Microbes and complex diseases: from experimental results to computational models
Published 2020 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Microbes and complex diseases: from experimental results to computational models
Authors
Keywords
-
Journal
BRIEFINGS IN BIOINFORMATICS
Volume -, Issue -, Pages -
Publisher
Oxford University Press (OUP)
Online
2020-06-23
DOI
10.1093/bib/bbaa158
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Editorial: Bioinformatics in Microbiota
- (2020) Xing Chen et al. Frontiers in Microbiology
- Identification and Analysis of Human Microbe-Disease Associations by Matrix Decomposition and Label Propagation
- (2019) Jia Qu et al. Frontiers in Microbiology
- Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation
- (2019) Andrew Maltez Thomas et al. NATURE MEDICINE
- M1CR0B1AL1Z3R—a user-friendly web server for the analysis of large-scale microbial genomics data
- (2019) Oren Avram et al. NUCLEIC ACIDS RESEARCH
- 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
- Prediction of potential miRNA-disease associations using matrix decomposition and label propagation
- (2019) Jia Qu et al. KNOWLEDGE-BASED SYSTEMS
- 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
- Integrating Bipartite Network Projection and KATZ Measure to Identify Novel CircRNA-Disease Associations
- (2019) Qi Zhao et al. IEEE TRANSACTIONS ON NANOBIOSCIENCE
- SNMFSMMA: using symmetric nonnegative matrix factorization and Kronecker regularized least squares to predict potential small molecule-microRNA association
- (2019) Yan Zhao et al. RNA Biology
- Predicting metabolite-disease associations based on KATZ model
- (2019) Xiujuan Lei et al. BioData Mining
- 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
- Computational drug repositioning using low-rank matrix approximation and randomized algorithms
- (2018) Huimin Luo et al. 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
- The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level
- (2018) Luis M Rodriguez-R et al. NUCLEIC ACIDS RESEARCH
- 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
- Prediction of new potential associations between LncRNAs and environmental factors based on KATZ measure
- (2018) Hüseyin Vural et al. COMPUTERS IN BIOLOGY AND MEDICINE
- Predicting the associations between microbes and diseases by integrating multiple data sources and path-based HeteSim scores
- (2018) Chunyan Fan et al. NEUROCOMPUTING
- A Novel Computational Method for the Identification of Potential miRNA-Disease Association Based on Symmetric Non-negative Matrix Factorization and Kronecker Regularized Least Square
- (2018) Yan Zhao et al. Frontiers in Genetics
- Supervised non-negative matrix factorization methods for MALDI imaging applications
- (2018) Johannes Leuschner et al. BIOINFORMATICS
- Accurate prediction of protein-lncRNA interactions by diffusion and HeteSim features across heterogeneous network
- (2018) Lei Deng et al. BMC BIOINFORMATICS
- Species-level functional profiling of metagenomes and metatranscriptomes
- (2018) Eric A. Franzosa et al. NATURE METHODS
- Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome
- (2018) Geoffrey D. Hannigan et al. mBio
- MDAD: A Special Resource for Microbe-Drug Associations
- (2018) Ya-Zhou Sun et al. Frontiers in Cellular and Infection Microbiology
- Human Microbe-Disease Association Prediction Based on Adaptive Boosting
- (2018) Li-Hong Peng et al. Frontiers in Microbiology
- In Silico Prediction of Small Molecule-miRNA Associations Based on the HeteSim Algorithm
- (2018) Jia Qu et al. Molecular Therapy-Nucleic Acids
- KATZLGO: Large-scale Prediction of LncRNA Functions by Using the KATZ Measure Based on Multiple Networks
- (2017) Zuping Zhang et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- Prediction and Validation of Disease Genes Using HeteSim Scores
- (2017) Xiangxiang Zeng et al. IEEE-ACM Transactions on Computational Biology and Bioinformatics
- A novel approach for predicting microRNA-disease associations by unbalanced bi-random walk on heterogeneous network
- (2017) Jiawei Luo et al. JOURNAL OF BIOMEDICAL INFORMATICS
- Prediction of protein-protein interactions by label propagation with protein evolutionary and chemical information derived from heterogeneous network
- (2017) Yu-Ting Wen et al. JOURNAL OF THEORETICAL BIOLOGY
- 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
- PRISM 3: expanded prediction of natural product chemical structures from microbial genomes
- (2017) Michael A. Skinnider et al. NUCLEIC ACIDS RESEARCH
- MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data
- (2017) Achal Dhariwal et al. NUCLEIC ACIDS RESEARCH
- Interactive microbial distribution analysis using BioAtlas
- (2017) Jesper Beltoft Lund et al. NUCLEIC ACIDS RESEARCH
- MCMDA: Matrix completion for MiRNA-disease association prediction
- (2017) Jian-Qiang Li et al. Oncotarget
- LRLSHMDA: Laplacian Regularized Least Squares for Human Microbe–Disease Association prediction
- (2017) Fan Wang et al. Scientific Reports
- PBHMDA: Path-Based Human Microbe-Disease Association Prediction
- (2017) Zhi-An Huang et al. Frontiers in Microbiology
- Graph Regularized Non-Negative Low-Rank Matrix Factorization for Image Clustering
- (2017) Xuelong Li et al. IEEE Transactions on Cybernetics
- Uncovering the trimethylamine-producing bacteria of the human gut microbiota
- (2017) Silke Rath et al. Microbiome
- A novel approach for predicting microbe-disease associations by bi-random walk on the heterogeneous network
- (2017) Shuai Zou et al. PLoS One
- Prediction and validation of association between microRNAs and diseases by multipath methods
- (2016) Xiangxiang Zeng et al. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS
- Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm
- (2016) Huimin Luo et al. BIOINFORMATICS
- An analysis of human microbe–disease associations
- (2016) Wei Ma et al. BRIEFINGS IN BIOINFORMATICS
- miREFRWR: a novel disease-related microRNA-environmental factor interactions prediction method
- (2016) Xing Chen Molecular BioSystems
- Relevance search for predicting lncRNA–protein interactions based on heterogeneous network
- (2016) Jianghong Yang et al. NEUROCOMPUTING
- Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing
- (2016) Emily Vogtmann et al. PLoS One
- Network Consistency Projection for Human miRNA-Disease Associations Inference
- (2016) Changlong Gu et al. Scientific Reports
- Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer
- (2015) Jun Yu et al. GUT
- MetaPhlAn2 for enhanced metagenomic taxonomic profiling
- (2015) Duy Tin Truong et al. NATURE METHODS
- The promise of metabolic phenotyping in gastroenterology and hepatology
- (2015) Elaine Holmes et al. Nature Reviews Gastroenterology & Hepatology
- HPMCD: the database of human microbial communities from metagenomic datasets and microbial reference genomes
- (2015) Samuel C. Forster et al. NUCLEIC ACIDS RESEARCH
- Using Dynamic Multi-Task Non-Negative Matrix Factorization to Detect the Evolution of User Preferences in Collaborative Filtering
- (2015) Bin Ju et al. PLoS One
- Gut microbiome development along the colorectal adenoma–carcinoma sequence
- (2015) Qiang Feng et al. Nature Communications
- KATZLDA: KATZ measure for the lncRNA-disease association prediction
- (2015) Xing Chen Scientific Reports
- A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics
- (2014) Mohamed S. Donia et al. CELL
- Aberrant gut microbiota composition at the onset of type 1 diabetes in young children
- (2014) Marcus C. de Goffau et al. DIABETOLOGIA
- Risk Prediction for Late-Stage Ovarian Cancer by Meta-analysis of 1525 Patient Samples
- (2014) Markus Riester et al. JNCI-Journal of the National Cancer Institute
- Potential of fecal microbiota for early-stage detection of colorectal cancer
- (2014) G. Zeller et al. Molecular Systems Biology
- Alterations of the human gut microbiome in liver cirrhosis
- (2014) Nan Qin et al. NATURE
- Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes
- (2014) H Bjørn Nielsen et al. NATURE BIOTECHNOLOGY
- A Network Based Method for Analysis of lncRNA-Disease Associations and Prediction of lncRNAs Implicated in Diseases
- (2014) Xiaofei Yang et al. PLoS One
- A Graph-based model for context-aware recommendation using implicit feedback data
- (2014) Weilong Yao et al. WORLD WIDE WEB-INTERNET AND WEB INFORMATION SYSTEMS
- Human symptoms–disease network
- (2014) XueZhong Zhou et al. Nature Communications
- Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer
- (2014) Janelle C. Arthur et al. Nature Communications
- Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders
- (2013) Elaine Y. Hsiao et al. CELL
- Richness of human gut microbiome correlates with metabolic markers
- (2013) Emmanuelle Le Chatelier et al. NATURE
- Diet rapidly and reproducibly alters the human gut microbiome
- (2013) Lawrence A. David et al. NATURE
- The gut microbiota — masters of host development and physiology
- (2013) Felix Sommer et al. NATURE REVIEWS MICROBIOLOGY
- A New Logistic Dynamic Particle Swarm Optimization Algorithm Based on Random Topology
- (2013) Qingjian Ni et al. TheScientificWorldJOURNAL
- The Impact of the Gut Microbiota on Human Health: An Integrative View
- (2012) Jose C. Clemente et al. CELL
- Asthma-associated differences in microbial composition of induced sputum
- (2012) Pradeep Reddy Marri et al. JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY
- RWRMDA: predicting novel human microRNA–disease associations
- (2012) Xing Chen et al. Molecular BioSystems
- Drug–target interaction prediction by random walk on the heterogeneous network
- (2012) Xing Chen et al. Molecular BioSystems
- A framework for human microbiome research
- (2012) NATURE
- Detecting overlapping protein complexes in protein-protein interaction networks
- (2012) Tamás Nepusz et al. NATURE METHODS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Microbial interactions: from networks to models
- (2012) Karoline Faust et al. NATURE REVIEWS MICROBIOLOGY
- Hierarchical non-negative matrix factorization (hNMF): a tissue pattern differentiation method for glioblastoma multiforme diagnosis using MRSI
- (2012) Yuqian Li et al. NMR IN BIOMEDICINE
- 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
- Human nutrition, the gut microbiome and the immune system
- (2011) Andrew L. Kau et al. NATURE
- Ranking Candidate Disease Genes from Gene Expression and Protein Interaction: A Katz-Centrality Based Approach
- (2011) Jing Zhao et al. PLoS One
- Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans
- (2011) B. D. Muegge et al. SCIENCE
- Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes
- (2011) G. D. Wu et al. SCIENCE
- Microbial Metagenomics: Beyond the Genome
- (2010) Jack A. Gilbert et al. Annual Review of Marine Science
- Graph Regularized Nonnegative Matrix Factorization for Data Representation
- (2010) Deng Cai et al. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE
- A hybrid content-based and item-based collaborative filtering approach to recommend TV programs enhanced with singular value decomposition
- (2010) Ana Belén Barragáns-Martínez et al. INFORMATION SCIENCES
- 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
- Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis
- (2008) Djahida Bouskra et al. NATURE
- A core gut microbiome in obese and lean twins
- (2008) Peter J. Turnbaugh et al. NATURE
- Genome-scale analyses of health-promoting bacteria: probiogenomics
- (2008) Marco Ventura et al. NATURE REVIEWS MICROBIOLOGY
- Worlds within worlds: evolution of the vertebrate gut microbiota
- (2008) Ruth E. Ley et al. NATURE REVIEWS MICROBIOLOGY
- Symbiotic gut microbes modulate human metabolic phenotypes
- (2008) M. Li et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Publish scientific posters with Peeref
Peeref publishes scientific posters from all research disciplines. Our Diamond Open Access policy means free access to content and no publication fees for authors.
Learn MoreCreate your own webinar
Interested in hosting your own webinar? Check the schedule and propose your idea to the Peeref Content Team.
Create Now