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

[1]  Gavin Sherlock,et al.  Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions , 2015, bioRxiv.

[2]  G. von Heijne,et al.  Tissue-based map of the human proteome , 2015, Science.

[3]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

[4]  Anatoly Dritschilo,et al.  Multi‐marker analysis of circulating cell‐free DNA toward personalized medicine for colorectal cancer , 2014, Molecular oncology.

[5]  W. Koh,et al.  Noninvasive in vivo monitoring of tissue-specific global gene expression in humans , 2014, Proceedings of the National Academy of Sciences.

[6]  V. Corces,et al.  CTCF: an architectural protein bridging genome topology and function , 2014, Nature Reviews Genetics.

[7]  Peter A. Jones,et al.  Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome , 2014, Genome research.

[8]  L. Diaz,et al.  Liquid biopsies: genotyping circulating tumor DNA. , 2014, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[9]  Jeff Vierstra,et al.  Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH , 2013, Nature Methods.

[10]  Michael A. Freitas,et al.  H1 histones: current perspectives and challenges , 2013, Nucleic acids research.

[11]  M. Meyer,et al.  Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA , 2013, Nature Protocols.

[12]  D. García-Olmo,et al.  Quantitation of cell-free DNA and RNA in plasma during tumor progression in rats , 2013, Molecular Cancer.

[13]  G. Parmigiani,et al.  Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing , 2012, Science Translational Medicine.

[14]  Daniel J. Gaffney,et al.  Controls of Nucleosome Positioning in the Human Genome , 2012, PLoS genetics.

[15]  J. Mallm,et al.  Genome-wide nucleosome positioning during embryonic stem cell development , 2012, Nature Structural &Molecular Biology.

[16]  Shane J. Neph,et al.  Systematic Localization of Common Disease-Associated Variation in Regulatory DNA , 2012, Science.

[17]  R. Kimmig,et al.  Impact of platinum‐based chemotherapy on circulating nucleic acid levels, protease activities in blood and disseminated tumor cells in bone marrow of ovarian cancer patients , 2011, International journal of cancer.

[18]  Steven M. Johnson,et al.  Determinants of nucleosome organization in primary human cells , 2011, Nature.

[19]  S. Quake,et al.  Universal noninvasive detection of solid organ transplant rejection , 2011, Proceedings of the National Academy of Sciences.

[20]  William Stafford Noble,et al.  FIMO: scanning for occurrences of a given motif , 2011, Bioinform..

[21]  Yama W. L. Zheng,et al.  Maternal Plasma DNA Sequencing Reveals the Genome-Wide Genetic and Mutational Profile of the Fetus , 2010, Science Translational Medicine.

[22]  M. Pellegrini,et al.  Relationship between nucleosome positioning and DNA methylation , 2010, Nature.

[23]  Richard Durbin,et al.  Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..

[24]  Jan Komorowski,et al.  Nucleosomes are well positioned in exons and carry characteristic histone modifications. , 2009, Genome research.

[25]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[26]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[27]  J. Hainsworth,et al.  Introduction: unknown primary cancer. , 2009, Seminars in oncology.

[28]  C. Cantor,et al.  Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma , 2008, Proceedings of the National Academy of Sciences.

[29]  H. C. Fan,et al.  Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood , 2008, Proceedings of the National Academy of Sciences.

[30]  Z. Weng,et al.  The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome , 2008, PLoS genetics.

[31]  Dustin E. Schones,et al.  Dynamic Regulation of Nucleosome Positioning in the Human Genome , 2008, Cell.

[32]  M. Fleischhacker,et al.  Circulating nucleic acids (CNAs) and cancer--a survey. , 2007, Biochimica et biophysica acta.

[33]  A. Kremer,et al.  Cell-free DNA in serum and plasma: comparison of ELISA and quantitative PCR. , 2005, Clinical Chemistry.

[34]  A. Stammati,et al.  The Caco-2 cell line as a model of the intestinal barrier: influence of cell and culture-related factors on Caco-2 cell functional characteristics , 2005, Cell Biology and Toxicology.

[35]  Y. Lo,et al.  Prognostic use of circulating plasma nucleic acid concentrations in patients with acute stroke. , 2003, Clinical chemistry.

[36]  Y. Lo,et al.  Cell-free nucleic acids in plasma, serum and urine: a new tool in molecular diagnosis , 2003, Annals of clinical biochemistry.

[37]  M. Galeazzi,et al.  Dosage and characterization of circulating DNA: present usage and possible applications in systemic autoimmune disorders. , 2003, Autoimmunity reviews.

[38]  K. Tsao,et al.  Elevated cell-free serum DNA detected in patients with myocardial infarction. , 2003, Clinica chimica acta; international journal of clinical chemistry.

[39]  C. Lam,et al.  Predominant hematopoietic origin of cell-free DNA in plasma and serum after sex-mismatched bone marrow transplantation. , 2002, Clinical chemistry.

[40]  Y. Lo,et al.  Rapid clearance of fetal DNA from maternal plasma. , 1999, American journal of human genetics.

[41]  A. Savitzky,et al.  Smoothing and Differentiation of Data by Simplified Least Squares Procedures. , 1964 .