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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
...that are incorporated into completed transcripts and allow for their identification, for example, by hybridization-based techniques with radiolabeling (Smale 2009). This approach was recently improved by including modified nucleotides that allow for enrichment of the emergent transcripts by affinity isolation. Some...
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Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
- Yang Xi,
- Jingjing Qi,
- Zhao Yang,
- Yutian Zeng,
- Huicong Zhang,
- Qiuyu Tao,
- Mengru Xu,
- Anqi Huang,
- Shenqiang Hu,
- Chunchun Han,
- Lili Bai,
- Jiwei Hu,
- Jiwen Wang,
- Liang Li,
- Lingzhao Fang,
- and Hehe Liu
Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
..., several modules were significantly correlated with modules in the liver (ME1, ME3, ME5). In contrast, no significant cross-tissue correlations were observed among the ovary, spleen, and shell gland themselves (Fig. 6A). We employed a Bayesian network-based approach to explore the potential causal...
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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
...changes (McLean et al. 2011; Hubisz and Pollard 2014). However, available methods rely on alignments and mutational analysis, often lacking the ability to identify the units of accelerated evolution at base pair resolution. The identification of the shortest genomic sequences unique to a species can...
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Method: Exon Nomenclature And Classification of Transcripts (ENACT) provides a systematic framework to annotate exon attributes
- Paras Verma,
- Deeksha Thakur,
- Deepanshi Awasthi,
- and Shashi Bhushan Pandit
Genome Res. June 2025 35: 1440-1455; Published in Advance May 7, 2025, doi:10.1101/gr.279878.124
...information is integrated (onto the available/annotated or new transcripts) while enabling tracking and assessing splice-site variability through unique yielded descriptors. The resulting annotation from the ENACT framework enables exon features to be tractable, facilitating a systematic analysis of isoform...
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Research: Global identification of mammalian host and nested gene pairs reveal tissue-specific transcriptional interplay
- Bertille Montibus,
- James A. Cain,
- Rocio T. Martinez-Nunez,
- and Rebecca J. Oakey
Genome Res. December 2024 34: 2163-2175; Published in Advance November 22, 2024, doi:10.1101/gr.279430.124
...through “premature” polyadenylation are key for cell functions (Singh et al. 2018).Thus, even though the role and the consequences of the host/nested gene organization are starting to be uncovered, an updated -wide analysis is urgently needed. As such, characterization and identification of all possible...
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Resource: Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes
- Guanjue Xiang,
- Xi He,
- Belinda M. Giardine,
- Kathryn J. Isaac,
- Dylan J. Taylor,
- Rajiv C. McCoy,
- Camden Jansen,
- Cheryl A. Keller,
- Alexander Q. Wixom,
- April Cockburn,
- Amber Miller,
- Qian Qi,
- Yanghua He,
- Yichao Li,
- Jens Lichtenberg,
- Elisabeth F. Heuston,
- Stacie M. Anderson,
- Jing Luan,
- Marit W. Vermunt,
- Feng Yue,
- Michael E.G. Sauria,
- Michael C. Schatz,
- James Taylor,
- Berthold Göttgens,
- Jim R. Hughes,
- Douglas R. Higgs,
- Mitchell J. Weiss,
- Yong Cheng,
- Gerd A. Blobel,
- David M. Bodine,
- Yu Zhang,
- Qunhua Li,
- Shaun Mahony,
- and Ross C. Hardison
Genome Res. July 2024 34: 1089-1105; Published in Advance July 1, 2024, doi:10.1101/gr.277950.123
...Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epis Guanjue Xiang1,2,3, Xi He1, Belinda M. Giardine4, Kathryn J. Isaac5, Dylan J. Taylor5, Rajiv C. McCoy5, Camden Jansen4, Cheryl A. Keller4, Alexander Q. Wixom4, April...
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Method: Systematic mapping of TF-mediated cell fate changes by a pooled induction coupled with scRNA-seq and multi-omics approaches
- Muyoung Lee,
- Qingqing Guo,
- Mijeong Kim,
- Joonhyuk Choi,
- Alia Segura,
- Alper Genceroglu,
- Lucy LeBlanc,
- Nereida Ramirez,
- Yu Jin Jang,
- Yeejin Jang,
- Bum-Kyu Lee,
- Edward M. Marcotte,
- and Jonghwan Kim
Genome Res. March 2024 34: 484-497; Published in Advance April 5, 2024, doi:10.1101/gr.277926.123
.... 2010; Rhee et al. 2014; Blij et al. 2015).Reprogramming has enormous potential for regenerative medicine, as it enables the generation of desired cell types. To systematically test the potential of individual TFs in converting cell fates, recent studies have performed large-scale overexpression screens...
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Method: Increased taxon sampling reveals thousands of hidden orthologs in flatworms
- José M. Martín-Durán,
- Joseph F. Ryan,
- Bruno C. Vellutini,
- Kevin Pang,
- and Andreas Hejnol
Genome Res. July 2017 27: 1263-1272; Published in Advance April 11, 2017, doi:10.1101/gr.216226.116
...putative hidden orthologs (Fig. 2). However, our results on an extensive data set of flatworm transcriptomes are likely an underestimation of the true number of hidden orthologs. First, we based our identification of hidden orthologs on reciprocal best BLAST hits, a valid and widely used approach (Tatusov...
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Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
- Samuel T. Horsfield,
- Gerry Tonkin-Hill,
- Nicholas J. Croucher,
- and John A. Lees
Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
...-caller based on DBGs. ggCaller uses population-frequency information to guide gene prediction, aiding the identification of homologous start codons across orthologs, as well as consistent scoring and functional annotation of orthologs. ggCaller also includes a query mode, enabling reference-agnostic functional...
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Method: Cross-species cell-type assignment from single-cell RNA-seq data by a heterogeneous graph neural network
- Xingyan Liu,
- Qunlun Shen,
- and Shihua Zhang
Genome Res. January 2023 33: 96-111; Published in Advance December 16, 2022, doi:10.1101/gr.276868.122
...(Fig. 6A). As a distance-based method, scmap fails to make effective cell-type assignment between zebrafish and chick owing to the systematic differences in gene expression space cross-species. It is worth mentioning that even for chick, CAME achieves superior cell typing accuracy (with >27...

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