Targeted expression profiling by RNA-Seq improves detection of cellular dynamics during pregnancy and identifies a role for T cells in term parturition

Comparative analysis of gene expression in maternal peripheral blood and monocytes during spontaneous preterm labor

(2018) Alison G. Paquette et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

Chronic inflammatory lesions of the placenta are associated with an up-regulation of amniotic fluid CXCR3: A marker of allograft rejection

(2018) Eli Maymon et al.   JOURNAL OF PERINATAL MEDICINE

Molecular signatures of circulating melanoma cells for monitoring early response to immune checkpoint therapy

(2018) Xin Hong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Noninvasive blood tests for fetal development predict gestational age and preterm delivery

(2018) Thuy T. M. Ngo et al.   SCIENCE

Alloreactive fetal T cells promote uterine contractility in preterm labor via IFN-γ and TNF-α

(2018) Michela Frascoli et al.   Science Translational Medicine

Decidual T Cells Exhibit a Highly Differentiated Phenotype and Demonstrate Potential Fetal Specificity and a Strong Transcriptional Response to IFN

(2017) Richard M. Powell et al.   JOURNAL OF IMMUNOLOGY

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

(2017) Jason C. H. Tsang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Changes in T Cell and Dendritic Cell Phenotype from Mid to Late Pregnancy Are Indicative of a Shift from Immune Tolerance to Immune Activation

(2017) Nishel Mohan Shah et al.   Frontiers in Immunology

Circulating mRNAs and miRNAs as candidate markers for the diagnosis and prognosis of prostate cancer

(2017) Marilesia Ferreira de Souza et al.   PLoS One

Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data

(2017) Celine Everaert et al.   Scientific Reports

In vivo T-cell activation by a monoclonal αCD3ε antibody induces preterm labor and birth

(2016) Nardhy Gomez-Lopez et al.   AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY

Invariant NKT Cell Activation Induces Late Preterm Birth That Is Attenuated by Rosiglitazone

(2016) Derek St. Louis et al.   JOURNAL OF IMMUNOLOGY

Maternal Whole Blood Gene Expression at 18 and 28 Weeks of Gestation Associated with Spontaneous Preterm Birth in Asymptomatic Women

(2016) Yujing J. Heng et al.   PLoS One

The Role of Vitamin D in the Transcriptional Program of Human Pregnancy

(2016) Amal Al-Garawi et al.   PLoS One

In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development

(2016) Ivan V. Ozerov et al.   Nature Communications

Chronic inflammation of the placenta: definition, classification, pathogenesis, and clinical significance

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

An imbalance between innate and adaptive immune cells at the maternal–fetal interface occurs prior to endotoxin-induced preterm birth

(2015) Marcia Arenas-Hernandez et al.   Cellular & Molecular Immunology

Interleukin-6 controls uterine Th9 cells and CD8+ T regulatory cells to accelerate parturition in mice

(2015) Nardhy Gomez-Lopez et al.   IMMUNOLOGY AND CELL BIOLOGY

How data analysis affects power, reproducibility and biological insight of RNA-seq studies in complex datasets

(2015) Lucia Peixoto et al.   NUCLEIC ACIDS RESEARCH

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Increased expression of perforin, granzyme B, and C5b-9 in villitis of unknown etiology

(2015) Y. Ito et al.   PLACENTA

Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge

(2014) Adel Dayarian et al.   BIOINFORMATICS

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

(2014)   NATURE BIOTECHNOLOGY

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Single-cell RNA-seq: advances and future challenges

(2014) Antoine-Emmanuel Saliba et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome

(2014) Lillian M. Zwemer et al.   PRENATAL DIAGNOSIS

Comparison of three different kits for extraction of high-quality RNA from frozen blood

(2014) Jin-Hee Kim et al.   SpringerPlus

Evidence for a Role for the Adaptive Immune Response in Human Term Parturition

(2013) Nardhy Gomez-Lopez et al.   AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY

Strengths and limitations of microarray-based phenotype prediction: lessons learned from the IMPROVER Diagnostic Signature Challenge

(2013) Adi L. Tarca et al.   BIOINFORMATICS

Transcriptome interrogation of human myometrium identifies differentially expressed sense-antisense pairs of protein-coding and long non-coding RNA genes in spontaneous labor at term

(2013) Roberto Romero et al.   Journal of Maternal-Fetal & Neonatal Medicine

Differences and similarities in the transcriptional profile of peripheral whole blood in early and late-onset preeclampsia: insights into the molecular basis of the phenotype of preeclampsiaa

(2013) Tinnakorn Chaiworapongsa et al.   JOURNAL OF PERINATAL MEDICINE

Count-based differential expression analysis of RNA sequencing data using R and Bioconductor

(2013) Simon Anders et al.   Nature Protocols

The immunological basis of villitis of unknown etiology – Review

(2013) J.A. Tamblyn et al.   PLACENTA

Chronic chorioamnionitis is the most common placental lesion in late preterm birth

(2013) J. Lee et al.   PLACENTA

A Comparison of Gene Set Analysis Methods in Terms of Sensitivity, Prioritization and Specificity

(2013) Adi L. Tarca et al.   PLoS One

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

Normal and Premature Rupture of Fetal Membranes at Term Delivery Differ in Regional Chemotactic Activity and Related Chemokine/Cytokine Production

(2012) Nardhy Gomez-Lopez et al.   Reproductive Sciences

Specific inflammatory microenvironments in the zones of the fetal membranes at term delivery

(2011) Nardhy Gomez-Lopez et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

Peripheral CD300a+CD8+ T Lymphocytes with a Distinct Cytotoxic Molecular Signature Increase in Pregnant Women with Chronic Chorioamnionitis

(2011) Yi Xu et al.   AMERICAN JOURNAL OF REPRODUCTIVE IMMUNOLOGY

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

A Signature of Maternal Anti-Fetal Rejection in Spontaneous Preterm Birth: Chronic Chorioamnionitis, Anti-Human Leukocyte Antigen Antibodies, and C4d

(2011) JoonHo Lee et al.   PLoS One

The “Great Obstetrical Syndromes” are associated with disorders of deep placentation

(2010) Ivo Brosens et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

A framework for oligonucleotide microarray preprocessing

(2010) Benilton S. Carvalho et al.   BIOINFORMATICS

Human Decidual Tissue Contains Differentiated CD8+ Effector-Memory T Cells with Unique Properties

(2010) T. Tilburgs et al.   JOURNAL OF IMMUNOLOGY

The frequency, clinical significance and pathological features of chronic chorioamnionitis: a lesion associated with spontaneous preterm birth

(2010) Chong Jai Kim et al.   MODERN PATHOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Resistance to Lipopolysaccharide-Induced Preterm Delivery Mediated by Regulatory T Cell Function in Mice1

(2009) Peyman Bizargity et al.   BIOLOGY OF REPRODUCTION

Detection call algorithms for high-throughput gene expression microarray data

(2009) K. J. Archer et al.   BRIEFINGS IN BIOINFORMATICS

Decidual CD8+CD28− T cells express CD103 but not perforin

(2009) Tamara Tilburgs et al.   HUMAN IMMUNOLOGY

Villitis of Unknown Etiology Is Associated with a Distinct Pattern of Chemokine Up-Regulation in the Feto-Maternal and Placental Compartments: Implications for Conjoint Maternal Allograft Rejection and Maternal Anti-Fetal Graft-versus-Host Disease

(2009) M. J. Kim et al.   JOURNAL OF IMMUNOLOGY

Expression of NK cell receptors on decidual T cells in human pregnancy

(2009) Tamara Tilburgs et al.   JOURNAL OF REPRODUCTIVE IMMUNOLOGY

Leukocytes are primed in peripheral blood for activation during term and preterm labour

(2009) M. Yuan et al.   MOLECULAR HUMAN REPRODUCTION

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

(2009) Chunlei Wu et al.   GENOME BIOLOGY

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Involvement of Hofbauer cells and maternal T cells in villitis of unknown aetiology

(2008) J-S Kim et al.   HISTOPATHOLOGY

Expression patterns of microRNAs in the chorioamniotic membranes: a role for microRNAs in human pregnancy and parturition

(2008) D Montenegro et al.   JOURNAL OF PATHOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS