PFmulDL: a novel strategy enabling multi-class and multi-label protein function annotation by integrating diverse deep learning methods

Molecular Mechanism for the Allosteric Inhibition of the Human Serotonin Transporter by Antidepressant Escitalopram

(2022) Weiwei Xue et al.   ACS Chemical Neuroscience

Hierarchical shared transfer learning for biomedical named entity recognition

(2022) Zhaoying Chai et al.   BMC BIOINFORMATICS

POSREG: proteomic signature discovered by simultaneously optimizing its reproducibility and generalizability

(2022) Fengcheng Li et al.   BRIEFINGS IN BIOINFORMATICS

In Silico Analysis Revealed a Unique Binding but Ineffective Mode of Amantadine to Influenza Virus B M2 Channel

(2021) Yue Zhang et al.   Journal of Physical Chemistry Letters

sgRNACNN: identifying sgRNA on-target activity in four crops using ensembles of convolutional neural networks

(2021) Mengting Niu et al.   PLANT MOLECULAR BIOLOGY

The miRNA: a small but powerful RNA for COVID-19

(2021) Song Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Identify DisorderedRegions of Intrinsically Disordered Proteins by Multi-FeaturesFusion

(2021) Sun Can Zhuang et al.   Current Bioinformatics

DeepDRK: a deep learning framework for drug repurposing through kernel-based multi-omics integration

(2021) Yongcui Wang et al.   BRIEFINGS IN BIOINFORMATICS

Pharmacometabonomics: data processing and statistical analysis

(2021) Jianbo Fu et al.   BRIEFINGS IN BIOINFORMATICS

Ant colony optimization with Cauchy and greedy Levy mutations for multilevel COVID 19 X-ray image segmentation

(2021) Lei Liu et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Prediction of off-target effects in crispr/cas9 system by ensemble learning

(2021) Yongxian Fan et al.   Current Bioinformatics

Structure-based protein function prediction using graph convolutional networks

(2021) Vladimir Gligorijević et al.   Nature Communications

Dynamic selective auditory attention detection using RNN and reinforcement learning

(2021) Masoud Geravanchizadeh et al.   Scientific Reports

RNA–RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection

(2021) Song Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Advances in understanding the specificity function of transporters by machine learning

(2021) Esmaeil Ebrahimie et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Erythropoiesis stimulating agent recommendation model using recurrent neural networks for patient with kidney failure with replacement therapy

(2021) Hae-Ryong Yun et al.   COMPUTERS IN BIOLOGY AND MEDICINE

iAtbP-Hyb-EnC: Prediction of antitubercular peptides via heterogeneous feature representation and genetic algorithm based ensemble learning model

(2021) Shahid Akbar et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Rethinking modeling Alzheimer's disease progression from a multi-task learning perspective with deep recurrent neural network

(2021) Wei Liang et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Differential analysis of Orientia tsutsugamushi genomes for therapeutic target identification and possible intervention through natural product inhibitor screening

(2021) Zarrin Basharat et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Machine learning-based prediction of drug and ligand binding in BCL-2 variants through molecular dynamics

(2021) John R. Hamre et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Class imbalance in out-of-distribution datasets: Improving the robustness of the TextCNN for the classification of rare cancer types

(2021) Kevin De Angeli et al.   JOURNAL OF BIOMEDICAL INFORMATICS

Optimization of metabolomic data processing using NOREVA

(2021) Jianbo Fu et al.   Nature Protocols

SYNBIP: synthetic binding proteins for research, diagnosis and therapy

(2021) Xiaona Wang et al.   NUCLEIC ACIDS RESEARCH

VARIDT 2.0: structural variability of drug transporter

(2021) Tingting Fu et al.   NUCLEIC ACIDS RESEARCH

An Economic Forecasting Method Based on the LightGBM-Optimized LSTM and Time-Series Model

(2021) Jiehua Lv et al.   Computational Intelligence and Neuroscience

SSizer: Determining the Sample Sufficiency for Comparative Biological Study

(2020) Fengcheng Li et al.   JOURNAL OF MOLECULAR BIOLOGY

Biophysical prediction of protein–peptide interactions and signaling networks using machine learning

(2020) Joseph M. Cunningham et al.   NATURE METHODS

ACNNT3: Attention-CNN Framework for Prediction of Sequence-Based Bacterial Type III Secreted Effectors

(2020) Jie Li et al.   Computational and Mathematical Methods in Medicine

Boosted binary Harris hawks optimizer and feature selection

(2020) Yanan Zhang et al.   ENGINEERING WITH COMPUTERS

NOREVA: enhanced normalization and evaluation of time-course and multi-class metabolomic data

(2020) Qingxia Yang et al.   NUCLEIC ACIDS RESEARCH

SDN2GO: An Integrated Deep Learning Model for Protein Function Prediction

(2020) Yideng Cai et al.   Frontiers in Bioengineering and Biotechnology

MetaFS: Performance assessment of biomarker discovery in metaproteomics

(2020) Jing Tang et al.   BRIEFINGS IN BIOINFORMATICS

NPalmitoylDeep-PseAAC: A Predictor for N-Palmitoylation sites in Proteins using Deep Representations of Proteins and PseAAC via modified 5-steps rule

(2020) Sheraz Naseer et al.   Current Bioinformatics

In Silico Study of Membrane Lipid Composition Regulating Conformation and Hydration of Influenza Virus B M2 Channel

(2020) Yue Zhang et al.   Journal of Chemical Information and Modeling

Towards Augmented Kernel Extreme Learning Models for Bankruptcy Prediction: Algorithmic Behavior and Comprehensive Analysis

(2020) Yanan Zhang et al.   NEUROCOMPUTING

INTEDE: interactome of drug-metabolizing enzymes

(2020) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

Prediction of bio-sequence modifications and the associations with diseases

(2020) Chunyan Ao et al.   Briefings in Functional Genomics

DeepAdd: Protein function prediction from k-mer embedding and additional features

(2020) Zhihua Du et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

MMEASE: Online meta-analysis of metabolomic data by enhanced metabolite annotation, marker selection and enrichment analysis

(2020) Qingxia Yang et al.   Journal of Proteomics

Orthogonal learning covariance matrix for defects of grey wolf optimizer: Insights, balance, diversity, and feature selection

(2020) Jiao Hu et al.   KNOWLEDGE-BASED SYSTEMS

Protein Secondary Structure Prediction Using Character Bi-gram Embedding and Bi-LSTM

(2020) Ashish Kumar Sharma et al.   Current Bioinformatics

MultiPredGO: Deep Multi-Modal Protein Function Prediction by Amalgamating Protein Structure, Sequence, and Interaction Information

(2020) Swagarika Jaharlal Giri et al.   IEEE Journal of Biomedical and Health Informatics

Bias in Cross-Entropy-Based Training of Deep Survival Networks

(2020) Shekoufeh Gorgi Zadeh et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Learning transferable features in deep convolutional neural networks for diagnosing unseen machine conditions

(2019) Te Han et al.   ISA TRANSACTIONS

How Does Chirality Determine the Selective Inhibition of Histone Deacetylase 6? A Lesson from Trichostatin A Enantiomers Based on Molecular Dynamics

(2019) Yang Zhang et al.   ACS Chemical Neuroscience

Deep Learning Predicts Lung Cancer Treatment Response from Serial Medical Imaging

(2019) Yiwen Xu et al.   CLINICAL CANCER RESEARCH

Simultaneous Improvement in the Precision, Accuracy and Robustness of Label-free Proteome Quantification by Optimizing Data Manipulation Chains

(2019) Jing Tang et al.   MOLECULAR & CELLULAR PROTEOMICS

DeepFunc: A Deep Learning Framework for Accurate Prediction of Protein Functions from Protein Sequences and Interactions

(2019) Fuhao Zhang et al.   PROTEOMICS

Coupling of ATPase activity, microtubule binding, and mechanics in the dynein motor domain

(2019) Stefan Niekamp et al.   EMBO JOURNAL

DEEPred: Automated Protein Function Prediction with Multi-task Feed-forward Deep Neural Networks

(2019) Ahmet Sureyya Rifaioglu et al.   Scientific Reports

Machine learning for discovering missing or wrong protein function annotations

(2019) Felipe Kenji Nakano et al.   BMC BIOINFORMATICS

VARIDT 1.0: variability of drug transporter database

(2019) Jiayi Yin et al.   NUCLEIC ACIDS RESEARCH

A novel bioinformatics approach to identify the consistently well-performing normalization strategy for current metabolomic studies

(2019) Qingxia Yang et al.   BRIEFINGS IN BIOINFORMATICS

Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery

(2019) Jiajun Hong et al.   BRIEFINGS IN BIOINFORMATICS

SimExact – An Efficient Method To Compute Function Similarity Between Proteins Using Gene Ontology

(2019) Najmul Ikram et al.   Current Bioinformatics

Accurate classification of membrane protein types based on sequence and evolutionary information using deep learning

(2019) Lei Guo et al.   BMC BIOINFORMATICS

Fast and accurate microRNA search using CNN

(2019) Xubo Tang et al.   BMC BIOINFORMATICS

Comparing different supervised machine learning algorithms for disease prediction

(2019) Shahadat Uddin et al.   BMC Medical Informatics and Decision Making

Deep learning for mining protein data

(2019) Qiang Shi et al.   BRIEFINGS IN BIOINFORMATICS

What Contributes to Serotonin–Norepinephrine Reuptake Inhibitors’ Dual-Targeting Mechanism? The Key Role of Transmembrane Domain 6 in Human Serotonin and Norepinephrine Transporters Revealed by Molecular Dynamics Simulation

(2018) Weiwei Xue et al.   ACS Chemical Neuroscience

Exploring the Binding Mechanism of Metabotropic Glutamate Receptor 5 Negative Allosteric Modulators in Clinical Trials by Molecular Dynamics Simulations

(2018) Tingting Fu et al.   ACS Chemical Neuroscience

GOLabeler: improving sequence-based large-scale protein function prediction by learning to rank

(2018) Ronghui You et al.   BIOINFORMATICS

DeepFam: deep learning based alignment-free method for protein family modeling and prediction

(2018) Seokjun Seo et al.   BIOINFORMATICS

Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes

(2018) Hervé Seligmann   BIOSYSTEMS

MetaGO: Predicting Gene Ontology of Non-homologous Proteins Through Low-Resolution Protein Structure Prediction and Protein–Protein Network Mapping

(2018) Chengxin Zhang et al.   JOURNAL OF MOLECULAR BIOLOGY

DeepText2GO: Improving large-scale protein function prediction with deep semantic text representation

(2018) Ronghui You et al.   METHODS

Computational identification of the binding mechanism of a triple reuptake inhibitor amitifadine for the treatment of major depressive disorder

(2018) Weiwei Xue et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Clinical Success of Drug Targets Prospectively Predicted by In Silico Study

(2018) Feng Zhu et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Discovery of the Consistently Well-Performed Analysis Chain for SWATH-MS Based Pharmacoproteomic Quantification

(2018) Jianbo Fu et al.   Frontiers in Pharmacology

ANPELA: analysis and performance assessment of the label-free quantification workflow for metaproteomic studies

(2018) Jing Tang et al.   BRIEFINGS IN BIOINFORMATICS

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Post-transcriptional Regulatory Functions of Mammalian Pumilio Proteins

(2018) Aaron C. Goldstrohm et al.   TRENDS IN GENETICS

Multiple Sclerosis Identification by 14-Layer Convolutional Neural Network With Batch Normalization, Dropout, and Stochastic Pooling

(2018) Shui-Hua Wang et al.   Frontiers in Neuroscience

Clinical trials, progression-speed differentiating features and swiftness rule of the innovative targets of first-in-class drugs

(2018) Ying Hong Li et al.   BRIEFINGS IN BIOINFORMATICS

NOREVA: normalization and evaluation of MS-based metabolomics data

(2017) Bo Li et al.   NUCLEIC ACIDS RESEARCH

COFACTOR: improved protein function prediction by combining structure, sequence and protein–protein interaction information

(2017) Chengxin Zhang et al.   NUCLEIC ACIDS RESEARCH

Continuous Dropout

(2017) Xu Shen et al.   IEEE Transactions on Neural Networks and Learning Systems

Reduction strategies for hierarchical multi-label classification in protein function prediction

(2016) Ricardo Cerri et al.   BMC BIOINFORMATICS

Protein–protein interaction inference based on semantic similarity of Gene Ontology terms

(2016) Shu-Bo Zhang et al.   JOURNAL OF THEORETICAL BIOLOGY

Protein function annotation using protein domain family resources

(2016) Sayoni Das et al.   METHODS

GoFDR: A sequence alignment based method for predicting protein functions

(2016) Qingtian Gong et al.   METHODS

An efficient hybrid kernel extreme learning machine approach for early diagnosis of Parkinson׳s disease

(2016) Hui-Ling Chen et al.   NEUROCOMPUTING

Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information

(2015) Hong Yang et al.   NUCLEIC ACIDS RESEARCH

Calcium homeostasis modulator (CALHM) ion channels

(2015) Zhongming Ma et al.   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

Neural network and SVM classifiers accurately predict lipid binding proteins, irrespective of sequence homology

(2014) Mohammad Reza Bakhtiarizadeh et al.   JOURNAL OF THEORETICAL BIOLOGY

Adenine nucleotide transporters in organelles: novel genes and functions

(2011) Javier Traba et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Therapeutic target database update 2012: a resource for facilitating target-oriented drug discovery

(2011) F. Zhu et al.   NUCLEIC ACIDS RESEARCH

Clustered patterns of species origins of nature-derived drugs and clues for future bioprospecting

(2011) F. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA