A survey on predicting microbe-disease associations: biological data and computational methods
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Title
A survey on predicting microbe-disease associations: biological data and computational methods
Authors
Keywords
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Journal
BRIEFINGS IN BIOINFORMATICS
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2020-06-23
DOI
10.1093/bib/bbaa157
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Note: Only part of the references are listed.- Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease
- (2020) F. J. Ryan et al. Nature Communications
- Identification and Analysis of Human Microbe-Disease Associations by Matrix Decomposition and Label Propagation
- (2019) Jia Qu et al. Frontiers in Microbiology
- deepDR: A network-based deep learning approach to in silico drug repositioning
- (2019) Xiangxiang Zeng et al. BIOINFORMATICS
- A Novel Human Microbe-Disease Association Prediction Method Based on the Bidirectional Weighted Network
- (2019) Hao Li et al. Frontiers in Microbiology
- A Bidirectional Label Propagation Based Computational Model for Potential Microbe-Disease Association Prediction
- (2019) Lei Wang et al. Frontiers in Microbiology
- RWHMDA: Random Walk on Hypergraph for Microbe-Disease Association Prediction
- (2019) Ya-Wei Niu et al. Frontiers in Microbiology
- Challenges in the construction of knowledge bases for human microbiome-disease associations
- (2019) Varsha Dave Badal et al. Microbiome
- “EviMass”: A Literature Evidence-Based Miner for Human Microbial Associations
- (2019) Divyanshu Srivastava et al. Frontiers in Genetics
- WMGHMDA: a novel weighted meta-graph-based model for predicting human microbe-disease association on heterogeneous information network
- (2019) Yahui Long et al. BMC BIOINFORMATICS
- A Novel Approach Based on Bipartite Network Recommendation and KATZ Model to Predict Potential Micro-Disease Associations
- (2019) Shiru Li et al. Frontiers in Genetics
- MCHMDA:Predicting Microbe-Disease Associations Based on Similarities and Low-Rank Matrix Completion
- (2019) Cheng Yan et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- Modeling polypharmacy side effects with graph convolutional networks
- (2018) Marinka Zitnik et al. BIOINFORMATICS
- Compound-protein Interaction Prediction with End-to-end Learning of Neural Networks for Graphs and Sequences
- (2018) Masashi Tsubaki et al. BIOINFORMATICS
- Disbiome database: linking the microbiome to disease
- (2018) Yorick Janssens et al. BMC MICROBIOLOGY
- Computational prediction of drug–target interactions using chemogenomic approaches: an empirical survey
- (2018) Ali Ezzat et al. BRIEFINGS IN BIOINFORMATICS
- A Novel Approach based on Bipartite Network to Predict Human Microbe-Disease Associations
- (2018) Lei Wang et al. Current Bioinformatics
- PRWHMDA: Human Microbe-Disease Association Prediction by Random Walk on the Heterogeneous Network with PSO
- (2018) Chuanyan Wu et al. International Journal of Biological Sciences
- CASNMF: A Converged Algorithm for symmetrical nonnegative matrix factorization
- (2018) Li-Ping Tian et al. NEUROCOMPUTING
- Novel human microbe-disease associations inference based on network consistency projection
- (2018) Shuai Zou et al. Scientific Reports
- The Bi-direction Similarity Integration Method for Predicting Microbe-disease Association
- (2018) Wen Zhang et al. IEEE Access
- Predicting the associations between microbes and diseases by integrating multiple data sources and path-based HeteSim scores
- (2018) Chunyan Fan et al. NEUROCOMPUTING
- OUP accepted manuscript
- (2018) NUCLEIC ACIDS RESEARCH
- Human Disease Ontology 2018 update: classification, content and workflow expansion
- (2018) Lynn M Schriml et al. NUCLEIC ACIDS RESEARCH
- STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
- (2018) Damian Szklarczyk et al. NUCLEIC ACIDS RESEARCH
- Human Microbe-Disease Association Prediction Based on Adaptive Boosting
- (2018) Li-Hong Peng et al. Frontiers in Microbiology
- Evaluating the Value of Defensins for Diagnosing Secondary Bacterial Infections in Influenza-Infected Patients
- (2018) Siyu Zhou et al. Frontiers in Microbiology
- Human Microbe-Disease Association Prediction With Graph Regularized Non-Negative Matrix Factorization
- (2018) Bin-Sheng He et al. Frontiers in Microbiology
- 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
- Prioritizing disease-causing microbes based on random walking on the heterogeneous network
- (2017) Xianjun Shen et al. METHODS
- DrugBank 5.0: a major update to the DrugBank database for 2018
- (2017) David S Wishart et al. NUCLEIC ACIDS RESEARCH
- Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis
- (2017) Jaeyun Sung et al. Nature Communications
- LRLSHMDA: Laplacian Regularized Least Squares for Human Microbe–Disease Association prediction
- (2017) Fan Wang et al. Scientific Reports
- MicroPattern: a web-based tool for microbe set enrichment analysis and disease similarity calculation based on a list of microbes
- (2017) Wei Ma et al. Scientific Reports
- Genome composition and phylogeny of microbes predict their co-occurrence in the environment
- (2017) Olga K. Kamneva PLoS Computational Biology
- PBHMDA: Path-Based Human Microbe-Disease Association Prediction
- (2017) Zhi-An Huang et al. Frontiers in Microbiology
- Gut microbiota dysbiosis contributes to the development of hypertension
- (2017) Jing Li et al. Microbiome
- A standard database for drug repositioning
- (2017) Adam S. Brown et al. Scientific Data
- A novel approach for predicting microbe-disease associations by bi-random walk on the heterogeneous network
- (2017) Shuai Zou et al. PLoS One
- Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing
- (2016) Ravi Ranjan et al. BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
- An analysis of human microbe–disease associations
- (2016) Wei Ma et al. BRIEFINGS IN BIOINFORMATICS
- Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China
- (2016) Bin Ma et al. ISME Journal
- Next-Generation Sequencing of the Bacterial 16S rRNA Gene for Forensic Soil Comparison: A Feasibility Study
- (2016) Ellen M. Jesmok et al. JOURNAL OF FORENSIC SCIENCES
- Microbiome-wide association studies link dynamic microbial consortia to disease
- (2016) Jack A. Gilbert et al. NATURE
- Predicting drug–target interaction using positive-unlabeled learning
- (2016) Wei Lan et al. NEUROCOMPUTING
- Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences
- (2016) Nathan A. Ahlgren et al. NUCLEIC ACIDS RESEARCH
- Linking Virus Genomes with Host Taxonomy
- (2016) Tomoko Mihara et al. Viruses-Basel
- Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation
- (2016) Matthew T. Agler et al. PLOS BIOLOGY
- Improving compound–protein interaction prediction by building up highly credible negative samples
- (2015) Hui Liu et al. BIOINFORMATICS
- NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation
- (2015) Roie Levy et al. BMC BIOINFORMATICS
- Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research
- (2015) Àlex Bravo et al. BMC BIOINFORMATICS
- HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes
- (2015) Samuel C. Forster et al. NUCLEIC ACIDS RESEARCH
- The Pfam protein families database: towards a more sustainable future
- (2015) Robert D. Finn et al. NUCLEIC ACIDS RESEARCH
- Computational methodology for predicting the landscape of the human–microbial interactome region level influence
- (2015) Edgar D. Coelho et al. Journal of Bioinformatics and Computational Biology
- Lactobacillus species as biomarkers and agents that can promote various aspects of vaginal health
- (2015) Mariya I. Petrova et al. Frontiers in Physiology
- Review article: fungal microbiota and digestive diseases
- (2014) Z. K. Wang et al. ALIMENTARY PHARMACOLOGY & THERAPEUTICS
- Conducting a Microbiome Study
- (2014) Julia K. Goodrich et al. CELL
- Facial bacterial infections: Folliculitis
- (2014) Ana Cristina Laureano et al. CLINICS IN DERMATOLOGY
- HeteSim: A General Framework for Relevance Measure in Heterogeneous Networks
- (2014) Chuan Shi et al. IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
- Similarity network fusion for aggregating data types on a genomic scale
- (2014) Bo Wang et al. NATURE METHODS
- The gut microbiota, bacterial metabolites and colorectal cancer
- (2014) Petra Louis et al. NATURE REVIEWS MICROBIOLOGY
- DINIES: drug–target interaction network inference engine based on supervised analysis
- (2014) Yoshihiro Yamanishi et al. NUCLEIC ACIDS RESEARCH
- The Augmented Lagrange Multipliers Method for Matrix Completion from Corrupted Samplings with Application to Mixed Gaussian-Impulse Noise Removal
- (2014) Fan Meng et al. PLoS One
- Identifying Gut Microbe-Host Phenotype Relationships Using Combinatorial Communities in Gnotobiotic Mice
- (2014) J. J. Faith et al. Science Translational Medicine
- Role of the gut microbiota in inflammatory bowel disease pathogenesis: What have we learnt in the past 10 years?
- (2014) Georgina L Hold WORLD JOURNAL OF GASTROENTEROLOGY
- Metatranscriptomics of the Human Oral Microbiome during Health and Disease
- (2014) P. Jorth et al. mBio
- Human symptoms–disease network
- (2014) XueZhong Zhou et al. Nature Communications
- A Fast Algorithm for Nonnegative Matrix Factorization and Its Convergence
- (2014) Li-Xin Li et al. IEEE Transactions on Neural Networks and Learning Systems
- Halogen Bond: Its Role beyond Drug–Target Binding Affinity for Drug Discovery and Development
- (2013) Zhijian Xu et al. Journal of Chemical Information and Modeling
- The gut microbiota and obesity: from correlation to causality
- (2013) Liping Zhao NATURE REVIEWS MICROBIOLOGY
- The Transporter Classification Database
- (2013) Milton H. Saier et al. NUCLEIC ACIDS RESEARCH
- Predictive Computational Modeling of the Mucosal Immune Responses during Helicobacter pylori Infection
- (2013) Adria Carbo et al. PLoS One
- Interpreting infective microbiota: the importance of an ecological perspective
- (2013) Geraint B. Rogers et al. TRENDS IN MICROBIOLOGY
- Predicting drug-target interactions from chemical and genomic kernels using Bayesian matrix factorization
- (2012) M. Gonen BIOINFORMATICS
- Host-microbe interactions that shape the pathogenesis ofAcinetobacter baumanniiinfection
- (2012) Brittany L. Mortensen et al. CELLULAR MICROBIOLOGY
- ENteric Immunity SImulator: A Tool for In Silico Study of Gastroenteric Infections
- (2012) K. V. Wendelsdorf et al. IEEE TRANSACTIONS ON NANOBIOSCIENCE
- Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease
- (2012) Luke Jostins et al. NATURE
- Microbial interactions: from networks to models
- (2012) Karoline Faust et al. NATURE REVIEWS MICROBIOLOGY
- EuPathDB: The Eukaryotic Pathogen database
- (2012) C. Aurrecoechea et al. NUCLEIC ACIDS RESEARCH
- The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
- (2012) Christian Quast et al. NUCLEIC ACIDS RESEARCH
- Interactions Between the Microbiota and the Immune System
- (2012) L. V. Hooper et al. SCIENCE
- Gaussian interaction profile kernels for predicting drug–target interaction
- (2011) Twan van Laarhoven et al. BIOINFORMATICS
- Manifold Regularized Discriminative Nonnegative Matrix Factorization With Fast Gradient Descent
- (2011) Naiyang Guan et al. IEEE TRANSACTIONS ON IMAGE PROCESSING
- The NCBI Taxonomy database
- (2011) S. Federhen NUCLEIC ACIDS RESEARCH
- Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease
- (2011) S. Greenblum et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Agent-based dynamic knowledge representation of Pseudomonas aeruginosa virulence activation in the stressed gut: Towards characterizing host-pathogen interactions in gut-derived sepsis
- (2011) John B Seal et al. Theoretical Biology and Medical Modelling
- Inferring the human microRNA functional similarity and functional network based on microRNA-associated diseases
- (2010) Dong Wang et al. BIOINFORMATICS
- Graph Regularized Nonnegative Matrix Factorization for Data Representation
- (2010) Deng Cai et al. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
- Mechanisms of disease: Helicobacter pylori virulence factors
- (2010) Yoshio Yamaoka Nature Reviews Gastroenterology & Hepatology
- A Singular Value Thresholding Algorithm for Matrix Completion
- (2010) Jian-Feng Cai et al. SIAM JOURNAL ON OPTIMIZATION
- The Human Oral Microbiome Database: a web accessible resource for investigating oral microbe taxonomic and genomic information
- (2010) T. Chen et al. Database-The Journal of Biological Databases and Curation
- Associating Genes and Protein Complexes with Disease via Network Propagation
- (2010) Oron Vanunu et al. PLoS Computational Biology
- Comparisons of Subgingival Microbial Profiles of Refractory Periodontitis, Severe Periodontitis, and Periodontal Health Using the Human Oral Microbe Identification Microarray
- (2009) Ana Paula V. Colombo et al. JOURNAL OF PERIODONTOLOGY
- DIANA-microT web server: elucidating microRNA functions through target prediction
- (2009) M. Maragkakis et al. NUCLEIC ACIDS RESEARCH
- Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis
- (2008) Djahida Bouskra et al. NATURE
- Bregman Iterative Algorithms for $\ell_1$-Minimization with Applications to Compressed Sensing
- (2008) Wotao Yin et al. SIAM Journal on Imaging Sciences
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