Searching journal content for articles similar to Tahri-Daizadeh et al. 13 (8): 1952.

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Research: Phylogenetic modeling of enhancer shifts in African mole-rats reveals regulatory changes associated with tissue-specific traits
- Elise Parey,
- Diego Fernandez-Aroca,
- Stephanie Frost,
- Ainhoa Uribarren,
- Thomas J. Park,
- Markus Zöttl,
- Ewan St. John Smith,
- Camille Berthelot,
- and Diego Villar
Genome Res. September 2023 33: 1513-1526; Published in Advance August 25, 2023, doi:10.1101/gr.277715.123
...of drift), the alpha parameter (strength of selection), the theta parameter (optimal trait value), and the beta parameter (ratio of intra- to interspecies variation). To detect significant shift in regulatory activity of enhancers and promoters on specific branches of the study phylogeny, we took advantage...
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Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
- Peter Orchard,
- Nandini Manickam,
- Christa Ventresca,
- Swarooparani Vadlamudi,
- Arushi Varshney,
- Vivek Rai,
- Jeremy Kaplan,
- Claudia Lalancette,
- Karen L. Mohlke,
- Katherine Gallagher,
- Charles F. Burant,
- and Stephen C.J. Parker
Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
...-related complex traits.Bulk profiling of skeletal muscle tissue ignores this heterogeneity and is dominated by the most common cell types (muscle fibers), but single-cell/-nucleus methods overcome this and allow profiling of the constituent cell types. In the case of skeletal muscle, the distinction between...
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Method: FIND: difFerential chromatin INteractions Detection using a spatial Poisson process
- Mohamed Nadhir Djekidel,
- Yang Chen,
- and Michael Q. Zhang
Genome Res. March 2018 28: 412-422; Published in Advance February 12, 2018, doi:10.1101/gr.212241.116
...reveal the advantage of our method over the count-based methods for high-resolution Hi-C contact map as it uses the nearest neighbors’ information to decide about the significance of a structural change. Compared to count-based methods, this strategy avoids the detection of noisy DCIs, because it borrows...
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Resource: Integrative chromatin state annotation of 234 human ENCODE4 cell types using Segway
- Marjan Farahbod,
- Aboud Diab,
- Paul Sud,
- Meenakshi S. Kagda,
- Ian Whaling,
- Mehdi Foroozandeh,
- Ishan Goel,
- Habib Daneshpajouh,
- Benjamin Hitz,
- J. Michael Cherry,
- and Maxwell W. Libbrecht
Genome Res. October 6, 2025 gr.280633.125; Published in Advance October 6, 2025, doi:10.1101/gr.280633.125
...“concatenated” approach (Kundaje et al. 2015) of using a single model for all samples, allows the pipeline to incorporate all data sets available for each sample. To handle the added challenge of interpreting independent models, we used an automated interpretation process as described. Doing so also obviates...
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Method: ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs
- Piotr J. Balwierz,
- Mikhail Pachkov,
- Phil Arnold,
- Andreas J. Gruber,
- Mihaela Zavolan,
- and Erik van Nimwegen
Genome Res. May 2014 24: 869-884; Published in Advance February 10, 2014, doi:10.1101/gr.169508.113
...ISMARA: automated modeling of genomic signals as a democracy of regulatory motifs Piotr J. Balwierz , Mikhail Pachkov , Phil Arnold , Andreas J. Gruber , Mihaela Zavolan and Erik van Nimwegen 1 Biozentrum, University...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...gene expression levels, reducing our power to detect convergence if no close control species can be included in the study design.The molecular convergences between distant lineages that have long adapted to aridity could be attributed to the fact that many separate adaptations in various traits have...
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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...be expected as module detection for WGCNA combines information across multiple gene pairs to identify modules and has been shown to work reasonably well even at small sample sizes. WGCNA module detection simply may not benefit as much from increased sample sizes. Thus, we conclude that PC-correction followed...
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Research: Haplotype-resolved telomere-to-telomere genome of Aphelenchus avenae implicates P5CS in nematode desiccation stress response
- Yali Zhang,
- Yayi Zhou,
- Yangyang Chen,
- Xueyu Wang,
- Boyan Hu,
- Shahid Siddique,
- Romnick A. Latina,
- Veronica I. Casey,
- Dexin Bo,
- Yucheng Liao,
- Min Zhang,
- Ming Sun,
- Fengjuan Zhang,
- and Dadong Dai
Genome Res. March 23, 2026 ; Published in Advance March 23, 2026, doi:10.1101/gr.281016.125
...diverse life forms, including plants, fungi, and nematodes. However, our understanding of its molecular basis, particularly in animals, remains limited. Aphelenchus avenae nematodes are notable for their exceptional tolerance to dehydration, and multiple genes related to this trait have been identified...
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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
...and the KZFP family (Marta et al. 2019a). 103 Furthermore, studying dynamic evolution of ruminant TE can help us reveal unique 104 phenotypic traits in ruminant species (Siqian et al. 2022). Yet, the characterization of KZFPs 105 and TEs as well as their coevolution patterns is limited in ruminants, because...
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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
...are prone to false positives, whereas fully endogenous systems, although biologically informative, carry a higher risk of false negatives owing to contextual dependencies such as chromatin state, cell cycle stage, and transcriptional noise. It is critical to carefully select experimental configurations...
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