More info in my Google Scholar profile.

Refereed Publications


Zeng H, Gifford DK.
Predicting the impact of non-coding variants on DNA methylation
Nucleic Acid Research [Journal]
Zeng H, Edwards MD, Guo Y, and Gifford DK.
Accurate eQTL prioritization with an ensemble-based framework.
Human Mutation [Journal]
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, Goke J, Mueller NS, Kellis M, Kundaje A, Beer MA, Keles S, Gifford DK and Yosef N.
Predicting gene expression in massively parallele reporter assays: a comparative study
Human Mutation [Journal]


Hashimoto T, Sherwood RI, Kang DD, Barkal AA, Zeng H, Emons BJM, Srinivasan S, Rajagopal N, Jaakkola T, and Gifford DK.
A DNA code governs chromatin accessibility.
Genome Research, 26(10), 1430-1440 [Journal]
Zeng H, Edwards M, Liu G, and Gifford DK.
Convolutional Neural Network Architectures for Predicting DNA-Protein Binding.
Intelligent Systems for Molecular Biology (ISMB), 2016
Bioinformatics, 32(12), i121-i127.[Journal]
Guo Y, Tian K, Zeng H, and Gifford DK.
K-mer Set Memory (KSM) motif representation enables accurate prediction of the impact of regulatory variants.
The 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB), 2017


Gymrek M, Willems T, Guilmatre A, Zeng H, Markus B, Georgiev S, Daly MJ, Price AL, Pritchard J, Sharp A and Erlich Y.
Abundant contribution of short tandem repeats to gene expression variation in humans
Nature Genetics, 48(1), 22–29. [Journal]
Zeng H, Hashimoto TB, Kang DD, and Gifford DK.
GERV: A statistical method for generative evaluation of regulatory variants for transcription factor binding
Bioinformatics, 32(4), 490-496. [Journal]


Bansal M, Yang J, Karan C, Menden MP, Costello JC, Tang H et al.
A community computational challenge to predict the activity of pairs of compounds
Nature Biotechnology, 32(12), 1213-1222. [Journal]
Sinha S, Tsang EK, Zeng H, Meister M, and Dill DL.
Mining TCGA data using Boolean implications
PLOS ONE, 9(7): e102119. [Journal]