Predicting ATP-Binding Cassette Transporters Using the Random Forest Method

MULTiPly: a novel multi-layer predictor for discovering general and specific types of promoters

(2019) Meng Zhang et al.   BIOINFORMATICS

deepDR: A network-based deep learning approach to in silico drug repositioning

(2019) Xiangxiang Zeng et al.   BIOINFORMATICS

Incorporating Distance-based Top-n-gram and Random Forest to Identify Electron Transport Proteins

(2019) Xiaoqing Ru et al.   JOURNAL OF PROTEOME RESEARCH

CLU-CNNs: Object detection for medical images

(2019) Zhuoling Li et al.   NEUROCOMPUTING

Identifying enhancer–promoter interactions with neural network based on pre-trained DNA vectors and attention mechanism

(2019) Zengyan Hong et al.   BIOINFORMATICS

A network embedding-based multiple information integration method for the MiRNA-disease association prediction

(2019) Yuchong Gong et al.   BMC BIOINFORMATICS

Evidential Decision Tree Based on Belief Entropy

(2019) Mujin Li et al.   Entropy

SFLLN: A sparse feature learning ensemble method with linear neighborhood regularization for predicting drug–drug interactions

(2019) Wen Zhang et al.   INFORMATION SCIENCES

A Random Forest Sub-Golgi Protein Classifier Optimized via Dipeptide and Amino Acid Composition Features

(2019) Zhibin Lv et al.   Frontiers in Bioengineering and Biotechnology

AOPs-SVM: A Sequence-Based Classifier of Antioxidant Proteins Using a Support Vector Machine

(2019) Chaolu Meng et al.   Frontiers in Bioengineering and Biotechnology

Predicting disease-associated circular RNAs using deep forests combined with positive-unlabeled learning methods

(2019) Xiangxiang Zeng et al.   BRIEFINGS IN BIOINFORMATICS

DeepSVM-fold: protein fold recognition by combining support vector machines and pairwise sequence similarity scores generated by deep learning networks

(2019) Bin Liu et al.   BRIEFINGS IN BIOINFORMATICS

A comprehensive comparison and analysis of computational predictors for RNA N6-methyladenosine sites of Saccharomyces cerevisiae

(2019) Xiaolei Zhu et al.   Briefings in Functional Genomics

Prediction of CYP450 Enzyme–Substrate Selectivity Based on the Network-Based Label Space Division Method

(2019) Xiaoqi Shan et al.   Journal of Chemical Information and Modeling

Genome-wide identification of ABC transporters in monogeneans

(2019) Víctor Caña-Bozada et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

iPromoter-2L2.0: Identifying Promoters and Their Types by Combining Smoothing Cutting Window Algorithm and Sequence-Based Features

(2019) Bin Liu et al.   Molecular Therapy-Nucleic Acids

RNAm5CPred: Prediction of RNA 5-Methylcytosine Sites Based on Three Different Kinds of Nucleotide Composition

(2019) Ting Fang et al.   Molecular Therapy-Nucleic Acids

A Fast Linear Neighborhood Similarity-Based Network Link Inference Method to Predict MicroRNA-Disease Associations

(2019) Wen Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

O-GlcNAcPRED-II: an integrated classification algorithm for identifying O-GlcNAcylation sites based on fuzzy undersampling and a K-means PCA oversampling technique

(2018) Cangzhi Jia et al.   BIOINFORMATICS

ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides

(2018) Leyi Wei et al.   BIOINFORMATICS

Protein-protein interface hot spots prediction based on a hybrid feature selection strategy

(2018) Yanhua Qiao et al.   BMC BIOINFORMATICS

Predicting Potential Drugs for Breast Cancer based on miRNA and Tissue Specificity

(2018) Liang Yu et al.   International Journal of Biological Sciences

The linear neighborhood propagation method for predicting long non-coding RNA–protein interactions

(2018) Wen Zhang et al.   NEUROCOMPUTING

PseUI: Pseudouridine sites identification based on RNA sequence information

(2018) Jingjing He et al.   BMC BIOINFORMATICS

Sequence clustering in bioinformatics: an empirical study

(2018) Quan Zou et al.   BRIEFINGS IN BIOINFORMATICS

Genome-wide analysis of ATP binding cassette (ABC) transporters in tomato

(2018) Peter Amoako Ofori et al.   PLoS One

Identification of Antioxidant Proteins With Deep Learning From Sequence Information

(2018) Lifen Shao et al.   Frontiers in Pharmacology

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

(2018) Quan Zou et al.   RNA

SFPEL-LPI: Sequence-based feature projection ensemble learning for predicting LncRNA-protein interactions

(2018) Wen Zhang et al.   PLoS Computational Biology

PredT4SE-Stack: Prediction of Bacterial Type IV Secreted Effectors From Protein Sequences Using a Stacked Ensemble Method

(2018) Yi Xiong et al.   Frontiers in Microbiology

Sparse fully convolutional network for face labeling

(2018) Minghui Dong et al.   NEUROCOMPUTING

Identification of protein subcellular localization via integrating evolutionary and physicochemical information into Chou’s general PseAAC

(2018) Yinan Shen et al.   JOURNAL OF THEORETICAL BIOLOGY

PhosPred-RF: A Novel Sequence-Based Predictor for Phosphorylation Sites Using Sequential Information Only

(2017) Leyi Wei et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Meta-path methods for prioritizing candidate disease miRNAs

(2017) Xuan Zhang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Prediction and Validation of Disease Genes Using HeteSim Scores

(2017) Xiangxiang Zeng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

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

Identification of drug-target interactions via multiple information integration

(2017) Yijie Ding et al.   INFORMATION SCIENCES

CPPred-RF: A Sequence-based Predictor for Identifying Cell-Penetrating Peptides and Their Uptake Efficiency

(2017) Leyi Wei et al.   JOURNAL OF PROTEOME RESEARCH

Identification of DNA–protein Binding Sites through Multi-Scale Local Average Blocks on Sequence Information

(2017) Cong Shen et al.   MOLECULES

Improved detection of DNA-binding proteins via compression technology on PSSM information

(2017) Yubo Wang et al.   PLoS One

A comprehensive overview and evaluation of circular RNA detection tools

(2017) Xiangxiang Zeng et al.   PLoS Computational Biology

Predicting protein-protein interactions via multivariate mutual information of protein sequences

(2016) Yijie Ding et al.   BMC BIOINFORMATICS

Pretata: predicting TATA binding proteins with novel features and dimensionality reduction strategy

(2016) Quan Zou et al.   BMC Systems Biology

A novel machine learning method for cytokine-receptor interaction prediction

(2016) Leyi Wei et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Plant ABC Transporters Enable Many Unique Aspects of a Terrestrial Plant's Lifestyle

(2016) Jae-Ung Hwang et al.   Molecular Plant

Mechanistic diversity in ATP-binding cassette (ABC) transporters

(2016) Kaspar P Locher   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mechanistic diversity in ATP-binding cassette (ABC) transporters

(2016) Kaspar P Locher   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structural basis for the mechanism of ABC transporters

(2015) K. Beis   BIOCHEMICAL SOCIETY TRANSACTIONS

The substrate-binding protein in bacterial ABC transporters: dissecting roles in the evolution of substrate specificity

(2015) A. Maqbool et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Inferring drug-disease associations based on known protein complexes

(2015) Liang Yu et al.   BMC Medical Genomics

Identifying DNA-binding proteins by combining support vector machine and PSSM distance transformation

(2015) Ruifeng Xu et al.   BMC Systems Biology

Computational approaches for the classification of seed storage proteins

(2014) V. Radhika et al.   JOURNAL OF FOOD SCIENCE AND TECHNOLOGY-MYSORE

Cloning and characterization of a novelNicotiana tabacumABC transporter involved in shoot branching

(2014) Xiaodong Xie et al.   PHYSIOLOGIA PLANTARUM

BinMemPredict: a Web Server and Software for Predicting Membrane Protein Types

(2013) Quan Zou et al.   Current Proteomics

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

Structures of P-glycoprotein reveal its conformational flexibility and an epitope on the nucleotide-binding domain

(2013) A. B. Ward et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Towards understanding promiscuity in multidrug efflux pumps

(2013) Kelvin Wong et al.   TRENDS IN BIOCHEMICAL SCIENCES

An Approach for Identifying Cytokines Based on a Novel Ensemble Classifier

(2013) Quan Zou et al.   Biomed Research International

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Improved method for predicting protein fold patterns with ensemble classifiers

(2012) W. Chen et al.   GENETICS AND MOLECULAR RESEARCH

ABC transporters involved in drug resistance in human parasites

(2011) Philippe Leprohon et al.   Essays in Biochemistry

ABC solute importers in bacteria

(2011) Jinming Cui et al.   Essays in Biochemistry

SVM-BASED METHOD FOR PROTEIN STRUCTURAL CLASS PREDICTION USING SECONDARY STRUCTURAL CONTENT AND STRUCTURAL INFORMATION OF AMINO ACIDS

(2011) TABREZ ANWAR SHAMIM MOHAMMAD et al.   Journal of Bioinformatics and Computational Biology

Supervised machine learning algorithms for protein structure classification

(2009) Pooja Jain et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Molecular basis of multidrug transport by ABC transporters

(2008) Markus A. Seeger et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Structure, Function, and Evolution of Bacterial ATP-Binding Cassette Systems

(2008) A. L. Davidson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Structure and mechanism of ATP-binding cassette transporters

(2008) K. P Locher   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Identification of two inner-membrane proteins required for the transport of lipopolysaccharide to the outer membrane of Escherichia coli

(2008) N. Ruiz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural Basis of Trans-Inhibition in a Molybdate/Tungstate ABC Transporter

(2008) S. Gerber et al.   SCIENCE

The High-Affinity E. coli Methionine ABC Transporter: Structure and Allosteric Regulation

(2008) N. S. Kadaba et al.   SCIENCE