Survey of Natural Language Processing Techniques in Bioinformatics

Community challenges in biomedical text mining over 10 years: success, failure and the future

(2015) Chung-Chi Huang et al.   BRIEFINGS IN BIOINFORMATICS

Crowdsourcing in biomedicine: challenges and opportunities

(2015) Ritu Khare et al.   BRIEFINGS IN BIOINFORMATICS

miRNA-dis: microRNA precursor identification based on distance structure status pairs

(2015) Bin Liu et al.   Molecular BioSystems

Predicting the subcellular localization of mycobacterial proteins by incorporating the optimal tripeptides into the general form of pseudo amino acid composition

(2015) Pan-Pan Zhu et al.   Molecular BioSystems

SynBioLGDB: a resource for experimentally validated logic gates in synthetic biology

(2015) Liqiang Wang et al.   Scientific Reports

Identification of Real MicroRNA Precursors with a Pseudo Structure Status Composition Approach

(2015) Bin Liu et al.   PLoS One

Identification of mitochondrial proteins of malaria parasite using analysis of variance

(2014) Hui Ding et al.   AMINO ACIDS

repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects

(2014) Bin Liu et al.   BIOINFORMATICS

Using distances between Top-n-gram and residue pairs for protein remote homology detection

(2014) Bin Liu et al.   BMC BIOINFORMATICS

Association Studies on mtDNA and Parkinson’s Disease Population Discrimination Using the Statistical Classification

(2014) Jun Wang et al.   Current Bioinformatics

Review of Protein Subcellular Localization Prediction

(2014) Zhen Wang et al.   Current Bioinformatics

Identifying the Subfamilies of Voltage-Gated Potassium Channels Using Feature Selection Technique

(2014) Wei-Xin Liu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Probabilistic Models for Capturing More Physicochemical Properties on Protein–Protein Interface

(2014) Fei Guo et al.   Journal of Chemical Information and Modeling

Identification of bacteriophage virion proteins by the ANOVA feature selection and analysis

(2014) Hui Ding et al.   Molecular BioSystems

PseDNA-Pro: DNA-Binding Protein Identification by Combining Chou’s PseAAC and Physicochemical Distance Transformation

(2014) Bin Liu et al.   Molecular Informatics

ViRBase: a resource for virus–host ncRNA-associated interactions

(2014) Yanhui Li et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2015 update

(2014) Andrew Chatr-aryamontri et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

iDNA-Prot|dis: Identifying DNA-Binding Proteins by Incorporating Amino Acid Distance-Pairs and Reduced Alphabet Profile into the General Pseudo Amino Acid Composition

(2014) Bin Liu et al.   PLoS One

RAID: a comprehensive resource for human RNA-associated (RNA-RNA/RNA-protein) interaction

(2014) X. Zhang et al.   RNA

Protein Binding Site Prediction by Combining Hidden Markov Support Vector Machine and Profile-Based Propensities

(2014) Bin Liu et al.   TheScientificWorldJOURNAL

Approaches for Recognizing Disease Genes Based on Network

(2014) Quan Zou et al.   Biomed Research International

iCTX-Type: A Sequence-Based Predictor for Identifying the Types of Conotoxins in Targeting Ion Channels

(2014) Hui Ding et al.   Biomed Research International

Prediction of protein structural classes based on feature selection technique

(2014) Hui Ding et al.   Interdisciplinary Sciences-Computational Life Sciences

Using Over-Represented Tetrapeptides to Predict Protein Submitochondria Locations

(2013) Hao Lin et al.   ACTA BIOTHEORETICA

Connect the dots

(2013) Yifei Li et al.   Autophagy

Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection

(2013) Bin Liu et al.   BIOINFORMATICS

Survey of MapReduce frame operation in bioinformatics

(2013) Q. Zou et al.   BRIEFINGS IN BIOINFORMATICS

Prediction of Golgi-resident protein types by using feature selection technique

(2013) Hui Ding et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Computational Approaches in Detecting Non- Coding RNA

(2013) Chunyu Wang et al.   CURRENT GENOMICS

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

(2013) Quan Zou et al.   Current Proteomics

Protein Function Prediction Using Multilabel Ensemble Classification

(2013) Guoxian Yu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Protein Function Prediction with Incomplete Annotations

(2013) Guoxian Yu et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Identifying Multi-Functional Enzyme by Hierarchical Multi-Label Classifier

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

Hybrid pseudo-relevance feedback for microblog retrieval

(2013) Lin Chen et al.   JOURNAL OF INFORMATION SCIENCE

Protein Remote Homology Detection by Combining Chou’s Pseudo Amino Acid Composition and Profile-Based Protein Representation

(2013) Bin Liu et al.   Molecular Informatics

PubTator: a web-based text mining tool for assisting biocuration

(2013) Chih-Hsuan Wei et al.   NUCLEIC ACIDS RESEARCH

Hierarchical Classification of Protein Folds Using a Novel Ensemble Classifier

(2013) Chen Lin et al.   PLoS One

AcalPred: A Sequence-Based Tool for Discriminating between Acidic and Alkaline Enzymes

(2013) Hao Lin et al.   PLoS One

PREDICTING SUBCHLOROPLAST LOCATIONS OF PROTEINS BASED ON THE GENERAL FORM OF CHOU'S PSEUDO AMINO ACID COMPOSITION: APPROACHED FROM OPTIMAL TRIPEPTIDE COMPOSITION

(2013) HAO LIN et al.   International Journal of Biomathematics

Mammalian ncRNA-disease repository: a global view of ncRNA-mediated disease network

(2013) Y Wang et al.   Cell Death & Disease

An Approach for Identifying Cytokines Based on a Novel Ensemble Classifier

(2013) Quan Zou et al.   Biomed Research International

Protein-protein binding site identification by enumerating the configurations

(2012) Fei Guo et al.   BMC BIOINFORMATICS

Improved method for predicting protein fold patterns with ensemble classifiers

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

Identify content quality in online social networks

(2012) C. Lin et al.   IET Communications

Identification of mycobacterial membrane proteins and their types using over-represented tripeptide compositions

(2012) Chen Ding et al.   Journal of Proteomics

A Global Characterization and Identification of Multifunctional Enzymes

(2012) Xian-Ying Cheng et al.   PLoS One

Using Amino Acid Physicochemical Distance Transformation for Fast Protein Remote Homology Detection

(2012) Bin Liu et al.   PLoS One

LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs

(2012) S. Will et al.   RNA

Prediction of the types of ion channel-targeted conotoxins based on radial basis function network

(2012) Lu-Feng Yuan et al.   TOXICOLOGY IN VITRO

Novel representation of RNA secondary structure used to improve prediction algorithms

(2011) Q. Zou et al.   GENETICS AND MOLECULAR RESEARCH

Protein–Protein Binding Sites Prediction by 3D Structural Similarities

(2011) Fei Guo et al.   Journal of Chemical Information and Modeling

Identify Golgi Protein Types with Modified Mahalanobis Discriminant Algorithm and Pseudo Amino Acid Composition

(2011) Hui Ding et al.   PROTEIN AND PEPTIDE LETTERS

Interactive and fuzzy search: a dynamic way to explore MEDLINE

(2010) J. Wang et al.   BIOINFORMATICS

Simple sequence-based kernels do not predict protein-protein interactions

(2010) J. Yu et al.   BIOINFORMATICS

Extracting causal relations on HIV drug resistance from literature

(2010) Quoc-Chinh Bui et al.   BMC BIOINFORMATICS

Mining SNPs from EST sequences using filters and ensemble classifiers

(2010) J. Wang et al.   GENETICS AND MOLECULAR RESEARCH

Prediction of thermophilic proteins using feature selection technique

(2010) Hao Lin et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Predicting ion channels and their types by the dipeptide mode of pseudo amino acid composition

(2010) Hao Lin et al.   JOURNAL OF THEORETICAL BIOLOGY

GeneCards Version 3: the human gene integrator

(2010) M. Safran et al.   Database-The Journal of Biological Databases and Curation

Prediction of Subcellular Localization of Apoptosis Protein Using Chou’s Pseudo Amino Acid Composition

(2009) Hao Lin et al.   ACTA BIOTHEORETICA

Bayesian inference of protein–protein interactions from biological literature

(2009) Rajesh Chowdhary et al.   BIOINFORMATICS

Large-scale prediction of long disordered regions in proteins using random forests

(2009) Pengfei Han et al.   BMC BIOINFORMATICS

Prediction of protein binding sites in protein structures using hidden Markov support vector machine

(2009) Bin Liu et al.   BMC BIOINFORMATICS

Exploiting three kinds of interface propensities to identify protein binding sites

(2009) Bin Liu et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Predicting RNA secondary structure based on the class information and Hopfield network

(2009) Quan Zou et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Prediction of subcellular location of mycobacterial protein using feature selection techniques

(2009) Hao Lin et al.   MOLECULAR DIVERSITY

Prediction of Protein–Protein Interaction Sites in Sequences and 3D Structures by Random Forests

(2009) Mile Šikić et al.   PLoS Computational Biology

Looking at Cerebellar Malformations through Text-Mined Interactomes of Mice and Humans

(2009) Ivan Iossifov et al.   PLoS Computational Biology

OnD-CRF: predicting order and disorder in proteins conditional random fields

(2008) L. Wang et al.   BIOINFORMATICS

A discriminative method for protein remote homology detection and fold recognition combining Top-n-grams and latent semantic analysis

(2008) Bin Liu et al.   BMC BIOINFORMATICS

The modified Mahalanobis Discriminant for predicting outer membrane proteins by using Chou's pseudo amino acid composition

(2008) Hao Lin   JOURNAL OF THEORETICAL BIOLOGY

PolySearch: a web-based text mining system for extracting relationships between human diseases, genes, mutations, drugs and metabolites

(2008) D. Cheng et al.   NUCLEIC ACIDS RESEARCH

miR2Disease: a manually curated database for microRNA deregulation in human disease

(2008) Q. Jiang et al.   NUCLEIC ACIDS RESEARCH

Predicting Subcellular Localization of Mycobacterial Proteins by Using Chous Pseudo Amino Acid Composition

(2008) Hao Lin et al.   PROTEIN AND PEPTIDE LETTERS

Analysis and prediction of protein local structure based on structure alphabets

(2008) Qiwen Dong et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Prediction of protein local structures and folding fragments based on building-block library

(2008) Qiwen Dong et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS