RFAmyloid: A Web Server for Predicting Amyloid Proteins

Machine-Learning-Based Prediction of Cell-Penetrating Peptides and Their Uptake Efficiency with Improved Accuracy

(2018) Balachandran Manavalan et al.   JOURNAL OF PROTEOME RESEARCH

Predicting drug-disease associations and their therapeutic function based on the drug-disease association bipartite network

(2018) Wen Zhang et al.   METHODS

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

(2018) Wen Zhang et al.   NEUROCOMPUTING

PVP-SVM: Sequence-Based Prediction of Phage Virion Proteins Using a Support Vector Machine

(2018) Balachandran Manavalan et al.   Frontiers in Microbiology

AIPpred: Sequence-Based Prediction of Anti-inflammatory Peptides Using Random Forest

(2018) Balachandran Manavalan et al.   Frontiers in Pharmacology

Integrating Multiple Heterogeneous Networks for Novel LncRNA-disease Association Inference

(2017) Jingpu Zhang 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

Proteus: a random forest classifier to predict disorder-to-order transitioning binding regions in intrinsically disordered proteins

(2017) Sankar Basu et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Recent Advances in Conotoxin Classification by Using Machine Learning Methods

(2017) Fu-Ying Dao et al.   MOLECULES

Identification of DNA-Binding Proteins Using Mixed Feature Representation Methods

(2017) Kaiyang Qu et al.   MOLECULES

Drug-Target Interaction Prediction through Label Propagation with Linear Neighborhood Information

(2017) Wen Zhang et al.   MOLECULES

AmyPro: a database of proteins with validated amyloidogenic regions

(2017) Mihaly Varadi et al.   NUCLEIC ACIDS RESEARCH

SODA: prediction of protein solubility from disorder and aggregation propensity

(2017) Lisanna Paladin et al.   NUCLEIC ACIDS RESEARCH

Sequence-based predictive modeling to identify cancerlectins

(2017) Hong-Yan Lai et al.   Oncotarget

DHSpred: support-vector-machine-based human DNase I hypersensitive sites prediction using the optimal features selected by random forest

(2017) Balachandran Manavalan et al.   Oncotarget

MLACP: machine-learning-based prediction of anticancer peptides

(2017) Balachandran Manavalan et al.   Oncotarget

Prediction of lncRNA-protein interactions using HeteSim scores based on heterogeneous networks

(2017) Yun Xiao et al.   Scientific Reports

Amyloidogenic motifs revealed by n-gram analysis

(2017) Michał Burdukiewicz et al.   Scientific Reports

Amyloid fibril proteins and amyloidosis: chemical identification and clinical classification International Society of Amyloidosis 2016 Nomenclature Guidelines

(2016) Jean D. Sipe et al.   AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS

A genetic algorithm-based weighted ensemble method for predicting transposon-derived piRNAs

(2016) Dingfang Li et al.   BMC BIOINFORMATICS

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

(2016) Quan Zou et al.   BMC Systems Biology

Use of a Novel Grammatical Inference Approach in Classification of Amyloidogenic Hexapeptides

(2016) Wojciech Wieczorek et al.   Computational and Mathematical Methods in Medicine

Protein Folds Prediction with Hierarchical Structured SVM

(2016) Dapeng Li et al.   Current Proteomics

Antimicrobial peptide (Cn-AMP2) from liquid endosperm ofCocos nuciferaforms amyloid-like fibrillar structure

(2016) Shalini Gour et al.   JOURNAL OF PEPTIDE SCIENCE

Predicting potential side effects of drugs by recommender methods and ensemble learning

(2016) Wen Zhang et al.   NEUROCOMPUTING

BP Neural Network Could Help Improve Pre-miRNA Identification in Various Species

(2016) Limin Jiang et al.   Biomed Research International

A structure-based approach to predict predisposition to amyloidosis

(2015) Abdullah B. Ahmed et al.   Alzheimers & Dementia

Prediction and analysis of cell-penetrating peptides using pseudo-amino acid composition and random forest models

(2015) Lei Chen et al.   AMINO ACIDS

WALTZ-DB: a benchmark database of amyloidogenic hexapeptides

(2015) J. Beerten et al.   BIOINFORMATICS

imDC: an ensemble learning method for imbalanced classification with miRNA data

(2015) C.Y. Wang et al.   GENETICS AND MOLECULAR RESEARCH

An Improved Protein Structural Classes Prediction Method by Incorporating Both Sequence and Structure Information

(2015) Leyi Wei et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

An Integrated Framework for Functional Annotation of Protein Structural Domains

(2015) Lei Deng et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Improving tRNAscan-SE Annotation Results via Ensemble Classifiers

(2015) Quan Zou et al.   Molecular Informatics

Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences

(2015) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

Accurate Prediction of Immunogenic T-Cell Epitopes from Epitope Sequences Using the Genetic Algorithm-Based Ensemble Learning

(2015) Wen Zhang et al.   PLoS One

Nomenclature 2014: Amyloid fibril proteins and clinical classification of the amyloidosis

(2014) Jean D. Sipe et al.   AMYLOID-JOURNAL OF PROTEIN FOLDING DISORDERS

Structural studies of “aggregation-prone” peptide-analogues of teleostean egg chorion ZPB proteins

(2014) Nikolaos N. Louros et al.   BIOPOLYMERS

nDNA-prot: identification of DNA-binding proteins based on unbalanced classification

(2014) Li Song et al.   BMC BIOINFORMATICS

Discriminating between deleterious and neutral non-frameshifting indels based on protein interaction networks and hybrid properties

(2014) Ning Zhang et al.   MOLECULAR GENETICS AND GENOMICS

Random Forest-Based Protein Model Quality Assessment (RFMQA) Using Structural Features and Potential Energy Terms

(2014) Balachandran Manavalan et al.   PLoS One

Predicting A-to-I RNA Editing by Feature Selection and Random Forest

(2014) Yang Shu et al.   PLoS One

Identification of cytokine via an improved genetic algorithm

(2014) Xiangxiang Zeng et al.   Frontiers of Computer Science

Prediction of protein modification sites of gamma-carboxylation using position specific scoring matrices based evolutionary information

(2013) Jianzhao Gao et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

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

(2013) Quan Zou et al.   Current Proteomics

Identifying Multi-Functional Enzyme by Hierarchical Multi-Label Classifier

(2013) Quan Zou et al.   Journal of Computational and Theoretical Nanoscience

LibD3C: Ensemble classifiers with a clustering and dynamic selection strategy

(2013) Chen Lin et al.   NEUROCOMPUTING

Prediction and Analysis of Antibody Amyloidogenesis from Sequences

(2013) Chyn Liaw et al.   PLoS One

Hierarchical Classification of Protein Folds Using a Novel Ensemble Classifier

(2013) Chen Lin et al.   PLoS One

Structural Analysis of Peptide-Analogues of Human Zona Pellucida ZP1 Protein with Amyloidogenic Properties: Insights into Mammalian Zona Pellucida Formation

(2013) Nikolaos N. Louros et al.   PLoS One

MetAmyl: A METa-Predictor for AMYLoid Proteins

(2013) Mathieu Emily et al.   PLoS One

Identification of an Amyloidogenic Peptide From the Bap Protein of Staphylococcus epidermidis

(2013) Pierre Lembré et al.   PROTEIN AND PEPTIDE LETTERS

An Approach for Identifying Cytokines Based on a Novel Ensemble Classifier

(2013) Quan Zou et al.   Biomed Research International

The prediction of protein structural class using averaged chemical shifts

(2012) Hao Lin et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Computational prediction and analysis of protein γ-carboxylation sites based on a random forest method

(2012) Ning Zhang et al.   Molecular BioSystems

Computational Prediction of Conformational B-Cell Epitopes from Antigen Primary Structures by Ensemble Learning

(2012) Wen Zhang et al.   PLoS One

Prediction of protein–RNA binding sites by a random forest method with combined features

(2010) Zhi-Ping Liu et al.   BIOINFORMATICS

Using simple artificial intelligence methods for predicting amyloidogenesis in antibodies

(2010) Maria Pamela C David et al.   BMC BIOINFORMATICS

Exploring the sequence determinants of amyloid structure using position-specific scoring matrices

(2010) Sebastian Maurer-Stroh et al.   NATURE METHODS

FoldAmyloid: a method of prediction of amyloidogenic regions from protein sequence

(2009) S. O. Garbuzynskiy et al.   BIOINFORMATICS

Prediction of amyloid fibril-forming segments based on a support vector machine

(2009) Jian Tian et al.   BMC BIOINFORMATICS

Amyloidogenic determinants are usually not buried

(2009) Kimon K Frousios et al.   BMC STRUCTURAL BIOLOGY