A practical guide to amplicon and metagenomic analysis of microbiome data

YX Liu, Y Qin, T Chen, M Lu, X Qian, X Guo… - Protein & cell, 2021 - academic.oup.com
Advances in high-throughput sequencing (HTS) have fostered rapid developments in the
field of microbiome research, and massive microbiome datasets are now being generated …

Probiotics, gut microbiota, and their influence on host health and disease

B Sánchez, S Delgado… - Molecular nutrition & …, 2017 - Wiley Online Library
The gastrointestinal tract of mammals hosts a high and diverse number of different
microorganisms, known as intestinal microbiota. Many probiotics were originally isolated …

The STRING database in 2017: quality-controlled protein–protein association networks, made broadly accessible

D Szklarczyk, JH Morris, H Cook, M Kuhn… - Nucleic acids …, 2016 - academic.oup.com
A system-wide understanding of cellular function requires knowledge of all functional
interactions between the expressed proteins. The STRING database aims to collect and …

[HTML][HTML] The phyllosphere microbiome shifts toward combating melanose pathogen

PD Li, ZR Zhu, Y Zhang, J Xu, H Wang, Z Wang, H Li - Microbiome, 2022 - Springer
Background Plants can recruit beneficial microbes to enhance their ability to defend against
pathogens. However, in contrast to the intensively studied roles of the rhizosphere …

[HTML][HTML] A guide to conquer the biological network era using graph theory

M Koutrouli, E Karatzas, D Paez-Espino… - … in bioengineering and …, 2020 - frontiersin.org
Networks are one of the most common ways to represent biological systems as complex sets
of binary interactions or relations between different bioentities. In this article, we discuss the …

PhosphoSitePlus, 2014: mutations, PTMs and recalibrations

PV Hornbeck, B Zhang, B Murray… - Nucleic acids …, 2015 - academic.oup.com
Abstract PhosphoSitePlus®(PSP, http://www. phosphosite. org/), a knowledgebase
dedicated to mammalian post-translational modifications (PTMs), contains over 330 000 non …

Identification of 153 new loci associated with heel bone mineral density and functional involvement of GPC6 in osteoporosis

JP Kemp, JA Morris, C Medina-Gomez, V Forgetta… - Nature …, 2017 - nature.com
Osteoporosis is a common disease diagnosed primarily by measurement of bone mineral
density (BMD). We undertook a genome-wide association study (GWAS) in 142,487 …

New genetic loci link adipose and insulin biology to body fat distribution

D Shungin, TW Winkler, DC Croteau-Chonka… - Nature, 2015 - nature.com
Body fat distribution is a heritable trait and a well-established predictor of adverse metabolic
outcomes, independent of overall adiposity. To increase our understanding of the genetic …

FunRich: An open access standalone functional enrichment and interaction network analysis tool

M Pathan, S Keerthikumar, CS Ang, L Gangoda… - …, 2015 - Wiley Online Library
As high‐throughput techniques including proteomics become more accessible to individual
laboratories, there is an urgent need for a user‐friendly bioinformatics analysis system …

The IBD interactome: an integrated view of aetiology, pathogenesis and therapy

HSP De Souza, C Fiocchi, D Iliopoulos - … Reviews Gastroenterology & …, 2017 - nature.com
Crohn's disease and ulcerative colitis are prototypical complex diseases characterized by
chronic and heterogeneous manifestations, induced by interacting environmental, genomic …