iDNA-MT: Identification DNA Modification Sites in Multiple Species by Using Multi-Task Learning Based a Neural Network Tool

Granular multiple kernel learning for identifying RNA-binding protein residues via integrating sequence and structure information

(2021) Chao Yang et al.   NEURAL COMPUTING & APPLICATIONS

DeepM6ASeq-EL: prediction of human N6-methyladenosine (m6A) sites with LSTM and ensemble learning

(2021) Juntao Chen et al.   Frontiers of Computer Science

StackCPPred: A Stacking and Pairwise Energy Content-based Prediction of Cell-Penetrating Peptides and Their Uptake Efficiency

(2020) Xiangzheng Fu et al.   BIOINFORMATICS

ECFS-DEA: an ensemble classifier-based feature selection for differential expression analysis on expression profiles

(2020) Xudong Zhao et al.   BMC BIOINFORMATICS

Identification of methylation states of DNA regions for Illumina methylation BeadChip

(2020) Ximei Luo et al.   BMC GENOMICS

Basic polar and hydrophobic properties are the main characteristics that affect the binding of transcription factors to methylation sites

(2020) Zijie Shen et al.   BIOINFORMATICS

A Novel Triple Matrix Factorization Method for Detecting Drug-Side Effect Association Based on Kernel Target Alignment

(2020) Xiaoyi Guo et al.   Biomed Research International

Identification of Drug–Target Interactions via Dual Laplacian Regularized Least Squares with Multiple Kernel Fusion

(2020) Yijie Ding et al.   KNOWLEDGE-BASED SYSTEMS

DeepYY1: a deep learning approach to identify YY1-mediated chromatin loops

(2020) Fu-Ying Dao et al.   BRIEFINGS IN BIOINFORMATICS

Exploring associations of non-coding RNAs in human diseases via three-matrix factorization with hypergraph-regular terms on center kernel alignment

(2020) Hao Wang et al.   BRIEFINGS IN BIOINFORMATICS

Identification of human microRNA-disease association via hypergraph embedded bipartite local model

(2020) Yijie Ding et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

i6mA-Pred: Identifying DNA N6-methyladenine sites in the rice genome

(2019) Wei Chen et al.   BIOINFORMATICS

Deep-Resp-Forest: A deep forest model to predict anti-cancer drug response

(2019) Ran Su et al.   METHODS

RMDB: An integrated database of single-cytosine-resolution DNA methylation in Oryza sativa

(2019) Tiansheng Zhu et al.   Current Bioinformatics

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

(2019) Peng Ni et al.   BIOINFORMATICS

Iterative feature representations improve N4-methylcytosine site prediction

(2019) Leyi Wei et al.   BIOINFORMATICS

Genome-wide differential-based analysis of the relationship between DNA methylation and gene expression

(2019) Yuanyuan Zhang et al.   Current Bioinformatics

Jump-seq: Genome-Wide Capture and Amplification of 5-Hydroxymethylcytosine Sites

(2019) Lulu Hu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DUNet: A deformable network for retinal vessel segmentation

(2019) Qiangguo Jin et al.   KNOWLEDGE-BASED SYSTEMS

Review of progress in predicting protein methylation sites

(2019) Chunyan Ao et al.   CURRENT ORGANIC CHEMISTRY

Meta-4mCpred: A Sequence-Based Meta-Predictor for Accurate DNA 4mC Site Prediction Using Effective Feature Representation

(2019) Balachandran Manavalan et al.   Molecular Therapy-Nucleic Acids

Analysis on epigenetic signature of cell reprogramming by computational DNA methylation profiles

(2019) Yongchun Zuo et al.   Current Bioinformatics

A comparison and assessment of computational method for identifying recombination hotspots in Saccharomyces cerevisiae

(2019) Hui Yang et al.   BRIEFINGS IN BIOINFORMATICS

Identification of drug–target interactions via fuzzy bipartite local model

(2019) Yijie Ding et al.   NEURAL COMPUTING & APPLICATIONS

i6mA-DNCP: Computational Identification of DNA N6-Methyladenine Sites in the Rice Genome Using Optimized Dinucleotide-Based Features

(2019) Liang Kong et al.   Genes

SNNRice6mA: A Deep Learning Method for Predicting DNA N6-Methyladenine Sites in Rice Genome

(2019) Haitao Yu et al.   Frontiers in Genetics

4mCpred-EL: An Ensemble Learning Framework for Identification of DNA N4-methylcytosine Sites in the Mouse Genome

(2019) Manavalan et al.   Cells

i4mC-ROSE, a bioinformatics tool for the identification of DNA N4-methylcytosine sites in the Rosaceae genome

(2019) Md. Mehedi Hasan et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Identification of membrane protein types via multivariate information fusion with Hilbert–Schmidt Independence Criterion

(2019) Hao Wang et al.   NEUROCOMPUTING

SDM6A: A Web-Based Integrative Machine-Learning Framework for Predicting 6mA Sites in the Rice Genome

(2019) Shaherin Basith et al.   Molecular Therapy-Nucleic Acids

Is There Any Sequence Feature in the RNA Pseudouridine Modification Prediction Problem?

(2019) Lijun Dou et al.   Molecular Therapy-Nucleic Acids

Clustering count-based RNA methylation data using a nonparametric generative model

(2018) Lin Zhang et al.   Current Bioinformatics

Prediction of human protein subcellular localization using deep learning

(2018) Leyi Wei et al.   JOURNAL OF PARALLEL AND DISTRIBUTED COMPUTING

Integration of deep feature representations and handcrafted features to improve the prediction of N 6 -methyladenosine sites

(2018) Leyi Wei et al.   NEUROCOMPUTING

M6APred-EL: A sequence-based predictor for identifying N6-methyladenosine sites using ensemble learning

(2018) Leyi Wei et al.   Molecular Therapy-Nucleic Acids

4mCPred: Machine Learning Methods for DNA N4-methylcytosine sites Prediction

(2018) Wenying He et al.   BIOINFORMATICS

Exploring sequence-based features for the improved prediction of DNA N4-methylcytosine sites in multiple species

(2018) Leyi Wei et al.   BIOINFORMATICS

Developing a Multi-Dose Computational Model for Drug-induced Hepatotoxicity Prediction based on Toxicogenomics Data

(2018) Ran Su et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

mAHTPred: a sequence-based meta-predictor for improving the prediction of anti-hypertensive peptides using effective feature representation

(2018) Balachandran Manavalan et al.   BIOINFORMATICS

FKL-Spa-LapRLS: an accurate method for identifying human microRNA-disease association

(2018) Limin Jiang et al.   BMC GENOMICS

Identification of drug-side effect association via multiple information integration with centered kernel alignment

(2018) Yijie Ding et al.   NEUROCOMPUTING

Gene2vec: gene subsequence embedding for prediction of mammalian N6-methyladenosine sites from mRNA

(2018) Quan Zou et al.   RNA

Empirical comparison and analysis of web-based cell-penetrating peptide prediction tools

(2018) Ran Su et al.   BRIEFINGS IN BIOINFORMATICS

Identification of Drug-Side Effect Association via Semisupervised Model and Multiple Kernel Learning

(2018) Yijie Ding et al.   IEEE Journal of Biomedical and Health Informatics

Fast prediction of protein methylation sites using a sequence-based feature selection technique

(2017) Leyi Wei et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Local-DPP: An improved DNA-binding protein prediction method by exploring local evolutionary information

(2017) Leyi Wei et al.   INFORMATION SCIENCES

Identification of drug-target interactions via multiple information integration

(2017) Yijie Ding et al.   INFORMATION SCIENCES

Widespread adenine N6-methylation of active genes in fungi

(2017) Stephen J Mondo et al.   NATURE GENETICS

The application of genome-wide 5-hydroxymethylcytosine studies in cancer research

(2017) John P Thomson et al.   Epigenomics

DNA methylation on N6-adenine in mammalian embryonic stem cells

(2016) Tao P. Wu et al.   NATURE

MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing

(2016) Pohao Ye et al.   NUCLEIC ACIDS RESEARCH

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

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

An Adenine Code for DNA: A Second Life for N6-Methyladenine

(2015) Holger Heyn et al.   CELL

DNA Methylation on N6-Adenine in C. elegans

(2015) Eric Lieberman Greer et al.   CELL

Improved and Promising Identification of Human MicroRNAs by Incorporating a High-Quality Negative Set

(2013) Leyi Wei et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

DNA methylation dynamics in health and disease

(2013) Yehudit Bergman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nucleic acid modifications with epigenetic significance

(2012) Ye Fu et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

(2012) Gang Fang et al.   NATURE BIOTECHNOLOGY

5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging

(2011) Keith E Szulwach et al.   NATURE NEUROSCIENCE

Bacterial genetics: past achievements, present state of the field, and future challenges

(2008) Herbert P. Schweizer   BIOTECHNIQUES