Green MR, Antunes DA, Futreal A, Hao D, Abbas HA. Single-Cell Profiling of CD8+ T Cells in Acute Myeloid Leukemia Reveals a Continuous Spectrum of Differentiation and Clonal Hyperexpansion. Cancer Immunol Res. 2023 Jun 07; OF1-OF18. PMID: 37285177.
      Citations: 2     Fields:    
    12. Lee SE, Wang F, Grefe M, Trujillo-Ocampo A, Ruiz-Vasquez W, Takahashi K, Abbas HA, Borges P, Antunes DA, Al-Atrash G, Daver N, Molldrem JJ, Futreal A, Garcia-Manero G, Im JS. Immunologic Predictors for Clinical Responses during Immune Checkpoint Blockade in Patients with Myelodysplastic Syndromes. Clin Cancer Res. 2023 05 15; 29(10):1938-1951. PMID: 36988276; PMCID: PMC10192218.
      Citations: 3     Fields:    Translation:Humans
    13. Klein S, Mischke J, Beruldsen F, Prinz I, Antunes DA, Cornberg M, Kraft ARM. Individual Epitope-Specific CD8+ T Cell Immune Responses Are Shaped Differently during Chronic Viral Infection. Pathogens. 2023 May 14; 12(5). PMID: 37242386; PMCID: PMC10221246.
      Citations:    
    14. Desai PN, Wang B, Fonseca A, Borges P, Jelloul FZ, Reville PK, Lee E, Ly C, Basi A, Root J, Baran N, Post SM, Deng Q, Sun H, Harmanci AO, Burks JK, Gomez JA, DiNardo CD, Daver NG, Alatrash G, Konopleva M, Green MR, Antunes DA, Futreal A, Hao D, Abbas HA. Single-Cell Profiling of CD8+ T Cells in Acute Myeloid Leukemia Reveals a Continuous Spectrum of Differentiation and Clonal Hyperexpansion. Cancer Immunol Res. 2023 May 10. PMID: 37163233.
      Citations: 8     Fields:    
    15. Conev A, Rigo MM, Devaurs D, Fonseca AF, Kalavadwala H, de Freitas MV, Clementi C, Zanatta G, Antunes DA, Kavraki L. EnGens: a computational framework for generation and analysis of representative protein conformational ensembles. bioRxiv. 2023 Apr 28. PMID: 37163076; PMCID: PMC10168271.
      Citations:    
    16. Hall-Swan S, Slone J, Rigo MM, Antunes DA, Liz?e G, Kavraki LE. PepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure. Front Immunol. 2023; 14:1108303. PMID: 37187737; PMCID: PMC10175663.
      Citations:    Fields:    Translation:Cells
    17. Sonnemann HM, Pazdrak B, Antunes DA, Roszik J, Liz?e G. Vestigial-like 1 (VGLL1): An ancient co-transcriptional activator linking wing, placenta, and tumor development. Biochim Biophys Acta Rev Cancer. 2023 05; 1878(3):188892. PMID: 37004960.
      Citations: 2     Fields:    Translation:HumansAnimals
    18. Alves CC, Arns T, Oliveira ML, Moreau P, Antunes DA, Castelli EC, Mendes-Junior CT, Giuliatti S, Donadi EA. Computational and atomistic studies applied to the understanding of the structural and behavioral features of the immune checkpoint HLA-G molecule and gene. Hum Immunol. 2023 Aug; 84(8):374-383. PMID: 36710086.
      Citations:    Fields:    Translation:Humans
    19. Jackson KR, Antunes DA, Talukder AH, Maleki AR, Amagai K, Salmon A, Katailiha AS, Chiu Y, Fasoulis R, Rigo MM, Abella JR, Melendez BD, Li F, Sun Y, Sonnemann HM, Belousov V, Frenkel F, Justesen S, Makaju A, Liu Y, Horn D, Lopez-Ferrer D, Huhmer AF, Hwu P, Roszik J, Hawke D, Kavraki LE, Liz?e G. Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules. PNAS Nexus. 2022 Jul; 1(3):pgac124. PMID: 36003074; PMCID: PMC9391200.
      Citations: 3     
    20. Rigo MM, Fasoulis R, Conev A, Hall-Swan S, Antunes DA, Kavraki LE. SARS-Arena: Sequence and Structure-Guided Selection of Conserved Peptides from SARS-related Coronaviruses for Novel Vaccine Development. Front Immunol. 2022; 13:931155. PMID: 35903104; PMCID: PMC9315150.
      Citations: 2     Fields:    Translation:HumansCells
    21. Conev A, Devaurs D, Rigo MM, Antunes DA, Kavraki LE. 3pHLA-score improves structure-based peptide-HLA binding affinity prediction. Sci Rep. 2022 06 24; 12(1):10749. PMID: 35750701; PMCID: PMC9232595.
      Citations: 5     Fields:    Translation:HumansCells
    22. Sapoval N, Aghazadeh A, Nute MG, Antunes DA, Balaji A, Baraniuk R, Barberan CJ, Dannenfelser R, Dun C, Edrisi M, Elworth RAL, Kille B, Kyrillidis A, Nakhleh L, Wolfe CR, Yan Z, Yao V, Treangen TJ. Current progress and open challenges for applying deep learning across the biosciences. Nat Commun. 2022 04 01; 13(1):1728. PMID: 35365602; PMCID: PMC8976012.
      Citations: 65     Fields:    
    23. Devaurs D, Antunes DA, Borysik AJ. Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data. J Am Soc Mass Spectrom. 2022 Feb 02; 33(2):215-237. PMID: 35077179.
      Citations: 7     Fields:    
    24. Hall-Swan S, Devaurs D, Rigo MM, Antunes DA, Kavraki LE, Zanatta G. DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins. Comput Biol Med. 2021 12; 139:104943. PMID: 34717233; PMCID: PMC8518241.
      Citations: 5     Fields:    
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