Searching journal content for articles similar to Hormozdiari et al. 19 (7): 1270.

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  1. 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
    ..., TF binding for each factor is highly variable across genotypes, as shown for two loci for Twist and Mef2 occupancy (Fig. 1F).Effects of genetic variation on TF binding are extensive and preferably detected in genomic regions with less bufferingTo disentangle the impact of genetic variation on TF...
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  2. Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
    • Hao Zhu,
    • Jiao Zhang,
    • Soumya Rao,
    • Matthew D. Durbin,
    • Ying Li,
    • Ruirui Lang,
    • Jiqiang Liu,
    • Baichuan Xiao,
    • Hailin Shan,
    • Ziqiu Meng,
    • Jinmo Wang,
    • Xiaokai Tang,
    • Zhenni Shi,
    • Liza L. Cox,
    • Shouqin Zhao,
    • Stephanie M. Ware,
    • Tiong Y. Tan,
    • Michelle de Silva,
    • Lyndon Gallacher,
    • Ting Liu,
    • Jie Mi,
    • Changqing Zeng,
    • Hou-Feng Zheng,
    • Qingguo Zhang,
    • Stylianos E. Antonarakis,
    • Timothy C. Cox,
    • and Yong-Biao Zhang
    Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
    ...ancestry. The patients and unaffected relatives were collected from Equador, Colombia, and the United States, as previously described (Quiat et al. 2022).High-throughput sequencing and variant callingFor the 2009 Chinese CFM patients, paired-end (2 × 150 bp) whole- sequencing was carried out on them...
  3. Method: A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
    • Siyuan Chen,
    • Jiuming Wang,
    • Inkyung Jung,
    • Zhaowen Qiu,
    • Xin Gao,
    • and Yu Li
    Genome Res. August 2024 34: 1174-1184; Published in Advance August 13, 2024, doi:10.1101/gr.279274.124
    ...involved in loop structures. Derived from chromosome conformation capture (3C) (Fullwood et al. 2009) technology, Hi-C (Lieberman-Aiden et al. 2009) utilizes high-throughput sequencing technology to study the relationship between the entire chromatin DNA in the whole , and obtains high...
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  4. Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
    • Scott Ferguson,
    • Ashley Jones,
    • Kevin Murray,
    • Rose Andrew,
    • Benjamin Schwessinger,
    • and Justin Borevitz
    Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
    ...in a population or species (Bayer et al. 2020; Lei et al. 2021) have revealed a significant amount of structural variation within s (Torkamaneh et al. 2021; Tang et al. 2022; Li et al. 2023).Shared architecture is measured by synteny. Synteny is the conservation of both the order and sequence of homologous...
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  5. Resource: Simultaneous structural variation discovery among multiple paired-end sequenced genomes
    • Fereydoun Hormozdiari,
    • Iman Hajirasouliha,
    • Andrew McPherson,
    • Evan E. Eichler,
    • and S. Cenk Sahinalp
    Genome Res. December 2011 21: 2203-2212; Published in Advance November 2, 2011, doi:10.1101/gr.120501.111
    ...for a comparative genome variation study involves two key steps: (1) each paired-end high-throughput sequenced genome is compared with a reference genome and its (structural) differences are identified; (2) the lists of structural variants in each genome are compared against each other. In this study we propose...
  6. Method: Effective sequence similarity detection with strobemers
    • Kristoffer Sahlin
    Genome Res. November 2021 31: 2080-2094; Published in Advance October 19, 2021, doi:10.1101/gr.275648.121
    ...(Wood and Salzberg 2014) and chromosome (Rangavittal et al. 2019) sequence classification, sequence clustering (Steinegger and Söding 2018), database searches (Solomon and Kingsford 2016; Harris and Medvedev 2020), structural variation detection (Abo et al. 2015; Standage et al. 2019; Khorsand...
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  7. Method: nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing
    • Andrew McPherson,
    • Chunxiao Wu,
    • Alexander W. Wyatt,
    • Sohrab Shah,
    • Colin Collins,
    • and S. Cenk Sahinalp
    Genome Res. November 2012 22: 2250-2261; Published in Advance June 28, 2012, doi:10.1101/gr.136572.111
    ...nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing Andrew McPherson 1 , 4 , Chunxiao Wu 2 , Alexander W. Wyatt 2 , Sohrab Shah 3 , Colin Collins 2 and S. Cenk Sahinalp 1 , 4...
  8. Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
    • Benjamin J. Auerbach,
    • Jian Hu,
    • Muredach P. Reilly,
    • and Mingyao Li
    Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
    ...the effect of perturbations in humans to improve health will require an unmasking of the complex regulation of the cell and improved understanding of how cell interactions shape human physiology.The advent of high-throughput single-cell genomics technologies has brought the scientific community one step...
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  9. Research: SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes
    • Yue Shen,
    • Giovanni Stracquadanio,
    • Yun Wang,
    • Kun Yang,
    • Leslie A. Mitchell,
    • Yaxin Xue,
    • Yizhi Cai,
    • Tai Chen,
    • Jessica S. Dymond,
    • Kang Kang,
    • Jianhui Gong,
    • Xiaofan Zeng,
    • Yongfen Zhang,
    • Yingrui Li,
    • Qiang Feng,
    • Xun Xu,
    • Jun Wang,
    • Jian Wang,
    • Huanming Yang,
    • Jef D. Boeke,
    • and Joel S. Bader
    Genome Res. January 2016 26: 36-49; Published in Advance November 13, 2015, doi:10.1101/gr.193433.115
    ...for understanding the structure, function, and evolution of s. Pioneering work established that native genomic DNA can be functionally replaced by synthetic DNA molecules encoding identical sequences. Milestones include the 7.5-kb synthetic poliovirus in 2002 (Cello et al. 2002), the 5.4-kb synthetic ϕX174 phage...
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  10. Methods: DNA Sudoku—harnessing high-throughput sequencing for multiplexed specimen analysis
    • Yaniv Erlich,
    • Kenneth Chang,
    • Assaf Gordon,
    • Roy Ronen,
    • Oron Navon,
    • Michelle Rooks,
    • and Gregory J. Hannon
    Genome Res. July 2009 19: 1243-1253; Published in Advance May 15, 2009, doi:10.1101/gr.092957.109
    ...GregoryJ Hannon Navon Oron Gordon Chang Kenneth Erlich, Y K Chang Kenneth, Chang Roy, Ronen Rooks Gregory J Hannon M Rooks Navon, O Erlich, Yaniv Yaniv Erlich Rooks Michelle genome;gr.092957.109 10.1101/gr.092957.109 1088-9051 DNA Sudoku—harnessing high-throughput sequencing for multiplexed specimen...
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