Cross-Cell-Type Prediction of TF-Binding Site by Integrating Convolutional Neural Network and Adversarial Network

EL_LSTM: Prediction of DNA-binding residue from Protein sequence by Combining Long Short-Term Memory and Ensemble Learning

(2018) Jiyun Zhou et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

How motif environment influences transcription factor search dynamics: Finding a needle in a haystack

(2016) Iris Dror et al.   BIOESSAYS

Convolutional neural network architectures for predicting DNA–protein binding

(2016) Haoyang Zeng et al.   BIOINFORMATICS

Predicting transcription factor site occupancy using DNA sequence intrinsic and cell-type specific chromatin features

(2016) Sunil Kumar et al.   BMC BIOINFORMATICS

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

PDNAsite: Identification of DNA-binding Site from Protein Sequence by Incorporating Spatial and Sequence Context

(2016) Jiyun Zhou et al.   Scientific Reports

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

Predicting effects of noncoding variants with deep learning–based sequence model

(2015) Jian Zhou et al.   NATURE METHODS

JASPAR 2016: a major expansion and update of the open-access database of transcription factor binding profiles

(2015) Anthony Mathelier et al.   NUCLEIC ACIDS RESEARCH

Contribution of Sequence Motif, Chromatin State, and DNA Structure Features to Predictive Models of Transcription Factor Binding in Yeast

(2015) Zing Tsung-Yeh Tsai et al.   PLoS Computational Biology

UniPROBE, update 2015: new tools and content for the online database of protein-binding microarray data on protein–DNA interactions

(2014) Maxwell A. Hume et al.   NUCLEIC ACIDS RESEARCH

Transcription Factor Binding Sites Prediction Based on Modified Nucleosomes

(2014) Mohammad Talebzadeh et al.   PLoS One

Motif discovery and transcription factor binding sites before and after the next-generation sequencing era

(2012) Federico Zambelli et al.   BRIEFINGS IN BIOINFORMATICS

Genome-wide prediction of transcription factor binding sites using an integrated model

(2010) Kyoung-Jae Won et al.   GENOME BIOLOGY

Understanding bag-of-words model: a statistical framework

(2010) Yin Zhang et al.   International Journal of Machine Learning and Cybernetics

A Survey on Transfer Learning

(2009) Sinno Jialin Pan et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

ModuleMiner - improved computational detection of cis-regulatory modules: are there different modes of gene regulation in embryonic development and adult tissues?

(2008) Peter Van Loo et al.   GENOME BIOLOGY