dPromoter-XGBoost: Detecting promoters and strength by combining multiple descriptors and feature selection using XGBoost

PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters

(2021) Wei Su et al.   JOURNAL OF MOLECULAR BIOLOGY

MUFFIN: multi-scale feature fusion for drug–drug interaction prediction

(2021) Yujie Chen et al.   BIOINFORMATICS

Alternate Roles of Sox Transcription Factors beyond Transcription Initiation

(2021) Yuli Zhang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

RFhy-m2G: Identification of RNA N2-methylguanosine modification sites based on random forest and hybrid features

(2021) Chunyan Ao et al.   METHODS

StackCPPred: A Stacking and Pairwise Energy Content-based Prediction of Cell-Penetrating Peptides and Their Uptake Efficiency

(2020) Xiangzheng Fu et al.   BIOINFORMATICS

Extremely Low Leakage Expression Systems Using Dual Transcriptional-Translational Control for Toxic Protein Production

(2020) Yusuke Kato   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Identification of Highest-Affinity Binding Sites of Yeast Transcription Factor Families

(2020) Zongyu Wang et al.   Journal of Chemical Information and Modeling

Application of deep learning methods in biological networks

(2020) Shuting Jin et al.   BRIEFINGS IN BIOINFORMATICS

Sequence-Based Identification of Allergen Proteins developed by Integration of PseAAC and Statistical Moments via 5-step Rule

(2020) Yaser Daanial Khan et al.   Current Bioinformatics

SAGA and TFIID: Friends of TBP drifting apart

(2020) H.Th. Marc Timmers   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

IDP-Seq2Seq: Identification of Intrinsically Disordered Regions based on Sequence to Sequence Learning

(2020) Yi-Jun Tang et al.   BIOINFORMATICS

Deep learning model for Pathogen Classification using Feature fusion and Data augmentation

(2020) Fareed Ahmad et al.   Current Bioinformatics

Repurpose Open Data to Discover Therapeutics for COVID-19 Using Deep Learning

(2020) Xiangxiang Zeng et al.   JOURNAL OF PROTEOME RESEARCH

Strigolactone Signaling: Repressor Proteins Are Transcription Factors

(2020) Jiuyou Tang et al.   TRENDS IN PLANT SCIENCE

Predicting preference of transcription factors for methylated DNA using sequence information

(2020) Meng-Lu Liu et al.   Molecular Therapy-Nucleic Acids

Predicting enhancer-promoter interactions by deep learning and matching heuristic

(2020) Xiaoping Min et al.   BRIEFINGS IN BIOINFORMATICS

Identification of Drug–Target Interactions via Dual Laplacian Regularized Least Squares with Multiple Kernel Fusion

(2020) Yijie Ding et al.   KNOWLEDGE-BASED SYSTEMS

The highly diverse TATA box-binding proteins among protists: A review

(2020) Olivia Parra-Marín et al.   MOLECULAR AND BIOCHEMICAL PARASITOLOGY

Prediction of transcription factors binding events based on epigenetic modifications in different human cells

(2020) Yan Huang et al.   Epigenomics

A computational framework for identifying the transcription factors involved in enhancer-promoter loop formation

(2020) Li Liu et al.   Molecular Therapy-Nucleic Acids

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

(2020) Ashish Kumar Sharma et al.   Current Bioinformatics

Prediction of Protein Ubiquitination Sites in Arabidopsis thaliana

(2019) Jiajing Chen et al.   Current Bioinformatics

Computational methods for identifying the critical nodes in biological networks

(2019) Xiangrong Liu et al.   BRIEFINGS IN BIOINFORMATICS

Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs

(2019) Christ Leemans et al.   CELL

HS-MMGKG: A Fast Multi-Objective Harmony Search Algorithm for Two-Locus Model Detection in GWAS

(2019) Liyan Sun et al.   Current Bioinformatics

iN6-methylat (5-step): identifying DNA N6-methyladenine sites in rice genome using continuous bag of nucleobases via Chou’s 5-step rule

(2019) Nguyen Quoc Khanh Le   MOLECULAR GENETICS AND GENOMICS

Feature subset selection combining maximal information entropy and maximal information coefficient

(2019) Kangfeng Zheng et al.   APPLIED INTELLIGENCE

Identify lysine carboxylation sites in proteins by integrating statistical moments and position relative features

(2019) Saba Amanat et al.   Current Bioinformatics

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data

(2019) Qian Liu et al.   Nature Communications

Xgboost application on bridge management systems for proactive damage estimation

(2019) Soram Lim et al.   ADVANCED ENGINEERING INFORMATICS

Identification of clathrin proteins by incorporating hyperparameter optimization in deep learning and PSSM profiles

(2019) Nguyen Quoc Khanh Le et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

Predicting LncRNA Subcellular Localization Using Unbalanced Pseudo-k Nucleotide Compositions

(2019) Xiao-Fei Yang et al.   Current Bioinformatics

iProEP: A Computational Predictor for Predicting Promoter

(2019) Hong-Yan Lai et al.   Molecular Therapy-Nucleic Acids

A comparison and assessment of computational method for identifying recombination hotspots in Saccharomyces cerevisiae

(2019) Hui Yang et al.   BRIEFINGS IN BIOINFORMATICS

A machine learning-based diagnosis of thyroid cancer using thyroid nodules ultrasound images

(2019) Xuesi Ma et al.   Current Bioinformatics

Prediction of ATP-binding sites in membrane proteins using a two-dimensional convolutional neural network

(2019) Trinh-Trung-Duong Nguyen et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Identification of drug–target interactions via fuzzy bipartite local model

(2019) Yijie Ding et al.   NEURAL COMPUTING & APPLICATIONS

Gene Expression Value Prediction Based on XGBoost Algorithm

(2019) Wei Li et al.   Frontiers in Genetics

Identification of membrane protein types via multivariate information fusion with Hilbert–Schmidt Independence Criterion

(2019) Hao Wang et al.   NEUROCOMPUTING

Bioinformatics analysis of real time PCR and reverse transcription PCR in detecting HCV RNA

(2018) Wei Liu et al.   Current Bioinformatics

iRSpot-PDI: Identification of recombination spots by incorporating dinucleotide property diversity information into Chou's pseudo components

(2018) Lichao Zhang et al.   GENOMICS

XGBFEMF: An XGBoost-based Framework for Essential Protein Prediction

(2018) Jiancheng Zhong et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Multitemporal field-based plant height estimation using 3D point clouds generated from small unmanned aerial systems high-resolution imagery

(2018) L. Malambo et al.   International Journal of Applied Earth Observation and Geoinformation

Using Multi-Spectral UAV Imagery to Extract Tree Crop Structural Properties and Assess Pruning Effects

(2018) Kasper Johansen et al.   Remote Sensing

Estimating Biomass and Nitrogen Amount of Barley and Grass Using UAV and Aircraft Based Spectral and Photogrammetric 3D Features

(2018) Roope Näsi et al.   Remote Sensing

iRNA(m6A)-PseDNC: Identifying N6-methyladenosine sites using pseudo dinucleotide composition

(2018) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

Developing a Multi-Dose Computational Model for Drug-induced Hepatotoxicity Prediction based on Toxicogenomics Data

(2018) Ran Su et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Identifying antimicrobial peptides using word embedding with deep recurrent neural networks

(2018) Md-Nafiz Hamid et al.   BIOINFORMATICS

iPSW(2L)-PseKNC: A two-layer predictor for identifying promoters and their strength by hybrid features via pseudo K-tuple nucleotide composition

(2018) Xuan Xiao et al.   GENOMICS

On String Languages Generated by Spiking Neural P Systems With Structural Plasticity

(2018) Francis George C. Cabarle et al.   IEEE TRANSACTIONS ON NANOBIOSCIENCE

Identifying sigma70 promoters with novel pseudo nucleotide composition

(2017) Hao Lin et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

A novel features ranking metric with application to scalable visual and bioinformatics data classification

(2016) Quan Zou et al.   NEUROCOMPUTING

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

Identification of mitochondrial proteins of malaria parasite using analysis of variance

(2014) Hui Ding et al.   AMINO ACIDS

Gene Sets of Gene Ontology are More Stable Diagnostic Biomarkers than Genes in Oral Squamous Cell Carcinoma

(2014) Tao Huang et al.   Current Bioinformatics

iPro54-PseKNC: a sequence-based predictor for identifying sigma-54 promoters in prokaryote with pseudo k-tuple nucleotide composition

(2014) Hao Lin et al.   NUCLEIC ACIDS RESEARCH

Equitability, mutual information, and the maximal information coefficient

(2014) Justin B. Kinney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CG methylated microarrays identify a novel methylated sequence bound by the CEBPB ATF4 heterodimer that is active in vivo

(2013) I. K. Mann et al.   GENOME RESEARCH

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

Predicting human microRNA-disease associations based on support vector machine

(2013) Qinghua Jiang et al.   International Journal of Data Mining and Bioinformatics

CD-HIT Suite: a web server for clustering and comparing biological sequences

(2010) Ying Huang et al.   BIOINFORMATICS

618 Five vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding

(2010) D. Odom   EJC SUPPLEMENTS