Searching journal content for articles similar to Fernandez et al. 22 (2): 407.

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  1. Mini-Review: Evolution of genome-wide methylation profiling technologies
    • Carolina Montano and
    • Winston Timp
    Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
    ...patterns, acting as molecular fingerprints that reveal their cellular origins. Scientists have developed highly specific “liquid biopsies,” noninvasive biomarkers that identify the DNA's tissue or cell-type source by analyzing cfDNA methylation patterns (Yu et al. 2023a). This has led to applications...
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  2. Method: Nanopore-based consensus sequencing enables accurate multimodal tumor cell-free DNA profiling
    • Li-Ting Chen,
    • Myrthe Jager,
    • Dàmi Rebergen,
    • Geertruid J. Brink,
    • Tom van den Ende,
    • Willem Vanderlinden,
    • Pauline Kolbeck,
    • Marc Pagès-Gallego,
    • Ymke van der Pol,
    • Nicolle Besselink,
    • Norbert Moldovan,
    • Nizar Hami,
    • Wigard P. Kloosterman,
    • Hanneke van Laarhoven,
    • Florent Mouliere,
    • Ronald Zweemer,
    • Jan Lipfert,
    • Sarah Derks,
    • Alessio Marcozzi,
    • and Jeroen de Ridder
    Genome Res. April 2025 35: 886-899; Published in Advance January 13, 2025, doi:10.1101/gr.279144.124
    ...RCS. It should be noted that, although NanoRCS enables more accurate SNV detection in cfDNA, native Nanopore sequencing has the advantage of incorporating methylation as an additional modality that can be captured (Simpson et al. 2017; Lau et al. 2023). Future improvements of NanoRCS include encompassing even...
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  3. Research: Characteristics, origin, and potential for cancer diagnostics of ultrashort plasma cell-free DNA
    • Irena Hudecova,
    • Christopher G. Smith,
    • Robert Hänsel-Hertsch,
    • Chandra S. Chilamakuri,
    • James A. Morris,
    • Aadhitthya Vijayaraghavan,
    • Katrin Heider,
    • Dineika Chandrananda,
    • Wendy N. Cooper,
    • Davina Gale,
    • Javier Garcia-Corbacho,
    • Simon Pacey,
    • Richard D. Baird,
    • Nitzan Rosenfeld,
    • and Florent Mouliere
    Genome Res. February 2022 32: 215-227; Published in Advance December 20, 2021, doi:10.1101/gr.275691.121
    ..., Victoria 3010, Australia Corresponding authors: f.mouliere@amsterdamumc.nl, nitzan.rosenfeld@cruk.cam.ac.ukAbstractCurrent evidence suggests that plasma cell-free DNA (cfDNA) is fragmented around a mode of 166 bp. Data supporting this view has been mainly acquired through the analysis of double-stranded cfDNA...
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  4. Research: DNA methylation contributes to natural human variation
    • Holger Heyn,
    • Sebastian Moran,
    • Irene Hernando-Herraez,
    • Sergi Sayols,
    • Antonio Gomez,
    • Juan Sandoval,
    • Dave Monk,
    • Kenichiro Hata,
    • Tomas Marques-Bonet,
    • Liewei Wang,
    • and Manel Esteller
    Genome Res. September 2013 23: 1363-1372; Published in Advance August 1, 2013, doi:10.1101/gr.154187.112
    ...DNA methylation contributes to natural human variation Holger Heyn 1 , 7 , Sebastian Moran 1 , 7 , Irene Hernando-Herraez 2 , Sergi Sayols 1 , Antonio Gomez 1 , Juan Sandoval 1 , Dave Monk 1 , Kenichiro Hata 3...
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  5. Research: Accessibility of promoter DNA is not the primary determinant of chromatin-mediated gene regulation
    • Răzvan V. Chereji,
    • Peter R. Eriksson,
    • Josefina Ocampo,
    • Hemant K. Prajapati,
    • and David J. Clark
    Genome Res. December 2019 29: 1985-1995; Published in Advance September 11, 2019, doi:10.1101/gr.249326.119
    ...important factor.Alternative methods for quantitative measurement of DNA accessibility involve the use of DNA methyltransferases. These enzymes can be used to methylate cytosines in accessible CpG or GpC dinucleotides, which can then be identified by their resistance to bisulfite conversion after sequencing...
  6. Method: Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin
    • Kun Sun,
    • Peiyong Jiang,
    • Suk Hang Cheng,
    • Timothy H.T. Cheng,
    • John Wong,
    • Vincent W.S. Wong,
    • Simon S.M. Ng,
    • Brigette B.Y. Ma,
    • Tak Y. Leung,
    • Stephen L. Chan,
    • Tony S.K. Mok,
    • Paul B.S. Lai,
    • Henry L.Y. Chan,
    • Hao Sun,
    • K.C. Allen Chan,
    • Rossa W.K. Chiu,
    • and Y.M. Dennis Lo
    Genome Res. March 2019 29: 418-427; Published in Advance February 26, 2019, doi:10.1101/gr.242719.118
    ...in DNA methylation patterns between tissues, we have previously demonstrated that circulating fetal-derived DNA in maternal plasma originated predominantly from the placenta (Chim et al. 2005). This work was based on the detection of unmethylated SERPINB5 sequences as a placental marker in maternal...
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  7. Research: Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs
    • Phuc-Loi Luu,
    • Hans R. Schöler,
    • and Marcos J. Araúzo-Bravo
    Genome Res. December 2013 23: 2013-2029; Published in Advance October 22, 2013, doi:10.1101/gr.155960.113
    ...Disclosing the crosstalk among DNA methylation, transcription factors, and histone marks in human pluripotent cells through discovery of DNA methylation motifs Phuc-Loi Luu 1 , Hans R. Schöler 2 , 3 and Marcos J. Araúzo-Bravo 1 , 4 1...
  8. Research: Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites
    • Amber Hogart,
    • Jens Lichtenberg,
    • Subramanian S. Ajay,
    • Stacie Anderson,
    • NIH Intramural Sequencing Center,
    • Elliott H. Margulies,
    • and David M. Bodine
    Genome Res. August 2012 22: 1407-1418; Published in Advance June 8, 2012, doi:10.1101/gr.132878.111
    ...Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites Amber Hogart 1 , Jens Lichtenberg 1 , Subramanian S. Ajay 2 , Stacie Anderson 1 , 3 , NIH...
  9. Research: H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells
    • Agustín F. Fernández,
    • Gustavo F. Bayón,
    • Rocío G. Urdinguio,
    • Estela G. Toraño,
    • María G. García,
    • Antonella Carella,
    • Sandra Petrus-Reurer,
    • Cecilia Ferrero,
    • Pablo Martinez-Camblor,
    • Isabel Cubillo,
    • Javier García-Castro,
    • Jesús Delgado-Calle,
    • Flor M. Pérez-Campo,
    • José A. Riancho,
    • Clara Bueno,
    • Pablo Menéndez,
    • Anouk Mentink,
    • Katia Mareschi,
    • Fabian Claire,
    • Corrado Fagnani,
    • Emanuela Medda,
    • Virgilia Toccaceli,
    • Sonia Brescianini,
    • Sebastián Moran,
    • Manel Esteller,
    • Alexandra Stolzing,
    • Jan de Boer,
    • Lorenza Nisticò,
    • Maria A. Stazi,
    • and Mario F. Fraga
    Genome Res. January 2015 25: 27-40; Published in Advance September 30, 2014, doi:10.1101/gr.169011.113
    ..., aging is associated with hypermethylation of DNA regions enriched in repressive histone post-translational modifications. However, the chromatin marks associated with changes in DNA methylation in adult stem cells during lifetime are still largely unknown. Here, DNA methylation profiling of mesenchymal...
  10. Letter: Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus
    • Biola M. Javierre,
    • Agustin F. Fernandez,
    • Julia Richter,
    • Fatima Al-Shahrour,
    • J. Ignacio Martin-Subero,
    • Javier Rodriguez-Ubreva,
    • Maria Berdasco,
    • Mario F. Fraga,
    • Terrance P. O'Hanlon,
    • Lisa G. Rider,
    • Filipe V. Jacinto,
    • F. Javier Lopez-Longo,
    • Joaquin Dopazo,
    • Marta Forn,
    • Miguel A. Peinado,
    • Luis Carreño,
    • Amr H. Sawalha,
    • John B. Harley,
    • Reiner Siebert,
    • Manel Esteller,
    • Frederick W. Miller,
    • and Esteban Ballestar
    Genome Res. February 2010 20: 170-179; Published in Advance December 22, 2009, doi:10.1101/gr.100289.109
    ...Changes in the pattern of DNA methylation associate with twin discordance in systemic lupus erythematosus Biola M. Javierre 1 , Agustin F. Fernandez 2 , Julia Richter 3 , Fatima Al-Shahrour 4 , 5 , 6 , J. Ignacio Martin-Subero 3...
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