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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
...et al. 2021), disease associations (Xiong et al. 2019; Yu et al. 2021), expanding gene set representations (Chen et al. 2018; Wang et al. 2020), among other applications (Gao et al. 2018; Kim et al. 2018; Mostavi et al. 2020; Bryant et al. 2022).Given the utility of gene embeddings for downstream...
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Review: Advancements in prospective single-cell lineage barcoding and their applications in research
- Xiaoli Zhang,
- Yirui Huang,
- Yajing Yang,
- Qi-En Wang,
- and Lang Li
Genome Res. December 2024 34: 2147-2162; Published in Advance November 21, 2024, doi:10.1101/gr.278944.124
...complexity. This integration allows for the connection of cells from the present to their historical lineage. Additionally, the refinement of clonal dynamics is achieved by leveraging transcriptome-derived differentiation trajectories and assessing gene expression changes over time (Kester and van...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...; carefully curated databases compile as many of them as possible, including JASPAR (Rauluseviciute et al. 2024) and ORegAnno (Lesurf et al. 2016), both available via the USCS Genome Browser. MSigDB contains curated gene sets from the literature; the most useful ones for the purpose described here...
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Research: A gene regulatory element modulates myosin expression and controls cardiomyocyte response to stress
- Taylor Anglen,
- Irene M. Kaplow,
- Baekgyu Choi,
- Enya Dewars,
- Robin M. Perelli,
- Kevin T. Hagy,
- Duc Tran,
- Megan E. Ramaker,
- Svati H. Shah,
- Inkyung Jung,
- Andrew P. Landstrom,
- Ravi Karra,
- Yarui Diao,
- and Charles A. Gersbach
Genome Res. November 2025 35: 2418-2432; Published in Advance October 22, 2025, doi:10.1101/gr.280825.125
...).Epigenetic landscape surrounding a gene regulatory element in human and mouse samplesTo understand the context in which these putative regulatory elements may be active, we analyzed multiple epigenetic data sets from human and mouse samples (Fig. 2; Supplemental Figs. S3–S7). We find that activity...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...assembly had the same problem as in mRatBN7.2, implying an origin in the RefSeq gene rather than the assembly. We used isoform sequencing (Iso-Seq) alignments to investigate 33 remaining genes with problematic concordance with the annotation gene set in GRCr8. Of these, 24 appeared to be problems arising...
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Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
- Aliza B. Rubenstein,
- Gregory R. Smith,
- Zidong Zhang,
- Xi Chen,
- Toby L. Chambers,
- Frederique Ruf-Zamojski,
- Natalia Mendelev,
- Wan Sze Cheng,
- Michel Zamojski,
- Mary Anne S. Amper,
- Venugopalan D. Nair,
- Andrew R. Marderstein,
- Stephen B. Montgomery,
- Olga G. Troyanskaya,
- Elena Zaslavsky,
- Todd Trappe,
- Scott Trappe,
- and Stuart C. Sealfon
Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
...National Institutes of Health Molecular Transducers of Physical Activity Consortium (MoTrPAC) program is developing a comprehensive multiomic whole-tissue-level molecular map of the responses to exercise in rat models and humans (Sanford et al. 2020). These tissue-level multiomic data sets support...
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Research: Analysis of canine gene constraint identifies new variants for orofacial clefts and stature
- Reuben M. Buckley,
- Nüket Bilgen,
- Alexander C. Harris,
- Peter Savolainen,
- Cafer Tepeli,
- Metin Erdoğan,
- Aitor Serres Armero,
- Dayna L. Dreger,
- Frank G. van Steenbeek,
- Marjo K. Hytönen,
- Heidi G. Parker,
- Jessica Hale,
- Hannes Lohi,
- Bengi Çınar Kul,
- Adam R. Boyko,
- and Elaine A. Ostrander
Genome Res. May 2025 35: 1080-1093; Published in Advance March 24, 2025, doi:10.1101/gr.280092.124
...constraint can therefore be used to prioritize likely trait-causing variants. To explore the utility of gene sequence constraint for this purpose, we assembled a data set of over 2291 high-quality s and used phylogenetic clustering to group them into 200 breeds/groups of five or more (Supplemental Figs. S1...
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Research: Snake venom gene expression is coordinated by novel regulatory architecture and the integration of multiple co-opted vertebrate pathways
- Blair W. Perry,
- Siddharth S. Gopalan,
- Giulia I.M. Pasquesi,
- Drew R. Schield,
- Aundrea K. Westfall,
- Cara F. Smith,
- Ivan Koludarov,
- Paul T. Chippindale,
- Mark W. Pellegrino,
- Edward B. Chuong,
- Stephen P. Mackessy,
- and Todd A. Castoe
Genome Res. June 2022 32: 1058-1073; Published in Advance June 1, 2022, doi:10.1101/gr.276251.121
...expression analyses described above to identify TFs with evidence of up-regulation in the venom gland compared with nonvenom tissues (IHW P-value < 0.05). Separately, we identified TF genes associated with SEs. These two TF sets were merged to form one master...
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Method: A transcriptome-based single-cell biological age model and resource for tissue-specific aging measures
- Shulin Mao,
- Jiayu Su,
- Longteng Wang,
- Xiaochen Bo,
- Cheng Li,
- and Hebing Chen
Genome Res. August 2023 33: 1381-1394; Published in Advance July 31, 2023, doi:10.1101/gr.277491.122
...across species. To test this hypothesis, we replaced selected mouse aging genes with corresponding homologs in other species and similarly calculated the SCALE scores in scRNA-seq data from humans and rats.Our first experiment involved a human brain data set with seven chronological age groups (Hodge et...
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Research: Identification of a transcriptional signature found in multiple models of ASD and related disorders
- Samuel Thudium,
- Katherine Palozola,
- Éloïse L'Her,
- and Erica Korb
Genome Res. September 2022 32: 1642-1654; Published in Advance September 14, 2022, doi:10.1101/gr.276591.122
...in regulating chromatin. Specifically, we depleted ASH1L, CHD8, CREBBP, EHMT1, and NSD1 in parallel in a highly controlled neuronal culture system. We then identified sets of shared genes, or transcriptional signatures, that are differentially expressed following loss of multiple ASD-linked chromatin modifiers...

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