Searching journal content for articles similar to Stendahl et al. 33 (12): 2053.

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  1. Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
    • Michael K.B. Ford,
    • Ananth Hari,
    • Meredith Yeager,
    • Lisa Mirabello,
    • Stephen Chanock,
    • Ibrahim Numanagić,
    • COVNET Consortium,
    • and S. Cenk Sahinalp
    Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
    ...approaches. In particular, germline adaptive immune system genes, like immunoglobulin (IG) and T cell receptor (TR) genes, are particularly hard to genotype using classic reference-based methods owing to their highly repetitive and homologous nature. In this paper, we present ImmunoTyper2, a new...
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  2. Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
    • Kai Otsuka,
    • Akihiko Sakashita,
    • So Maezawa,
    • Richard M. Schultz,
    • and Satoshi H. Namekawa
    Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
    ...KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and evolution Kai Otsuka1,2, Akihiko Sakashita3,4, So Maezawa2, Richard M. Schultz1,5 and Satoshi H. Namekawa1,3 1Department of Microbiology and Molecular Genetics, University of California, Davis...
  3. 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
    ...repertoire, we combined sequencing of the germline IG loci with single-cell transcriptome sequencing of B cells from the same donor. Sequencing and assembly of the germline IG loci captured the IGH locus in a single fully phased contig where the maternal and paternal contributions to the germline V, D, and J...
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  4. Research: Extensive variation in germline de novo mutations in Poecilia reticulata
    • Yuying Lin,
    • Iulia Darolti,
    • Wouter van der Bijl,
    • Jake Morris,
    • and Judith E. Mank
    Genome Res. August 2023 33: 1317-1324; Published in Advance July 13, 2023, doi:10.1101/gr.277936.123
    ...-based variant filtering criteria to accurately identify and quantify the number of DNMs, providing insights into the role of germline mutations in the rapid evolution of this species. Moreover, our large families, each with ten offspring, allow us to estimate the timing of mutations across germline development...
  5. Method: A somatic hypermutation–based machine learning model stratifies individuals with Crohn's disease and controls
    • Modi Safra,
    • Lael Werner,
    • Ayelet Peres,
    • Pazit Polak,
    • Naomi Salamon,
    • Michael Schvimer,
    • Batia Weiss,
    • Iris Barshack,
    • Dror S. Shouval,
    • and Gur Yaari
    Genome Res. January 2023 33: 71-79; Published in Advance December 16, 2022, doi:10.1101/gr.276683.122
    ..., the B cell receptor (BCR) is formed after VDJ recombination. Somatic hypermutation (SHM) is an additional B cell–specific mode of diversification that relies on the introduction of mutations in BCR sequences. These mutations occur mostly at known “hotspots” in the DNA, which are concentrated...
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  6. Method: Analytical validation of germline small variant detection using long-read HiFi genome sequencing
    • Nathan Hammond,
    • Linda Liao,
    • Pun Wai Tong,
    • Zena Ng,
    • Thuy-Mi P. Nguyen,
    • Chandler Ho,
    • Yao Yang,
    • and Stuart A. Scott
    Genome Res. June 2025 35: 1391-1399; Published in Advance April 11, 2025, doi:10.1101/gr.278836.123
    ...Analytical validation of germline small variant detection using long-read HiFi sequencing Nathan Hammond1,3, Linda Liao1, Pun Wai Tong1, Zena Ng1, Thuy-Mi P. Nguyen2, Chandler Ho1, Yao Yang1,2 and Stuart A. Scott1,2 1Clinical Genomics Laboratory, Stanford Medicine, Palo Alto, California 94304, USA...
  7. Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
    • Daffodil M. Canson,
    • Michael T. Parsons,
    • Gemma Moir-Meyer,
    • Troy Dumenil,
    • Gemma Montalban,
    • Erica Lin,
    • Terri P. McVeigh,
    • Aimee L. Davidson,
    • Shaun M. Bouckaert,
    • Matt Trau,
    • Darren Korbie,
    • and Amanda B. Spurdle
    Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
    ...that construct-derived results for variants showing low or no splicing impact provide reliable evidence against variant pathogenicity, whereas—for variants demonstrating splicing impact—construct design and naturally occurring alternative splicing are important considerations for assigning and weighting evidence...
  8. Research: Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids
    • Carina F. Mugal,
    • Mi Wang,
    • Niclas Backström,
    • David Wheatcroft,
    • Murielle Ålund,
    • Marie Sémon,
    • S. Eryn McFarlane,
    • Ludovic Dutoit,
    • Anna Qvarnström,
    • and Hans Ellegren
    Genome Res. December 2020 30: 1727-1739; Published in Advance November 3, 2020, doi:10.1101/gr.254508.119
    ...-specific nature of cis-regulatory evolution bypassing constraints associated with pleiotropic effects of genes.Following the seminal work of King and Wilson (1975) postulating that evolution occurs at two levels, the relative importance of changes in protein sequences and changes in gene expression has been...
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  9. Method: BayesRVAT enhances rare-variant association testing through Bayesian aggregation of functional annotations
    • Antonio Nappi,
    • Liubov Shilova,
    • Theofanis Karaletsos,
    • Na Cai,
    • and Francesco Paolo Casale
    Genome Res. December 2025 35: 2682-2690; Published in Advance October 24, 2025, doi:10.1101/gr.280689.125
    ...Corresponding author: francescopaolo.casale@helmholtz-munich.deAbstractGene-level rare variant association tests (RVATs) are essential for uncovering disease mechanisms and identifying therapeutic targets. Advances in sequence-based machine learning have generated diverse variant pathogenicity scores, creating...
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  10. Research: Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T
    • Luis F. Paulin,
    • Jeremy Fan,
    • Kieran O'Neill,
    • Erin Pleasance,
    • Vanessa L. Porter,
    • Steven J.M. Jones,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 621-631; Published in Advance March 17, 2025, doi:10.1101/gr.279352.124
    ...) variant calls, especially with larger rearrangements or duplications (Aganezov et al. 2020). We recently developed the SV caller Sniffles2 to identify SVs using LRS data (Smolka et al. 2024). While Sniffles2 has been applied in germline contexts such as neurological and Mendelian disorders, its utility...
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