Zeng H - Search Results

1

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: zeng h. Bioinformatics. 2021 Oct 11;37(19):3160-3167. doi: 10.1093/bioinformatics/btab131. Bioinformatics. 2021. PMID: 33705522 Free PMC article.

2

GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding.

Zeng H, Hashimoto T, Kang DD, Gifford DK. Zeng H, et al. Bioinformatics. 2016 Feb 15;32(4):490-6. doi: 10.1093/bioinformatics/btv565. Epub 2015 Oct 17. Bioinformatics. 2016. PMID: 26476779 Free PMC article.

3

Convolutional neural network architectures for predicting DNA-protein binding.

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

4

A synergistic DNA logic predicts genome-wide chromatin accessibility.

Hashimoto T, Sherwood RI, Kang DD, Rajagopal N, Barkal AA, Zeng H, Emons BJ, Srinivasan S, Jaakkola T, Gifford DK. Hashimoto T, et al. Among authors: zeng h. Genome Res. 2016 Oct;26(10):1430-1440. doi: 10.1101/gr.199778.115. Epub 2016 Jul 25. Genome Res. 2016. PMID: 27456004 Free PMC article.

5

Predicting gene expression in massively parallel reporter assays: A comparative study.

Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Tewhey R, Sabeti PC, Goke J, Mueller NS, Kellis M, Kundaje A, Beer MA, Keles S, Gifford DK, Yosef N. Kreimer A, et al. Among authors: zeng h. Hum Mutat. 2017 Sep;38(9):1240-1250. doi: 10.1002/humu.23197. Epub 2017 Mar 9. Hum Mutat. 2017. PMID: 28220625 Free PMC article.

6

Accurate eQTL prioritization with an ensemble-based framework.

Zeng H, Edwards MD, Guo Y, Gifford DK. Zeng H, et al. Hum Mutat. 2017 Sep;38(9):1259-1265. doi: 10.1002/humu.23198. Epub 2017 Apr 19. Hum Mutat. 2017. PMID: 28224684 Free PMC article.

7

Predicting the impact of non-coding variants on DNA methylation.

Zeng H, Gifford DK. Zeng H, et al. Nucleic Acids Res. 2017 Jun 20;45(11):e99. doi: 10.1093/nar/gkx177. Nucleic Acids Res. 2017. PMID: 28334830 Free PMC article.

8

A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction.

Guo Y, Tian K, Zeng H, Guo X, Gifford DK. Guo Y, et al. Among authors: zeng h. Genome Res. 2018 Jun;28(6):891-900. doi: 10.1101/gr.226852.117. Epub 2018 Apr 13. Genome Res. 2018. PMID: 29654070 Free PMC article.

9

Quantification of Uncertainty in Peptide-MHC Binding Prediction Improves High-Affinity Peptide Selection for Therapeutic Design.

Zeng H, Gifford DK. Zeng H, et al. Cell Syst. 2019 Aug 28;9(2):159-166.e3. doi: 10.1016/j.cels.2019.05.004. Epub 2019 Jun 5. Cell Syst. 2019. PMID: 31176619 Free PMC article.

10

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

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

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