Facile single-stranded DNA sequencing of human plasma DNA via thermostable group II intron reverse transcriptase template switching
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[1] F. O. Fackelmayer,et al. DNA fragments in the blood plasma of cancer patients: quantitations and evidence for their origin from apoptotic and necrotic cells. , 2001, Cancer research.
[2] Christoph Grunau,et al. Bisulfite genomic sequencing: systematic investigation of critical experimental parameters , 2001, Nucleic Acids Res..
[3] Éric Renault,et al. MethDB - a public database for DNA methylation data , 2001, Nucleic Acids Res..
[4] M. Belfort,et al. Recruitment of host functions suggests a repair pathway for late steps in group II intron retrohoming. , 2005, Genes & development.
[5] D. Pisetsky,et al. The role of macrophages in the in vitro generation of extracellular DNA from apoptotic and necrotic cells , 2005, Immunology.
[6] I. Grivicich,et al. Role of plasma DNA as a predictive marker of fatal outcome following severe head injury in males. , 2007, Journal of neurotrauma.
[7] John D. Hunter,et al. Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.
[8] Travis E. Oliphant,et al. Python for Scientific Computing , 2007, Computing in Science & Engineering.
[9] 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.
[10] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[11] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[12] Pedro M. Valero-Mora,et al. ggplot2: Elegant Graphics for Data Analysis , 2010 .
[13] 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.
[14] Richard Durbin,et al. Fast and accurate long-read alignment with Burrows–Wheeler transform , 2010, Bioinform..
[15] Travis White. Group II intron and gene targeting reactions in Drosophila melanogaster , 2011 .
[16] K. Kinzler,et al. Detection and quantification of rare mutations with massively parallel sequencing , 2011, Proceedings of the National Academy of Sciences.
[17] Brent S. Pedersen,et al. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations , 2011, Bioinform..
[18] T. Glenn. Field guide to next‐generation DNA sequencers , 2011, Molecular ecology resources.
[19] G. Parmigiani,et al. Detection of Chromosomal Alterations in the Circulation of Cancer Patients with Whole-Genome Sequencing , 2012, Science Translational Medicine.
[20] D. Cook,et al. ggbio: an R package for extending the grammar of graphics for genomic data , 2012, Genome Biology.
[21] N. Kyrpides,et al. Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample , 2012, PloS one.
[22] N. Lennon,et al. Characterizing and measuring bias in sequence data , 2013, Genome Biology.
[23] Daniel J. Gaffney,et al. Controls of Nucleosome Positioning in the Human Genome , 2012, PLoS genetics.
[24] F. Syed,et al. EpiGnome™ Methyl-Seq Kit: a novel post–bisulfite conversion library prep method for methylation analysis , 2013, Nature Methods.
[25] N. Rosenfeld,et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA , 2013, Nature.
[26] A. Lambowitz,et al. Genetic and Biochemical Assays Reveal a Key Role for Replication Restart Proteins in Group II Intron Retrohoming , 2013, PLoS genetics.
[27] V. Iyer,et al. Thermostable group II intron reverse transcriptase fusion proteins and their use in cDNA synthesis and next-generation RNA sequencing , 2013, RNA.
[28] M. Meyer,et al. Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA , 2013, Nature Protocols.
[29] Yiliang Ding,et al. A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation. , 2013, Analytical biochemistry.
[30] Jeffrey A. Hussmann,et al. High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing , 2013, Proceedings of the National Academy of Sciences.
[31] N. Neff,et al. Temporal Response of the Human Virome to Immunosuppression and Antiviral Therapy , 2013, Cell.
[32] Brent S. Pedersen,et al. Fast and accurate alignment of long bisulfite-seq reads , 2014, 1401.1129.
[33] A. Quinlan. BEDTools: The Swiss‐Army Tool for Genome Feature Analysis , 2014, Current protocols in bioinformatics.
[34] R. Spriggs,et al. Evaluating bias-reducing protocols for RNA sequencing library preparation , 2014, BMC Genomics.
[35] Björn Usadel,et al. Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..
[36] Ash A. Alizadeh,et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage , 2013, Nature Medicine.
[37] Brendan F. Kohrn,et al. Detecting ultralow-frequency mutations by Duplex Sequencing , 2014, Nature Protocols.
[38] S. Linnarsson,et al. Amplification-free sequencing of cell-free DNA for prenatal non-invasive diagnosis of chromosomal aberrations. , 2015, Genomics.
[39] Yue Hu,et al. Non-invasive Analysis of Genomic Copy Number Variation in Patients with Hepatocellular Carcinoma by Next Generation DNA Sequencing , 2015, Journal of Cancer.
[40] Nicholas J. Wang,et al. Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary Disease , 2015, PloS one.
[41] M. Belfort,et al. Mobile Bacterial Group II Introns at the Crux of Eukaryotic Evolution. , 2015, Microbiology spectrum.
[42] Brent S. Pedersen,et al. Efficient "pythonic" access to FASTA files using pyfaidx , 2015, PeerJ Prepr..
[43] N. Thorne,et al. High-resolution characterization of sequence signatures due to non-random cleavage of cell-free DNA , 2015, BMC Medical Genomics.
[44] R. Strausberg,et al. Circulating tumor DNA as an early marker of therapeutic response in patients with metastatic colorectal cancer. , 2015, Annals of oncology : official journal of the European Society for Medical Oncology.
[45] G. von Heijne,et al. Tissue-based map of the human proteome , 2015, Science.
[46] V. Wong,et al. Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients , 2015, Proceedings of the National Academy of Sciences.
[47] E. Ma,et al. Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments , 2015, Proceedings of the National Academy of Sciences.
[48] C. Ling,et al. Genome-wide analysis of DNA methylation in subjects with type 1 diabetes identifies epigenetic modifications associated with proliferative diabetic retinopathy , 2015, BMC Medicine.
[49] R. Price,et al. Artemether-lumefantrine treatment of uncomplicated Plasmodium falciparum malaria: a systematic review and meta-analysis of day 7 lumefantrine concentrations and therapeutic response using individual patient data , 2015, BMC Medicine.
[50] Min Seong Kim,et al. Single-stranded DNA library preparation uncovers the origin and diversity of ultrashort cell-free DNA in plasma , 2015, Scientific Reports.
[51] A. Lambowitz,et al. RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase , 2016, RNA.
[52] Matthew W. Snyder,et al. Cell-free DNA Comprises an In Vivo Nucleosome Footprint that Informs Its Tissues-Of-Origin , 2016, Cell.
[53] A. Lambowitz,et al. High-throughput sequencing of human plasma RNA by using thermostable group II intron reverse transcriptases , 2016, RNA.
[54] Ash A. Alizadeh,et al. Integrated digital error suppression for improved detection of circulating tumor DNA , 2016, Nature Biotechnology.
[55] R. Strausberg,et al. Circulating tumor DNA analysis detects minimal residual disease and predicts recurrence in patients with stage II colon cancer , 2016, Science Translational Medicine.
[56] J. McPherson,et al. Coming of age: ten years of next-generation sequencing technologies , 2016, Nature Reviews Genetics.
[57] Alon Goren,et al. Biases in the SMART-DNA library preparation method associated with genomic poly dA/dT sequences , 2017, PloS one.
[58] R. Batey,et al. Recurrent RNA motifs as scaffolds for genetically encodable small molecule biosensors , 2016, Nature chemical biology.
[59] J. Weissman,et al. DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo , 2016, Nature Methods.
[60] M. Meyer,et al. Single-stranded DNA library preparation from highly degraded DNA using T4 DNA ligase , 2017, Nucleic acids research.
[61] R. Schekman,et al. A broad role for YBX1 in defining the small non-coding RNA composition of exosomes , 2017, bioRxiv.