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Method: Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences
- Chencheng Xu,
- Suying Bao,
- Ye Wang,
- Wenxing Li,
- Hao Chen,
- Yufeng Shen,
- Tao Jiang,
- and Chaolin Zhang
Genome Res. July 2024 34: 1052-1065; Published in Advance July 26, 2024, doi:10.1101/gr.279044.124
...of in silico mutations in each nucleotide position in the region on the two splice sites is shown in the heatmaps at the bottom. The nucleotide base in each position of the human gene sequence is indicated by “x.”Prediction of lineage-specific splicing changesGiven the imperfect accuracy of all compared...
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Research: Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer
- Myrthe Jager,
- Francis Blokzijl,
- Ewart Kuijk,
- Johanna Bertl,
- Maria Vougioukalaki,
- Roel Janssen,
- Nicolle Besselink,
- Sander Boymans,
- Joep de Ligt,
- Jakob Skou Pedersen,
- Jan Hoeijmakers,
- Joris Pothof,
- Ruben van Boxtel,
- and Edwin Cuppen
Genome Res. July 2019 29: 1067-1077; Published in Advance June 20, 2019, doi:10.1101/gr.246223.118
...al. 1995; Sijbers et al. 1996a; Kirschner and Melton 2010; Iyama and Wilson 2013). ERCC1 is mutated in ∼4.5% of all human tumors, and single nucleotide polymorphisms in ERCC1 have been linked to an increased risk of developing colorectal cancer (Ni et al. 2014). Ercc1−/Δ mice are hemizygous...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...to a particular MHC-I gene (Supplemental Tables S8 and S9; Supplemental Fig. S9). Combining expression patterns with these polymorphism estimates (Fig. 8) suggests that sequences highly expressed in adults, which are also highly polymorphic, represent classical (MHC-Ia) genes. Sequences with high relative...
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Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
- Clotilde Garrido,
- Cintia Gómez-Muñoz,
- Etienne Kornobis,
- Nicolas Agier,
- Oana Ilioaia,
- Gilles Fischer,
- and Zhou Xu
Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
..., relatively little is known about TL regulation and distribution in natural yeast strains. Recent large-scale population genomics studies revealed great genetic diversity encompassing, beyond single-nucleotide polymorphisms, structural variations, aneuploidies, and polyploidies (Peter et al. 2018; O...
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Method: Efficient identification of Y chromosome sequences in the human and Drosophila genomes
- Antonio Bernardo Carvalho and
- Andrew G. Clark
Genome Res. November 2013 23: 1894-1907; Published in Advance August 6, 2013, doi:10.1101/gr.156034.113
...in the middle of the reference scaffold NT_011875 (Supplemental Table S3). We later found that this insertion is a polymorphism covered by high-quality sequence (fosmid AC236424, obtained as part of the Human Genome Structural Variation Project [Kidd et al. 2008] and BAC clone AC245170). The rediscovery...
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Research: Degrees of convergent evolution in rodent adaptations to arid environments
- Domitille Chalopin,
- Carine Rey,
- Jeremy Ganofsky,
- Juliana Blin,
- Pascale Chevret,
- Marion Mouginot,
- Laurent Guéguen,
- Bastien Boussau,
- Sophie Pantalacci,
- and Marie Sémon
Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
...the whole kidney transcriptome down to the coding sequences and expression level of individual genes. Transcriptome-level signatures reflect convergent changes in cell proportions, suggesting convergent structural adaptations of the kidney. A large proportion of genes shows convergent substitutions...
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Research: Natural variation of histone modification and its impact on gene expression in the rat genome
- Carola Rintisch,
- Matthias Heinig,
- Anja Bauerfeind,
- Sebastian Schafer,
- Christin Mieth,
- Giannino Patone,
- Oliver Hummel,
- Wei Chen,
- Stuart Cook,
- Edwin Cuppen,
- Maria Colomé-Tatché,
- Frank Johannes,
- Ritsert C. Jansen,
- Helen Neil,
- Michel Werner,
- Michal Pravenec,
- Martin Vingron,
- and Norbert Hubner
Genome Res. June 2014 24: 942-953; Published in Advance May 2, 2014, doi:10.1101/gr.169029.113
...). In line with our previous observation in parental rats, H3K27me3 peaks were much broader with lower sequencing coverage and thus, only 117 QTLs were observed for this modification. Furthermore, 252 H3K4me3 peaks showed linkage to two or more quantitative trait loci (QTLs), emphasizing the complex nature...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...and Wasserman 2013). PWMs, often displayed as sequence logos, which are bar graphs with bars made of nucleotide symbol letters, help illustrate binding motif conservation. Energy matrices, an alternative to PWMs, account for binding energy contributions. Still, PWMs remain dominant owing to early statistical...
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Research: The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
- Santosh S. Atanur,
- İnanç Birol,
- Victor Guryev,
- Martin Hirst,
- Oliver Hummel,
- Catherine Morrissey,
- Jacques Behmoaras,
- Xose M. Fernandez-Suarez,
- Michelle D. Johnson,
- William M. McLaren,
- Giannino Patone,
- Enrico Petretto,
- Charles Plessy,
- Kathleen S. Rockland,
- Charles Rockland,
- Kathrin Saar,
- Yongjun Zhao,
- Piero Carninci,
- Paul Flicek,
- Ted Kurtz,
- Edwin Cuppen,
- Michal Pravenec,
- Norbert Hubner,
- Steven J.M. Jones,
- Ewan Birney,
- and Timothy J. Aitman
Genome Res. June 2010 20: 791-803; Published in Advance April 29, 2010, doi:10.1101/gr.103499.109
...of heterozygous nucleotide variants. However, laboratory rat strains such as SHR have been inbred for more than 130 generations and are therefore homozygous at almost all loci across the . Lower depth of sequence coverage may therefore be required for such inbred s, because a single allele is present at almost...
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LETTER: In Silico Model-Driven Assessment of the Effects of Single Nucleotide Polymorphisms (SNPs) on Human Red Blood Cell Metabolism
- Neema Jamshidi,
- Sharon J. Wiback,
- and Bernhard Ø. Palsson
Genome Res. November 1, 2002 12: 1687-1692; doi:10.1101/gr.329302
...project and the construction of single nucleotide polymorphism (SNP) maps have lead to significant efforts to find SNPs that can be linked to pathophysiology. In silico models of complete biochemical reaction networks relate a cell's individual reactions to the function of the entire network. Sequence...

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