Haoyang Zeng
Haoyang Zeng
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Convolutional neural network architectures for predicting DNA–protein binding
H Zeng, MD Edwards, G Liu, DK Gifford
Bioinformatics 32 (12), i121-i127, 2016
Training gans with optimism
C Daskalakis, A Ilyas, V Syrgkanis, H Zeng
arXiv preprint arXiv:1711.00141, 2017
Abundant contribution of short tandem repeats to gene expression variation in humans
M Gymrek, T Willems, A Guilmatre, H Zeng, B Markus, S Georgiev, ...
Nature genetics 48 (1), 22-29, 2016
A community computational challenge to predict the activity of pairs of compounds
M Bansal, J Yang, C Karan, MP Menden, JC Costello, H Tang, G Xiao, ...
Nature biotechnology 32 (12), 1213-1222, 2014
Predicting the impact of non-coding variants on DNA methylation
H Zeng, DK Gifford
Nucleic Acid Research 45 (11), e99, 2017
Antibody complementarity determining region design using high-capacity machine learning
G Liu, H Zeng, J Mueller, B Carter, Z Wang, J Schilz, G Horny, ...
Bioinformatics 36 (7), 2126-2133, 2020
GERV: A Statistical Method for Generative Evaluation of Regulatory Variants for Transcription Factor Binding
H Zeng, T Hashimoto, DD Kang, DK Gifford
Bioinformatics, 2015
A novel k-mer set memory (KSM) motif representation improves regulatory variant prediction
Y Guo, K Tian, H Zeng, X Guo, DK Gifford
Genome research 28 (6), 891-900, 2018
Predicting gene expression in massively parallel reporter assays: A comparative study
A Kreimer, H Zeng, MD Edwards, Y Guo, K Tian, S Shin, R Welch, ...
Human mutation 38 (9), 1240-1250, 2017
Quantification of uncertainty in peptide-MHC binding prediction improves high-affinity peptide selection for therapeutic design
H Zeng, DK Gifford
Cell systems 9 (2), 159-166. e3, 2019
DeepLigand: accurate prediction of MHC class I ligands using peptide embedding
H Zeng, DK Gifford
Bioinformatics 35 (14), i278-i283, 2019
A synergistic DNA logic predicts genome-wide chromatin accessibility
T Hashimoto, RI Sherwood, DD Kang, N Rajagopal, AA Barkal, H Zeng, ...
Genome research 26 (10), 1430-1440, 2016
Visualizing complex feature interactions and feature sharing in genomic deep neural networks
G Liu, H Zeng, DK Gifford
BMC bioinformatics 20 (1), 1-14, 2019
Accurate eQTL prioritization with an ensemble‐based framework
H Zeng, MD Edwards, Y Guo, DK Gifford
Human mutation 38 (9), 1259-1265, 2017
Mining TCGA data using Boolean implications
S Sinha, EK Tsang, H Zeng, M Meister, DL Dill
PloS one 9 (7), e102119, 2014
Machine learning optimization of peptides for presentation by class II MHCs
Z Dai, BD Huisman, H Zeng, B Carter, S Jain, ME Birnbaum, DK Gifford
Bioinformatics 37 (19), 3160-3167, 2021
Discovering DNA motifs and genomic variants associated with DNA methylation
H Zeng, DK Gifford
bioRxiv, 073809, 2016
Machine learning based antibody design
DK Gifford, H Zeng, G Liu
US Patent App. 16/171,596, 2019
Machine learning models for functional genomics and therapeutic design
H Zeng
Massachusetts Institute of Technology, 2019
K-mer Set Memory (KSM) Motif Representation Enables Accurate Prediction of the Impact of Regulatory Variants.
Y Guo, K Tian, H Zeng, DK Gifford
RECOMB, 372-374, 2017
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