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Research: Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth
- Clarence Zheng,
- Sherwood R. Casjens,
- Alan R. Davidson,
- Susan K. Amundsen,
- and Gerald R. Smith
Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
...that it is a typical lambdoid phage except that it appears to have no Rec module and has abundant Chi sites. Among the 314 previously sequenced Enterobacteriales lambdoid phage s that we analyzed, 68 have no recognizable Rec module genes (Table 1; Supplemental Table S3). Sixty-two of these phages have eight or more...
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Research: Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells
- Johannes Hiltunen,
- Laura Helminen,
- Niina Aaltonen,
- Kaisa-Mari Launonen,
- Hanna Laakso,
- Marjo Malinen,
- Einari A. Niskanen,
- Jorma J. Palvimo,
- and Ville Paakinaho
Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
...changes in cell growth.To further investigate the relationship between ESRRG and steroid receptors in PCa, we analyzed data from TCGA patient data sets. High ESRRG expression was associated with improved disease-free survival in PCa patients, a benefit not observed with high ESR1 expression (Supplemental...
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Research: Translation-dependent and -independent mRNA decay occur through mutually exclusive pathways defined by ribosome density during T cell activation
- Blandine C. Mercier,
- Emmanuel Labaronne,
- David Cluet,
- Laura Guiguettaz,
- Nicolas Fontrodona,
- Alicia Bicknell,
- Antoine Corbin,
- Mélanie Wencker,
- Fabien Aube,
- Laurent Modolo,
- Karina Jouravleva,
- Didier Auboeuf,
- Melissa J. Moore,
- and Emiliano P. Ricci
Genome Res. March 2024 34: 394-409; Published in Advance March 20, 2024, doi:10.1101/gr.277863.123
...determinants of TDD magnitude. Consistently, all transcripts that undergo changes in ribosome density within their coding sequence upon T cell activation display a corresponding change in their TDD level. Moreover, we reveal a dynamic modulation in the relationship between GC3 content and TDD upon T cell...
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Method: Variations in antibody repertoires correlate with vaccine responses
- Yana Safonova,
- Sung Bong Shin,
- Luke Kramer,
- James Reecy,
- Corey T. Watson,
- Timothy P.L. Smith,
- and Pavel A. Pevzner
Genome Res. April 2022 32: 791-804; Published in Advance March 31, 2022, doi:10.1101/gr.276027.121
...in CDR3s derived from IGHV1-7 at four time points.Serum from each of the sequenced animals was also assayed for BRD-specific antibody titers at the same time points (Kramer et al. 2017) to quantify pre-existing immunity (e.g., resulting from maternal antibodies that are passed through milk from the dam...
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Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
...preprocessing”). For query data with m cells, C = {c1, …, cm}, suppose we have the clustering results U = {U1, …, Us} with s clusters, where Ui denotes the ith cluster set and the annotation results are V = {V1, …, Vt} with t cell types, where Vi denotes the cell set of type i. It should be noted that for all i...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
...transcription of 7SL RNAs, which are RIGI ligands. RNA modifications play roles in adaptive immunity: (E) Deletion of ADAR results in excessive ISG expression, thus impairing T cell receptor (TCR) signaling. (F) Loss of m6A leads to destabilization of Tcf7 transcripts, consequently impairing naïve T cell...
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Method: Identification of the shortest species-specific oligonucleotide sequences
- Ioannis Mouratidis,
- Maxwell A. Konnaris,
- Nikol Chantzi,
- Candace S.Y. Chan,
- Michail Patsakis,
- Kimonas Provatas,
- Austin Montgomery,
- Fotis A. Baltoumas,
- Congzhou M. Sha,
- Manvita Mareboina,
- Georgios A. Pavlopoulos,
- Dionysios V. Chartoumpekis,
- and Ilias Georgakopoulos-Soares
Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
...with that organism (Bussi et al. 2021). The set of k-mers in a species's can serve as a signature of its underlying sequence. Comparing these k-mers and their frequencies enables the identification of distinct characteristics among species. For example, extremophile s exhibit some of the most distinct and unique k...
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Method: k-mer manifold approximation and projection for visualizing DNA sequences
- Chengbo Fu,
- Einari A. Niskanen,
- Gong-Hong Wei,
- Zhirong Yang,
- Marta Sanvicente-García,
- Marc Güell,
- and Lu Cheng
Genome Res. May 2025 35: 1234-1246; Published in Advance April 10, 2025, doi:10.1101/gr.279458.124
..., patterns are often represented by sets of k-mers, the fundamental building blocks of DNA sequences. To visually unveil these patterns, one could project each k-mer onto a point in two-dimensional (2D) space. However, this projection poses challenges owing to the high-dimensional nature of k...
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Method: Accurate detection of tandem repeats from error-prone sequences with EquiRep
- Zhezheng Song,
- Tasfia Zahin,
- Xiang Li,
- and Mingfu Shao
Genome Res. December 2025 35: 2714-2721; Published in Advance August 21, 2025, doi:10.1101/gr.280750.125
...circular RNAs from rolling-circular long-read sequencing data, using both simulated and raw sequencing data sets. Our results show that EquiRep consistently outperforms or matches state-of-the-art methods, demonstrating robustness to sequencing errors and superior performance on long repeat units and low...
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Method: A best-match approach for gene set analyses in embedding spaces
- Lechuan Li,
- Ruth Dannenfelser,
- Charlie Cruz,
- and Vicky Yao
Genome Res. September 2024 34: 1421-1433; Published in Advance September 4, 2024, doi:10.1101/gr.279141.124
...://www.ncbi.nlm.nih.gov/geo/) GSE14924 data set seem to benefit slightly from using the blood tissue network whereas the CD4 samples from the same data set perform worse. These results suggest that the general blood tissue network may better capture and highlight CD8-related T cell signal rather than CD4 signal. In general, we...
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