Searching journal content for articles similar to Liang et al. 19 (10): 1912.

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Resource: Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal expanded transporter repertoire and duplication of entire chromosome ends including subtelomeric regions
- Rodrigo P. Baptista,
- Yiran Li,
- Adam Sateriale,
- Mandy J. Sanders,
- Karen L. Brooks,
- Alan Tracey,
- Brendan R.E. Ansell,
- Aaron R. Jex,
- Garrett W. Cooper,
- Ethan D. Smith,
- Rui Xiao,
- Jennifer E. Dumaine,
- Peter Georgeson,
- Bernard J. Pope,
- Matthew Berriman,
- Boris Striepen,
- James A. Cotton,
- and Jessica C. Kissinger
Genome Res. January 2022 32: 203-213; Published in Advance November 11, 2021, doi:10.1101/gr.275325.121
...and compared CpIRef, CpIA, Ch30976, and CtUGA55 which have >95% identity to assess differences in gene content. The new annotation for each species was generated with three de novo approaches and evidence-based manual annotation. Curation of the annotation was performed pairwise between each assembly to take...
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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
...genomic-, transcriptomic-, and protein-derived evidence that has been developed with a focus on large plant and animal s. GeneMark-ETP first identifies genomic loci where extrinsic data are sufficient for making gene predictions with “high confidence.” The genes situated in the genomic space between...
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Research: Multiple Pristionchus pacificus genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes
- Neel Prabh and
- Christian Rödelsperger
Genome Res. July 2022 32: 1315-1327; Published in Advance May 26, 2022, doi:10.1101/gr.276431.121
...of duplicated and de novo genes (Rödelsperger et al. 2019). One major prediction of this rapid turnover model is that the contribution of both categories of origin will depend on the evolutionary distance of the comparison. In this study, we explicitly test this model using genomic data of the nematode...
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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...species, and the intrinsic uncertainty in the discovery of functional coding and noncoding elements in newly assembled s (Yandell and Ence 2012).Currently, annotation approaches can be broadly divided into three main types: evidence-based methods, ab initio, and evidence-driven gene predictions (Yandell...
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PERSPECTIVE: Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity
- Michael Freeling and
- Brian C. Thomas
Genome Res. July 2006 16: 805-814; doi:10.1101/gr.3681406
...Gene-balanced duplications, like tetraploidy, provide predictable drive to increase morphological complexity Michael Freeling 1 , 3 and Brian C. Thomas 2 1 Department of Plant and Molecular Biology, University of California–Berkeley, Berkeley, California...
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Research: De novo genome assemblies of two cryptodiran turtles with ZZ/ZW and XX/XY sex chromosomes provide insights into patterns of genome reshuffling and uncover novel 3D genome folding in amniotes
- Basanta Bista,
- Laura González-Rodelas,
- Lucía Álvarez-González,
- Zhi-qiang Wu,
- Eugenia E. Montiel,
- Ling Sze Lee,
- Daleen B. Badenhorst,
- Srihari Radhakrishnan,
- Robert Literman,
- Beatriz Navarro-Dominguez,
- John B. Iverson,
- Simon Orozco-Arias,
- Josefa González,
- Aurora Ruiz-Herrera,
- and Nicole Valenzuela
Genome Res. October 2024 34: 1553-1569; Published in Advance October 16, 2024, doi:10.1101/gr.279443.124
.... 2014). As architecture and function are interdependent (Rowley and Corces 2018), 3D chromatin folding is expected to coevolve along with functional genomic changes. This view predicts that 3D chromatin remodeling should underlie phenotypic evolution and adaptation to changing environments...
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Resource: Building better genome annotations across the tree of life
- Adam H. Freedman and
- Timothy B. Sackton
Genome Res. May 2025 35: 1261-1276; Published in Advance April 15, 2025, doi:10.1101/gr.280377.124
...(Table 2, below). Although “ annotation” is often treated as an omnibus term that includes both the prediction of the genomic positions of genes and constituent isoforms and the assigning of gene symbols and functions, we focus on the first of these two components. Our goals are to determine (1) which...
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Resource: The pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation
- Zhengcao Li,
- Xiaohong Liu,
- Chen Wang,
- Zhenyang Li,
- Bo Jiang,
- Ruifeng Zhang,
- Lu Tong,
- Youping Qu,
- Sheng He,
- Haifan Chen,
- Yafei Mao,
- Qingnan Li,
- Torsten Pook,
- Yu Wu,
- Yanjun Zan,
- Hui Zhang,
- Lu Li,
- Keying Wen,
- and Yaosheng Chen
Genome Res. October 2023 33: 1833-1847; Published in Advance November 1, 2023, doi:10.1101/gr.277638.122
...2002; Maccari et al. 2017).Gene annotationAn annotation pipeline integrating ab initio prediction, homologous-based prediction, and expression evidence-based prediction was performed for gene model prediction. Repeat sequences were first masked using RepeatMasker with a repeat library downloaded from...
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Resource: The fine-scale recombination rate variation and associations with genomic features in a butterfly
- Aleix Palahí i Torres,
- Lars Höök,
- Karin Näsvall,
- Daria Shipilina,
- Christer Wiklund,
- Roger Vila,
- Peter Pruisscher,
- and Niclas Backström
Genome Res. May 2023 33: 810-823; Published in Advance June 12, 2023, doi:10.1101/gr.277414.122
...and the density of different classes of transposable elements, most notably a significant enrichment of short interspersed nucleotide elements in genomic regions with higher recombination rate. Finally, the analyses unveiled significant enrichment of genes involved in farnesyltranstransferase activity...
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Resource: Global networks of functional coupling in eukaryotes from comprehensive data integration
- Andrey Alexeyenko and
- Erik L.L. Sonnhammer
Genome Res. June 2009 19: 1107-1116; Published in Advance February 25, 2009, doi:10.1101/gr.087528.108
.... However, the user is typically interested in smaller subnetworks around a set of query genes. The user can control the subnetwork retrieval and thus its information content. The evidence base can be limited to particular species or data types (e.g., “mammalian” or “coexpression” only). The query...

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