MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease-2019 (COVID-19): The epidemic and the challenges

(2020) Chih-Cheng Lai et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

(2020) Roujian Lu et al.   LANCET

Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study

(2020) Nanshan Chen et al.   LANCET

Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China

(2020) Chaolin Huang et al.   LANCET

What we know so far: COVID-19 current clinical knowledge and research

(2020) Mary A Lake   CLINICAL MEDICINE

PLA2G1B is involved in CD4 anergy and CD4 lymphopenia in HIV-infected patients

(2020) Julien Pothlichet et al.   JOURNAL OF CLINICAL INVESTIGATION

The late stage of Parkinson's –results of a large multinational study on motor and non-motor complications

(2020) A. Schrag et al.   PARKINSONISM & RELATED DISORDERS

Phase IA/IB study of single-agent tislelizumab, an investigational anti-PD-1 antibody, in solid tumors

(2020) Jayesh Desai et al.   Journal for ImmunoTherapy of Cancer

Evidence for an association of gut microbial Clostridia with brain functional connectivity and gastrointestinal sensorimotor function in patients with irritable bowel syndrome, based on tripartite network analysis

(2019) Jennifer S. Labus et al.   Microbiome

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Disbiome database: linking the microbiome to disease

(2018) Yorick Janssens et al.   BMC MICROBIOLOGY

A Systematic Review and Narrative Synthesis to Explore the Effectiveness of Exercise-Based Interventions in Improving Fatigue, Dyspnea, and Depression in Lung Cancer Survivors

(2018) Catherine L. Henshall et al.   CANCER NURSING

The Human Gut Microbiome: From Association to Modulation

(2018) Thomas S.B. Schmidt et al.   CELL

Gut microbiota associations with common diseases and prescription medications in a population-based cohort

(2018) Matthew A. Jackson et al.   Nature Communications

Detection of Pulmonary Infectious Pathogens From Lung Biopsy Tissues by Metagenomic Next-Generation Sequencing

(2018) Henan Li et al.   Frontiers in Cellular and Infection Microbiology

A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiologya

(2018) J Michael Miller et al.   CLINICAL INFECTIOUS DISEASES

Alteration of the cutaneous microbiome in psoriasis and potential role in Th17 polarization

(2018) Hsin-Wen Chang et al.   Microbiome

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2018) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

(2018) Sebastian Köhler et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

New nucleic acid testing devices to diagnose infectious diseases in resource-limited settings

(2017) P. Maffert et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets

(2017) Yasset Perez-Riverol et al.   PROTEOMICS

Disnea de esfuerzo en las enfermedades respiratorias crónicas: de la fisiología a la aplicación clínica

(2017) Bruno-Pierre Dubé et al.   ARCHIVOS DE BRONCONEUMOLOGIA

An analysis of human microbe–disease associations

(2016) Wei Ma et al.   BRIEFINGS IN BIOINFORMATICS

Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans

(2016) Ron Sender et al.   CELL

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

(2016) Christopher J. Mungall et al.   NUCLEIC ACIDS RESEARCH

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

(2016) Jacqueline MacArthur et al.   NUCLEIC ACIDS RESEARCH

Gut microbiome in health and disease: Linking the microbiome–gut–brain axis and environmental factors in the pathogenesis of systemic and neurodegenerative diseases

(2016) Shivani Ghaisas et al.   PHARMACOLOGY & THERAPEUTICS

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

Altered gut microbiota in Rett syndrome

(2016) Francesco Strati et al.   Microbiome

Hepatopulmonary Syndrome Is a Frequent Cause of Dyspnea in the Short Telomere Disorders

(2015) Amany I. Gorgy et al.   CHEST

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

VFDB 2016: hierarchical and refined dataset for big data analysis—10 years on

(2015) Lihong Chen et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

The EMBL-EBI bioinformatics web and programmatic tools framework

(2015) Weizhong Li et al.   NUCLEIC ACIDS RESEARCH

DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

(2015) J. Pinero et al.   Database-The Journal of Biological Databases and Curation

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

Gut microbiome-host interactions in health and disease

(2011) James M Kinross et al.   Genome Medicine

Modeling sample variables with an Experimental Factor Ontology

(2010) James Malone et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Pneumococcal pneumonia presenting with septic shock: host- and pathogen-related factors and outcomes

(2009) C Garcia-Vidal et al.   THORAX