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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
...-transformed along with gene-specific and sample-specific filters. Based on the data source, normalized gene expression was processed to merge replicates and exclude miRNA and scRNA-seq samples. (B) Number of samples which were annotated to be noncancerous and cancerous based on available metadata across GTEx, SRA...
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Perspective: Decrypting noncoding RNA interactions, structures, and functional networks
- Muller Fabbri,
- Leonard Girnita,
- Gabriele Varani,
- and George A. Calin
Genome Res. September 2019 29: 1377-1388; Published in Advance August 21, 2019, doi:10.1101/gr.247239.118
...grammar and the ncRNA structure grammar. (A) The elements of the ncRNA language grammar. A schematic view of IEs, SEs, structural domains of a ncRNA, and the noncoding RNA interactor network (NIN) composed by the ncRNA, interactor RNAs (such as miRNAs), interactor proteins (such as P1), interactor DNA...
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Research: Loss of transcriptional control over endogenous retroelements during reprogramming to pluripotency
- Marc Friedli,
- Priscilla Turelli,
- Adamandia Kapopoulou,
- Benjamin Rauwel,
- Nathaly Castro-Díaz,
- Helen M. Rowe,
- Gabriela Ecco,
- Carmen Unzu,
- Evarist Planet,
- Angelo Lombardo,
- Bastien Mangeat,
- Barbara E. Wildhaber,
- Luigi Naldini,
- and Didier Trono
Genome Res. August 2014 24: 1251-1259; Published in Advance May 30, 2014, doi:10.1101/gr.172809.114
.... Genome Biol 11: R106. Barde I, Rauwel B, Marin-Florez RM, Corsinotti A, Laurenti E, Verp S, Offner S, Marquis J, Kapopoulou A, Vanicek J et al. 2013. A KRAB/KAP1-miRNA cascade regulates erythropoiesis through stage-specific control of mitophagy. Science 340: 350–353. Birraux J, Menzel O, Wildhaber B...
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Method: Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs
- Ziyan Rao,
- Min Zhang,
- Shaodong Huang,
- Chenyang Wu,
- Yuheng Zhou,
- Weijie Zhang,
- Xia Lin,
- and Dongyu Zhao
Genome Res. August 2025 35: 1842-1858; Published in Advance May 27, 2025, doi:10.1101/gr.280235.124
...throughput sequencing methods can be integrated to enhance the accuracy of lncRNA–DNA interactions. On the other hand, lncRNAs have the capacity to influence coding gene expression through various mechanisms, including liquid–liquid phase separation (Adnane et al. 2022) and miRNA sponging (Du et al. 2016...
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Research: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells
- Jennifer Y. Tan,
- Tamara Sirey,
- Frantisek Honti,
- Bryony Graham,
- Allison Piovesan,
- Matthias Merkenschlager,
- Caleb Webber,
- Chris P. Ponting,
- and Ana C. Marques
Genome Res. May 2015 25: 655-666; Published in Advance March 19, 2015, doi:10.1101/gr.181974.114
...Corresponding author: anaclaudia.marques@unil.ch Abstract Recently, a handful of intergenic long noncoding RNAs (lncRNAs) have been shown to compete with mRNAs for binding to miRNAs and to contribute to development and disease. Beyond these reports, little is yet known of the extent and functional...
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Resource: Single-nucleus transcriptomic mapping uncovers targets for traumatic brain injury
- Qiuyun Yang,
- Lingxuan Zhang,
- Manrui Li,
- Yang Xu,
- Xiaogang Chen,
- Ruixuan Yuan,
- Xiaofeng Ou,
- Min He,
- Miao Liao,
- Lin Zhang,
- Hao Dai,
- Meili Lv,
- Xiaoqi Xie,
- Weibo Liang,
- and Xiameng Chen
Genome Res. October 2023 33: 1818-1832; Published in Advance September 20, 2023, doi:10.1101/gr.277881.123
...) SCENIC results of the control and mTBI group. Major regulators were shown; their corresponding enriched DNA-binding motifs are shown in right column. (F) Ridge plot showing the expression of Tcf7l1. (G) Protein–protein interaction (PPI) networks of TFs and miRNAs in neuroblast (upper) and astrocyte, q...
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Method: A novel approach for data integration and disease subtyping
- Tin Nguyen,
- Rebecca Tagett,
- Diana Diaz,
- and Sorin Draghici
Genome Res. December 2017 27: 2025-2039; Published in Advance October 24, 2017, doi:10.1101/gr.215129.116
...profiles.Subtyping by integrating mRNA, miRNA, and methylation dataWe analyzed six different cancers which have curated level-three data, available at the TCGA website (https://cancer.nih.gov): KIRC, glioblastoma multiforme (GBM), acute myeloid leukemia (LAML), lung squamous cell carcinoma (LUSC), breast...
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Method: Identification and dynamic quantification of regulatory elements using total RNA
- Sascha H. Duttke,
- Max W. Chang,
- Sven Heinz,
- and Christopher Benner
Genome Res. November 2019 29: 1836-1846; Published in Advance October 24, 2019, doi:10.1101/gr.253492.119
...functionality. Other unstable RNAs include diverse precursor RNAs, such as pri-miRNAs that avoid detection owing to being rapidly processed into their mature forms such as miRNAs (Lee et al. 2002). Furthermore, the process of transcription rather than the RNA itself has been shown to impact conformation (Heinz...
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Method: Accurate transcriptome-wide identification and quantification of alternative polyadenylation from RNA-seq data with APAIQ
- Yongkang Long,
- Bin Zhang,
- Shuye Tian,
- Jia Jia Chan,
- Juexiao Zhou,
- Zhongxiao Li,
- Yisheng Li,
- Zheng An,
- Xingyu Liao,
- Yu Wang,
- Shiwei Sun,
- Ying Xu,
- Yvonne Tay,
- Wei Chen,
- and Xin Gao
Genome Res. April 2023 33: 644-657; Published in Advance April 28, 2023, doi:10.1101/gr.277177.122
...μg total RNA, using the ZYMO RNA Clean & Concentrator-5 kit (Zymo R1015). The rRNA-depleted RNA (5 μL) was then mixed with 1 μL 50 pmol Universal miRNA cloning linker (NEB S1315S; 5′ rAppCTGTAGGCACCATCAAT–NH2 3′) at 65°C for 5 min, and then ligated using T4 RNA Ligase 2, truncated KQ (NEB M0373S...
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Method: Models of human core transcriptional regulatory circuitries
- Violaine Saint-André,
- Alexander J. Federation,
- Charles Y. Lin,
- Brian J. Abraham,
- Jessica Reddy,
- Tong Ihn Lee,
- James E. Bradner,
- and Richard A. Young
Genome Res. March 2016 26: 385-396; Published in Advance February 3, 2016, doi:10.1101/gr.197590.115
...regulators DNMT3B, JARID2, and SETDB1, and the miRNA miR-371a, all of which have established roles in pluripotency, self-renewal, or differentiation (detailed functions and associated references in Supplemental Table S5). Among the SE-assigned genes, some transcriptional regulators may create feedforward...

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