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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
...of the OMKar method. (A) Input data. OMKar takes structural variant (SV) calls, copy number variation (CNV) calls, and sequence alignments as input. (B) Preprocessing and filtering. Low-confidence SVs and CNVs are removed. Chromosomes are segmented based on CNV boundaries and breakpoints, and a breakpoint...
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Research: AGAP duplicons associate with structural diversity at Chromosome 10q11.22
- Stefania Fornezza,
- Vincenza Simona Delvecchio,
- William T. Harvey,
- Philip C. Dishuck,
- Evan E. Eichler,
- and Giuliana Giannuzzi
Genome Res. October 2024 34: 1487-1499; Published in Advance September 25, 2024, doi:10.1101/gr.279454.124
...orientation and mediate the deletion of one copy in H10 haplotype. Genes mapped at the breakpoints are specified.Finally, we evaluated features that have been previously associated with breakpoint sequences of NAHR events, that is, long stretches of homology between nonallelic sequences, high GC content...
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Resource: Chromosome-level subgenome-aware de novo assembly provides insight into Saccharomyces bayanus genome divergence after hybridization
- Cory Gardner,
- Junhao Chen,
- Christina Hadfield,
- Zhaolian Lu,
- David Debruin,
- Yu Zhan,
- Maureen J. Donlin,
- Tae-Hyuk Ahn,
- and Zhenguo Lin
Genome Res. November 2024 34: 2133-2146; Published in Advance September 17, 2024, doi:10.1101/gr.279364.124
..., probably by sporulation, created some heterozygous chromosomes, such as Chr III, and some homozygous chromosomes, such as Chr XI.To validate the accuracy of inference of parental genomic regions by the BLAST approach, we mapped the raw sequences reads that were assigned to S. uvarum and S. eubayanus by spp...
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Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
- Qian Qin,
- Victoria Popic,
- Kirsty Wienand,
- Houlin Yu,
- Emily White,
- Akanksha Khorgade,
- Asa Shin,
- Christophe Georgescu,
- Catarina D. Campbell,
- Arthur Dondi,
- Niko Beerenwinkel,
- Francisca Vazquez,
- Aziz M. Al'Khafaji,
- and Brian J. Haas
Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
...-cell sequencing assays, pose further limitations for fusion detection as short reads are far less likely to span the breakpoint of the fusion transcript.Long-read isoform sequencing is made possible by Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT), enabling full-length isoform sequences via...
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Research: Genomic architecture constrained placental mammal X Chromosome evolution
- Wesley A. Brashear,
- Kevin R. Bredemeyer,
- and William J. Murphy
Genome Res. August 2021 31: 1353-1365; Published in Advance July 22, 2021, doi:10.1101/gr.275274.121
...of targeted BAC clone sequence) to the pig, human, and mouse assemblies. A comprehensive analysis of annotated X-linked orthologs in public databases demonstrated that the majority of ampliconic gene families were present on the ancestral placental X Chromosome. We generated a domestic cat Hi-C contact map...
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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
.... For example, the 2009 identification of the mutation that causes SCA31 was achieved solely by “traditional” methods: bacterial artificial chromosome (BAC)-based cloning, Sanger sequencing, and Southern blot, with targeted shotgun resequencing (Sato et al. 2009).The techniques employed by the Human Genome...
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Research: Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation
- Xin Li,
- San-Gang He,
- Wen-Rong Li,
- Ling-Yun Luo,
- Ze Yan,
- Dong-Xin Mo,
- Xing Wan,
- Feng-Hua Lv,
- Ji Yang,
- Ya-Xi Xu,
- Juan Deng,
- Qiang-Hui Zhu,
- Xing-Long Xie,
- Song-Song Xu,
- Chen-Xi Liu,
- Xin-Rong Peng,
- Bin Han,
- Zhong-Hui Li,
- Lei Chen,
- Jian-Lin Han,
- Xue-Zhi Ding,
- Renqing Dingkao,
- Yue-Feng Chu,
- Jin-Yan Wu,
- Li-Min Wang,
- Ping Zhou,
- Ming-Jun Liu,
- and Meng-Hua Li
Genome Res. September 2022 32: 1669-1684; Published in Advance August 10, 2022, doi:10.1101/gr.276769.122
...chromosomes of domestic sheep and the proposed molecular basis of fertility for the F1-hybrid. (A) Repeated sequences surrounding the breakpoints on the chromosomes involved in chromosome fusions in goat (C. hircus), argali (O. ammon polii), and domestic sheep (O. aries). (B) Schematic representation...
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Research: Large palindromes on the primate X Chromosome are preserved by natural selection
- Emily K. Jackson,
- Daniel W. Bellott,
- Ting-Jan Cho,
- Helen Skaletsky,
- Jennifer F. Hughes,
- Tatyana Pyntikova,
- and David C. Page
Genome Res. August 2021 31: 1337-1352; Published in Advance July 21, 2021, doi:10.1101/gr.275188.120
...of sex-chromosome palindromes conserved between species. We identified 26 palindromes on the human X Chromosome, constituting more than 2% of its sequence, and characterized orthologous palindromes in the chimpanzee and the rhesus macaque using a clone-based sequencing approach that incorporates full...
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Resource: Assembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history
- Yang Zhou,
- Lv Yang,
- Xiaotao Han,
- Jiazheng Han,
- Yan Hu,
- Fan Li,
- Han Xia,
- Lingwei Peng,
- Clarissa Boschiero,
- Benjamin D. Rosen,
- Derek M. Bickhart,
- Shujun Zhang,
- Aizhen Guo,
- Curtis P. Van Tassell,
- Timothy P.L. Smith,
- Liguo Yang,
- and George E. Liu
Genome Res. August 2022 32: 1585-1601; Published in Advance August 17, 2022, doi:10.1101/gr.276550.122
...repetitive sequences like MEI, interfering with accurate read mapping and introducing ambiguity in breakpoint definition (Abel et al. 2020; Collins et al. 2020; Ho et al. 2020). Multiple solutions to this problem have been applied for detecting and genotyping SV, including read-pair (RP) or paired...
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Method: Detection of simple and complex de novo mutations with multiple reference sequences
- Kiran V. Garimella,
- Zamin Iqbal,
- Michael A. Krause,
- Susana Campino,
- Mihir Kekre,
- Eleanor Drury,
- Dominic Kwiatkowski,
- Juliana M. Sá,
- Thomas E. Wellems,
- and Gil McVean
Genome Res. August 2020 30: 1154-1169; Published in Advance August 19, 2020, doi:10.1101/gr.255505.119
...to the reference sequence in order to identify SVs. Manta similarly identifies SR/SC/PE reads and constructs a breakend association graph whose edges denote long-range adjacencies. Reads associated to individual edges are then assembled and aligned to the reference to facilitate SV identification.Many SV detection...
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