Searching journal content for articles similar to Engelhardt et al. 21 (11): 1969.

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Research: Plant 24-nt reproductive phasiRNAs from intramolecular duplex mRNAs in diverse monocots
- Atul Kakrana,
- Sandra M. Mathioni,
- Kun Huang,
- Reza Hammond,
- Lee Vandivier,
- Parth Patel,
- Siwaret Arikit,
- Olga Shevchenko,
- Alex E. Harkess,
- Bruce Kingham,
- Brian D. Gregory,
- James H. Leebens-Mack,
- and Blake C. Meyers
Genome Res. September 2018 28: 1333-1344; Published in Advance July 12, 2018, doi:10.1101/gr.228163.117
...-meiotic anthers (Supplemental Table S1). In total, we generated 23 sRNA libraries combined with 15 published but not extensively characterized libraries (Harkess et al. 2017). We recently annotated 166 miRNA precursors (105 unique miRNAs from 78 families) in asparagus, including known/conserved and novel mi...
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Research: The identification and functional annotation of RNA structures conserved in vertebrates
- Stefan E. Seemann,
- Aashiq H. Mirza,
- Claus Hansen,
- Claus H. Bang-Berthelsen,
- Christian Garde,
- Mikkel Christensen-Dalsgaard,
- Elfar Torarinsson,
- Zizhen Yao,
- Christopher T. Workman,
- Flemming Pociot,
- Henrik Nielsen,
- Niels Tommerup,
- Walter L. Ruzzo,
- and Jan Gorodkin
Genome Res. August 2017 27: 1371-1383; Published in Advance May 9, 2017, doi:10.1101/gr.208652.116
...for this article.] Computational analyses have suggested many conserved structured RNAs in vertebrate s (Washietl et al. 2005; Torarinsson et al. 2008; Parker et al. 2011; Smith et al. 2013). Recent transcriptome-wide experiments also support a diverse RNA structure landscape (Ding et al. 2014; Rouskin et al. 2014...
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RESEARCH: GAIA: Framework Annotation of Genomic Sequence
- L. Charles Bailey, Jr.,
- Stephen Fischer,
- Jonathan Schug,
- Jonathan Crabtree,
- Mark Gibson,
- and G. Christian Overton
Genome Res. March 1, 1998 8: 234-250; doi:10.1101/gr.8.3.234
...the region, which has guided the interpretation of the sequence data. Genome-scale sequencing imposes new conditions of quantity and context on the problem of understanding sequence data. As the name ‘‘-scale’’ implies, the goal is to make readily available sequence for at least one allele of any region from...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
....ResultsDistribution and phylogenetic analysis of SET domain proteins in fungiTo understand the diversity of SET domain proteins in fungal evolution, we performed domain-based functional annotations for all 23.64 million proteins from 1038 publicly available fungal s across nine phyla. This analysis identified 18,718 SET domain...
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Research: Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster
- Anna Grandchamp,
- Lucas Kühl,
- Marie Lebherz,
- Kathrin Brüggemann,
- John Parsch,
- and Erich Bornberg-Bauer
Genome Res. June 2023 33: 872-890; Published in Advance July 13, 2023, doi:10.1101/gr.277482.122
...phylogenetic studies that used long evolutionary distances, and population level studies that either used sparsely annotated reference s or did not investigate the genetic mechanisms underlying the creation of neORFs. A major result of our work is that neORF emergence is a frequent event, even when viewed from...
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Research: Competition for DNA binding between paralogous transcription factors determines their genomic occupancy and regulatory functions
- Yuning Zhang,
- Tiffany D. Ho,
- Nicolas E. Buchler,
- and Raluca Gordân
Genome Res. July 2021 31: 1216-1229; Published in Advance May 11, 2021, doi:10.1101/gr.275145.120
..., North Carolina 27708, USA Corresponding author: raluca.gordan@duke.eduAbstractMost eukaryotic transcription factors (TFs) are part of large protein families, with members of the same family (i.e., paralogous TFs) recognizing similar DNA-binding motifs but performing different regulatory functions. Many...
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Research: Comparative analysis of mammalian Y chromosomes illuminates ancestral structure and lineage-specific evolution
- Gang Li,
- Brian W. Davis,
- Terje Raudsepp,
- Alison J. Pearks Wilkerson,
- Victor C. Mason,
- Malcolm Ferguson-Smith,
- Patricia C. O'Brien,
- Paul D. Waters,
- and William J. Murphy
Genome Res. September 2013 23: 1486-1495; Published in Advance June 20, 2013, doi:10.1101/gr.154286.112
...36: 518–522. Bourque G, Pevzner PA. 2002. Genome-scale evolution: Reconstructing gene orders in the ancestral species. Genome Res 12: 26–36. Carvalho AB, Koerich LB, Clark AG. 2009. Origin and evolution of Y chromosomes: Drosophila tales. Trends Genet 25: 270–277. Chang TC, Klabnik JL, LiuWS. 2011...
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Resource: Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment
- Martin Ebeling,
- Erich Küng,
- Angela See,
- Clemens Broger,
- Guido Steiner,
- Marco Berrera,
- Tobias Heckel,
- Leonardo Iniguez,
- Thomas Albert,
- Roland Schmucki,
- Hermann Biller,
- Thomas Singer,
- and Ulrich Certa
Genome Res. October 2011 21: 1746-1756; Published in Advance August 23, 2011, doi:10.1101/gr.123117.111
...singlenucleotide polymorphisms (SNPs) and used homology-based annotation for transcript identification to design a M. fascicularisspecific gene expression microarray. With focus on drug safety, we performed a phylogenetic analysis of the SLCO drug transporter family and transcript profiling of cytokines...
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Research: Extensive de novo mutation rate variation between individuals and across the genome of Chlamydomonas reinhardtii
- Rob W. Ness,
- Andrew D. Morgan,
- Radhakrishnan B. Vasanthakrishnan,
- Nick Colegrave,
- and Peter D. Keightley
Genome Res. November 2015 25: 1739-1749; Published in Advance August 10, 2015, doi:10.1101/gr.191494.115
...predictors of mutation rate (Michaelson et al. 2012; Neale et al. 2012; Samocha et al. 2014; Zhu et al. 2014). However, investigations concerning the underlying mechanisms and the consistency of sequence context effects on mutability are only now emerging. At a broader genomic scale, evidence for mutation...
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Letter: Evolution of gene function and regulatory control after whole-genome duplication: Comparative analyses in vertebrates
- Karin S. Kassahn,
- Vinh T. Dang,
- Simon J. Wilkins,
- Andrew C. Perkins,
- and Mark A. Ragan
Genome Res. August 2009 19: 1404-1418; Published in Advance May 13, 2009, doi:10.1101/gr.086827.108
...the consequences of WGD, because the teleost lineage experienced an additional WGD soon after divergence from tetrapods and because five teleost genomes are available for comparative analysis. Here we present an integrated approach to characterize these post-duplication genomes based on genome-scale synteny...

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