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Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
- Tomáš Brůna,
- Alexandre Lomsadze,
- and Mark Borodovsky
Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
...GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic s Tomáš Brůna1,4,5, Alexandre Lomsadze2,4 and Mark Borodovsky1,2,3 1School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA; 2Wallace H. Coulter Department of Biomedical...
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Research: Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists
- Marcin P. Sajek,
- Danielle Y. Bilodeau,
- Michael A. Beer,
- Emma Horton,
- Yukiko Miyamoto,
- Katrina B. Velle,
- Lars Eckmann,
- Lillian Fritz-Laylin,
- Olivia S. Rissland,
- and Neelanjan Mukherjee
Genome Res. October 2024 34: 1570-1581; Published in Advance September 26, 2024, doi:10.1101/gr.279526.124
...found that G. lamblia assemblage A does not use any known auxiliary element (Bilodeau et al. 2022), highlighting the potential diversity of cleavage site recognition within the eukaryotic tree.View larger version: In this window In a new window Figure 1. Characterization of poly(A) signals in diverse...
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Perspective: Ribosome decision graphs for the representation of eukaryotic RNA translation complexity
- Jack A.S. Tierney,
- Michał Świrski,
- Håkon Tjeldnes,
- Jonathan M. Mudge,
- Joanna Kufel,
- Nicola Whiffin,
- Eivind Valen,
- and Pavel V. Baranov
Genome Res. April 2024 34: 530-538; Published in Advance May 7, 2024, doi:10.1101/gr.278810.123
...representation of eukaryotic translation complexity and focuses on locations critical for translation regulation. We show how RDGs can be used for depicting translated regions and for analyzing genetic variation and quantitative -wide data on translation for characterization of regulatory modulators...
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RECOMB 2022 Special/Methods: Learning probabilistic protein–DNA recognition codes from DNA-binding specificities using structural mappings
- Joshua L. Wetzel,
- Kaiqian Zhang,
- and Mona Singh
Genome Res. September 2022 32: 1776-1786; Published in Advance September 19, 2022, doi:10.1101/gr.276606.122
...to predict specificities for uncharacterized TFs or TFs mutated in disease. Here we introduce recognition code learning via automated mapping of protein–DNA structural interfaces (rCLAMPS), a probabilistic approach that uses DNA-binding specificities for TFs from the same structural family to simultaneously...
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Perspective: Recognition of the polycistronic nature of human genes is critical to understanding the genotype-phenotype relationship
- Marie A. Brunet,
- Sébastien A. Levesque,
- Darel J. Hunting,
- Alan A. Cohen,
- and Xavier Roucou
Genome Res. May 2018 28: 609-624; Published in Advance April 6, 2018, doi:10.1101/gr.230938.117
...). Although two decades have passed since the first eukaryotic was sequenced, assigning translated ORFs to genetic loci remains a daunting task (Basrai et al. 1997; Claverie et al. 1997; Ladoukakis et al. 2011). Indeed, current annotations rely partly on ORF prediction algorithms that are only reliable...
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Research: HNRNPA1 promotes recognition of splice site decoys by U2AF2 in vivo
- Jonathan M. Howard,
- Hai Lin,
- Andrew J. Wallace,
- Garam Kim,
- Jolene M. Draper,
- Maximilian Haeussler,
- Sol Katzman,
- Masoud Toloue,
- Yunlong Liu,
- and Jeremy R. Sanford
Genome Res. May 2018 28: 689-698; Published in Advance April 12, 2018, doi:10.1101/gr.229062.117
...) with myriad cis-regulatory elements scattered throughout pre-mRNAs. These molecular recognition events are critical for defining the protein-coding sequences (exons) within pre-mRNAs and directing spliceosome assembly on noncoding regions (introns). One of the earliest events in this process is recognition...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...outperformed local k-mer encoding by 10.19% in C. elegans, suggesting animals’ reliance on nucleotide-level chemical features for methylation recognition (Feng et al. 2010).Microbial groups displayed significant prokaryotic-eukaryotic differentiation. Prokaryotes (E. coli, G. subterraneus, G. pickeringii...
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Research: Exploring the DNA-recognition potential of homeodomains
- Stephanie W. Chu,
- Marcus B. Noyes,
- Ryan G. Christensen,
- Brian G. Pierce,
- Lihua J. Zhu,
- Zhiping Weng,
- Gary D. Stormo,
- and Scot A. Wolfe
Genome Res. October 2012 22: 1889-1898; Published in Advance April 26, 2012, doi:10.1101/gr.139014.112
...positions within most eukaryotes (Fig. 1), and there is a corresponding paucity in the diversity of preferred recognition sequences observed for the characterized HD population (Berger et al. 2008; Noyes et al. 2008a). This focused sequence preference is similar to many other families of DNA-binding domains...
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Research: Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome
- Tim R. Mercer,
- Marcel E. Dinger,
- Cameron P. Bracken,
- Gabriel Kolle,
- Jan M. Szubert,
- Darren J. Korbie,
- Marjan E. Askarian-Amiri,
- Brooke B. Gardiner,
- Gregory J. Goodall,
- Sean M. Grimmond,
- and John S. Mattick
Genome Res. December 2010 20: 1639-1650; Published in Advance November 2, 2010, doi:10.1101/gr.112128.110
...Regulated post-transcriptional RNA cleavage diversifies the eukaryotic transcriptome Tim R. Mercer 1 , 4 , Marcel E. Dinger 1 , 4 , Cameron P. Bracken 2 , 3 , Gabriel Kolle 1 , Jan M. Szubert 2 , Darren J. Korbie 1...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...MutSꞵ 221 complex, which repairs larger insertions and deletions. Alternatively, if MSH6 and MSH2 form 222 an MMR recognition heterodimer MutSɑ, one to two base pair mismatches and indels are 223 repaired. MSH6 is found in P3, indicating a differential regulation of these portions of the MMR 224...
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