AptaNet as a deep learning approach for aptamer–protein interaction prediction

Reconstruction and analysis of a carbon-core metabolic network for Dunaliella salina

(2020) Melanie Fachet et al.   BMC BIOINFORMATICS

Prediction of Protein–Protein Interaction Sites Using Convolutional Neural Network and Improved Data Sets

(2020) Zengyan Xie et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A deep neural network based hierarchical multi-label classification method

(2020) Shou Feng et al.   REVIEW OF SCIENTIFIC INSTRUMENTS

Re-epithelialization and immune cell behaviour in an ex vivo human skin model

(2020) Ana Rakita et al.   Scientific Reports

Multi-Task Network Representation Learning

(2020) Yu Xie et al.   Frontiers in Neuroscience

Accuracy improvement of quantification information using super-resolution with convolutional neural network for microscopy images

(2020) Mi-Sun Kang et al.   Biomedical Signal Processing and Control

Computational predictive approaches for interaction and structure of aptamers

(2020) Neda Emami et al.   JOURNAL OF THEORETICAL BIOLOGY

Meta-i6mA: an interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework

(2020) Md Mehedi Hasan et al.   BRIEFINGS IN BIOINFORMATICS

ProIn-Fuse: improved and robust prediction of proinflammatory peptides by fusing of multiple feature representations

(2020) Mst. Shamima Khatun et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Deep learning model for classification and bioactivity prediction of essential oil-producing plants from Egypt

(2020) Noha E. El-Attar et al.   Scientific Reports

ACCBN: ant-Colony-clustering-based bipartite network method for predicting long non-coding RNA–protein interactions

(2019) Rong Zhu et al.   BMC BIOINFORMATICS

DBS: a fast and informative segmentation algorithm for DNA copy number analysis

(2019) Jun Ruan et al.   BMC BIOINFORMATICS

Protein–Phenolic Interactions as a Factor Affecting the Physicochemical Properties of White Bean Proteins

(2019) Łukasz Sęczyk et al.   MOLECULES

Chemical methods for the modification of RNA

(2019) Marie Flamme et al.   METHODS

RPITER: A Hierarchical Deep Learning Framework for ncRNA–Protein Interaction Prediction

(2019) Cheng Peng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

BGFE: A Deep Learning Model for ncRNA-Protein Interaction Predictions Based on Improved Sequence Information

(2019) Zhao-Hui Zhan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Prediction of aptamer–protein interacting pairs based on sparse autoencoder feature extraction and an ensemble classifier

(2019) Qing Yang et al.   MATHEMATICAL BIOSCIENCES

LPI-IBNRA: Long Non-coding RNA-Protein Interaction Prediction Based on Improved Bipartite Network Recommender Algorithm

(2019) Guobo Xie et al.   Frontiers in Genetics

A Hybrid Prediction Method for Plant lncRNA-Protein Interaction

(2019) Jael Sanyanda Wekesa et al.   Cells

Automated feature engineering improves prediction of protein–protein interactions

(2019) Neven Sumonja et al.   AMINO ACIDS

Selection and application of ssDNA aptamers against spermine based on Capture-SELEX

(2019) Huili Tian et al.   ANALYTICA CHIMICA ACTA

MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks

(2019) Chieh Lo et al.   BMC BIOINFORMATICS

Prediction of MoRFs in Protein Sequences with MLPs Based on Sequence Properties and Evolution Information

(2019) Hao He et al.   Entropy

Evolution of multi-functional capillary electrophoresis for high-efficiency selection of aptamers

(2019) Chao Zhu et al.   BIOTECHNOLOGY ADVANCES

A classification model for lncRNA and mRNA based on k-mers and a convolutional neural network

(2019) Jianghui Wen et al.   BMC BIOINFORMATICS

New sulfonamide complexes with essential metal ions [Cu (II), Co (II), Ni (II) and Zn (II)]. Effect of the geometry and the metal ion on DNA binding and nuclease activity. BSA protein interaction

(2019) Tamara Tŏpala et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

A Comparative Assessment Study of Known Small-Molecule Keap1−Nrf2 Protein–Protein Interaction Inhibitors: Chemical Synthesis, Binding Properties, and Cellular Activity

(2019) Kim T. Tran et al.   JOURNAL OF MEDICINAL CHEMISTRY

Impact of the Position of the Chemically Modified 5-Furyl-2′-Deoxyuridine Nucleoside on the Thrombin DNA Aptamer–Protein Complex: Structural Insights into Aptamer Response from MD Simulations

(2019) Preethi Seelam Prabhakar et al.   MOLECULES

Novel Human Bispecific Aptamer–Antibody Conjugates for Efficient Cancer Cell Killing

(2019) Margherita Passariello et al.   Cancers

DM-RPIs: Predicting ncRNA-protein interactions using stacked ensembling strategy

(2019) Shuping Cheng et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

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

Predicting RNA–protein binding sites and motifs through combining local and global deep convolutional neural networks

(2018) Xiaoyong Pan et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

iFeature: a Python package and web server for features extraction and selection from protein and peptide sequences

(2018) Zhen Chen et al.   BIOINFORMATICS

Prediction of citrullination sites by incorporating k-spaced amino acid pairs into Chou's general pseudo amino acid composition

(2018) Zhe Ju et al.   GENE

PrESOgenesis: A two-layer multi-label predictor for identifying fertility-related proteins using support vector machine and pseudo amino acid composition approach

(2018) Mohammad Reza Bakhtiarizadeh et al.   Scientific Reports

Prediction of HIV-1 and HIV-2 proteins by using Chou’s pseudo amino acid compositions and different classifiers

(2018) Juan Mei et al.   Scientific Reports

Classification of riboswitch sequences using k-mer frequencies

(2018) Hugo A. Guillén-Ramírez et al.   BIOSYSTEMS

Unique Physicochemical Patterns of Residues in Protein-Protein Interfaces

(2018) Tamas Lazar et al.   Journal of Chemical Information and Modeling

Evolution of In Silico Strategies for Protein-Protein Interaction Drug Discovery

(2018) Stephani Joy Y. Macalino et al.   MOLECULES

Functional classification of long non-coding RNAs by k-mer content

(2018) Jessime M. Kirk et al.   NATURE GENETICS

A computational method for prediction of xylanase enzymes activity in strains of Bacillus subtilis based on pseudo amino acid composition features

(2018) Shohreh Ariaeenejad et al.   PLoS One

In situ immune response and mechanisms of cell damage in central nervous system of fatal cases microcephaly by Zika virus

(2018) Raimunda S. S. Azevedo et al.   Scientific Reports

Identifying sequence features that drive ribosomal association for lncRNA

(2018) Chao Zeng et al.   BMC GENOMICS

iPPI-PseAAC(CGR): Identify protein-protein interactions by incorporating chaos game representation into PseAAC

(2018) Jianhua Jia et al.   JOURNAL OF THEORETICAL BIOLOGY

pLoc_bal-mVirus: predict subcellular localization of multi-label virus proteins by PseAAC and IHTS treatment to balance training dataset

(2018) Xuan Xiao et al.   Medicinal Chemistry

Double-slit photoelectron interference in strong-field ionization of the neon dimer

(2018) Maksim Kunitski et al.   Nature Communications

Physicochemical properties of quinoa flour as affected by starch interactions

(2017) Guantian Li et al.   FOOD CHEMISTRY

Prediction of protein structural class for low-similarity sequences using Chou’s pseudo amino acid composition and wavelet denoising

(2017) Bin Yu et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Image based fruit category classification by 13-layer deep convolutional neural network and data augmentation

(2017) Yu-Dong Zhang et al.   MULTIMEDIA TOOLS AND APPLICATIONS

Effect of physicochemical properties of peptides from soy protein on their antimicrobial activity

(2017) Ning Xiang et al.   PEPTIDES

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

(2016) Yijie Ding et al.   BMC BIOINFORMATICS

Prediction of aptamer-protein interacting pairs using an ensemble classifier in combination with various protein sequence attributes

(2016) Lina Zhang et al.   BMC BIOINFORMATICS

Boosting compound-protein interaction prediction by deep learning

(2016) Kai Tian et al.   METHODS

Support vector machine with hypergraph-based pairwise constraints

(2016) Qiuling Hou et al.   SpringerPlus

TP53 Polymorphisms and Colorectal Cancer Risk in Patients with Lynch Syndrome in Taiwan: A Retrospective Cohort Study

(2016) Abram Bunya Kamiza et al.   PLoS One

Molecular Weight, Protein Binding Affinity and Methane Mitigation of Condensed Tannins from Mangosteen-peel (Garcinia mangostana L)

(2015) P. Paengkoum et al.   ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES

A novel method based on physicochemical properties of amino acids and one class classification algorithm for disease gene identification

(2015) Abdulaziz Yousef et al.   JOURNAL OF BIOMEDICAL INFORMATICS

DNA Aptamers in the Diagnosis and Treatment of Human Diseases

(2015) Qinchang Zhu et al.   MOLECULES

Support vector machine applications in the field of hydrology: A review

(2014) Sujay Raghavendra. N et al.   APPLIED SOFT COMPUTING

Ligand induced stabilization of the melting temperature of the HSV-1 single-strand DNA binding protein using the thermal shift assay

(2014) Kanchi Ravi Rupesh et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

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

Optimizing parameters of support vector machine using fast messy genetic algorithm for dispute classification

(2014) Jui-Sheng Chou et al.   EXPERT SYSTEMS WITH APPLICATIONS

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

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

Prediction of Aptamer-Target Interacting Pairs with Pseudo-Amino Acid Composition

(2014) Bi-Qing Li et al.   PLoS One

Aptamers as Both Drugs and Drug-Carriers

(2014) Md. Ashrafuzzaman   Biomed Research International

Development of RNA Aptamers Targeting Ebola Virus VP35

(2013) Jennifer M. Binning et al.   BIOCHEMISTRY

Complex formation with nucleic acids and aptamers alters the antigenic properties of platelet factor 4

(2013) M. E. Jaax et al.   BLOOD

Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments

(2012) Jose Cruz-Toledo et al.   Database-The Journal of Biological Databases and Curation

Aptamer in Bioanalytical Applications

(2011) Anton B. Iliuk et al.   ANALYTICAL CHEMISTRY

Aptamers as Therapeutics in Cardiovascular Diseases

(2011) P. Wang et al.   CURRENT MEDICINAL CHEMISTRY

Probing the links between in vitro potency, ADMET and physicochemical parameters

(2011) M. Paul Gleeson et al.   NATURE REVIEWS DRUG DISCOVERY

Protein–protein interaction networks: how can a hub protein bind so many different partners?

(2009) Chung-Jung Tsai et al.   TRENDS IN BIOCHEMICAL SCIENCES