Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin

Liver- and Colon-Specific DNA Methylation Markers in Plasma for Investigation of Colorectal Cancers With or Without Liver Metastases

(2018) Wanxia Gai et al.   CLINICAL CHEMISTRY

CancerDetector: ultrasensitive and non-invasive cancer detection at the resolution of individual reads using cell-free DNA methylation sequencing data

(2018) Wenyuan Li et al.   NUCLEIC ACIDS RESEARCH

Size-tagged preferred ends in maternal plasma DNA shed light on the production mechanism and show utility in noninvasive prenatal testing

(2018) Kun Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and localization of surgically resectable cancers with a multi-analyte blood test

(2018) Joshua D. Cohen et al.   SCIENCE

Non-invasive detection of human cardiomyocyte death using methylation patterns of circulating DNA

(2018) Hai Zemmour et al.   Nature Communications

Early circulating tumor DNA dynamics and clonal selection with palbociclib and fulvestrant for breast cancer

(2018) Ben O’Leary et al.   Nature Communications

Preferred end coordinates and somatic variants as signatures of circulating tumor DNA associated with hepatocellular carcinoma

(2018) Peiyong Jiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Origin and clinical relevance of chromosomal aberrations other than the common trisomies detected by genome-wide NIPS: results of the TRIDENT study

(2017) Diane Van Opstal et al.   GENETICS IN MEDICINE

Patient monitoring through liquid biopsies using circulating tumor DNA

(2017) Peter Ulz et al.   INTERNATIONAL JOURNAL OF CANCER

Reversion of BRCA1/2 Germline Mutations Detected in Circulating Tumor DNA From Patients With High-Grade Serous Ovarian Cancer

(2017) Elizabeth L. Christie et al.   JOURNAL OF CLINICAL ONCOLOGY

Analysis of Plasma Epstein–Barr Virus DNA to Screen for Nasopharyngeal Cancer

(2017) K.C. Allen Chan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Direct detection of early-stage cancers using circulating tumor DNA

(2017) Jillian Phallen et al.   Science Translational Medicine

Genomic Landscape of Cell-Free DNA in Patients with Colorectal Cancer

(2017) John H. Strickler et al.   Cancer Discovery

Graft-derived cell-free DNA, a noninvasive early rejection and graft damage marker in liver transplantation: A prospective, observational, multicenter cohort study

(2017) Ekkehard Schütz et al.   PLOS MEDICINE

Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin

(2016) Matthew W. Snyder et al.   CELL

Early Detection of Lung Cancer Using DNA Promoter Hypermethylation in Plasma and Sputum

(2016) Alicia Hulbert et al.   CLINICAL CANCER RESEARCH

Inferring expressed genes by whole-genome sequencing of plasma DNA

(2016) Peter Ulz et al.   NATURE GENETICS

Identification of tissue-specific cell death using methylation patterns of circulating DNA

(2016) Roni Lehmann-Werman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends

(2016) K. C. Allen Chan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The International Human Epigenome Consortium Data Portal

(2016) David Bujold et al.   Cell Systems

Better prediction of functional effects for sequence variants

(2015) Maximilian Hecht et al.   BMC GENOMICS

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

(2015) Alicia N. Schep et al.   GENOME RESEARCH

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments

(2015) Kun Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients

(2015) Peiyong Jiang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Peiyong Jiang et al.   PLoS One

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

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

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

(2013) J. S. Pedersen et al.   GENOME RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Determinants of nucleosome positioning

(2013) Kevin Struhl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasma DNA bisulfite sequencing

(2013) K. C. A. Chan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Controls of Nucleosome Positioning in the Human Genome

(2012) Daniel J. Gaffney et al.   PLoS Genetics

Targeted enrichment of genomic DNA regions for next-generation sequencing

(2011) F. Mertes et al.   Briefings in Functional Genomics

Determinants of nucleosome organization in primary human cells

(2011) Anton Valouev et al.   NATURE

Maternal Plasma DNA Sequencing Reveals the Genome-Wide Genetic and Mutational Profile of the Fetus

(2010) Y. M. D. Lo et al.   Science Translational Medicine

Nucleosome positioning: How is it established, and why does it matter?

(2009) Marta Radman-Livaja et al.   DEVELOPMENTAL BIOLOGY

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY