High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA

Whole genome bisulfite sequencing of cell-free DNA and its cellular contributors uncovers placenta hypomethylated domains

(2015) Taylor J Jensen et al.   GENOME BIOLOGY

Investigating and Correcting Plasma DNA Sequencing Coverage Bias to Enhance Aneuploidy Discovery

(2014) Dineika Chandrananda et al.   PLoS One

Methy-Pipe: An Integrated Bioinformatics Pipeline for Whole Genome Bisulfite Sequencing Data Analysis

(2014) Peiyong Jiang et al.   PLoS One

Plasma DNA aberrations in systemic lupus erythematosus revealed by genomic and methylomic sequencing

(2014) Rebecca W. Y. Chan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circulating Cell-Free DNA Enables Noninvasive Diagnosis of Heart Transplant Rejection

(2014) I. De Vlaminck et al.   Science Translational Medicine

Non-random DNA fragmentation in next-generation sequencing

(2014) Maria S. Poptsova et al.   Scientific Reports

High-Resolution Profiling of Fetal DNA Clearance from Maternal Plasma by Massively Parallel Sequencing

(2013) S. C. Y. Yu et al.   CLINICAL CHEMISTRY

Circulating Fetal Cell-Free DNA Fractions Differ in Autosomal Aneuploidies and Monosomy X

(2013) R. P. Rava et al.   CLINICAL CHEMISTRY

Noninvasive Prenatal Methylomic Analysis by Genomewide Bisulfite Sequencing of Maternal Plasma DNA

(2013) F. M. F. Lun et al.   CLINICAL CHEMISTRY

The concentration of cell-free DNA in focal epilepsy

(2013) Suvi P. Liimatainen et al.   EPILEPSY RESEARCH

Cell-free nucleic acids as biomarkers in dialyzed patients

(2013) Marie Korabecna et al.   JOURNAL OF NEPHROLOGY

Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer

(2013) Sarah-Jane Dawson et al.   NEW ENGLAND JOURNAL OF MEDICINE

High-Throughput Massively Parallel Sequencing for Fetal Aneuploidy Detection from Maternal Plasma

(2013) Taylor J. Jensen et al.   PLoS One

Gestational age and maternal weight effects on fetal cell-free DNA in maternal plasma

(2013) Eric Wang et al.   PRENATAL DIAGNOSIS

Pleural fluid cell-free DNA integrity index to identify cytologically negative malignant pleural effusions including mesotheliomas

(2012) Krishna B Sriram et al.   BMC CANCER

Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing

(2012) K. C. A. Chan et al.   CLINICAL CHEMISTRY

A comparative study of cell-free apoptotic and genomic DNA using FISH and massive parallel sequencing

(2012) Evgeniy S Morozkin et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

Fetal Fraction in Maternal Plasma Cell-Free DNA at 11–13 Weeks’ Gestation: Effect of Maternal and Fetal Factors

(2012) Ghalia Ashoor et al.   FETAL DIAGNOSIS AND THERAPY

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia

(2012) Marta Kulis et al.   NATURE GENETICS

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

High Resolution Size Analysis of Fetal DNA in the Urine of Pregnant Women by Paired-End Massively Parallel Sequencing

(2012) Nancy B. Y. Tsui et al.   PLoS One

Clinical application of massively parallel sequencing-based prenatal noninvasive fetal trisomy test for trisomies 21 and 18 in 11 105 pregnancies with mixed risk factors

(2012) Shan Dan et al.   PRENATAL DIAGNOSIS

Noninvasive Whole-Genome Sequencing of a Human Fetus

(2012) J. O. Kitzman et al.   Science Translational Medicine

Fetal fraction in maternal plasma cell-free DNA at 11-13 weeks' gestation: relation to maternal and fetal characteristics

(2012) G. Ashoor et al.   ULTRASOUND IN OBSTETRICS & GYNECOLOGY

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

Origin, translocation and destination of extracellular occurring DNA — A new paradigm in genetic behaviour

(2011) Dimetrie L. Peters et al.   CLINICA CHIMICA ACTA

Nonhematopoietically Derived DNA Is Shorter than Hematopoietically Derived DNA in Plasma: A Transplantation Model

(2011) Y. W. L. Zheng et al.   CLINICAL CHEMISTRY

Gestation-dependent changes in human placental global DNA methylation levels

(2011) Preeti Chavan-Gautam et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Reducing the exome search space for Mendelian diseases using genetic linkage analysis of exome genotypes

(2011) Katherine R Smith et al.   GENOME BIOLOGY

Analysis of the Size Distributions of Fetal and Maternal Cell-Free DNA by Paired-End Sequencing

(2010) H. C. Fan et al.   CLINICAL CHEMISTRY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Clinical Relevance of Circulating Nucleosomes in Cancer

(2009) Stefan Holdenrieder et al.   Annals of the New York Academy of Sciences

Metabolic DNA as the Origin of Spontaneously Released DNA?

(2009) Peter B. Gahan et al.   Annals of the New York Academy of Sciences

A Method for Characterization of Total Circulating DNA

(2009) Maniesh van der Vaart et al.   Annals of the New York Academy of Sciences

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Profile of the Circulating DNA in Apparently Healthy Individuals

(2009) J. Beck et al.   CLINICAL CHEMISTRY

High-Resolution Mapping of Sequence-Directed Nucleosome Positioning on Genomic DNA

(2009) Ross M. Fraser et al.   JOURNAL OF MOLECULAR BIOLOGY

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Microfluidics Digital PCR Reveals a Higher than Expected Fraction of Fetal DNA in Maternal Plasma

(2008) F. M. F. Lun et al.   CLINICAL CHEMISTRY