DeepSite: bidirectional LSTM and CNN models for predicting DNA–protein binding

Identification of DNA–protein binding sites by bootstrap multiple convolutional neural networks on sequence information

(2019) Yongqing Zhang et al.   ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE

Discovering the Relationship Between Generalization and Uncertainty by Incorporating Complexity of Classification

(2018) Xi-Zhao Wang et al.   IEEE Transactions on Cybernetics

TEPIC 2—an extended framework for transcription factor binding prediction and integrative epigenomic analysis

(2018) Florian Schmidt et al.   BIOINFORMATICS

Simple tricks of convolutional neural network architectures improve DNA–protein binding prediction

(2018) Zhen Cao et al.   BIOINFORMATICS

Incorporating Diversity and Informativeness in Multiple-Instance Active Learning

(2017) Ran Wang et al.   IEEE TRANSACTIONS ON FUZZY SYSTEMS

Noniterative Deep Learning: Incorporating Restricted Boltzmann Machine Into Multilayer Random Weight Neural Networks

(2017) Xi-Zhao Wang et al.   IEEE Transactions on Systems Man Cybernetics-Systems

ISMB 2016 Proceedings

(2016) Pierre Baldi et al.   BIOINFORMATICS

Convolutional neural network architectures for predicting DNA–protein binding

(2016) Haoyang Zeng et al.   BIOINFORMATICS

Predicting CpG methylation levels by integrating Infinium HumanMethylation450 BeadChip array data

(2016) Shicai Fan et al.   GENOMICS

DiscMLA: An Efficient Discriminative Motif Learning Algorithm over High-Throughput Datasets

(2016) Hongbo Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

GeNemo: a search engine for web-based functional genomic data

(2016) Yongqing Zhang et al.   NUCLEIC ACIDS RESEARCH

A Study on Relationship Between Generalization Abilities and Fuzziness of Base Classifiers in Ensemble Learning

(2015) Xi-Zhao Wang et al.   IEEE TRANSACTIONS ON FUZZY SYSTEMS

A Two-Stage Geometric Method for Pruning Unreliable Links in Protein-Protein Networks

(2015) Lin Zhu et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction

(2015) Matt Spencer et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

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

(2015) Jian Zhou et al.   NATURE METHODS

By the company they keep: interaction networks define the binding ability of transcription factors

(2015) Davide Cirillo et al.   NUCLEIC ACIDS RESEARCH

Quantitative modeling of transcription factor binding specificities using DNA shape

(2015) Tianyin Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Continuous Distributed Representation of Biological Sequences for Deep Proteomics and Genomics

(2015) Ehsaneddin Asgari et al.   PLoS One

MACE: model based analysis of ChIP-exo

(2014) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

Using ensemble methods to deal with imbalanced data in predicting protein–protein interactions

(2012) Yongqing Zhang et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

ChIP–seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions

(2012) Terrence S. Furey   NATURE REVIEWS GENETICS

Convolutional Neural Networks for P300 Detection with Application to Brain-Computer Interfaces

(2010) H Cecotti et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE