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Corrigendum: Corrigendum: TRUB1 is the predominant pseudouridine synthase acting on mammalian mRNA via a predictable and conserved code
- Modi Safra,
- Ronit Nir,
- Daneyal Farouq,
- Ilya Vainberg Slutskin,
- and Schraga Schwartz
Genome Res. August 2017 27: 1460; doi:10.1101/gr.225870.117
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Research: Functional genomics analysis of developing zebrafish and human endoderm reveals highly conserved cis-regulatory modules acting during vertebrate organogenesis
- Daniela M Riley,
- Randa Elsayed,
- Mark D Walsh,
- Simaran Johal,
- Ying Lin,
- Harry Walton,
- Till Bretschneider,
- Sascha Ott,
- and Andrew C Nelson
Genome Res. March 4, 2026 gr.280838.125; Published in Advance March 4, 2026, doi:10.1101/gr.280838.125
...1 Functional genomics analysis of developing zebrafish and human endoderm reveals 1 highly conserved cis-regulatory modules acting during vertebrate organogenesis 2 3 Daniela M. Riley1,†, Randa Elsayed1,†, Mark D. Walsh2,†, Simaran Johal2, Ying Lin3,4, Harry 4 Walton1, Till Bretschneider5, Sascha...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 gr.281113.125; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...1 Title 1 Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals 2 conserved gene alterations linked to Parkinson’s disease 3 Running title: Substantia nigra aging linked to Parkinson 4 Kangli Wang1, Weikun Xia1, Yingli Gu1, Songpeng Zu1, Qian Yang2, Maria Luisa Amaral1...
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Research: Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes
- Yu-Chi Chen,
- David L.J. Vendrami,
- Maximilian L. Huber,
- Luisa E.Y. Handel,
- Christopher R. Cooney,
- Joseph I. Hoffman,
- and Toni I. Gossmann
Genome Res. June 2025 35: 1313-1324; Published in Advance March 31, 2025, doi:10.1101/gr.279428.124
...of NUMTs with at least one intact coding gene (cNUMTs) identified using the vertebrate mitochondrial genetic code. Of the 114,047 NUMTs identified, 6429 (5229 in 379 mammalian species and 1200 in 319 avian species) retained at least one intact mitochondrial gene. In mammals, the number of c...
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Research: Endonucleolytic cleavage is the primary mechanism of decay elicited by C. elegans nonsense-mediated mRNA decay
- Marcus J. Viscardi,
- Enisha Sehgal,
- and Joshua A. Arribere
Genome Res. June 2025 35: 1337-1348; Published in Advance May 9, 2025, doi:10.1101/gr.280046.124
...truncated and dominantly acting proteins that harm cells. Eukaryotic cells protect themselves by degrading such mRNAs via the nonsense-mediated mRNA decay (NMD) pathway. The precise reactions by which cells attack NMD-target mRNAs remain obscure, precluding a biochemical understanding of NMD and hampering...
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Method: CodonBERT large language model for mRNA vaccines
- Sizhen Li,
- Saeed Moayedpour,
- Ruijiang Li,
- Michael Bailey,
- Saleh Riahi,
- Lorenzo Kogler-Anele,
- Milad Miladi,
- Jacob Miner,
- Fabien Pertuy,
- Dinghai Zheng,
- Jun Wang,
- Akshay Balsubramani,
- Khang Tran,
- Minnie Zacharia,
- Monica Wu,
- Xiaobo Gu,
- Ryan Clinton,
- Carla Asquith,
- Joseph Skaleski,
- Lianne Boeglin,
- Sudha Chivukula,
- Anusha Dias,
- Tod Strugnell,
- Fernando Ulloa Montoya,
- Vikram Agarwal,
- Ziv Bar-Joseph,
- and Sven Jager
Genome Res. July 2024 34: 1027-1035; Published in Advance July 1, 2024, doi:10.1101/gr.278870.123
.... The pretrained model can also be generalized to a diverse set of supervised learning tasks. We pretrained CodonBERT using 10 million mRNA coding sequences (CDSs) spanning an evolutionarily diverse set of organisms. Next, we used it to perform several mRNA prediction tasks, including protein expression and mRNA...
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Research: Convergent relaxation of molecular constraint in herbivores reveals the changing role of liver and kidney functions across mammalian diets
- Matthew D. Pollard,
- Wynn K. Meyer,
- and Emily E. Puckett
Genome Res. December 2024 34: 2176-2189; Published in Advance November 22, 2024, doi:10.1101/gr.278930.124
...to increases.The weaker signal we observed in genes with positive correlations than in those with negative correlations could also indicate that constraint on coding sequence is less predictable during adaptation to increased herbivory than to increased carnivory. Low predictability may be mediated by diverse...
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Research: Modeling alternative translation initiation sites in plants reveals evolutionarily conserved cis-regulatory codes in eukaryotes
- Ting-Ying Wu,
- Ya-Ru Li,
- Kai-Jyun Chang,
- Jhen-Cheng Fang,
- Daisuke Urano,
- and Ming-Jung Liu
Genome Res. February 2024 34: 272-285; Published in Advance March 13, 2024, doi:10.1101/gr.278100.123
...-specific sequence features. We explored their conserved regulatory role across dicot and monocot plants, viruses, and humans.ResultsML enables cross-species TIS predictions in plantsTo comprehensively and precisely build models that predict TISs in plant mRNAs, we used tomato ribosome profiling data sets...
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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
...heterochromatin dissociation during meiotic diplotene. PLoS Genet 17: e1009778. doi:10.1371/journal.pgen.1009778 ↵Cowley M, Wood AJ, Böhm S, Schulz R, Oakey RJ. 2012. Epigenetic control of alternative mRNA processing at the imprinted Herc3/Nap1l5 locus. Nucleic Acids Res 40: 8917–8926. doi:10.1093/nar/gks654...
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Resource: A spatiotemporally resolved atlas of mRNA decay in the C. elegans embryo reveals differential regulation of mRNA stability across stages and cell types
- Felicia Peng,
- C. Erik Nordgren,
- and John Isaac Murray
Genome Res. August 2024 34: 1235-1252; Published in Advance August 14, 2024, doi:10.1101/gr.278980.124
..., experimental tractability, and conservation of RNA decay machinery with humans. In this study, we undertook the first global measurement of mRNA decay rates throughout C. elegans embryogenesis at high resolution by pairing a transcription inhibition approach with both bulk and single-cell RNA sequencing. Using...

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