Searching journal content for articles similar to Edderkaoui et al. 17 (5): 577.

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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
...sequences and their association with expression quantitative trait loci (eQTLs) to form the most comprehensive resource of this type, accessible through the UCSC Genome Browser. If your GOI and/or candidate TF are known to be expressed in human cancer, two useful tools that are relevant are DepMap, which...
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Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
- Paul Ashford,
- Alexander M. Frankell,
- Zofia Piszka,
- Camilla S.M. Pang,
- Mahnaz Abbasian,
- Maise Al Bakir,
- Mariam Jamal-Hanjani,
- Nicholas McGranahan,
- Charles Swanton,
- and Christine A. Orengo
Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
...applied distinct approaches both to the identification of drivers (i.e., by predicting FIEs) and to their analysis with respect to gene duplication.FunVar was designed to detect mutations with impacts on functional sites, predict rare drivers, and provide insights into the structural and functional...
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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
...activation of quasi-prime-containing gene associations related to cancer, whereas simultaneously suppressing quasi-prime-containing genes are associated with cognitive, mental, and developmental disorders. We also show that human disease–causing variants, eQTLs, mQTLs, and sQTLs are 4.43-fold, 4.34-fold, 4...
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Resource: Cell type–specific gene regulatory atlas prioritizes drug targets and repurposable medicines in Alzheimer's disease
- Yunxiao Ren,
- Ming Hu,
- Yang E. Li,
- Andrew A. Pieper,
- Jeffrey Cummings,
- and Feixiong Cheng
Genome Res. March 2026 36: 645-659; Published in Advance January 21, 2026, doi:10.1101/gr.280436.125
...significantly enriched in pathways related to the response Aβ, including key genes such as triggering receptor expressed on myeloid cells 2 (TREM2), ADRB2, and GJA1 (Fig. 3D). TREM2 is involved in Aβ clearance by microglia, playing a pivotal role in mitigating Aβ plaque accumulation in AD (Gratuze et al. 2018...
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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
...because it can increase the DHT-induced chromatin accessibility and BRD4 chromatin occupancy.Coactivation of AR and GR leads to synergistic expression of a subset of target genesBecause GR at AR-assisted GRBs has added effect on chromatin accessibility, we next measured if coactivation of both receptors...
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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
...confirmed (TEC)” and “immunoglobulin (IG) variable chain or T cell receptor (TR) genes” biotypes were removed. In addition, complex loci where alternative promoter or recombined segments are annotated with different gene names but cannot be considered as independent genes were also removed (Jung et al. 2006...
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Method: Robust and efficient annotation of cell states through gene signature scoring
- Laure Ciernik,
- Agnieszka Kraft,
- Florian Barkmann,
- Josephine Yates,
- and Valentina Boeva
Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
...of the Austrian Academy of Sciences, 1090 Vienna, Austria; 11Eric and Wendy Schmidt Center, The Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA Corresponding author: valentina.boeva@inf.ethz.chAbstractGene signature scoring is integral to single-cell RNA sequencing (scRNA-seq) data analysis...
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Method: Systematic identification of interchromosomal interaction networks supports the existence of specialized RNA factories
- Borislav Hrisimirov Hristov,
- William Stafford Noble,
- and Alessandro Bertero
Genome Res. October 2024 34: 1610-1623; Published in Advance September 25, 2024, doi:10.1101/gr.278327.123
...genes responsible for the antigenic variation of the parasite and evasion of the host immune system. Only a single var gene is active at a given time, the other var genes being maintained in a perinuclear cluster of heterochromatic telomeres (Fig. 2A; Duffy et al. 2017). This cluster is an excellent...
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Method: Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes
- Philipp Rentzsch,
- Aaron Kollotzek,
- Kaushik Ram Ganapathy,
- Pejman Mohammadi,
- and Tuuli Lappalainen
Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
...previously introduced ANEVA, a method for assessing the gene expression distribution based on allelic expression (AE) of heterozygotic SNPs or eQTLs (Mohammadi et al. 2019). Recently, we have further extended this principle to use allelic expression over entire haplotypes (ANEVA-h), improving robustness...
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Method: Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP
- Lin Li,
- Xianbin Su,
- and Ze-Guang Han
Genome Res. October 2025 35: 2300-2315; Published in Advance August 21, 2025, doi:10.1101/gr.279689.124
...programs were most enriched in focal adhesion and ECM–receptor interaction (Supplemental Fig. S26B). These results support the potential regulatory effects of TGFB and Wnt signaling on focal adhesion, accompanied by interactions between the invasive tumor and the TME.View larger version: In this window...

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