Computational prediction of promotors in Agrobacterium tumefaciens strain C58 by using the machine learning technique

An Effective Integrated Machine Learning Framework for Identifying Severity of Tomato Yellow Leaf Curl Virus and Their Experimental Validation

(2023) Nattanong Bupi et al.   Research

Bitter-RF: A random forest machine model for recognizing bitter peptides

(2023) Yu-Fei Zhang et al.   Frontiers in Medicine

Repositioning linifanib as a potent anti-necroptosis agent for sepsis

(2023) Liang Yu et al.   Cell Death Discovery

ToxIBTL: prediction of peptide toxicity based on information bottleneck and transfer learning

(2022) Lesong Wei et al.   BIOINFORMATICS

Deep-4mCGP: A Deep Learning Approach to Predict 4mC Sites in Geobacter pickeringii by Using Correlation-Based Feature Selection Technique

(2022) Hasan Zulfiqar et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2022) Hongfei Li et al.   METHODS

Towards a better prediction of subcellular location of long non-coding RNA

(2022) Zhao-Yue Zhang et al.   Frontiers of Computer Science

i6mA-Vote: Cross-Species Identification of DNA N6-Methyladenine Sites in Plant Genomes Based on Ensemble Learning With Voting

(2022) Zhixia Teng et al.   Frontiers in Plant Science

Supervised graph co-contrastive learning for drug–target interaction prediction

(2022) Yang Li et al.   BIOINFORMATICS

MLCPP 2.0: An Updated Cell-penetrating Peptides and Their Uptake Efficiency Predictor

(2022) Balachandran Manavalan et al.   JOURNAL OF MOLECULAR BIOLOGY

THRONE: A New Approach for Accurate Prediction of Human RNA N7-Methylguanosine Sites

(2022) Watshara Shoombuatong et al.   JOURNAL OF MOLECULAR BIOLOGY

Deepm5C: A deep-learning-based hybrid framework for identifying human RNA N5-methylcytosine sites using a stacking strategy

(2022) Md Mehedi Hasan et al.   MOLECULAR THERAPY

iLoc-miRNA: extracellular/intracellular miRNA prediction using deep BiLSTM with attention mechanism

(2022) Zhao-Yue Zhang et al.   BRIEFINGS IN BIOINFORMATICS

GSAML-DTA: An interpretable drug-target binding affinity prediction model based on graph neural networks with self-attention mechanism and mutual information

(2022) Jiaqi Liao et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Analysis and modeling of myopia-related factors based on questionnaire survey

(2022) Jianqiang Xiao et al.   COMPUTERS IN BIOLOGY AND MEDICINE

A Statistical Analysis of the Sequence and Structure of Thermophilic and Non-Thermophilic Proteins

(2022) Zahoor Ahmed et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

MultiscaleDTA: A multiscale-based method with a self-attention mechanism for drug-target binding affinity prediction

(2022) Haoyang Chen et al.   METHODS

DeepIDC: A Prediction Framework of Injectable Drug Combination Based on Heterogeneous Information and Deep Learning

(2022) Yuhe Yang et al.   CLINICAL PHARMACOKINETICS

iRNA-ac4C: A novel computational method for effectively detecting N4-acetylcytidine sites in human mRNA

(2022) Wei Su et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

AcrPred: A hybrid optimization with enumerated machine learning algorithm to predict Anti-CRISPR proteins

(2022) Fu-Ying Dao et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

iBLP: An XGBoost-Based Predictor for Identifying Bioluminescent Proteins

(2021) Dan Zhang et al.   Computational and Mathematical Methods in Medicine

Risk Prediction of Diabetes: Big data mining with fusion of multifarious physical examination indicators

(2021) Hui Yang et al.   Information Fusion

PPD: A Manually Curated Database for Experimentally Verified Prokaryotic Promoters

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

ATSE: a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural network and attention mechanism

(2021) Lesong Wei et al.   BRIEFINGS IN BIOINFORMATICS

StackIL6: a stacking ensemble model for improving the prediction of IL-6 inducing peptides

(2021) Phasit Charoenkwan et al.   BRIEFINGS IN BIOINFORMATICS

iDNA-MT: Identification DNA Modification Sites in Multiple Species by Using Multi-Task Learning Based a Neural Network Tool

(2021) Xiao Yang et al.   Frontiers in Genetics

Deep-4mCW2V: A sequence-based predictor to identify N4-methylcytosine sites in Escherichia coli

(2021) Hasan Zulfiqar et al.   METHODS

CellCall: integrating paired ligand–receptor and transcription factor activities for cell–cell communication

(2021) Yang Zhang et al.   NUCLEIC ACIDS RESEARCH

Detection of transcription factors binding to methylated DNA by deep recurrent neural network

(2021) Hongfei Li et al.   BRIEFINGS IN BIOINFORMATICS

NmRF: identification of multispecies RNA 2’-O-methylation modification sites from RNA sequences

(2021) Chunyan Ao et al.   BRIEFINGS IN BIOINFORMATICS

webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study

(2021) Chen Cao et al.   NUCLEIC ACIDS RESEARCH

FTWSVM-SR: DNA-Binding Proteins Identification via Fuzzy Twin Support Vector Machines on Self-Representation

(2021) Yi Zou et al.   Interdisciplinary Sciences-Computational Life Sciences

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

(2021) Chunyan Ao et al.   METHODS

HLPpred-Fuse: improved and robust prediction of hemolytic peptide and its activity by fusing multiple feature representation

(2020) Md Mehedi Hasan et al.   BIOINFORMATICS

Bayesian functional mixed-effects models with grouped smoothness for analyzing time-course gene expression data

(2020) Shangyuan Ye et al.   Current Bioinformatics

Incorporating K-mers Highly Correlated to Epigenetic Modifications for Bayesian Inference of Gene Interactions

(2020) Dariush Salimi et al.   Current Bioinformatics

A Method for Identifying Vesicle Transport Proteins Based on LibSVM and MRMD

(2020) Zhiyu Tao et al.   Computational and Mathematical Methods in Medicine

MNDR v3.0: mammal ncRNA–disease repository with increased coverage and annotation

(2020) Lin Ning et al.   NUCLEIC ACIDS RESEARCH

Early Diagnosis of Pancreatic Ductal Adenocarcinoma by Combining Relative Expression Orderings With Machine-Learning Method

(2020) Zi-Mei Zhang et al.   Frontiers in Cell and Developmental Biology

DeePromoter: Robust Promoter Predictor Using Deep Learning

(2019) Mhaned Oubounyt et al.   Frontiers in Genetics

iProEP: A Computational Predictor for Predicting Promoter

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

Specific breast cancer prognosis-subtype distinctions based on DNA methylation patterns

(2018) Shumei Zhang et al.   Molecular Oncology

Gene2vec: gene subsequence embedding for prediction of mammalian N6-methyladenosine sites from mRNA

(2018) Quan Zou et al.   RNA

Methods of MicroRNA Promoter Prediction and Transcription Factor Mediated Regulatory Network

(2017) Yuming Zhao et al.   Biomed Research International

Pro54DB: a database for experimentally verified sigma-54 promoters

(2016) Zhi-Yong Liang et al.   BIOINFORMATICS

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

(2016) Quan Zou et al.   BMC Systems Biology

Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: a technical assessment

(2014) Rachael Doherty et al.   Frontiers in Genetics

PePPER: a webserver for prediction of prokaryote promoter elements and regulons

(2012) Anne de Jong et al.   BMC GENOMICS

XanthomonasAvrBs3 Family-Type III Effectors: Discovery and Function

(2010) Jens Boch et al.   Annual Review of Phytopathology

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS