Searching journal content for articles similar to Eyheramendy et al. 17 (1): 88.

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  1. Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
    • Maria Grazia Mendoza-Ferri,
    • Gwendoline Lozachmeur,
    • Maximilien Duvina,
    • Laetitia Perret,
    • Didier Merciris,
    • Anne Gigout,
    • and Marco Antonio Mendoza-Parra
    Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
    ...for capturing chromatin histone modification signatures across tissue sections by taking advantage of a double-barcoded DNA arrays design compatible with in situ Protein A–transposase Tn5 tagmentation. This approach has been validated in presence of fresh-frozen mouse brain tissues but also in decalcified...
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  2. Resource: A ChIP-exo screen of 887 Protein Capture Reagents Program transcription factor antibodies in human cells
    • William K.M. Lai,
    • Luca Mariani,
    • Gerson Rothschild,
    • Edwin R. Smith,
    • Bryan J. Venters,
    • Thomas R. Blanda,
    • Prashant K. Kuntala,
    • Kylie Bocklund,
    • Joshua Mairose,
    • Sarah N. Dweikat,
    • Katelyn Mistretta,
    • Matthew J. Rossi,
    • Daniela James,
    • James T. Anderson,
    • Sabrina K. Phanor,
    • Wanwei Zhang,
    • Zibo Zhao,
    • Avani P. Shah,
    • Katherine Novitzky,
    • Eileen McAnarney,
    • Michael-C. Keogh,
    • Ali Shilatifard,
    • Uttiya Basu,
    • Martha L. Bulyk,
    • and B. Franklin Pugh
    Genome Res. September 2021 31: 1663-1679; Published in Advance August 23, 2021, doi:10.1101/gr.275472.121
    ...milieu. However, antibody availability and reliability can be problematic, whereas epitope tagging can be impractical in many cases. To address these limitations, the Protein Capture Reagents Program (PCRP) generated over a thousand renewable monoclonal antibodies (mAbs) against human presumptive...
  3. Research: Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies
    • PingHsun Hsieh,
    • August E. Woerner,
    • Jeffrey D. Wall,
    • Joseph Lachance,
    • Sarah A. Tishkoff,
    • Ryan N. Gutenkunst,
    • and Michael F. Hammer
    Genome Res. March 2016 26: 291-300; Published in Advance February 17, 2016, doi:10.1101/gr.196634.115
    ...Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies PingHsun Hsieh 1 , August E. Woerner 2 , 3 , Jeffrey D. Wall 4 , Joseph Lachance 5 , 6 , Sarah A...
  4. 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
    ...indicated that introgression from wild relatives is a very important source of new genetic variation when adapting to a new environment (Wu et al. 2018; Mabry et al. 2021). Our results suggest that these species do not evolve in genetic isolation and point out future directions in the germplasm collection...
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  5. 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
    ...great strides toward this goal in the near future.Modeling the effect of genotypic variation on transcriptional regulationThe development of precision medicine therapies will benefit from predictive models to interpret how genetic variants influence gene expression. At present, eQTL studies have largely...
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  6. Research: Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans
    • Tess E. Jeffers and
    • Jason D. Lieb
    Genome Res. January 2017 27: 75-86; Published in Advance November 14, 2016, doi:10.1101/gr.208173.116
    ...immediately surrounding TFBSs in the C. elegans on average show strong affinity to histones in vitro (Locke et al. 2013). A nucleosome occupancy model based solely on DNA sequence also predicted C. elegans TFBSs to be nucleosome bound (Fig. 2A; Kaplan et al. 2009). In vivo, however, these sites show a local...
  7. Resource: Impact of regulatory variation across human iPSCs and differentiated cells
    • Nicholas E. Banovich,
    • Yang I. Li,
    • Anil Raj,
    • Michelle C. Ward,
    • Peyton Greenside,
    • Diego Calderon,
    • Po Yuan Tung,
    • Jonathan E. Burnett,
    • Marsha Myrthil,
    • Samantha M. Thomas,
    • Courtney K. Burrows,
    • Irene Gallego Romero,
    • Bryan J. Pavlovic,
    • Anshul Kundaje,
    • Jonathan K. Pritchard,
    • and Yoav Gilad
    Genome Res. January 2018 28: 122-131; Published in Advance December 5, 2017, doi:10.1101/gr.224436.117
    ...in chromatin accessibility and, more importantly, to predict effects of genetic variation in a cell-type–specific manner.iPSC-differentiated cells capture effects of disease variantsUltimately, the iPSCs and their derived cell types may be valuable for developing a variety of models of human disease, provided...
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  8. Research: Impact of the X Chromosome and sex on regulatory variation
    • Kimberly R. Kukurba,
    • Princy Parsana,
    • Brunilda Balliu,
    • Kevin S. Smith,
    • Zachary Zappala,
    • David A. Knowles,
    • Marie-Julie Favé,
    • Joe R. Davis,
    • Xin Li,
    • Xiaowei Zhu,
    • James B. Potash,
    • Myrna M. Weissman,
    • Jianxin Shi,
    • Anshul Kundaje,
    • Douglas F. Levinson,
    • Philip Awadalla,
    • Sara Mostafavi,
    • Alexis Battle,
    • and Stephen B. Montgomery
    Genome Res. June 2016 26: 768-777; Published in Advance April 21, 2016, doi:10.1101/gr.197897.115
    ...with differential chromatin accessibility between males and females, we used the R package DESeq (Anders and Huber 2010). The data were normalized by the effective library size, and variance was estimated for each group. We tested for differential chromatin accessibility using a model based on the negative binomial...
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  9. Method: Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change
    • Pejman Mohammadi,
    • Stephane E. Castel,
    • Andrew A. Brown,
    • and Tuuli Lappalainen
    Genome Res. November 2017 27: 1872-1884; Published in Advance October 11, 2017, doi:10.1101/gr.216747.116
    .... In addition to the aFC that captures the molecular effect, the proportion of expression variation explained by an eQTL in population data remains useful as a complementary measure valuable for describing population-level effect of an eQTL. aFC provides uniform estimates from both allelic expression and cis...
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  10. Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
    • Aayush Grover,
    • Till Muser,
    • Liine Kasak,
    • Lin Zhang,
    • Ekaterina Krymova,
    • and Valentina Boeva
    Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
    .... 2012), making it sufficient to capture relevant regulatory variation. The 2048-bp input window also provides adequate genomic context for the models to learn both local and distal sequence features.View larger version: In this window In a new window Figure 1. Overview of the benchmarking setup. (A...
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