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Research: The 22q11 low copy repeats are characterized by unprecedented size and structural variability
- Wolfram Demaerel,
- Yulia Mostovoy,
- Feyza Yilmaz,
- Lisanne Vervoort,
- Steven Pastor,
- Matthew S. Hestand,
- Ann Swillen,
- Elfi Vergaelen,
- Elizabeth A. Geiger,
- Curtis R. Coughlin,
- Stephen K. Chow,
- Donna McDonald-McGinn,
- Bernice Morrow,
- Pui-Yan Kwok,
- Ming Xiao,
- Beverly S. Emanuel,
- Tamim H. Shaikh,
- and Joris R. Vermeesch
Genome Res. September 2019 29: 1389-1401; doi:10.1101/gr.248682.119
..., driving variability and evolution. The Chromosome 22 LCRs (LCR22s) mediate nonallelic homologous recombination (NAHR) leading to the 22q11 deletion syndrome (22q11DS). However, LCR22s are among the most complex regions in the , and their structure remains unresolved. The difficulty in generating accurate...
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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
...and structurally variable regions in the , shaped by a complex dynamics of host-pathogen coevolution (for review, see Radwan et al. 2020). Beyond immunological significance, the MHC has thus become a prime model in evolutionary and comparative genomics, offering insights into birth-and-death processes, concerted...
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Research: Unraveling the architecture of major histocompatibility complex class II haplotypes in rhesus macaques
- Nanine de Groot,
- Marit van der Wiel,
- Ngoc Giang Le,
- Natasja G. de Groot,
- Jesse Bruijnesteijn,
- and Ronald E. Bontrop
Genome Res. November 2024 34: 1811-1824; Published in Advance October 23, 2024, doi:10.1101/gr.278968.124
...) in concert with adaptive sampling. In particular, the expansion and contraction of the primate DRB-region appear to be a dynamic process that involves the rearrangement of different cassettes of paralogous genes. These chromosomal recombination events are propagated by a conserved pseudogene, DRB6, which...
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Resource: The PanOryza pangene catalog of Asian cultivated rice
- Bruno Contreras-Moreira,
- Eshan Sharma,
- Shradha Saraf,
- Guy Naamati,
- Parul Gupta,
- Justin Elser,
- Dmytro Chebotarov,
- Kapeel Chougule,
- Zhenyuan Lu,
- Sharon Wei,
- Andrew Olson,
- Ian Tsang,
- Disha Lodha,
- Yong Zhou,
- Zhichao Yu,
- Wen Zhao,
- Jianwei Zhang,
- Sandeep Amberkar,
- Kawinnat Sue-Ob,
- Zhi Sun,
- Maria Martin,
- Kenneth L. McNally,
- Doreen Ware,
- Eric W. Deutsch,
- Dario Copetti,
- Rod A. Wing,
- Pankaj Jaiswal,
- Sarah Dyer,
- and Andrew R. Jones
Genome Res. January 2026 36: 226-238; Published in Advance December 12, 2025, doi:10.1101/gr.280790.125
..., pseudogenization, or gene model inaccuracies, which can be explored.Other groups have also explored or generated pans for rice. For example, Shang et al. (2022) sequenced, assembled, and annotated a 251 accession panel, demonstrating, as in our work, that LRR genes have variable copy number across s. Wu et al...
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Method: Genotyping of selected germline adaptive immune system loci using short-read sequencing data
- Michael K.B. Ford,
- Ananth Hari,
- Meredith Yeager,
- Lisa Mirabello,
- Stephen Chanock,
- Ibrahim Numanagić,
- COVNET Consortium,
- and S. Cenk Sahinalp
Genome Res. September 2025 35: 2076-2086; Published in Advance August 5, 2025, doi:10.1101/gr.280314.124
..., the variable class is a primary determinant of receptor binding structural diversity. These genes are highly duplicated and contain many pseudogenes, in some cases located on other chromosomes, as summarized in Table 1. These duplications, in conjunction with high sequence similarity and short length (on...
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Letter: Extreme variability among mammalian V1R gene families
- Janet M. Young,
- Hillary F. Massa,
- Li Hsu,
- and Barbara J. Trask
Genome Res. January 2010 20: 10-18; Published in Advance December 1, 2009, doi:10.1101/gr.098913.109
...appearing especially variable. There are over 100 functional V1Rs in the rat and mouse s, but only five (or fewer) intact V1Rs in the human and chimpanzee s along with a large number of pseudogenes (Liman 2006). The platypus possesses the largest V1R repertoire of any mammal studied to date, with more than...
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Research: Shared evolutionary trajectories of three independent neo-sex chromosomes in Drosophila
- Masafumi Nozawa,
- Yohei Minakuchi,
- Kazuhiro Satomura,
- Shu Kondo,
- Atsushi Toyoda,
- and Koichiro Tamura
Genome Res. November 2021 31: 2069-2079; Published in Advance October 21, 2021, doi:10.1101/gr.275503.121
...-X are under accelerated pseudogenization. To examine the generality of this pattern, we investigated the evolution of two additional neo-sex chromosomes that emerged independently in D. albomicans and D. americana and reanalyzed neo-sex chromosome evolution in D. miranda. Comparative genomic...
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Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
- A. Bernardo Carvalho,
- Bernard Y. Kim,
- and Fabiana Uno
Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
...window Figure 3. Sequence composition of selected regions of the D. melanogaster Y Chromosome, along with a control euchromatic region (white gene). Coding exons are shown as numbered black rectangles (unlabeled when pseudogenes), transposable elements in pink, simple satellites in blue (with darker...
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Resource: Complete sequencing of a cynomolgus macaque major histocompatibility complex haplotype
- Julie A. Karl,
- Trent M. Prall,
- Hailey E. Bussan,
- Joshua M. Varghese,
- Aparna Pal,
- Roger W. Wiseman,
- and David H. O'Connor
Genome Res. March 2023 33: 448-462; Published in Advance February 28, 2023, doi:10.1101/gr.277429.122
...in the MHC-I region. Unlike human leukocyte antigen (HLA) haplotypes, which contain three highly polymorphic class I genes (HLA-A, HLA-B, and HLA-C), the macaque MHC genomic region has undergone complex duplication, deletion, and rearrangement events such that different haplotypes contain a variable number...
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Research: Assessing the readiness of Oxford Nanopore sequencing for clinical genomics applications
- Judith Arres,
- Santosh Elavalli,
- Shalini Behl,
- Daniel Matias Sanchez,
- Ayesha Al Ali,
- Abdelrahman Ahmed Yehia Abdelaziz Saad,
- Azza Attia,
- Cyla Minas,
- Sharika Pariyachery,
- Shariq Ahmed,
- Fatmah Aldhuhoori,
- Nitu Thulasidharan,
- Gurunath Katagi,
- Omar Soliman,
- Shilp Purohit,
- Vinay Kusuma,
- Raony Cardenas,
- Thyago Cardoso,
- Luis F. Paulin,
- Philippe Sanio,
- Joseph Mafofo,
- Haiguo Wu,
- Val Zvereff,
- Albarah El-Khani,
- Fahed Al Marzooqi,
- Tiago R. Magalhães,
- Fritz J. Sedlazeck,
- and Javier Quilez
Genome Res. March 2026 36: 460-471; Published in Advance February 11, 2026, doi:10.1101/gr.280134.124
...regions underlying disorders like fragile X syndrome (FXS) (Stevanovski et al. 2022). ONT also enables variant phasing for inheritance and de novo mutation analyses (Cretu Stancu et al. 2017) and can distinguish clinically relevant genes from pseudogenes, improving diagnostic accuracy (Leija-Salazar et al...

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