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Research: A genome-wide long noncoding RNA CRISPRi screen identifies PRANCR as a novel regulator of epidermal homeostasis
- Pengfei Cai,
- Auke B.C. Otten,
- Binbin Cheng,
- Mitsuhiro A. Ishii,
- Wen Zhang,
- Beibei Huang,
- Kun Qu,
- and Bryan K. Sun
Genome Res. January 2020 30: 22-34; Published in Advance December 4, 2019, doi:10.1101/gr.251561.119
...association studies (GWAS) indicate that >93% of disease-linked single-nucleotide polymorphisms (SNPs) map to the noncoding (Tak and Farnham 2015). These observations therefore suggest a potential underappreciated disease relevance of noncoding elements such as enhancers and noncoding RNAs (Zhang and Lupski...
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Method: Ultrafast and scalable variant annotation and prioritization with big functional genomics data
- Dandan Huang,
- Xianfu Yi,
- Yao Zhou,
- Hongcheng Yao,
- Hang Xu,
- Jianhua Wang,
- Shijie Zhang,
- Wenyan Nong,
- Panwen Wang,
- Lei Shi,
- Chenghao Xuan,
- Miaoxin Li,
- Junwen Wang,
- Weidong Li,
- Hoi Shan Kwan,
- Pak Chung Sham,
- Kai Wang,
- and Mulin Jun Li
Genome Res. December 2020 30: 1789-1801; Published in Advance October 15, 2020, doi:10.1101/gr.267997.120
...result of Affymetrix Genome-Wide Human SNP Array 6.0 data for A375 cell line (A375_chip), and somatic mutation call result of whole-exome sequencing data for A375 cell line (A375_SM). These data sets span the highly unbalanced and sparse queries to the highly balanced and dense queries. (B) The genomic...
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Method: Accurate typing of short tandem repeats from genome-wide sequencing data and its applications
- Arkarachai Fungtammasan,
- Guruprasad Ananda,
- Suzanne E. Hile,
- Marcia Shu-Wei Su,
- Chen Sun,
- Robert Harris,
- Paul Medvedev,
- Kristin Eckert,
- and Kateryna D. Makova
Genome Res. May 2015 25: 736-749; Published in Advance March 30, 2015, doi:10.1101/gr.185892.114
...by a linked genetic marker (e.g., a SNP). To demonstrate this capability, we genotyped a sample of two plasmids with cloned mtDNA D-loop sequence, premixed at five different ratios—98:2, 99:1, 99.5:0.5, 99.75:0.25, and 99.9:0.1. The two plasmids differ at only one STR-containing region: the plasmid Z1...
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Research: A ChIP-seq defined genome-wide map of vitamin D receptor binding: Associations with disease and evolution
- Sreeram V. Ramagopalan,
- Andreas Heger,
- Antonio J. Berlanga,
- Narelle J. Maugeri,
- Matthew R. Lincoln,
- Amy Burrell,
- Lahiru Handunnetthi,
- Adam E. Handel,
- Giulio Disanto,
- Sarah-Michelle Orton,
- Corey T. Watson,
- Julia M. Morahan,
- Gavin Giovannoni,
- Chris P. Ponting,
- George C. Ebers,
- and Julian C. Knight
Genome Res. October 2010 20: 1352-1360; Published in Advance August 24, 2010, doi:10.1101/gr.107920.110
.... We analyzed GWAS intervals for T1D, Crohn’s disease (CD), andMS together with 44 other common traits listed in the Catalog of Published Genome-Wide Association Studies (http://www. .gov/gwastudies) (traits and marker single nucleotide polymorphisms [SNPs] used are detailed in Supplemental Table 5...
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Method: Highly accurate quantification of allelic gene expression for population and disease genetics
- Anna Saukkonen,
- Helena Kilpinen,
- and Alan Hodgkinson
Genome Res. August 2022 32: 1565-1572; Published in Advance July 6, 2022, doi:10.1101/gr.276296.121
...of variant calls that can be achieved with current methods. We used phased variant calls (VCF file) for NA12877 that included indels and SNPs to generate a diploid reference using AlleleSeq (Rozowsky et al. 2011) and the hg19 version of the human reference .Simulated WGS dataThe maternal and paternal s from...
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Method: Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation
- Mark D. Robinson,
- Clare Stirzaker,
- Aaron L. Statham,
- Marcel W. Coolen,
- Jenny Z. Song,
- Shalima S. Nair,
- Dario Strbenac,
- Terence P. Speed,
- and Susan J. Clark
Genome Res. December 2010 20: 1719-1729; Published in Advance November 2, 2010, doi:10.1101/gr.110601.110
...in the Figure 7. Effects of copy number changes on differential methylation detection. (A) Differential methylation Z-score for between LNCaP and PrEC cells, using MBD-SF-seq, for human chromosome 13. (B) Smoothed Affymetrix SNP 6.0 array data showing corresponding changes in copy number. (C ) Genome-wide...
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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
...autoimmune diseases (Onengut-Gumuscu et al. 2015). This suggests that the risk alleles at these SNPs modify genes acting on the immune system rather than on disease-specific target tissues. Fine mapping has revealed that themajority of the potentially causal SNPs are located in noncoding regions (Cortes...
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Research: Dynamic A-to-I RNA editing in response to gut microbiome in honey bees
- Yuange Duan,
- Min Huang,
- Lin Ye,
- Ling Ma,
- Yashuai Wu,
- Yating Du,
- Jiyao Liu,
- Fan Song,
- Li Tian,
- Wanzhi Cai,
- Hu Li,
- Xin Zhou,
- and Shiqi Luo
Genome Res. March 4, 2026 gr.280291.124; Published in Advance March 4, 2026, doi:10.1101/gr.280291.124
...recorded in VCF (variant calling format) and subsequently annotated 475 with SnpEff version 4.5 (Cingolani et al. 2012). VCF contains the location (chromosome 476 and position) and mutation (reference allele/reads count and alternative allele/reads count) 477 information of each variant. To annotate each...
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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
...the attributes and context dependence of functional noncoding SNPs and provide new mechanisms underlying vascular disease risk.Genome-wide association studies (GWASs) have revealed thousands of associations between genetic variants and clinical phenotypes. A large majority of disease-associated loci, and thus...
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Method: Allele-specific RNA N⁶-methyladenosine modifications reveal functional genetic variants in human tissues
- Shuo Cao,
- Haoran Zhu,
- Jinru Cui,
- Sun Liu,
- Yuhe Li,
- Junfang Shi,
- Junyuan Mo,
- Zihan Wang,
- Hailan Wang,
- Jiaxin Hu,
- Lizhi Chen,
- Yuan Li,
- Laixin Xia,
- and Shan Xiao
Genome Res. August 2023 33: 1369-1380; Published in Advance September 15, 2023, doi:10.1101/gr.277704.123
...corresponding to m6A peaks in human tissues are enriched for disease-associated variants (Xiao et al. 2019; Zhang et al. 2020a). We therefore sought to explore if there is a link between ASm6A and human complex traits and common diseases. To assess this, we considered GWAS risk SNPs collected from the GWAS...

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