| scholarly article | Q13442814 |
| P356 | DOI | 10.1038/NMETH.3582 |
| P2888 | exact match | https://scigraph.springernature.com/pub.10.1038/nmeth.3582 |
| P8608 | Fatcat ID | release_q3dupcbuxzbvxchgiy7ff2wuvm |
| P932 | PMC publication ID | 4626402 |
| P698 | PubMed publication ID | 26366987 |
| P50 | author | Jonathan K. Pritchard | Q6273523 |
| P2093 | author name string | Yoav Gilad | |
| Graham McVicker | |||
| Bryce van de Geijn | |||
| P2860 | cites work | Differential expression analysis for sequence count data | Q21184103 |
| The Sequence Alignment/Map format and SAMtools | Q27860966 | ||
| Summarizing and correcting the GC content bias in high-throughput sequencing | Q28728245 | ||
| Understanding mechanisms underlying human gene expression variation with RNA sequencing | Q29614412 | ||
| Transcriptome genetics using second generation sequencing in a Caucasian population | Q29614413 | ||
| Differential analysis of gene regulation at transcript resolution with RNA-seq | Q29614490 | ||
| Comparing computational methods for identification of allele-specific expression based on next generation sequencing data. | Q30847251 | ||
| Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data | Q33508980 | ||
| A statistical framework for eQTL mapping using RNA-seq data | Q33991900 | ||
| A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data | Q34004487 | ||
| Transcriptome and genome sequencing uncovers functional variation in humans | Q34371227 | ||
| Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies | Q34416687 | ||
| Analysis and design of RNA sequencing experiments for identifying isoform regulation | Q34565989 | ||
| Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. | Q35286142 | ||
| QuASAR: quantitative allele-specific analysis of reads | Q35367079 | ||
| AlleleSeq: analysis of allele-specific expression and binding in a network framework | Q35526123 | ||
| DNase I sensitivity QTLs are a major determinant of human expression variation | Q36408973 | ||
| Identification of genetic variants that affect histone modifications in human cells | Q39077207 | ||
| Streaming fragment assignment for real-time analysis of sequencing experiments | Q41849422 | ||
| P433 | issue | 11 | |
| P921 | main subject | software | Q7397 |
| quantitative trait locus | Q853421 | ||
| P304 | page(s) | 1061-1063 | |
| P577 | publication date | 2015-09-14 | |
| P1433 | published in | Nature Methods | Q680640 |
| P1476 | title | WASP: allele-specific software for robust molecular quantitative trait locus discovery | |
| P478 | volume | 12 |
| Q31040539 | A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes |
| Q36130267 | A haplotype-based normalization technique for the analysis and detection of allele specific expression |
| Q28071394 | A survey of best practices for RNA-seq data analysis |
| Q36815060 | A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals |
| Q49614247 | AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection. |
| Q47304474 | ASElux: An Ultra-Fast and Accurate Allelic Reads Counter |
| Q52716413 | Advances in Transcriptomics: Investigating Cardiovascular Disease at Unprecedented Resolution. |
| Q89467805 | Allele-Specific QTL Fine Mapping with PLASMA |
| Q90391364 | Allele-specific NKX2-5 binding underlies multiple genetic associations with human electrocardiographic traits |
| Q89748473 | Allele-specific expression changes dynamically during T cell activation in HLA and other autoimmune loci |
| Q38771570 | Allele-specific expression reveals interactions between genetic variation and environment |
| Q47617386 | An empirical Bayes test for allelic-imbalance detection in ChIP-seq. |
| Q91582055 | Analysis of genetically driven alternative splicing identifies FBXO38 as a novel COPD susceptibility gene |
| Q47327079 | Annotation-free quantification of RNA splicing using LeafCutter |
| Q55643159 | Association mapping from sequencing reads using k-mers. |
| Q58715751 | Balancing selection on a recessive lethal deletion with pleiotropic effects on two neighboring genes in the porcine genome |
| Q33698275 | Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations |
| Q91773699 | Brain Banks Spur New Frontiers in Neuropsychiatric Research and Strategies for Analysis and Validation |
| Q37076768 | Buffering of Genetic Regulatory Networks in Drosophila melanogaster. |
| Q88718519 | Characterization of noncoding regulatory DNA in the human genome |
| Q39751160 | Coregulation of tandem duplicate genes slows evolution of subfunctionalization in mammals |
| Q38993206 | Decreased STARD10 Expression Is Associated with Defective Insulin Secretion in Humans and Mice |
| Q55291410 | Determining the genetic basis of anthracycline-cardiotoxicity by molecular response QTL mapping in induced cardiomyocytes. |
| Q55322123 | Development and application of an integrated allele-specific pipeline for methylomic and epigenomic analysis (MEA). |
| Q36370820 | Discover hidden splicing variations by mapping personal transcriptomes to personal genomes. |
| Q31138145 | Discovering Single Nucleotide Polymorphisms Regulating Human Gene Expression Using Allele Specific Expression from RNA-seq Data |
| Q93087302 | Dynamic genetic regulation of gene expression during cellular differentiation |
| Q91692005 | Dynamic reorganization of the genome shapes the recombination landscape in meiotic prophase |
| Q90681462 | Elimination of Reference Mapping Bias Reveals Robust Immune Related Allele-Specific Expression in Crossbred Sheep |
| Q57329654 | Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks |
| Q50093911 | Enhancing GTEx by bridging the gaps between genotype, gene expression, and disease. |
| Q89920127 | Estimating the Allele-Specific Expression of SNVs From 10× Genomics Single-Cell RNA-Sequencing Data |
| Q37472956 | Evaluating the impact of single nucleotide variants on transcription factor binding. |
| Q60931579 | False positives in trans-eQTL and co-expression analyses arising from RNA-sequencing alignment errors |
| Q36899905 | Fast and efficient QTL mapper for thousands of molecular phenotypes. |
| Q47752654 | Fine Mapping and Functional Analysis Reveal a Role of SLC22A1 in Acylcarnitine Transport |
| Q61447699 | Fine-mapping -regulatory variants in diverse human populations |
| Q34047556 | Genetic Adaptation and Neandertal Admixture Shaped the Immune System of Human Populations |
| Q37429886 | Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells |
| Q56334063 | Genetic Regulatory Mechanisms of Smooth Muscle Cells Map to Coronary Artery Disease Risk Loci |
| Q96817052 | Genetic analyses support the contribution of mRNA N6-methyladenosine (m6A) modification to human disease heritability |
| Q37305746 | Genetic and transcriptional analysis of human host response to healthy gut microbiota. |
| Q38844789 | Genetic architecture of gene expression underlying variation in host response to porcine reproductive and respiratory syndrome virus infection. |
| Q37682430 | Genetic regulatory signatures underlying islet gene expression and type 2 diabetes |
| Q90638861 | Genetic regulatory variation in populations informs transcriptome analysis in rare disease |
| Q59807751 | Genetic variant at coronary artery disease and ischemic stroke locus 1p32.2 regulates endothelial responses to hemodynamics |
| Q38944185 | Genetics and Genomics of Coronary Artery Disease |
| Q90238984 | Genome wide analyses uncover allele-specific RNA editing in human and mouse |
| Q90576513 | Genome-wide germline correlates of the epigenetic landscape of prostate cancer |
| Q36084287 | Genomic approaches for understanding the genetics of complex disease |
| Q91451590 | Heritability of skewed X-inactivation in female twins is tissue-specific and associated with age |
| Q49999942 | Hierarchical Analysis of RNA-Seq Reads Improves the Accuracy of Allele-specific Expression. |
| Q37461558 | High-throughput allele-specific expression across 250 environmental conditions |
| Q93117338 | High-throughput identification of human SNPs affecting regulatory element activity |
| Q90099986 | Identification of human genetic variants controlling circular RNA expression |
| Q45990501 | Impact of regulatory variation across human iPSCs and differentiated cells. |
| Q42775818 | Impacts of Neanderthal-Introgressed Sequences on the Landscape of Human Gene Expression. |
| Q92534622 | Insight into genetic predisposition to chronic lymphocytic leukemia from integrative epigenomics |
| Q90468480 | Insights into the Mutational Burden of Human Induced Pluripotent Stem Cells from an Integrative Multi-Omics Approach |
| Q36302177 | Integrating molecular QTL data into genome-wide genetic association analysis: Probabilistic assessment of enrichment and colocalization |
| Q48089880 | Integration of human pancreatic islet genomic data refines regulatory mechanisms at Type 2 Diabetes susceptibility loci. |
| Q92978032 | Integrative analysis reveals RNA G-quadruplexes in UTRs are selectively constrained and enriched for functional associations |
| Q63433322 | Integrative detection and analysis of structural variation in cancer genomes |
| Q57295527 | Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer's disease susceptibility |
| Q92531267 | Is it time to change the reference genome? |
| Q90391378 | Landscape of stimulation-responsive chromatin across diverse human immune cells |
| Q52427399 | Large, Diverse Population Cohorts of hiPSCs and Derived Hepatocyte-like Cells Reveal Functional Genetic Variation at Blood Lipid-Associated Loci. |
| Q46686884 | Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. |
| Q91959027 | Leveraging allelic imbalance to refine fine-mapping for eQTL studies |
| Q28597150 | Local Adaptation of Sun-Exposure-Dependent Gene Expression Regulation in Human Skin |
| Q89813831 | Local rewiring of genome-nuclear lamina interactions by transcription |
| Q37290372 | Loss of genetic diversity as a consequence of selection in response to high pCO2. |
| Q56475859 | MMARGE: Motif Mutation Analysis for Regulatory Genomic Elements |
| Q97520866 | Modern epigenetics methods in biological research |
| Q64228207 | Multiomic Profiling Identifies cis-Regulatory Networks Underlying Human Pancreatic β Cell Identity and Function |
| Q39110191 | No Excess of Cis-Regulatory Variation Associated with Intraspecific Selection in Wild Pearl Millet (Cenchrus americanus). |
| Q38663531 | Novel risk genes for systemic lupus erythematosus predicted by random forest classification |
| Q92666113 | Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits |
| Q64064136 | Pancreatic islet chromatin accessibility and conformation reveals distal enhancer networks of type 2 diabetes risk |
| Q58752176 | Parent of origin gene expression in a founder population identifies two new candidate imprinted genes at known imprinted regions |
| Q61446374 | Parent-of-origin effects on quantitative phenotypes in a large Hutterite pedigree |
| Q36828596 | Pooled ChIP-Seq Links Variation in Transcription Factor Binding to Complex Disease Risk |
| Q102379133 | Population-scale study of eRNA transcription reveals bipartite functional enhancer architecture |
| Q64082784 | Prioritizing Parkinson's disease genes using population-scale transcriptomic data |
| Q48248042 | Promoter shape varies across populations and affects promoter evolution and expression noise |
| Q42696193 | QuASAR-MPRA: Accurate allele-specific analysis for massively parallel reporter assays |
| Q64101391 | Quantification of allelic differential expression using a simple Fluorescence primer PCR-RFLP-based method |
| Q41235268 | Quantification of transplant-derived circulating cell-free DNA in absence of a donor genotype |
| Q43794949 | Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change. |
| Q38774701 | RNA splicing is a primary link between genetic variation and disease |
| Q64904210 | RNA-Seq in 296 phased trios provides a high-resolution map of genomic imprinting. |
| Q47143371 | Rare non-coding variants are associated with plasma lipid traits in a founder population |
| Q90557541 | ReQTL: identifying correlations between expressed SNVs and gene expression using RNA-sequencing data |
| Q37395043 | Reference-based phasing using the Haplotype Reference Consortium panel |
| Q36080499 | SNPsplit: Allele-specific splitting of alignments between genomes with known SNP genotypes. |
| Q58084808 | Spatially varying cis-regulatory divergence in Drosophila embryos elucidates cis-regulatory logic |
| Q64064266 | Subtle changes in chromatin loop contact propensity are associated with differential gene regulation and expression |
| Q89449610 | The effects of common structural variants on 3D chromatin structure |
| Q90024199 | Tissue-Specific cis-Regulatory Divergence Implicates eloF in Inhibiting Interspecies Mating in Drosophila |
| Q35779348 | Tools and best practices for data processing in allelic expression analysis |
| Q37220917 | Topoisomerase II beta interacts with cohesin and CTCF at topological domain borders |
| Q41854365 | Transcriptional networks specifying homeostatic and inflammatory programs of gene expression in human aortic endothelial cells |
| Q58462188 | Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights |
| Q41412946 | Type 2 Diabetes Variants Disrupt Function of SLC16A11 through Two Distinct Mechanisms |
| Q63916436 | Type 2 diabetes risk alleles in PAM impact insulin release from human pancreatic β-cells |
| Q37005532 | Using genomic annotations increases statistical power to detect eGenes |
| Q31119904 | scphaser: haplotype inference using single-cell RNA-seq data |
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