Identifying polyadenylation signals with biological embedding via self-attentive gated convolutional highway networks

SANPolyA: a deep learning method for identifying Poly(A) signals

(2020) Haitao Yu et al.   BIOINFORMATICS

Attentive gated neural networks for identifying chromatin accessibility

(2020) Yanbu Guo et al.   NEURAL COMPUTING & APPLICATIONS

iEnhancer-5Step: Identifying enhancers using hidden information of DNA sequences via Chou's 5-step rule and word embedding

(2019) Nguyen Quoc Khanh Le et al.   ANALYTICAL BIOCHEMISTRY

DeepPASTA: deep neural network based polyadenylation site analysis

(2019) Ashraful Arefeen et al.   BIOINFORMATICS

To Embed or Not: Network Embedding as a Paradigm in Computational Biology

(2019) Walter Nelson et al.   Frontiers in Genetics

DeepACLSTM: deep asymmetric convolutional long short-term memory neural models for protein secondary structure prediction

(2019) Yanbu Guo et al.   BMC BIOINFORMATICS

Unsupervised word embeddings capture latent knowledge from materials science literature

(2019) Vahe Tshitoyan et al.   NATURE

DeepANF: A deep attentive neural framework with distributed representation for chromatin accessibility prediction

(2019) Yanbu Guo et al.   NEUROCOMPUTING

LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks

(2018) Juhua Zhang et al.   BIOINFORMATICS

Residual Highway Convolutional Neural Networks for in-loop Filtering in HEVC

(2018) Yongbing Zhang et al.   IEEE TRANSACTIONS ON IMAGE PROCESSING

A Comprehensive Survey of Graph Embedding: Problems, Techniques and Applications

(2018) HongYun Cai et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Learning distributed representations of RNA sequences and its application for predicting RNA-protein binding sites with a convolutional neural network

(2018) Xiaoyong Pan et al.   NEUROCOMPUTING

DeepPolyA: A Convolutional Neural Network Approach for Polyadenylation Site Prediction

(2018) Xin Gao et al.   IEEE Access

DeepGSR: an optimized deep-learning structure for the recognition of genomic signals and regions

(2018) Manal Kalkatawi et al.   BIOINFORMATICS

Protein secondary structure prediction improved by recurrent neural networks integrated with 2-dimensional convolutional neural networks

(2018) Yanbu Guo et al.   Journal of Bioinformatics and Computational Biology

DeeReCT-PolyA: a robust and generic deep learning method for PAS identification

(2018) Zhihao Xia et al.   BIOINFORMATICS

Functional and Contextual Attention-Based LSTM for Service Recommendation in Mashup Creation

(2018) Min Shi et al.   IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS

The Ensembl gene annotation system

(2016) Bronwen L. Aken et al.   Database-The Journal of Biological Databases and Curation

Deep learning

(2015) Yann LeCun et al.   NATURE

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

Poly(A) motif prediction using spectral latent features from human DNA sequences

(2013) Bo Xie et al.   BIOINFORMATICS

Alternative cleavage and polyadenylation: extent, regulation and function

(2013) Ran Elkon et al.   NATURE REVIEWS GENETICS

Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences

(2011) Manal Kalkatawi et al.   BIOINFORMATICS

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

POLYAR, a new computer program for prediction of poly(A) sites in human sequences

(2010) Malik Akhtar et al.   BMC GENOMICS

A classification-based prediction model of messenger RNA polyadenylation sites

(2010) Guoli Ji et al.   JOURNAL OF THEORETICAL BIOLOGY

The completion of the Mammalian Gene Collection (MGC)

(2009) et al.   GENOME RESEARCH