Formalin-Fixed Paraffin-Embedded (FFPE) samples are not a beneficial replacement for frozen tissues in fetal membrane microbiota research

A new pipeline for clinico-pathological and molecular placental research utilizing FFPE tissues

(2021) Jiaqi J. O'Reilly et al.   PLACENTA

Evaluation of the Use of Formalin-Fixed and Paraffin-Embedded Archive Gastric Tissues for Microbiota Characterization Using Next-Generation Sequencing

(2020) Ines Pinto-Ribeiro et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Fetal membrane bacterial load is increased in histologically confirmed inflammatory chorioamnionitis: A retrospective cohort study

(2020) Rochelle Hockney et al.   PLACENTA

The human tumor microbiome is composed of tumor type–specific intracellular bacteria

(2020) Deborah Nejman et al.   SCIENCE

Laboratory contamination over time during low‐biomass sample analysis

(2019) Laura S. Weyrich et al.   Molecular Ecology Resources

Human placenta has no microbiome but can contain potential pathogens

(2019) Marcus C. de Goffau et al.   NATURE

FEAST: fast expectation-maximization for microbial source tracking

(2019) Liat Shenhav et al.   NATURE METHODS

Controlling for Contaminants in Low-Biomass 16S rRNA Gene Sequencing Experiments

(2019) Lisa Karstens et al.   mSystems

A standardized method for collection of human placenta samples in the age of functional magnetic resonance imaging

(2019) Victoria HJ Roberts et al.   BIOTECHNIQUES

Deep microbial analysis of multiple placentas shows no evidence for a placental microbiome

(2019) AA Kuperman et al.   BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY

Re‐assessing microbiomes in the low‐biomass reproductive niche

(2019) JL O’Callaghan et al.   BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

Phylogenomics using formalin-fixed and 100+ year-old intractable natural history specimens

(2017) Sara Ruane et al.   Molecular Ecology Resources

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

(2017) Achal Dhariwal et al.   NUCLEIC ACIDS RESEARCH

Bacterial communities found in placental tissues are associated with severe chorioamnionitis and adverse birth outcomes

(2017) Ronan M. Doyle et al.   PLoS One

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Acute chorioamnionitis and funisitis: definition, pathologic features, and clinical significance

(2015) Chong Jai Kim et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

Comparison of eight commercially available kits for DNA extraction from formalin-fixed paraffin-embedded tissues

(2015) Anna Janecka et al.   ANALYTICAL BIOCHEMISTRY

Placental Infection WithUreaplasmaspecies Is Associated With Histologic Chorioamnionitis and Adverse Outcomes in Moderately Preterm and Late-Preterm Infants

(2015) Emma L. Sweeney et al.   JOURNAL OF INFECTIOUS DISEASES

Robustness of Next Generation Sequencing on Older Formalin-Fixed Paraffin-Embedded Tissue

(2015) Danielle Mercatante Carrick et al.   PLoS One

Inflammatory Signalling in Fetal Membranes: Increased Expression Levels of TLR 1 in the Presence of Preterm Histological Chorioamnionitis

(2015) Gareth J. Waring et al.   PLoS One

Comparison of Methods for the Extraction of DNA from Formalin-Fixed, Paraffin-Embedded Archival Tissues

(2014) Burcu Sengüven et al.   International Journal of Medical Sciences

Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes

(2014) Martin Laurence et al.   PLoS One

The Placenta Harbors a Unique Microbiome

(2014) K. Aagaard et al.   Science Translational Medicine

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Comparison of Clinical Targeted Next-Generation Sequence Data from Formalin-Fixed and Fresh-Frozen Tissue Specimens

(2013) David H. Spencer et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples

(2013) Michele Simbolo et al.   PLoS One

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Improved PCR Performance Using Template DNA from Formalin-Fixed and Paraffin-Embedded Tissues by Overcoming PCR Inhibition

(2013) Dimo Dietrich et al.   PLoS One

Reducing bias in bacterial community analysis of lower respiratory infections

(2012) Geraint B Rogers et al.   ISME Journal

Will PAXgene substitute formalin? A morphological and molecular comparative study using a new fixative system

(2012) Benedetta Belloni et al.   JOURNAL OF CLINICAL PATHOLOGY

Gene Expression Profiles from Formalin Fixed Paraffin Embedded Breast Cancer Tissue Are Largely Comparable to Fresh Frozen Matched Tissue

(2011) Lorenza Mittempergher et al.   PLoS One

Maternal Microbe-Specific Modulation of Inflammatory Response in Extremely Low-Gestational-Age Newborns

(2011) R. N. Fichorova et al.   mBio

Colonization of second-trimester placenta parenchyma

(2008) Andrew B. Onderdonk et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY