BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures
出版年份 2023 全文链接
标题
BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures
作者
关键词
-
出版物
NATURE BIOTECHNOLOGY
Volume -, Issue -, Pages -
出版商
Springer Science and Business Media LLC
发表日期
2023-09-12
DOI
10.1038/s41587-023-01872-y
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- The role of the microbiota in the management of intensive care patients
- (2022) Piotr Szychowiak et al. Annals of Intensive Care
- CBEA: Competitive balances for taxonomic enrichment analysis
- (2022) Quang P. Nguyen et al. PLoS Computational Biology
- OpenContami: a web-based application for detecting microbial contaminants in next-generation sequencing data
- (2021) Sung-Joon Park et al. BIOINFORMATICS
- Alterations in the human oral and gut microbiomes and lipidomics in COVID-19
- (2021) Zhigang Ren et al. GUT
- The Impact of Gut Microbiota-Derived Metabolites in Autism Spectrum Disorders
- (2021) Lucía N. Peralta-Marzal et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Reporting guidelines for human microbiome research: the STORMS checklist
- (2021) Chloe Mirzayi et al. NATURE MEDICINE
- BacDive in 2022: the knowledge base for standardized bacterial and archaeal data
- (2021) Lorenz Christian Reimer et al. NUCLEIC ACIDS RESEARCH
- Roseburia intestinalis: A Beneficial Gut Organism From the Discoveries in Genus and Species
- (2021) Kai Nie et al. Frontiers in Cellular and Infection Microbiology
- Role of gut microbiota in type 2 diabetes pathophysiology
- (2020) Manoj Gurung et al. EBioMedicine
- Disrupted tongue microbiota and detection of nonindigenous bacteria on the day of allogeneic hematopoietic stem cell transplantation
- (2020) Saori Oku et al. PLoS Pathogens
- Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women
- (2020) Despina Tsementzi et al. Cancer Medicine
- Periodontal Disease, Tooth Loss, and Risk of Serrated Polyps and Conventional Adenomas
- (2020) Chun-Han Lo et al. Cancer Prevention Research
- Effect of a Nutritional Intervention on the Intestinal Microbiota of Vertically HIV-Infected Children: The Pediabiota Study
- (2020) Talía Sainz et al. Nutrients
- Thyroid-Gut-Axis: How Does the Microbiota Influence Thyroid Function?
- (2020) Jovana Knezevic et al. Nutrients
- The Genus Alistipes: Gut Bacteria With Emerging Implications to Inflammation, Cancer, and Mental Health
- (2020) Bianca J. Parker et al. Frontiers in Immunology
- The Oral Microbiome and Cancer
- (2020) Muhammad Irfan et al. Frontiers in Immunology
- Text mining approaches for dealing with the rapidly expanding literature on COVID-19
- (2020) Lucy Lu Wang et al. BRIEFINGS IN BIOINFORMATICS
- Autism spectrum disorder and kidney disease
- (2020) Joanna Clothier et al. PEDIATRIC NEPHROLOGY
- Antibiotics as Major Disruptors of Gut Microbiota
- (2020) Jaime Ramirez et al. Frontiers in Cellular and Infection Microbiology
- Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study
- (2019) Modupe O. Coker et al. BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY
- 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
- Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer
- (2019) Jakob Wirbel et al. NATURE MEDICINE
- Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer
- (2019) Shinichi Yachida et al. NATURE MEDICINE
- Oral microbial dysbiosis linked to worsened periodontal condition in rheumatoid arthritis patients
- (2019) Jôice Dias Corrêa et al. Scientific Reports
- Association of prenatal antibiotics with measures of infant adiposity and the gut microbiome
- (2019) Mingyu Zhang et al. Annals of Clinical Microbiology and Antimicrobials
- HIV, Cancer, and the Microbiota: Common Pathways Influencing Different Diseases
- (2019) Sabina Herrera et al. Frontiers in Immunology
- Inflammatory and immunometabolic consequences of gut dysfunction in HIV: Parallels with IBD and implications for reservoir persistence and non-AIDS comorbidities
- (2019) Jehad Alzahrani et al. EBioMedicine
- Pathogenicity of Enterococci
- (2019) Elizabeth Fiore et al. Microbiology Spectrum
- BioBERT: a pre-trained biomedical language representation model for biomedical text mining
- (2019) Jinhyuk Lee et al. BIOINFORMATICS
- Oral Bacteria and Intestinal Dysbiosis in Colorectal Cancer
- (2019) Ioannis Koliarakis et al. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
- Consistent and correctable bias in metagenomic sequencing experiments
- (2019) Michael R McLaren et al. eLife
- Alterations to the Gastrointestinal Microbiome Associated with Methamphetamine Use among Young Men who have Sex with Men
- (2019) Ryan R. Cook et al. Scientific Reports
- Association of Flavonifractor plautii, a Flavonoid-Degrading Bacterium, with the Gut Microbiome of Colorectal Cancer Patients in India
- (2019) Ankit Gupta et al. mSystems
- Jaccard/Tanimoto similarity test and estimation methods for biological presence-absence data
- (2019) Neo Christopher Chung et al. BMC BIOINFORMATICS
- Alterations in the gut microbiota of patients with acquired immune deficiency syndrome
- (2018) Youlian Zhou et al. JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
- Gut microbiome of Moroccan colorectal cancer patients
- (2018) Imane Allali et al. MEDICAL MICROBIOLOGY AND IMMUNOLOGY
- Identifying and Overcoming Threats to Reproducibility, Replicability, Robustness, and Generalizability in Microbiome Research
- (2018) Patrick D. Schloss mBio
- Prenatal and postnatal antibiotic exposure influences the gut microbiota of preterm infants in neonatal intensive care units
- (2018) Zhi-Hui Zou et al. Annals of Clinical Microbiology and Antimicrobials
- Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging
- (2018) Chia-Yu Yang et al. Frontiers in Microbiology
- Higher Prevalence of “Low T3 Syndrome” in Patients With Chronic Fatigue Syndrome: A Case–Control Study
- (2018) Begoña Ruiz-Núñez et al. Frontiers in Endocrinology
- Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome
- (2018) Geoffrey D. Hannigan et al. mBio
- Protection of the Human Gut Microbiome From Antibiotics
- (2017) Jean de Gunzburg et al. JOURNAL OF INFECTIOUS DISEASES
- Shotgun metagenomics, from sampling to analysis
- (2017) Christopher Quince et al. NATURE BIOTECHNOLOGY
- Accessible, curated metagenomic data through ExperimentHub
- (2017) Edoardo Pasolli et al. NATURE METHODS
- MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data
- (2017) Achal Dhariwal et al. NUCLEIC ACIDS RESEARCH
- Microbiome Datasets Are Compositional: And This Is Not Optional
- (2017) Gregory B. Gloor et al. Frontiers in Microbiology
- Enterotypes in the landscape of gut microbial community composition
- (2017) Paul I. Costea et al. Nature Microbiology
- Bioconductor’s EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis
- (2016) Ludwig Geistlinger et al. BMC BIOINFORMATICS
- Sequencing of 16S rRNA reveals a distinct salivary microbiome signature in Behçet's disease
- (2016) Patrick Coit et al. CLINICAL IMMUNOLOGY
- Diabetes and Schizophrenia
- (2016) Jaana Suvisaari et al. Current Diabetes Reports
- TSHZ3 deletion causes an autism syndrome and defects in cortical projection neurons
- (2016) Xavier Caubit et al. NATURE GENETICS
- Role of gut microbiota in atherosclerosis
- (2016) Annika Lindskog Jonsson et al. Nature Reviews Cardiology
- Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center
- (2016) Alice R. Wattam et al. NUCLEIC ACIDS RESEARCH
- Population-level analysis of gut microbiome variation
- (2016) Gwen Falony et al. SCIENCE
- Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing
- (2016) Emily Vogtmann et al. PLoS One
- Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods
- (2015) Mamun-Ur Rashid et al. CLINICAL INFECTIOUS DISEASES
- Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer
- (2015) Jun Yu et al. GUT
- Orchestrating high-throughput genomic analysis with Bioconductor
- (2015) Wolfgang Huber et al. NATURE METHODS
- limma powers differential expression analyses for RNA-sequencing and microarray studies
- (2015) Matthew E. Ritchie et al. NUCLEIC ACIDS RESEARCH
- Gut microbiome development along the colorectal adenoma–carcinoma sequence
- (2015) Qiang Feng et al. Nature Communications
- The Molecular Signatures Database Hallmark Gene Set Collection
- (2015) Arthur Liberzon et al. Cell Systems
- Microbiome Changes in Healthy Volunteers Treated with GSK1322322, a Novel Antibiotic Targeting Bacterial Peptide Deformylase
- (2014) Seda Arat et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- Microbiota in the Throat and Risk Factors for Laryngeal Carcinoma
- (2014) Hongli Gong et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Reagent and laboratory contamination can critically impact sequence-based microbiome analyses
- (2014) Susannah J Salter et al. BMC BIOLOGY
- Potential of fecal microbiota for early-stage detection of colorectal cancer
- (2014) G. Zeller et al. Molecular Systems Biology
- The pathogenicity of the Streptococcus genus
- (2013) W. Krzyściak et al. EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
- Dysbiosis Signature of Fecal Microbiota in Colorectal Cancer Patients
- (2013) Na Wu et al. MICROBIAL ECOLOGY
- Differential abundance analysis for microbial marker-gene surveys
- (2013) Joseph N Paulson et al. NATURE METHODS
- A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity
- (2013) Adi L. Tarca et al. PLoS One
- Copy-Number Disorders Are a Common Cause of Congenital Kidney Malformations
- (2012) Simone Sanna-Cherchi et al. AMERICAN JOURNAL OF HUMAN GENETICS
- High-Throughput Sequencing Reveals the Incomplete, Short-Term Recovery of Infant Gut Microbiota following Parenteral Antibiotic Treatment with Ampicillin and Gentamicin
- (2012) Fiona Fouhy et al. ANTIMICROBIAL AGENTS AND CHEMOTHERAPY
- Down-weighting overlapping genes improves gene set analysis
- (2012) Adi Tarca et al. BMC BIOINFORMATICS
- PSEA: Phenotype Set Enrichment Analysis-A New Method for Analysis of Multiple Phenotypes
- (2012) Janina S. Ried et al. GENETIC EPIDEMIOLOGY
- Alterations in intestinal microbiota of elderly Irish subjects post-antibiotic therapy
- (2012) O. O'Sullivan et al. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY
- Genomic variation landscape of the human gut microbiome
- (2012) Siegfried Schloissnig et al. NATURE
- Camera: a competitive gene set test accounting for inter-gene correlation
- (2012) Di Wu et al. NUCLEIC ACIDS RESEARCH
- Microbial Co-occurrence Relationships in the Human Microbiome
- (2012) Karoline Faust et al. PLoS Computational Biology
- Uberon, an integrative multi-species anatomy ontology
- (2012) Christopher J Mungall et al. GENOME BIOLOGY
- From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems
- (2011) L. Geistlinger et al. BIOINFORMATICS
- Molecular signatures database (MSigDB) 3.0
- (2011) A. Liberzon et al. BIOINFORMATICS
- GeneSigDB: a manually curated database and resource for analysis of gene expression signatures
- (2011) A. C. Culhane et al. NUCLEIC ACIDS RESEARCH
- The NCBI Taxonomy database
- (2011) S. Federhen NUCLEIC ACIDS RESEARCH
- A similarity measure for indefinite rankings
- (2010) William Webber et al. ACM TRANSACTIONS ON INFORMATION SYSTEMS
- Modeling sample variables with an Experimental Factor Ontology
- (2010) James Malone et al. BIOINFORMATICS
- A human gut microbial gene catalogue established by metagenomic sequencing
- (2010) Junjie Qin et al. NATURE
- GREAT improves functional interpretation of cis-regulatory regions
- (2010) Cory Y McLean et al. NATURE BIOTECHNOLOGY
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- Semantic Similarity in Biomedical Ontologies
- (2009) Catia Pesquita et al. PLoS Computational Biology
- Metrics for GO based protein semantic similarity: a systematic evaluation
- (2008) Catia Pesquita et al. BMC BIOINFORMATICS
- Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
- (2008) Da Wei Huang et al. NUCLEIC ACIDS RESEARCH
Find the ideal target journal for your manuscript
Explore over 38,000 international journals covering a vast array of academic fields.
SearchAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started