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1.
APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries.
J Chem Inf Model
; 64(5): 1730-1750, 2024 Mar 11.
Article
in English
| MEDLINE | ID: mdl-38415656
2.
APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations.
Molecules
; 24(5)2019 Mar 02.
Article
in English
| MEDLINE | ID: mdl-30832312
3.
Revealing Unknown Protein Structures Using Computational Conformational Sampling Guided by Experimental Hydrogen-Exchange Data.
Int J Mol Sci
; 19(11)2018 Oct 31.
Article
in English
| MEDLINE | ID: mdl-30384411
4.
Frequency, Private Specificity, and Cross-Reactivity of Preexisting Hepatitis C Virus (HCV)-Specific CD8+ T Cells in HCV-Seronegative Individuals: Implications for Vaccine Responses.
J Virol
; 89(16): 8304-17, 2015 Aug.
Article
in English
| MEDLINE | ID: mdl-26041301
5.
Comprehensive characterization of IFNγ signaling in acute myeloid leukemia reveals prognostic and therapeutic strategies.
Nat Commun
; 15(1): 1821, 2024 Feb 28.
Article
in English
| MEDLINE | ID: mdl-38418901
6.
CrossDome: an interactive R package to predict cross-reactivity risk using immunopeptidomics databases.
Front Immunol
; 14: 1142573, 2023.
Article
in English
| MEDLINE | ID: mdl-37377956
7.
Vestigial-like 1 (VGLL1): An ancient co-transcriptional activator linking wing, placenta, and tumor development.
Biochim Biophys Acta Rev Cancer
; 1878(3): 188892, 2023 05.
Article
in English
| MEDLINE | ID: mdl-37004960
8.
PepSim: T-cell cross-reactivity prediction via comparison of peptide sequence and peptide-HLA structure.
Front Immunol
; 14: 1108303, 2023.
Article
in English
| MEDLINE | ID: mdl-37187737
9.
Individual Epitope-Specific CD8+ T Cell Immune Responses Are Shaped Differently during Chronic Viral Infection.
Pathogens
; 12(5)2023 May 14.
Article
in English
| MEDLINE | ID: mdl-37242386
10.
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
; 84(8): 374-383, 2023 Aug.
Article
in English
| MEDLINE | ID: mdl-36710086
11.
Single-Cell Profiling of CD8+ T Cells in Acute Myeloid Leukemia Reveals a Continuous Spectrum of Differentiation and Clonal Hyperexpansion.
Cancer Immunol Res
; : OF1-OF18, 2023 Jun 07.
Article
in English
| MEDLINE | ID: mdl-37285177
12.
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.
Article
in English
| MEDLINE | ID: mdl-37163233
13.
Computational Modeling of Molecular Structures Guided by Hydrogen-Exchange Data.
J Am Soc Mass Spectrom
; 33(2): 215-237, 2022 Feb 02.
Article
in English
| MEDLINE | ID: mdl-35077179
14.
Current progress and open challenges for applying deep learning across the biosciences.
Nat Commun
; 13(1): 1728, 2022 04 01.
Article
in English
| MEDLINE | ID: mdl-35365602
15.
Charge-based interactions through peptide position 4 drive diversity of antigen presentation by human leukocyte antigen class I molecules.
PNAS Nexus
; 1(3): pgac124, 2022 Jul.
Article
in English
| MEDLINE | ID: mdl-36003074
16.
DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins.
bioRxiv
; 2021 Jan 22.
Article
in English
| MEDLINE | ID: mdl-33501448
17.
DINC-COVID: A webserver for ensemble docking with flexible SARS-CoV-2 proteins.
Comput Biol Med
; 139: 104943, 2021 12.
Article
in English
| MEDLINE | ID: mdl-34717233
18.
Computational analysis of complement inhibitor compstatin using molecular dynamics.
J Mol Model
; 26(9): 231, 2020 Aug 12.
Article
in English
| MEDLINE | ID: mdl-32789582
19.
Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests.
Front Immunol
; 11: 1583, 2020.
Article
in English
| MEDLINE | ID: mdl-32793224
20.
HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy.
JCO Clin Cancer Inform
; 4: 623-636, 2020 07.
Article
in English
| MEDLINE | ID: mdl-32667823