Interaction Networks Are Driven by Community-Responsive Phenotypes in a Chitin-Degrading Consortium of Soil Microbes

Characterisation of cellulose-degrading organisms in an anaerobic digester

(2022) Jan Struckmann Poulsen et al.   BIORESOURCE TECHNOLOGY

Climate warming enhances microbial network complexity and stability

(2021) Mengting Maggie Yuan et al.   Nature Climate Change

Reproducibility of mass spectrometry based metabolomics data

(2021) Tusharkanti Ghosh et al.   BMC BIOINFORMATICS

Network structure of resource use and niche overlap within the endophytic microbiome

(2021) Matthew Michalska-Smith et al.   ISME Journal

Obligate cross-feeding expands the metabolic niche of bacteria

(2021) Leonardo Oña et al.   Nature Ecology & Evolution

Fate, cytotoxicity and cellular metabolomic impact of ingested nanoscale carbon dots using simulated digestion and a triculture small intestinal epithelial model

(2021) Xiaoqiong Cao et al.   NanoImpact

Emergent properties of microbial communities drive accelerated biogeochemical cycling in disturbed temperate forests

(2021) Ernest D. Osburn et al.   ECOLOGY

Research Advances of Beneficial Microbiota Associated with Crop Plants

(2020) Lei Tian et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Feeding on fungi: Genomic and proteomic analysis of the enzymatic machinery of bacteria decomposing fungal biomass

(2020) Robert Starke et al.   ENVIRONMENTAL MICROBIOLOGY

DRAM for distilling microbial metabolism to automate the curation of microbiome function

(2020) Michael Shaffer et al.   NUCLEIC ACIDS RESEARCH

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations

(2020) Ryan S. McClure et al.   Scientific Reports

Trophic Interactions and the Drivers of Microbial Community Assembly

(2020) Matti Gralka et al.   CURRENT BIOLOGY

Relationships between nitrogen cycling microbial community abundance and composition reveal the indirect effect of soil pH on oak decline

(2020) K. Scarlett et al.   ISME Journal

Development and Analysis of a Stable, Reduced Complexity Model Soil Microbiome

(2020) Ryan McClure et al.   Frontiers in Microbiology

Artificial consortium demonstrates emergent properties of enhanced cellulosic-sugar degradation and biofuel synthesis

(2020) Heejoon Park et al.   npj Biofilms and Microbiomes

Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems

(2019) Alan R. Pacheco et al.   Nature Communications

Microbial Degradation of Cellulosic Material and Gas Generation: Implications for the Management of Low- and Intermediate-Level Radioactive Waste

(2019) Danielle Beaton et al.   Frontiers in Microbiology

Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales

(2019) Regina L. Wilpiszeski et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Regulatory mechanisms underlying coordination of amino acid and glucose catabolism in Escherichia coli

(2019) Mattia Zampieri et al.   Nature Communications

Metaphenomic Responses of a Native Prairie Soil Microbiome to Moisture Perturbations

(2019) Taniya Roy Chowdhury et al.   mSystems

Metagenomic and chemical characterization of soil cobalamin production

(2019) Xinda Lu et al.   ISME Journal

KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold

(2019) Takuya Aramaki et al.   BIOINFORMATICS

A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome

(2019) Siwen Deng et al.   Scientific Reports

Chitin degradation and the temporary response of bacterial chitinolytic communities to chitin amendment in soil under different fertilization regimes

(2019) Cai Hui et al.   SCIENCE OF THE TOTAL ENVIRONMENT

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

The composition, localization and function of low-temperature-adapted microbial communities involved in methanogenic degradations of cellulose and chitin from Qinghai-Tibetan Plateau wetland soils

(2016) Y. Dai et al.   JOURNAL OF APPLIED MICROBIOLOGY

Microbial Community Metabolic Modeling: A Community Data-Driven Network Reconstruction

(2016) Christopher S. Henry et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Deciphering the Principles of Bacterial Nitrogen Dietary Preferences: a Strategy for Nutrient Containment

(2016) Jilong Wang et al.   mBio

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

(2016) Ernesto S. Nakayasu et al.   mSystems

Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems

(2016) Rubén López-Mondéjar et al.   Scientific Reports

Anthropogenic warming has increased drought risk in California

(2015) Noah S. Diffenbaugh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

(2014) Jennifer D Rocca et al.   ISME Journal

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Bacterial chitin degradation—mechanisms and ecophysiological strategies

(2013) Sara Beier et al.   Frontiers in Microbiology

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genome analyses highlight the different biological roles of cellulases

(2012) Felix Mba Medie et al.   NATURE REVIEWS MICROBIOLOGY

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

FiehnLib: Mass Spectral and Retention Index Libraries for Metabolomics Based on Quadrupole and Time-of-Flight Gas Chromatography/Mass Spectrometry

(2009) Tobias Kind et al.   ANALYTICAL CHEMISTRY

Higher trends but larger uncertainty and geographic variability in 21st century temperature and heat waves

(2009) A. R. Ganguly et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA