Searching journal content for articles similar to Boursot and Belkhir 16 (10): 1191.

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  1. Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    • Qiang Su,
    • Yi Long,
    • Deming Gou,
    • Junmin Quan,
    • Xiaoming Zhou,
    • and Qizhou Lian
    Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
    ...properties shape spike-in representation in RNA-seq data.In the handling of spike-in raw data, utilizing entire spike-in sequences is crucial for accurately determining the read counts of individual RNA sequences. To ascertain the consistency and intricacy of the sequencing biases, we conducted two...
  2. Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
    • Meilin Zhang,
    • Heng Du,
    • Yu Zhang,
    • Yue Zhuo,
    • Zhen Liu,
    • Yahui Xue,
    • Lei Zhou,
    • Sixuan Zhou,
    • Wanying Li,
    • and Jian-Feng Liu
    Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
    ..., China ↵3 These authors contributed equally to this work. Corresponding author: liujf@cau.edu.cnAbstractAs the scale of deep whole- sequencing (WGS) data has grown exponentially, hundreds of millions of single nucleotide polymorphisms (SNPs) have been identified in livestock. Utilizing these massive SNP...
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  3. Method: Three assays for in-solution enrichment of ancient human DNA at more than a million SNPs
    • Nadin Rohland,
    • Swapan Mallick,
    • Matthew Mah,
    • Robert Maier,
    • Nick Patterson,
    • and David Reich
    Genome Res. November/December 2022 32: 2068-2078; Published in Advance December 14, 2022, doi:10.1101/gr.276728.122
    ...both for all SNPs targets (left) and after applying the bias filter retaining a subset of 42% of autosomal SNPs (right). Results for this figure reflect data after removal of duplicated sequences.To explicitly study population genetic biases associated with coanalysis of data generated on different...
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  4. Research: Functional noncoding SNPs in human endothelial cells fine-map vascular trait associations
    • Anu Toropainen,
    • Lindsey K. Stolze,
    • Tiit Örd,
    • Michael B. Whalen,
    • Paula Martí Torrell,
    • Verena M. Link,
    • Minna U. Kaikkonen,
    • and Casey E. Romanoski
    Genome Res. March 2022 32: 409-424; Published in Advance February 22, 2022, doi:10.1101/gr.276064.121
    ...to ascertain despite demonstrated associations to common, complex disease traits. To elucidate properties of functional noncoding SNPs with effects in human endothelial cells (ECs), we utilized our previous molecular quantitative trait locus (molQTL) analysis for transcription factor binding, chromatin...
  5. Method: Correcting signal biases and detecting regulatory elements in STARR-seq data
    • Young-Sook Kim,
    • Graham D. Johnson,
    • Jungkyun Seo,
    • Alejandro Barrera,
    • Thomas N. Cowart,
    • William H. Majoros,
    • Alejandro Ochoa,
    • Andrew S. Allen,
    • and Timothy E. Reddy
    Genome Res. May 2021 31: 877-889; Published in Advance March 15, 2021, doi:10.1101/gr.269209.120
    ...regulatory region sequencing (STARR-seq) have made it possible to measure regulatory element activity across the entire human at once. The resulting data, however, present substantial analytical challenges. Here, we identify technical biases that explain most of the variance in STARR-seq data. We...
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  6. Research: Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits
    • Peter Orchard,
    • Nandini Manickam,
    • Christa Ventresca,
    • Swarooparani Vadlamudi,
    • Arushi Varshney,
    • Vivek Rai,
    • Jeremy Kaplan,
    • Claudia Lalancette,
    • Karen L. Mohlke,
    • Katherine Gallagher,
    • Charles F. Burant,
    • and Stephen C.J. Parker
    Genome Res. December 2021 31: 2258-2275; Published in Advance November 23, 2021, doi:10.1101/gr.268482.120
    ...these chromatin accessibility maps on GWAS data to nominate causal cell types, SNPs, transcription factor motifs, and target genes for type 2 diabetes signals. These chromatin accessibility profiles for human and rat skeletal muscle cell types are a useful resource for nominating causal GWAS SNPs and cell types...
  7. Research: Estrogen receptor 1 chromatin profiling in human breast tumors reveals high inter-patient heterogeneity with enrichment of risk SNPs and enhancer activity at most-conserved regions
    • Stacey E.P. Joosten,
    • Sebastian Gregoricchio,
    • Suzan Stelloo,
    • Elif Yapıcı,
    • Chia-Chi Flora Huang,
    • Kerim Yavuz,
    • Maria Donaldson Collier,
    • Tunç Morova,
    • Umut Berkay Altintaş,
    • Yongsoo Kim,
    • Sander Canisius,
    • Cathy B. Moelans,
    • Paul J. van Diest,
    • Gozde Korkmaz,
    • Nathan A. Lack,
    • Michiel Vermeulen,
    • Sabine C. Linn,
    • and Wilbert Zwart
    Genome Res. April 2024 34: 539-555; Published in Advance May 6, 2024, doi:10.1101/gr.278680.123
    ...sites show the highest estrogen-driven enhancer activity and are most engaged in long-range chromatin interactions. In addition, the most commonly shared ESR1-occupied enhancers are enriched for breast cancer risk SNP loci. We experimentally confirm SNVs to impact chromatin binding potential for ESR1...
  8. Research: Disease-specific biases in alternative splicing and tissue-specific dysregulation revealed by multitissue profiling of lymphocyte gene expression in type 1 diabetes
    • Jeremy R.B. Newman,
    • Ana Conesa,
    • Matthew Mika,
    • Felicia N. New,
    • Suna Onengut-Gumuscu,
    • Mark A. Atkinson,
    • Stephen S. Rich,
    • Lauren M. McIntyre,
    • and Patrick Concannon
    Genome Res. November 2017 27: 1807-1815; Published in Advance October 12, 2017, doi:10.1101/gr.217984.116
    ...identified more than 50 non-MHC loci containing single-nucleotide polymorphisms (SNPs) exhibiting -wide significant evidence of association with T1D (Burton et al. 2007; Hakonarson et al. 2007; Barrett et al. 2009; Concannon et al. 2009). The majority of these loci also display associations with additional...
  9. LETTER: A periodic pattern of SNPs in the human genome
    • Bo Eskerod Madsen,
    • Palle Villesen,
    • and Carsten Wiuf
    Genome Res. October 2007 17: 1414-1419; Published in Advance August 2, 2007, doi:10.1101/gr.6223207
    ...compiled a set of high-quality SNPs, that is, SNPs that map to a unique position in the , and with an exact match between the flanking regions and the reference sequence. In this way, all SNPs that might be wrongly placed in the are excluded. Furthermore, to avoid study-specific ascertainment biases, we...
  10. Method: Sasquatch: predicting the impact of regulatory SNPs on transcription factor binding from cell- and tissue-specific DNase footprints
    • Ron Schwessinger,
    • Maria C. Suciu,
    • Simon J. McGowan,
    • Jelena Telenius,
    • Stephen Taylor,
    • Doug R. Higgs,
    • and Jim R. Hughes
    Genome Res. October 2017 27: 1730-1742; Published in Advance September 13, 2017, doi:10.1101/gr.220202.117
    ...Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom In the era of -wide association studies (GWAS) and personalized medicine, predicting the impact of single nucleotide polymorphisms (SNPs) in regulatory elements is an important goal. Current approaches to determine the potential of regulatory...
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