Integrated proteomics and metabolomics suggests symbiotic metabolism and multimodal regulation in a fungal-endobacterial system

Mycoavidus cysteinexigens gen. nov., sp. nov., an endohyphal bacterium isolated from a soil isolate of the fungus Mortierella elongata

(2016) Shoko Ohshima et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

An interdomain network: the endobacterium of a mycorrhizal fungus promotes antioxidative responses in both fungal and plant hosts

(2016) Candida Vannini et al.   NEW PHYTOLOGIST

Symbiosis with an endobacterium increases the fitness of a mycorrhizal fungus, raising its bioenergetic potential

(2015) Alessandra Salvioli et al.   ISME Journal

Mosaic genome of endobacteria in arbuscular mycorrhizal fungi: Transkingdom gene transfer in an ancient mycoplasma-fungus association

(2015) Gloria Torres-Cortés et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Minimal genomes of mycoplasma-related endobacteria are plastic and contain host-derived genes for sustained life within Glomeromycota

(2015) Mizue Naito et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MIDAS: A Database-Searching Algorithm for Metabolite Identification in Metabolomics

(2014) Yingfeng Wang et al.   ANALYTICAL CHEMISTRY

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam

(2014) Juanjuan Chai et al.   BMC EVOLUTIONARY BIOLOGY

Nutrients drive transcriptional changes that maintain metabolic homeostasis but alter genome architecture in Microcystis

(2014) Morgan M Steffen et al.   ISME Journal

Sipros/ProRata: a versatile informatics system for quantitative community proteomics

(2013) Yingfeng Wang et al.   BIOINFORMATICS

P3DB 3.0: From plant phosphorylation sites to protein networks

(2013) Qiuming Yao et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

A Multifactor Analysis of Fungal and Bacterial Community Structure in the Root Microbiome of Mature Populus deltoides Trees

(2013) Migun Shakya et al.   PLoS One

Exhaustive database searching for amino acid mutations in proteomes

(2012) Doug Hyatt et al.   BIOINFORMATICS

A cross-platform toolkit for mass spectrometry and proteomics

(2012) Matthew C Chambers et al.   NATURE BIOTECHNOLOGY

P3DB: An Integrated Database for Plant Protein Phosphorylation

(2012) Qiuming Yao et al.   Frontiers in Plant Science

Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types

(2011) Neil R. Gottel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Effector Analogues Detect Varied Allosteric Roles for Conserved Protein−Effector Interactions in Pyruvate Kinase Isozymes

(2011) Aileen Y. Alontaga et al.   BIOCHEMISTRY

The genome of the obligate endobacterium of an AM fungus reveals an interphylum network of nutritional interactions

(2011) Stefano Ghignone et al.   ISME Journal

Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos

(2011) Zhou Li et al.   JOURNAL OF PROTEOME RESEARCH

Quantitative Tracking of Isotope Flows in Proteomes of Microbial Communities

(2011) Chongle Pan et al.   MOLECULAR & CELLULAR PROTEOMICS

Metabolomic Analysis and Visualization Engine for LC−MS Data

(2010) Eugene Melamud et al.   ANALYTICAL CHEMISTRY

Metabolomic Analysis via Reversed-Phase Ion-Pairing Liquid Chromatography Coupled to a Stand Alone Orbitrap Mass Spectrometer

(2010) Wenyun Lu et al.   ANALYTICAL CHEMISTRY

Complete Genome Sequence of Burkholderia rhizoxinica, an Endosymbiont of Rhizopus microsporus

(2010) G. Lackner et al.   JOURNAL OF BACTERIOLOGY

Dealing with the unknown: Metabolomics and Metabolite Atlases

(2010) Benjamin P. Bowen et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Chitin Deacetylases: Properties and Applications

(2010) Yong Zhao et al.   Marine Drugs

mzML—a Community Standard for Mass Spectrometry Data

(2010) Lennart Martens et al.   MOLECULAR & CELLULAR PROTEOMICS

Plants, Mycorrhizal Fungi, and Bacteria: A Network of Interactions

(2009) Paola Bonfante et al.   Annual Review of Microbiology

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Detection and identification of bacteria intimately associated with fungi of the orderSebacinales

(2008) Monica Sharma et al.   CELLULAR MICROBIOLOGY

NITROGEN LIMITATION OF NET PRIMARY PRODUCTIVITY IN TERRESTRIAL ECOSYSTEMS IS GLOBALLY DISTRIBUTED

(2008) David S. LeBauer et al.   ECOLOGY

Analytical strategies for LC–MS-based targeted metabolomics

(2008) Wenyun Lu et al.   JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES