Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta

Replicated association between the European GWAS locus rs10503253 at CSMD1 and schizophrenia in Asian population

(2017) Weiqing Liu et al.   NEUROSCIENCE LETTERS

Loss of CSMD1 expression disrupts mammary duct formation while enhancing proliferation, migration and invasion

(2017) Mohamed Kamal et al.   ONCOLOGY REPORTS

The pregnancy outcome prediction (POP) study: Investigating the relationship between serial prenatal ultrasonography, biomarkers, placental phenotype and adverse pregnancy outcomes

(2017) Francesca Gaccioli et al.   PLACENTA

Sexual epigenetic dimorphism in the human placenta: implications for susceptibility during the prenatal period

(2017) Elizabeth Martin et al.   Epigenomics

Allele-Specific Methylome and Transcriptome Analysis Reveals Widespread Imprinting in the Human Placenta

(2016) Hirotaka Hamada et al.   AMERICAN JOURNAL OF HUMAN GENETICS

An integrative transcriptomic atlas of organogenesis in human embryos

(2016) Dave T Gerrard et al.   eLife

Sexual Dimorphism in Adverse Pregnancy Outcomes - A Retrospective Australian Population Study 1981-2011

(2016) Petra E. Verburg et al.   PLoS One

Sex differences in DNA methylation assessed by 450 K BeadChip in newborns

(2015) Paul Yousefi et al.   BMC GENOMICS

Screening for fetal growth restriction with universal third trimester ultrasonography in nulliparous women in the Pregnancy Outcome Prediction (POP) study: a prospective cohort study

(2015) Ulla Sovio et al.   LANCET

The complement system and adverse pregnancy outcomes

(2015) Jean F. Regal et al.   MOLECULAR IMMUNOLOGY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The European Genome-phenome Archive of human data consented for biomedical research

(2015) Ilkka Lappalainen et al.   NATURE GENETICS

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

(2014) S. Anders et al.   BIOINFORMATICS

Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation

(2014) Allison M. Cotton et al.   HUMAN MOLECULAR GENETICS

Comprehensive analysis of DNA methylation data with RnBeads

(2014) Yassen Assenov et al.   NATURE METHODS

Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine

(2013) Michael J Booth et al.   Nature Protocols

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

The human placenta methylome

(2013) D. I. Schroeder et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

(2012) M. J. Booth et al.   SCIENCE

‘Leveling’ the playing field for analyses of single-base resolution DNA methylomes

(2012) Matthew D. Schultz et al.   TRENDS IN GENETICS

ggbio: an R package for extending the grammar of graphics for genomic data

(2012) Tengfei Yin et al.   GENOME BIOLOGY

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

DNA methylation profiles of human active and inactive X chromosomes

(2011) A. J. Sharp et al.   GENOME RESEARCH

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

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

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA

(2010) Colm Nestor et al.   BIOTECHNIQUES

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Inactive X chromosome-specific reduction in placental DNA methylation

(2009) Allison M. Cotton et al.   HUMAN MOLECULAR GENETICS

Study protocol. A prospective cohort study of unselected primiparous women: the pregnancy outcome prediction study

(2008) Dharmintra Pasupathy et al.   BMC Pregnancy and Childbirth