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Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
- John Beaulaurier,
- Lynn Ly,
- J. Andrew Duty,
- Carly Tyer,
- Christian Stevens,
- Chuan-Tien Hung,
- Akash Sookdeo,
- Alex W. Drong,
- Shreyas Kowdle,
- Axel Guzman-Solis,
- Domenico Tortorella,
- Daniel J. Turner,
- Sissel Juul,
- Scott Hickey,
- and Benhur Lee
Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
...significant consensus accuracy improvements could be expected using the newer R10 flow cells. We sequenced leftover cDNA from the MBC gate using an R10 flow cell and compared the resulting consensus VDJ regions to the cell barcode- and IG locus-matched sequences from the R9 data. Overall, the proportion...
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Research: Characterization of DNA methylation reader proteins in Arabidopsis thaliana
- Jonathan Cahn,
- James P.B. Lloyd,
- Ino D. Karemaker,
- Pascal W.T.C. Jansen,
- Jahnvi Pflueger,
- Owen Duncan,
- Jakob Petereit,
- Ozren Bogdanovic,
- A. Harvey Millar,
- Michiel Vermeulen,
- and Ryan Lister
Genome Res. December 2024 34: 2229-2243; Published in Advance December 4, 2024, doi:10.1101/gr.279379.124
...DNA methylation levels in all three contexts and is associated with transcriptional silencing of transposable elements (TEs) (Cokus et al. 2008; Lister et al. 2008; Lloyd and Lister 2022). In addition to an important role in silencing TEs in plants, notably in germline cells, mC is also involved...
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Research: Somatic retrotransposition in the developing rhesus macaque brain
- Victor Billon,
- Francisco J. Sanchez-Luque,
- Jay Rasmussen,
- Gabriela O. Bodea,
- Daniel J. Gerhardt,
- Patricia Gerdes,
- Seth W. Cheetham,
- Stephanie N. Schauer,
- Prabha Ajjikuttira,
- Thomas J. Meyer,
- Cora E. Layman,
- Kimberly A. Nevonen,
- Natasha Jansz,
- Jose L. Garcia-Perez,
- Sandra R. Richardson,
- Adam D. Ewing,
- Lucia Carbone,
- and Geoffrey J. Faulkner
Genome Res. July 2022 32: 1298-1314; Published in Advance June 21, 2022, doi:10.1101/gr.276451.121
...somatic TE insertions. Bulk liver DNA was analyzed with Illumina WGS to discriminate germline and somatic variants. (B) Percentages of exonic, intronic, and intergenic nonreference L1 (top left) and Alu (top right) insertions. Genomic features were annotated according to RefSeq coordinates...
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Research: Evolution and genomic signatures of spontaneous somatic mutation in Drosophila intestinal stem cells
- Nick Riddiford,
- Katarzyna Siudeja,
- Marius van den Beek,
- Benjamin Boumard,
- and Allison J. Bardin
Genome Res. August 2021 31: 1419-1432; Published in Advance June 24, 2021, doi:10.1101/gr.268441.120
...) During aging, normal cells (gray) acquire somatic mutations (colored), typically restricted to small populations of cells. Bulk DNA-sequencing of such tissues fails to detect somatic mutations, as they are present in such small numbers. Somatic mutations occurring in an ISC (green) are inherited...
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Method: Quantification of somatic mutation flow across individual cell division events by lineage sequencing
- Yehuda Brody,
- Robert J. Kimmerling,
- Yosef E. Maruvka,
- David Benjamin,
- Juniper J. Elacqua,
- Nicholas J. Haradhvala,
- Jaegil Kim,
- Kent W. Mouw,
- Kristjana Frangaj,
- Amnon Koren,
- Gad Getz,
- Scott R. Manalis,
- and Paul C. Blainey
Genome Res. December 2018 28: 1901-1918; Published in Advance November 20, 2018, doi:10.1101/gr.238543.118
...sharing POLE deficiency and, among COSMIC exome mutation signatures, to the COSMIC POLE signature (Supplemental Fig. S6). These observations highlight the need for quantitative -wide signature assessment to take full advantage of somatic mutations to discriminate specific mechanisms of mutagenesis and DNA...
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Research: Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment
- Franck Court,
- Chiharu Tayama,
- Valeria Romanelli,
- Alex Martin-Trujillo,
- Isabel Iglesias-Platas,
- Kohji Okamura,
- Naoko Sugahara,
- Carlos Simón,
- Harry Moore,
- Julie V. Harness,
- Hans Keirstead,
- Jose Vicente Sanchez-Mut,
- Eisuke Kaneki,
- Pablo Lapunzina,
- Hidenobu Soejima,
- Norio Wake,
- Manel Esteller,
- Tsutomu Ogata,
- Kenichiro Hata,
- Kazuhiko Nakabayashi,
- and David Monk
Genome Res. April 2014 24: 554-569; Published in Advance January 8, 2014, doi:10.1101/gr.164913.113
...Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment Franck Court 1 , 15 , Chiharu Tayama 2 , 15 , Valeria Romanelli 1 , 15 , Alex...
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Research: Transcriptional alterations in glioma result primarily from DNA methylation–independent mechanisms
- Franck Court,
- Elisa Le Boiteux,
- Anne Fogli,
- Mélanie Müller-Barthélémy,
- Catherine Vaurs-Barrière,
- Emmanuel Chautard,
- Bruno Pereira,
- Julian Biau,
- Jean-Louis Kemeny,
- Toufic Khalil,
- Lucie Karayan-Tapon,
- Pierre Verrelle,
- and Philippe Arnaud
Genome Res. October 2019 29: 1605-1621; Published in Advance September 18, 2019, doi:10.1101/gr.249219.119
.... Indeed, an increasing number of studies have shown that in tumors, DNA hypermethylation affects primarily CGI/promoters that control genes already repressed in the matched normal tissue (Gal-Yam et al. 2008; Sproul et al. 2011, 2012; Hinoue et al. 2012; Court and Arnaud 2017). Moreover, in some tumor...
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Research: Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers
- Bettina Meier,
- Nadezda V. Volkova,
- Ye Hong,
- Pieta Schofield,
- Peter J. Campbell,
- Moritz Gerstung,
- and Anton Gartner
Genome Res. May 2018 28: 666-675; Published in Advance April 10, 2018, doi:10.1101/gr.226845.117
...in C. elegans due to the lack of cytosine methylation. The associated human signature, “Clock-1,” together with MMR-1 explains the majority of mutations occurring in MMR-defective cancers not apparently affected by hypermutation.Matching mutational signatures to DNA repair deficiency has a tremendous...
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Research: APOBEC3A/B-induced mutagenesis is responsible for 20% of heritable mutations in the TpCpW context
- Vladimir B. Seplyarskiy,
- Maria A. Andrianova,
- and Georgii A. Bazykin
Genome Res. February 2017 27: 175-184; Published in Advance December 9, 2016, doi:10.1101/gr.210336.116
...of DNA repair and replication, and to exposure to external and internal mutagens (Alexandrov et al. 2013; Lawrence et al. 2013). APOBEC3A/B-induced mutations were described for many cancer types (Alexandrov et al. 2013; Burns et al. 2013b; Roberts et al. 2013). Mutations produced by APOBEC3A/B have known...
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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
...for the regions where the DNA methylation motifs have the best match. For each motif, the scanning method produces two matching distributions, one for low- and another for high-methylation regions. Their statistically significant dissimilarity is addressed with two checks. Two examples of matching discriminative...

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