Searching journal content for articles similar to Hormozdiari et al. 21 (12): 2203.

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  1. Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
    • Damira Veseljak,
    • Evelin Despot-Slade,
    • Marin Volarić,
    • Lucija Horvat,
    • Tanja Vojvoda Zeljko,
    • Nevenka Meštrović,
    • and Brankica Mravinac
    Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
    ...Zagreb, Croatia Corresponding author: Brankica.Mravinac@irb.hrAbstractTandemly repeated satellite DNAs (satDNAs) are among the most abundant and fastest-evolving eukaryotic sequences, but the way they model s is still elusive. Here, we investigate the evolutionary dynamics of satDNAs in the extremely sat...
  2. Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
    • Olga M. Sigalova,
    • Mattia Forneris,
    • Frosina Stojanovska,
    • Bingqing Zhao,
    • Rebecca R. Viales,
    • Adam Rabinowitz,
    • Fayrouz Hammal,
    • Benoît Ballester,
    • Judith B. Zaugg,
    • and Eileen E.M. Furlong
    Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
    ...). Because we used paired-end (PE) sequencing for the ChIP-seq, we reasoned that indels could be included without creating mappability issues. Relatively long-read PE sequencing also raises the proportion of reads overlapping indels, thus increasing the number of reads that would be discarded if indels were...
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  3. Research: The rate of de novo structural variation is increased in in vitro–produced offspring and preferentially affects the paternal genome
    • Young-Lim Lee,
    • Aniek C. Bouwman,
    • Chad Harland,
    • Mirte Bosse,
    • Gabriel Costa Monteiro Moreira,
    • Roel F. Veerkamp,
    • Erik Mullaart,
    • Nadine Cambisano,
    • Martien A.M. Groenen,
    • Latifa Karim,
    • Wouter Coppieters,
    • Michel Georges,
    • and Carole Charlier
    Genome Res. September 2023 33: 1455-1464; Published in Advance October 4, 2023, doi:10.1101/gr.277884.123
    .... All samples were then sequenced on Illumina HiSeq 2000 instruments, using the 2 × 100-bp paired-end protocol, by the GIGA Genomics platform (University of Liège). The sequence data were mapped using BWA-MEM 0.7.5a (Li 2013) to bovine reference ARS-UCD1.2. Afterward, SAMtools 1.9 (Li and Durbin 2009...
  4. Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
    • Angelo A. Ruggieri,
    • Luca Livraghi,
    • James J. Lewis,
    • Elizabeth Evans,
    • Francesco Cicconardi,
    • Laura Hebberecht,
    • Yadira Ortiz-Ruiz,
    • Stephen H. Montgomery,
    • Alfredo Ghezzi,
    • José Arcadio Rodriguez-Martinez,
    • Chris D. Jiggins,
    • W. Owen McMillan,
    • Brian A. Counterman,
    • Riccardo Papa,
    • and Steven M. Van Belleghem
    Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
    ...for structural variation to serve as raw material for adaptive evolution.Structural variants (SVs) in s are a ubiquitous component of within and between species genomic variation (Mérot et al. 2020; Zhang et al. 2021). The larger size of SVs, when compared with single nucleotide polymorphisms (SNPs), may...
  5. Method: Simultaneous profiling of host expression and microbial abundance by spatial metatranscriptome sequencing
    • Lin Lyu,
    • Xue Li,
    • Ru Feng,
    • Xin Zhou,
    • Tuhin K. Guha,
    • Xiaofei Yu,
    • Guo Qiang Chen,
    • Yufeng Yao,
    • Bing Su,
    • Duowu Zou,
    • Michael P. Snyder,
    • and Lei Chen
    Genome Res. March 2023 33: 401-411; Published in Advance March 27, 2023, doi:10.1101/gr.277178.122
    ..., and then the P7 and P5 adapters were added. Sequencing was performed using Illumina NovaSeq 6000 sequencer with a sequencing depth targeting at least 50,000 reads per spot with a paired-end 150-bp (PE150) reading strategy.ST data processing and analysisRaw reads were aligned to the human transcriptome GRCh38...
  6. Research: Small polymorphisms are a source of ancestral bias in structural variant breakpoint placement
    • Peter A. Audano and
    • Christine R. Beck
    Genome Res. January 2024 34: 7-19; Published in Advance January 4, 2024, doi:10.1101/gr.278203.123
    ...are subject to systematic bias affecting variant representation. To understand why SV breakpoints are inconsistent across samples, we reanalyzed 64 phased haplotypes constructed from long-read assemblies released by the Human Genome Structural Variation Consortium (HGSVC). We identify 882 SV insertions...
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  7. 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 evolutionary forces affecting evolution and divergence in holocentric organisms.Results84 Leptidea sinapis males were sampled across Sweden and used for paired-end Illumina sequencing. Chromosome-specific demographic histories were inferred with SMC++ (Terhorst et al. 2017) using six “distinguished...
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  8. Resource: Genome variation and population structure among 1142 mosquitoes of the African malaria vector species Anopheles gambiae and Anopheles coluzzii
    • The Anopheles gambiae 1000 Genomes Consortium
    Genome Res. October 2020 30: 1533-1546; Published in Advance September 28, 2020, doi:10.1101/gr.262790.120
    ...and ecological processes and help to further accelerate scientific discovery and applied research.The Anopheles gambiae 1000 Genomes (Ag1000G) Project (https://www.malariagen.net/projects/ag1000g) was established in 2013 to build a large-scale open data resource on natural genetic variation in malaria mosquito...
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  9. Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
    • Alejandro Martin-Trujillo,
    • Paras Garg,
    • Nihir Patel,
    • Bharati Jadhav,
    • and Andrew J. Sharp
    Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
    ...-mapping methods such as CAVIAR allow the integration of LD structure and association statistics in the model, allowing the evaluation of multiple variants simultaneously and providing an estimate of causality for each. In summary, our results highlight the importance of integrating fine-mapping analysis...
  10. Review: Advancing genomic technologies and clinical awareness accelerates discovery of disease-associated tandem repeat sequences
    • Terence Gall-Duncan,
    • Nozomu Sato,
    • Ryan K.C. Yuen,
    • and Christopher E. Pearson
    Genome Res. January 2022 32: 1-27; Published in Advance December 29, 2021, doi:10.1101/gr.269530.120
    .... TRs are a common form of genetic variation with biological consequences, observed, so far, in humans, dogs, plants, oysters, and yeast. Repeat diseases show atypical clinical features, genetic anticipation, and multiple and partially penetrant phenotypes among family members. Discovery of disease...
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