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Research: Transcriptome-wide systematic search does not detect A-to-I RNA editing in cis-antisense RNA duplexes
- Zohar Rosenwasser,
- Roni Cohen-Fultheim,
- Ofir Shliefer,
- Erez Y. Levanon,
- and Eli Eisenberg
Genome Res. March 12, 2026 gr.280820.125; Published in Advance March 12, 2026, doi:10.1101/gr.280820.125
...indices (negative strand). Figure 4C shows the distribution of correlation coefficients across all qualifying regions. The resulting correlation coefficients are distributed around zero, and positive coefficients are less frequent than negative ones (Figure 4C). This finding further supports independent...
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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
...-3 lacks a prodomain in the N-terminal region, suggesting constitutive metalloproteinase activity. As a consequence, ISF-3 loses two of four glycosylation sites from the prodomain (Srinivasan et al. 2014) but preserves the conserved glutamate (158E), which is essential for prodomain's catalytic...
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Method: The oligogenic inheritance test GCOD detects risk genes and their interactions in congenital heart defects
- Maureen Pittman,
- Kihyun Lee,
- Franco Felix,
- Yu Huang,
- Adrienne Lam,
- Mauro W. Costa,
- Deepak Srivastava,
- and Katherine S. Pollard
Genome Res. February 2026 36: 330-347; Published in Advance December 12, 2025, doi:10.1101/gr.281141.125
...“oligogenic transmission” and “oligogenic inheritance” to describe an event in which qualifying variants were inherited separately from both parents or include a de novo mutation, such that an unaffected parent did not also carry that same combination of variants. The count of observed oligogenic...
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Resource: Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform
- Liubomir Chorbadjiev,
- Murat Cokol,
- Zohar Weinstein,
- Kevin Shi,
- Christopher Fleisch,
- Nikolay Dimitrov,
- Svetlin Mladenov,
- Ivo Todorov,
- Iordan Ivanov,
- Simon Xu,
- Steven Ford,
- Yoon-ha Lee,
- Boris Yamrom,
- Steven Marks,
- Adriana Munoz,
- Alex Lash,
- Natalia Volfovsky,
- and Ivan Iossifov
Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
...populations like gnomAD (Chen et al. 2024), conservation metrics like phyloP (Pollard et al. 2010) and phastCons (Siepel et al. 2005), pathogenicity scores like MPC (Samocha et al. 2017) and CADD (Kircher et al. 2014), and gene intolerance scores like RVIS (Petrovski et al. 2013) and pLI (Lek et al. 2016...
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Method: A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS
- Sahar Gelfman,
- Sarah Dugger,
- Cristiane de Araujo Martins Moreno,
- Zhong Ren,
- Charles J. Wolock,
- Neil A. Shneider,
- Hemali Phatnani,
- Elizabeth T. Cirulli,
- Brittany N. Lasseigne,
- Tim Harris,
- Tom Maniatis,
- Guy A. Rouleau,
- Robert H. Brown, Jr,
- Aaron D. Gitler,
- Richard M. Myers,
- Slavé Petrovski,
- Andrew Allen,
- David B. Goldstein,
- and Matthew B. Harms
Genome Res. May 2019 29: 809-818; Published in Advance April 2, 2019, doi:10.1101/gr.243592.118
...was a conserved armadillo repeat domain spanning exons 12–14 of PKP4 (plakophilin 4, also known as p0071). Qualifying variants occurred in 0.61% of ALS cases and 0.13% of controls (OR = 4.6, P = 4.1 × 10−5). While not -wide significant, PKP4 is a relevant candidate gene that has been previously linked to various...
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Resource: RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse
- Catherine M. Farrell,
- Tamara Goldfarb,
- Sanjida H. Rangwala,
- Alexander Astashyn,
- Olga D. Ermolaeva,
- Vichet Hem,
- Kenneth S. Katz,
- Vamsi K. Kodali,
- Frank Ludwig,
- Craig L. Wallin,
- Kim D. Pruitt,
- and Terence D. Murphy
Genome Res. January 2022 32: 175-188; Published in Advance December 7, 2021, doi:10.1101/gr.275819.121
...,B), and feature qualifiers for metadata displays. Terms from the Sequence Ontology (SO) (Eilbeck et al. 2005) were additionally used to provide further specificity for features lacking a specific INSDC feature or class, and SO terms were also used to define -anchored features in GFF3- and big...
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Research: An iPSC-based model of 47,XYY Jacobs syndrome reveals a DNA methylation-independent transcriptional dysregulation shared with male X aneuploid cells
- Veronica Astro,
- Kelly Yojanna Cardona-Londoño,
- Lorena Viridiana Cortés-Medina,
- Rawan Alghamdi,
- Gustavo Ramírez-Calderón,
- Fotios Kefalas,
- Jair Dilmé-Capó,
- Santiago Radío,
- and Antonio Adamo
Genome Res. July 2025 35: 1503-1517; Published in Advance June 10, 2025, doi:10.1101/gr.279716.124
...enrichment for processes related to neurological functions. However, although this transcriptomic convergence underscores potential commonalities in the molecular pathways underpinning the pathophysiology of male sex-chromosome aneuploidies, whether this common transcriptional dysregulation is conserved...
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Research: Deciphering the largest disease-associated transcript isoforms in the human neural retina with advanced long-read sequencing approaches
- Merel Stemerdink,
- Tabea Riepe,
- Nick Zomer,
- Renee Salz,
- Michael Kwint,
- Jaap Oostrik,
- Raoul Timmermans,
- Barbara Ferrari,
- Stefano Ferrari,
- Alfredo Dueñas Rey,
- Emma Delanote,
- Suzanne E. de Bruijn,
- Hannie Kremer,
- Susanne Roosing,
- Frauke Coppieters,
- Alexander Hoischen,
- Frans P.M. Cremers,
- Peter A.C. ‘t Hoen,
- Erwin van Wijk,
- and Erik de Vrieze
Genome Res. April 2025 35: 725-739; Published in Advance March 4, 2025, doi:10.1101/gr.280060.124
.... 2021; Linnert et al. 2023). Therefore, CIB2 is included in our analyses as these results could add to the discussion of whether it qualifies as an Usher syndrome–associated gene.Obtaining a comprehensive understanding of the Usher syndrome–associated transcript isoforms in the human retina is crucial...
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Research: SWATH-MS-based proteogenomic analysis reveals the involvement of alternative splicing in poplar upon lead stress
- Fu-Yuan Zhu,
- Xin Chen,
- Yu-Chen Song,
- Lydia Pui Ying Lam,
- Yuki Tobimatsu,
- Bei Gao,
- Mo-Xian Chen,
- and Fu-Liang Cao
Genome Res. March 2023 33: 371-385; Published in Advance March 24, 2023, doi:10.1101/gr.277473.122
...of Educational Department of China and the Key Lab of Tree Genetics and Silvicultural Sciences of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China; 2Key Laboratory of State Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology...
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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
...suggested a greater functional relevance for conserved regulatory activity (Arnold et al. 2014; Castelijns et al. 2020; VanOudenhove et al. 2020; Wong et al. 2020). In contrast, lineage-specific elements appear partly compensatory of proximally lost events (Arnold et al. 2014; Berthelot et al. 2018...
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