Gifford DK - Search Results

1

A pan-variant mRNA-LNP T cell vaccine protects HLA transgenic mice from mortality after infection with SARS-CoV-2 Beta.

Carter B, Huang P, Liu G, Liang Y, Lin PJC, Peng BH, McKay LGA, Dimitrakakis A, Hsu J, Tat V, Saenkham-Huntsinger P, Chen J, Kaseke C, Gaiha GD, Xu Q, Griffiths A, Tam YK, Tseng CK, Gifford DK. Carter B, et al. Among authors: gifford dk. Front Immunol. 2023 Mar 9;14:1135815. doi: 10.3389/fimmu.2023.1135815. eCollection 2023. Front Immunol. 2023. PMID: 36969239 Free PMC article.

2

Convolutional neural network architectures for predicting DNA-protein binding.

Zeng H, Edwards MD, Liu G, Gifford DK. Zeng H, et al. Among authors: gifford dk. Bioinformatics. 2016 Jun 15;32(12):i121-i127. doi: 10.1093/bioinformatics/btw255. Bioinformatics. 2016. PMID: 27307608 Free PMC article.

3

Visualizing complex feature interactions and feature sharing in genomic deep neural networks.

Liu G, Zeng H, Gifford DK. Liu G, et al. Among authors: gifford dk. BMC Bioinformatics. 2019 Jul 19;20(1):401. doi: 10.1186/s12859-019-2957-4. BMC Bioinformatics. 2019. PMID: 31324140 Free PMC article.

4

Antibody complementarity determining region design using high-capacity machine learning.

Liu G, Zeng H, Mueller J, Carter B, Wang Z, Schilz J, Horny G, Birnbaum ME, Ewert S, Gifford DK. Liu G, et al. Among authors: gifford dk. Bioinformatics. 2020 Apr 1;36(7):2126-2133. doi: 10.1093/bioinformatics/btz895. Bioinformatics. 2020. PMID: 31778140 Free PMC article.

5

Robust computational design and evaluation of peptide vaccines for cellular immunity with application to SARS-CoV-2.

Liu G, Carter B, Bricken T, Jain S, Viard M, Carrington M, Gifford DK. Liu G, et al. Among authors: gifford dk. bioRxiv [Preprint]. 2020 May 17:2020.05.16.088989. doi: 10.1101/2020.05.16.088989. bioRxiv. 2020. Update in: Cell Syst. 2020 Aug 26;11(2):131-144.e6. doi: 10.1016/j.cels.2020.06.009 PMID: 32511351 Free PMC article. Updated. Preprint.

6

Computationally Optimized SARS-CoV-2 MHC Class I and II Vaccine Formulations Predicted to Target Human Haplotype Distributions.

Liu G, Carter B, Bricken T, Jain S, Viard M, Carrington M, Gifford DK. Liu G, et al. Among authors: gifford dk. Cell Syst. 2020 Aug 26;11(2):131-144.e6. doi: 10.1016/j.cels.2020.06.009. Epub 2020 Jul 27. Cell Syst. 2020. PMID: 32721383 Free PMC article.

7

Predicted Cellular Immunity Population Coverage Gaps for SARS-CoV-2 Subunit Vaccines and Their Augmentation by Compact Peptide Sets.

Liu G, Carter B, Gifford DK. Liu G, et al. Among authors: gifford dk. Cell Syst. 2021 Jan 20;12(1):102-107.e4. doi: 10.1016/j.cels.2020.11.010. Epub 2020 Nov 27. Cell Syst. 2021. PMID: 33321075 Free PMC article.

8

Machine learning optimization of peptides for presentation by class II MHCs.

Dai Z, Huisman BD, Zeng H, Carter B, Jain S, Birnbaum ME, Gifford DK. Dai Z, et al. Among authors: gifford dk. Bioinformatics. 2021 Oct 11;37(19):3160-3167. doi: 10.1093/bioinformatics/btab131. Bioinformatics. 2021. PMID: 33705522 Free PMC article.

9

Computational counterselection identifies nonspecific therapeutic biologic candidates.

Saksena SD, Liu G, Banholzer C, Horny G, Ewert S, Gifford DK. Saksena SD, et al. Among authors: gifford dk. Cell Rep Methods. 2022 Jul 11;2(7):100254. doi: 10.1016/j.crmeth.2022.100254. eCollection 2022 Jul 18. Cell Rep Methods. 2022. PMID: 35880012 Free PMC article.

10

A high-throughput yeast display approach to profile pathogen proteomes for MHC-II binding.

Huisman BD, Dai Z, Gifford DK, Birnbaum ME. Huisman BD, et al. Among authors: gifford dk. Elife. 2022 Jul 4;11:e78589. doi: 10.7554/eLife.78589. Elife. 2022. PMID: 35781135 Free PMC article.

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