- Home
- Publications
- Publication Search
- Publication Details
Title
Application of Machine Learning in Microbiology
Authors
Keywords
-
Journal
Frontiers in Microbiology
Volume 10, Issue -, Pages -
Publisher
Frontiers Media SA
Online
2019-04-18
DOI
10.3389/fmicb.2019.00827
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Prediction of potential disease-associated microRNAs using structural perturbation method
- (2018) Xiangxiang Zeng et al. BIOINFORMATICS
- MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples
- (2018) Ehsaneddin Asgari et al. BIOINFORMATICS
- ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides
- (2018) Leyi Wei et al. BIOINFORMATICS
- BNPMDA: Bipartite Network Projection for MiRNA–Disease Association prediction
- (2018) Xing Chen et al. BIOINFORMATICS
- Predicting miRNA–disease association based on inductive matrix completion
- (2018) Xing Chen et al. BIOINFORMATICS
- Deep learning models for bacteria taxonomic classification of metagenomic data
- (2018) Antonino Fiannaca et al. BMC BIOINFORMATICS
- Taxonomy-aware feature engineering for microbiome classification
- (2018) Mai Oudah et al. BMC BIOINFORMATICS
- Targeted sequencing of clade-specific markers from skin microbiomes for forensic human identification
- (2018) Sarah E. Schmedes et al. Forensic Science International-Genetics
- Predicting Potential Drugs for Breast Cancer based on miRNA and Tissue Specificity
- (2018) Liang Yu et al. International Journal of Biological Sciences
- iRSpot-Pse6NC: Identifying recombination spots in Saccharomyces cerevisiae by incorporating hexamer composition into general PseKNC
- (2018) Hui Yang et al. International Journal of Biological Sciences
- A Novel Computational Method for Detecting DNA Methylation Sites with DNA Sequence Information and Physicochemical Properties
- (2018) Gaofeng Pan et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- SeqSVM: A Sequence-Based Support Vector Machine Method for Identifying Antioxidant Proteins
- (2018) Lei Xu et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- HLPI-Ensemble: Prediction of human lncRNA-protein interactions based on ensemble strategy
- (2018) Huan Hu et al. RNA Biology
- EGBMMDA: Extreme Gradient Boosting Machine for MiRNA-Disease Association prediction
- (2018) Xing Chen et al. Cell Death & Disease
- A Novel Hybrid Sequence-Based Model for Identifying Anticancer Peptides
- (2018) Lei Xu et al. Genes
- M6APred-EL: A sequence-based predictor for identifying N6-methyladenosine sites using ensemble learning
- (2018) Leyi Wei et al. Molecular Therapy-Nucleic Acids
- IRWNRLPI: Integrating Random Walk and Neighborhood Regularized Logistic Matrix Factorization for lncRNA-Protein Interaction Prediction
- (2018) Qi Zhao et al. Frontiers in Genetics
- Metatranscriptome Analysis of the Vaginal Microbiota Reveals Potential Mechanisms for Protection against Metronidazole in Bacterial Vaginosis
- (2018) Zhi-Luo Deng et al. mSphere
- Data and Statistical Methods To Analyze the Human Microbiome
- (2018) Levi Waldron mSystems
- 4mCPred: Machine Learning Methods for DNA N4-methylcytosine sites Prediction
- (2018) Wenying He et al. BIOINFORMATICS
- BMCMDA: a novel model for predicting human microbe-disease associations via binary matrix completion
- (2018) Jian-Yu Shi et al. BMC BIOINFORMATICS
- Sequence clustering in bioinformatics: an empirical study
- (2018) Quan Zou et al. BRIEFINGS IN BIOINFORMATICS
- Computational models for lncRNA function prediction and functional similarity calculation
- (2018) Xing Chen et al. Briefings in Functional Genomics
- 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
- Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities
- (2018) Marinka Zitnik et al. Information Fusion
- Predicting the associations between microbes and diseases by integrating multiple data sources and path-based HeteSim scores
- (2018) Chunyan Fan et al. NEUROCOMPUTING
- RWLPAP: Random Walk for lncRNA-protein Associations Prediction
- (2018) Qi Zhao et al. PROTEIN AND PEPTIDE LETTERS
- MDHGI: Matrix Decomposition and Heterogeneous Graph Inference for miRNA-disease association prediction
- (2018) Xing Chen et al. PLoS Computational Biology
- The Bipartite Network Projection Recommended Algorithm for predicting long non-coding RNA–protein interactions
- (2018) Qi Zhao et al. Molecular Therapy-Nucleic Acids
- IDTAXA: a novel approach for accurate taxonomic classification of microbiome sequences
- (2018) Adithya Murali et al. Microbiome
- MARVEL, a Tool for Prediction of Bacteriophage Sequences in Metagenomic Bins
- (2018) Deyvid Amgarten et al. Frontiers in Genetics
- Microbiomics and Plant Health: An Interdisciplinary and International Workshop on the Plant Microbiome
- (2018) Kabin Xie et al. Molecular Plant
- An Efficient Classifier for Alzheimer’s Disease Genes Identification
- (2018) Lei Xu et al. MOLECULES
- Human Microbe-Disease Association Prediction Based on Adaptive Boosting
- (2018) Li-Hong Peng et al. Frontiers in Microbiology
- Novel Human miRNA-Disease Association Inference Based on Random Forest
- (2018) Xing Chen et al. Molecular Therapy-Nucleic Acids
- Predicting Diabetes Mellitus With Machine Learning Techniques
- (2018) Quan Zou et al. Frontiers in Genetics
- Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks
- (2018) Demetrius DiMucci et al. mSystems
- CountNet: Estimating the Number of Concurrent Speakers Using Supervised Learning
- (2018) Fabian-Robert Stoter et al. IEEE-ACM Transactions on Audio Speech and Language Processing
- Predicting the Ecological Quality Status of Marine Environments from eDNA Metabarcoding Data Using Supervised Machine Learning
- (2017) Tristan Cordier et al. ENVIRONMENTAL SCIENCE & TECHNOLOGY
- Spiking Neural P Systems With Scheduled Synapses
- (2017) Francis George C. Cabarle et al. IEEE TRANSACTIONS ON NANOBIOSCIENCE
- Meta-path methods for prioritizing candidate disease miRNAs
- (2017) Xuan Zhang et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- Prediction of Novel Drugs for Hepatocellular Carcinoma Based on Multi-Source Random Walk
- (2017) Liang Yu et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- Inferring MicroRNA-Disease Associations by Random Walk on a Heterogeneous Network with Multiple Data Sources
- (2017) Yuansheng Liu et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- Identification of drug-target interactions via multiple information integration
- (2017) Yijie Ding et al. INFORMATION SCIENCES
- Identification of Protein–Ligand Binding Sites by Sequence Information and Ensemble Classifier
- (2017) Yijie Ding et al. Journal of Chemical Information and Modeling
- Prediction of microbe–disease association from the integration of neighbor and graph with collaborative recommendation model
- (2017) Yu-An Huang et al. Journal of Translational Medicine
- LPI-ETSLP: lncRNA–protein interaction prediction using eigenvalue transformation-based semi-supervised link prediction
- (2017) Huan Hu et al. Molecular BioSystems
- Identification of DNA-Binding Proteins Using Mixed Feature Representation Methods
- (2017) Kaiyang Qu et al. MOLECULES
- RKNNMDA: Ranking-based KNN for MiRNA-Disease Association prediction
- (2017) Xing Chen et al. RNA Biology
- LRLSHMDA: Laplacian Regularized Least Squares for Human Microbe–Disease Association prediction
- (2017) Fan Wang et al. Scientific Reports
- LRSSLMDA: Laplacian Regularized Sparse Subspace Learning for MiRNA-Disease Association prediction
- (2017) Xing Chen et al. PLoS Computational Biology
- A comprehensive overview and evaluation of circular RNA detection tools
- (2017) Xiangxiang Zeng et al. PLoS Computational Biology
- PBHMDA: Path-Based Human Microbe-Disease Association Prediction
- (2017) Zhi-An Huang et al. Frontiers in Microbiology
- Predicting the HMA-LMA Status in Marine Sponges by Machine Learning
- (2017) Lucas Moitinho-Silva et al. Frontiers in Microbiology
- Metagenome-Wide Association Study and Machine Learning Prediction of Bulk Soil Microbiome and Crop Productivity
- (2017) Hao-Xun Chang et al. Frontiers in Microbiology
- VirFinder: a novel k-mer based tool for identifying viral sequences from assembled metagenomic data
- (2017) Jie Ren et al. Microbiome
- Spiking Neural P Systems with Colored Spikes
- (2017) Tao Song et al. IEEE Transactions on Cognitive and Developmental Systems
- A Machine Learning Approach for Using the Postmortem Skin Microbiome to Estimate the Postmortem Interval
- (2017) Hunter R. Johnson et al. PLoS One
- Statistical analysis of co-occurrence patterns in microbial presence-absence datasets
- (2017) Kumar P. Mainali et al. PLoS One
- AOD: the antioxidant protein database
- (2017) Pengmian Feng et al. Scientific Reports
- A novel approach based on KATZ measure to predict associations of human microbiota with non-infectious diseases
- (2016) Xing Chen et al. BIOINFORMATICS
- Predicting existing targets for new drugs base on strategies for missing interactions
- (2016) Jian-Yu Shi et al. BMC BIOINFORMATICS
- The extraction of drug-disease correlations based on module distance in incomplete human interactome
- (2016) Liang Yu et al. BMC Systems Biology
- A comprehensive review and comparison of different computational methods for protein remote homology detection
- (2016) Junjie Chen et al. BRIEFINGS IN BIOINFORMATICS
- Long non-coding RNAs and complex diseases: from experimental results to computational models
- (2016) Xing Chen et al. BRIEFINGS IN BIOINFORMATICS
- Learning from real imbalanced data of 14-3-3 proteins binding specificity
- (2016) Zhao Li et al. NEUROCOMPUTING
- Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation
- (2016) Ana Laura Grazziotin et al. NUCLEIC ACIDS RESEARCH
- iACP: a sequence-based tool for identifying anticancer peptides
- (2016) Wei Chen et al. Oncotarget
- Identification of Bacterial Cell Wall Lyases via Pseudo Amino Acid Composition
- (2016) Xin-Xin Chen et al. Biomed Research International
- Identification of Secretory Proteins inMycobacterium tuberculosisUsing Pseudo Amino Acid Composition
- (2016) Huan Yang et al. Biomed Research International
- Predicting the Organelle Location of Noncoding RNAs Using Pseudo Nucleotide Compositions
- (2016) Pengmian Feng et al. Interdisciplinary Sciences-Computational Life Sciences
- Prediction of new drug indications based on clinical data and network modularity
- (2016) Liang Yu et al. Scientific Reports
- Electro-assisted groundwater bioremediation: Fundamentals, challenges and future perspectives
- (2015) Wen-Wei Li et al. BIORESOURCE TECHNOLOGY
- Inferring drug-disease associations based on known protein complexes
- (2015) Liang Yu et al. BMC Medical Genomics
- Similarity computation strategies in the microRNA-disease network: a survey
- (2015) Quan Zou et al. Briefings in Functional Genomics
- Pse-in-One: a web server for generating various modes of pseudo components of DNA, RNA, and protein sequences
- (2015) Bin Liu et al. NUCLEIC ACIDS RESEARCH
- The global ocean microbiome
- (2015) M. A. Moran SCIENCE
- Constructing lncRNA functional similarity network based on lncRNA-disease associations and disease semantic similarity
- (2015) Xing Chen et al. Scientific Reports
- VirSorter: mining viral signal from microbial genomic data
- (2015) Simon Roux et al. PeerJ
- A Network Based Method for Analysis of lncRNA-Disease Associations and Prediction of lncRNAs Implicated in Diseases
- (2014) Xiaofei Yang et al. PLoS One
- Machine Learning Techniques Accurately Classify Microbial Communities by Bacterial Vaginosis Characteristics
- (2014) Daniel Beck et al. PLoS One
- Human symptoms–disease network
- (2014) XueZhong Zhou et al. Nature Communications
- Ecological Consistency of SSU rRNA-Based Operational Taxonomic Units at a Global Scale
- (2014) Thomas S. B. Schmidt et al. PLoS Computational Biology
- iHSP-PseRAAAC: Identifying the heat shock protein families using pseudo reduced amino acid alphabet composition
- (2013) Peng-Mian Feng et al. ANALYTICAL BIOCHEMISTRY
- Novel human lncRNA–disease association inference based on lncRNA expression profiles
- (2013) Xing Chen et al. BIOINFORMATICS
- Naïve Bayes Classifier with Feature Selection to Identify Phage Virion Proteins
- (2013) Peng-Mian Feng et al. Computational and Mathematical Methods in Medicine
- Identification of Antioxidants from Sequence Information Using Naïve Bayes
- (2013) Peng-Mian Feng et al. Computational and Mathematical Methods in Medicine
- Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences
- (2013) Morgan G I Langille et al. NATURE BIOTECHNOLOGY
- A comprehensive evaluation of multicategory classification methods for microbiomic data
- (2013) Alexander Statnikov et al. Microbiome
- Bacterial Communities in Women with Bacterial Vaginosis: High Resolution Phylogenetic Analyses Reveal Relationships of Microbiota to Clinical Criteria
- (2012) Sujatha Srinivasan et al. PLoS One
- Microbial ecosystems therapeutics: a new paradigm in medicine?
- (2012) E.O. Petrof et al. Beneficial Microbes
- Quantitative Assessment of the Human Gut Microbiome Using Multitag Pyrosequencing
- (2010) Patrick Gillevet et al. CHEMISTRY & BIODIVERSITY
- Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems
- (2010) Minou Nowrousian EUKARYOTIC CELL
- Vaginal microbiome of reproductive-age women
- (2010) J. Ravel et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Inflammatory bowel disease, gut bacteria and probiotic therapy
- (2009) Caroline Reiff et al. INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY
- Microbial disease and the coral holobiont
- (2009) David G. Bourne et al. TRENDS IN MICROBIOLOGY
- Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples
- (2009) James Robert White et al. PLoS Computational Biology
- Comment on “On Discriminative vs. Generative Classifiers: A Comparison of Logistic Regression and Naive Bayes”
- (2008) Jing-Hao Xue et al. NEURAL PROCESSING LETTERS
- A polymicrobial perspective of pulmonary infections exposes an enigmatic pathogen in cystic fibrosis patients
- (2008) C. D. Sibley et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Discover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversationBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started