Statistical analysis of co-occurrence patterns in microbial presence-absence datasets

Stochastic neutral modelling of the Gut Microbiota’s relative species abundance from next generation sequencing data

(2016) Claudia Sala et al.   BMC BIOINFORMATICS

A method for automated pathogenic content estimation with application to rheumatoid arthritis

(2016) Xiaoyuan Zhou et al.   BMC Systems Biology

The geography of forest diversity and community changes under future climate conditions in the eastern United States

(2016) Adam Bauer et al.   ECOSCIENCE

Plastic ingestion by Newell’s (Puffinus newelli) and wedge-tailed shearwaters (Ardenna pacifica) in Hawaii

(2016) Elizabeth C. Kain et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

bioOTU: An Improved Method for Simultaneous Taxonomic Assignments and Operational Taxonomic Units Clustering of 16s rRNA Gene Sequences

(2016) Shi-Yi Chen et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

cooccur: Probabilistic Species Co-Occurrence Analysis inR

(2016) Daniel M. Griffith et al.   Journal of Statistical Software

Selectivity of flesh-footed shearwaters for plastic colour: Evidence for differential provisioning in adults and fledglings

(2016) Jennifer L. Lavers et al.   MARINE ENVIRONMENTAL RESEARCH

Do indirect bite count surveys accurately represent diet selection of white-tailed deer in a forested environment?

(2016) Marcus A. Lashley et al.   WILDLIFE RESEARCH

Strain Dependent Genetic Networks for Antibiotic-Sensitivity in a Bacterial Pathogen with a Large Pan-Genome

(2016) Tim van Opijnen et al.   PLoS Pathogens

Unexpectedly High Beta-Diversity of Root-Associated Fungal Communities in the Bolivian Andes

(2016) Christopher J. Barnes et al.   Frontiers in Microbiology

Distributional congruence of mammalian herbivores in the Trans-Himalayan Mountains

(2016) Tsewang Namgail et al.   Current Zoology

Diversity and characterization of airborne bacteria at two health institutions

(2015) María Guadalupe Frías-De León et al.   AEROBIOLOGIA

Projecting future expansion of invasive species: comparing and improving methodologies for species distribution modeling

(2015) Kumar P. Mainali et al.   GLOBAL CHANGE BIOLOGY

fuzzySim: applying fuzzy logic to binary similarity indices in ecology

(2015) A. Márcia Barbosa   Methods in Ecology and Evolution

Tree Species Composition, Breeding Systems, and Pollination and Dispersal Syndromes in Three Forest Successional Stages in a Tropical Dry Forest in Mesoamerica

(2015) Branko Hilje et al.   Tropical Conservation Science

Biogeography of epiphytic Angiosperms in the Brazilian Atlantic forest, a world biodiversity hotspot

(2015) Luiz Menini Neto et al.   Brazilian Journal of Botany

The shared microbiota of humans and companion animals as evaluated from Staphylococcus carriage sites

(2015) Ana M Misic et al.   Microbiome

Habitat Preferences and Spatial Overlap Between Three Species of Bunting (Emberiza hortulana, emberiza cirlus, miliaria calandra) in Farmlands of Central Italy

(2015) Federico Morelli et al.   POLISH JOURNAL OF ECOLOGY

Biotic interactions and temporal dynamics of the human gastrointestinal microbiota

(2014) Pål Trosvik et al.   ISME Journal

Biogeography of western Mediterranean butterflies: combining turnover and nestedness components of faunal dissimilarity

(2014) Leonardo Dapporto et al.   JOURNAL OF BIOGEOGRAPHY

Biogeography and individuality shape function in the human skin metagenome

(2014) Julia Oh et al.   NATURE

rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development

(2014) Steven F. Stoddard et al.   NUCLEIC ACIDS RESEARCH

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

Hydroid assemblages from the Bellingshausen Sea (Antarctica): environmental factors behind their spatial distribution

(2014) Álvaro L. Peña Cantero et al.   POLAR BIOLOGY

Fluvial network organization imprints on microbial co-occurrence networks

(2014) S. Widder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Longitudinal analysis of microbial interaction between humans and the indoor environment

(2014) S. Lax et al.   SCIENCE

Deciphering microbial interactions and detecting keystone species with co-occurrence networks

(2014) David Berry et al.   Frontiers in Microbiology

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Mapping Hotspots of Threatened Species Traded in Bushmeat Markets in the Cross-Sanaga Rivers Region

(2013) JOHN E. FA et al.   CONSERVATION BIOLOGY

Amphibian diversity on the roof of Africa: unveiling the effects of habitat degradation, altitude and biogeography

(2013) Giulia Zancolli et al.   DIVERSITY AND DISTRIBUTIONS

The dynamics of gut-associated microbial communities during inflammation

(2013) Sebastian E Winter et al.   EMBO REPORTS

Dispersal in microbes: fungi in indoor air are dominated by outdoor air and show dispersal limitation at short distances

(2013) Rachel I Adams et al.   ISME Journal

Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota

(2013) Zhigang Zhang et al.   ISME Journal

Ecological services performed by the bonobo (Pan paniscus): seed dispersal effectiveness in tropical forest

(2013) David Beaune et al.   JOURNAL OF TROPICAL ECOLOGY

Herbicide Treatment and Timing for Controlling Kentucky Bluegrass (Poa pratensis) and Tall Fescue (Festuca arundinacea) in Cool Season Grasslands of Central Kentucky, USA

(2013) Joshua K. Adkins et al.   NATURAL AREAS JOURNAL

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses

(2013) Tomáš Větrovský et al.   PLoS One

Habitat characterization and modeling of the potential distribution of the Military Macaw (Ara militaris) in Mexico

(2013) Francisco A. Rivera-Ortíz et al.   Revista Mexicana de Biodiversidad

Significant changes in the skin microbiome mediated by the sport of roller derby

(2013) James F. Meadow et al.   PeerJ

Co-occurrence of anaerobic bacteria in colorectal carcinomas

(2013) René L Warren et al.   Microbiome

Ecological and zoogeographical significance of terrestrial isopods from the Carei Plain natural reserve (Romania)

(2012) Sára Ferenţi et al.   Archives of Biological Sciences

A probabilistic model for analysing species co-occurrence

(2012) Joseph A. Veech   GLOBAL ECOLOGY AND BIOGEOGRAPHY

New insights into the biogeography of south-western Europe: spatial patterns from vascular plants using cluster analysis and parsimony

(2012) Juan Carlos Moreno Saiz et al.   JOURNAL OF BIOGEOGRAPHY

Delimiting the geographical background in species distribution modelling

(2012) Pelayo Acevedo et al.   JOURNAL OF BIOGEOGRAPHY

Atlas versus range maps: robustness of chorological relationships to distribution data types in European mammals

(2012) A. Márcia Barbosa et al.   JOURNAL OF BIOGEOGRAPHY

Lepidopteran species richness of alpine sites in the High Sudetes Mts.: effect of area and isolation

(2012) Karolina Bila et al.   JOURNAL OF INSECT CONSERVATION

Species presence/absence sometimes represents a plant community as well as species abundances do, or better

(2012) J. Bastow Wilson   JOURNAL OF VEGETATION SCIENCE

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

(2012) Charles K. Lee et al.   PLoS One

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Incorporating 16S Gene Copy Number Information Improves Estimates of Microbial Diversity and Abundance

(2012) Steven W. Kembel et al.   PLoS Computational Biology

BIODIVERSITY RESEARCH: Nestedness for different reasons: the distributions of birds, lizards and small mammals on islands of an inundated lake

(2010) Yanping Wang et al.   DIVERSITY AND DISTRIBUTIONS

Biogeographic regions of the Iberian Peninsula: butterflies as biogeographical indicators

(2010) H. Romo et al.   JOURNAL OF ZOOLOGY

Detecting plant spatial patterns, using multidimensional scaling and cluster analysis, in rural landscapes in Central Iberian Peninsula

(2010) Juan-Javier García-Abad et al.   LANDSCAPE AND URBAN PLANNING

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Assessment of spatial and habitat use overlap between Himalayan tahr and livestock in Kedarnath Wildlife Sanctuary, India

(2009) Swati Kittur et al.   EUROPEAN JOURNAL OF WILDLIFE RESEARCH

Isolation of faecal coliform bacteria from the American alligator (Alligator mississippiensis)

(2009) M.A. Johnston et al.   JOURNAL OF APPLIED MICROBIOLOGY

Geohistorical and current environmental influences on floristic differentiation in the Ryukyu Archipelago, Japan

(2009) Koh Nakamura et al.   JOURNAL OF BIOGEOGRAPHY

DIFFERENCES IN GYPSUM PLANT COMMUNITIES ASSOCIATED WITH HABITAT FRAGMENTATION AND LIVESTOCK GRAZING

(2008) Y. Pueyo et al.   ECOLOGICAL APPLICATIONS

A diversity profile of the human skin microbiota

(2008) E. A. Grice et al.   GENOME RESEARCH

Fish assemblages of the Casiquiare River, a corridor and zoogeographical filter for dispersal between the Orinoco and Amazon basins

(2008) Kirk O. Winemiller et al.   JOURNAL OF BIOGEOGRAPHY

Testate Amoebae (Arcellinida and Euglyphida) vs. Ericoid Mycorrhizal and DSE Fungi: A Possible Novel Interaction in the Mycorrhizosphere of Ericaceous Plants?

(2008) M. Vohník et al.   MICROBIAL ECOLOGY

Germination of Invasive Plant Seeds after Digestion by Horses in California

(2008) Lauren D. Quinn et al.   NATURAL AREAS JOURNAL