The healthy human microbiome

J Lloyd-Price, G Abu-Ali, C Huttenhower - Genome medicine, 2016 - Springer
Humans are virtually identical in their genetic makeup, yet the small differences in our DNA
give rise to tremendous phenotypic diversity across the human population. By contrast, the …

Estimating the success of enzyme bioprospecting through metagenomics: current status and future trends

M Ferrer, M Martínez‐Martínez, R Bargiela… - Microbial …, 2016 - Wiley Online Library
Recent reports have suggested that the establishment of industrially relevant enzyme
collections from environmental genomes has become a routine procedure. Across the …

Expanded microbial genome coverage and improved protein family annotation in the COG database

MY Galperin, KS Makarova, YI Wolf… - Nucleic acids …, 2015 - academic.oup.com
Microbial genome sequencing projects produce numerous sequences of deduced proteins,
only a small fraction of which have been or will ever be studied experimentally. This leaves …

The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function

S Ghatak, ZA King, A Sastry… - Nucleic acids research, 2019 - academic.oup.com
Experimental studies of Escherichia coli K-12 MG1655 often implicate poorly annotated
genes in cellular phenotypes. However, we lack a systematic understanding of these genes …

Metatranscriptomics for the human microbiome and microbial community functional profiling

Y Zhang, KN Thompson, T Branck, Y Yan… - Annual Review of …, 2021 - annualreviews.org
Shotgun metatranscriptomics (MTX) is an increasingly practical way to survey microbial
community gene function and regulation at scale. This review begins by summarizing the …

The Chlamydomonas genome project: a decade on

IK Blaby, CE Blaby-Haas, N Tourasse, EFY Hom… - Trends in plant …, 2014 - cell.com
The green alga Chlamydomonas reinhardtii is a popular unicellular organism for studying
photosynthesis, cilia biogenesis, and micronutrient homeostasis. Ten years since its …

Determinants and prediction of esterase substrate promiscuity patterns

M Martínez-Martínez, C Coscolín, G Santiago… - ACS chemical …, 2017 - ACS Publications
Esterases receive special attention because of their wide distribution in biological systems
and environments and their importance for physiology and chemical synthesis. The …

The ocean sampling day consortium

A Kopf, M Bicak, R Kottmann, J Schnetzer, I Kostadinov… - Gigascience, 2015 - Springer
Abstract Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial
Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine …

HAMAP in 2015: updates to the protein family classification and annotation system

I Pedruzzi, C Rivoire, AH Auchincloss… - Nucleic acids …, 2015 - academic.oup.com
HAMAP (High-quality Automated and Manual Annotation of Proteins—available at
http://hamap. expasy. org/) is a system for the automatic classification and annotation of …

An open invitation to the understudied proteins initiative

G Kustatscher, T Collins, AC Gingras, T Guo… - Nature …, 2022 - nature.com
To the Editor—Much of life science research revolves around understanding the biological
function of proteins. Some proteins, such as the tumor suppressor p53, have been studied …