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Functional annotation of rare structural variation in the human brain
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1001/jama.2015.4845openalex-snapshot
Copy Number Variations and Cognitive Phenotypes in Unselected Populations
inferredcites →https://doi.org/10.1002/ana.20732openalex-snapshot
Spastic paraplegia type 2 associated with axonal neuropathy and apparent PLP1 position effect
inferredcites →https://doi.org/10.1007/s00439-009-0736-4openalex-snapshot
Deletion of an enhancer near DLX5 and DLX6 in a family with hearing loss, craniofacial defects, and an inv(7)(q21.3q35)
inferredcites →https://doi.org/10.1016/j.ajhg.2009.03.001openalex-snapshot
Duplications Involving a Conserved Regulatory Element Downstream of BMP2 Are Associated with Brachydactyly Type A2
inferredcites →https://doi.org/10.1016/j.ajhg.2012.05.011openalex-snapshot
Genome-wide Transcriptome Profiling Reveals the Functional Impact of Rare De Novo and Recurrent CNVs in Autism Spectrum Disorders
inferredcites →https://doi.org/10.1016/j.ajhg.2014.05.004openalex-snapshot
Transcriptional Consequences of 16p11.2 Deletion and Duplication in Mouse Cortex and Multiplex Autism Families
inferredcites →https://doi.org/10.1016/j.ccr.2014.07.021openalex-snapshot
When Deletions Gain Functions: Commandeering Epigenetic Mechanisms
inferredcites →https://doi.org/10.1037/h0071325openalex-snapshot
Analysis of a complex of statistical variables into principal components.
inferredcites →https://doi.org/10.1038/75556openalex-snapshot
Gene Ontology: tool for the unification of biology
inferredcites →https://doi.org/10.1038/ejhg.2009.186openalex-snapshot
Copy number variation upstream of PMP22 in Charcot–Marie–Tooth disease
inferredcites →https://doi.org/10.1038/nature09534openalex-snapshot
A map of human genome variation from population-scale sequencing
inferredcites →https://doi.org/10.1038/nature11247openalex-snapshot
An integrated encyclopedia of DNA elements in the human genome
inferredcites →https://doi.org/10.1038/nature12818openalex-snapshot
CNVs conferring risk of autism or schizophrenia affect cognition in controls
inferredcites →https://doi.org/10.1038/nature14248openalex-snapshot
Integrative analysis of 111 reference human epigenomes
inferredcites →https://doi.org/10.1038/nature15394openalex-snapshot
An integrated map of structural variation in 2,504 human genomes
inferredcites →https://doi.org/10.1038/nature24267openalex-snapshot
The impact of rare variation on gene expression across tissues
inferredcites →https://doi.org/10.1038/nature24277openalex-snapshot
Genetic effects on gene expression across human tissues
inferredcites →https://doi.org/10.1038/nature25983openalex-snapshot
De novo mutations in regulatory elements in neurodevelopmental disorders
inferredcites →https://doi.org/10.1038/ng.3200openalex-snapshot
Large multiallelic copy number variations in humans
inferredcites →https://doi.org/10.1038/ng.3638openalex-snapshot
Patterns of genic intolerance of rare copy number variation in 59,898 human exomes
inferredcites →https://doi.org/10.1038/ng.3725openalex-snapshot
Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects
inferredcites →https://doi.org/10.1038/ng.3834openalex-snapshot
The impact of structural variation on human gene expression
inferredcites →https://doi.org/10.1038/nmeth0410-248openalex-snapshot
A method and server for predicting damaging missense mutations
inferredcites →https://doi.org/10.1038/nn.4399openalex-snapshot
Gene expression elucidates functional impact of polygenic risk for schizophrenia
inferredcites →https://doi.org/10.1038/npp.2014.216openalex-snapshot
Copy Number Variation in Schizophrenia
inferredcites →https://doi.org/10.1038/nprot.2009.86openalex-snapshot
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
inferredcites →https://doi.org/10.1038/nrg2484openalex-snapshot
RNA-Seq: a revolutionary tool for transcriptomics
inferredcites →https://doi.org/10.1038/nrg2958openalex-snapshot
Genome structural variation discovery and genotyping
inferredcites →https://doi.org/10.1038/nrg3373openalex-snapshot
Phenotypic impact of genomic structural variation: insights from and for human disease
inferredcites →https://doi.org/10.1038/s41588-018-0107-yopenalex-snapshot
An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder
inferredcites →https://doi.org/10.1038/s41597-020-00642-8openalex-snapshot
Large eQTL meta-analysis reveals differing patterns between cerebral cortical and cerebellar brain regions
inferredcites →https://doi.org/10.1073/pnas.1808631116openalex-snapshot
Chromatin features constrain structural variation across evolutionary timescales
inferredcites →https://doi.org/10.1080/14786440109462720openalex-snapshot
LIII. On lines and planes of closest fit to systems of points in space
inferredcites →https://doi.org/10.1086/519795openalex-snapshot
PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses
inferredcites →https://doi.org/10.1093/bfgp/elv017openalex-snapshot
The impact of human copy number variation on gene expression: Figure 1
inferredcites →https://doi.org/10.1093/bib/bbq072openalex-snapshot
PHAST and RPHAST: phylogenetic analysis with space/time models
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
inferredcites →https://doi.org/10.1093/bioinformatics/bts378openalex-snapshot
DELLY: structural variant discovery by integrated paired-end and split-read analysis
inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot
STAR: ultrafast universal RNA-seq aligner
inferredcites →https://doi.org/10.1093/bioinformatics/btt656openalex-snapshot
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
inferredcites →https://doi.org/10.1093/bioinformatics/btv710openalex-snapshot
Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications
inferredcites →https://doi.org/10.1093/biostatistics/kxr054openalex-snapshot
Removing technical variability in RNA-seq data using conditional quantile normalization
inferredcites →https://doi.org/10.1093/hmg/ddv259openalex-snapshot
Non-coding genetic variants in human disease: Figure 1.
inferredcites →https://doi.org/10.1093/nar/29.1.308openalex-snapshot
dbSNP: the NCBI database of genetic variation
inferredcites →https://doi.org/10.1093/nar/gkj143openalex-snapshot
TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes
inferredcites →https://doi.org/10.1093/nar/gkm967openalex-snapshot
ORegAnno: an open-access community-driven resource for regulatory annotation
inferredcites →https://doi.org/10.1093/nar/gkv007openalex-snapshot
limma powers differential expression analyses for RNA-sequencing and microarray studies
inferredcites →https://doi.org/10.1101/531210openalex-snapshot
The mutational constraint spectrum quantified from variation in 141,456 humans
inferredcites →https://doi.org/10.1101/578674openalex-snapshot
An open resource of structural variation for medical and population genetics
inferredcites →https://doi.org/10.1101/gr.114876.110openalex-snapshot
CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing
inferredcites →https://doi.org/10.1101/gr.137323.112openalex-snapshot
Annotation of functional variation in personal genomes using RegulomeDB
inferredcites →https://doi.org/10.1101/gr.218032.116openalex-snapshot
The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biology
inferredcites →https://doi.org/10.1101/gr.3577405openalex-snapshot
Distribution and intensity of constraint in mammalian genomic sequence
inferredcites →https://doi.org/10.1126/science.1105136openalex-snapshot
The ENCODE (ENCyclopedia Of DNA Elements) Project
inferredcites →https://doi.org/10.1126/science.1136678openalex-snapshot
Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes
inferredcites →https://doi.org/10.1126/science.aat8464openalex-snapshot
Comprehensive functional genomic resource and integrative model for the human brain
inferredcites →https://doi.org/10.1146/annurev-med-100708-204735openalex-snapshot
Structural Variation in the Human Genome and its Role in Disease
inferredcites →https://doi.org/10.1186/gb-2014-15-2-r29openalex-snapshot
voom: precision weights unlock linear model analysis tools for RNA-seq read counts
inferredcites →https://doi.org/10.1186/gb-2014-15-6-r84openalex-snapshot
LUMPY: a probabilistic framework for structural variant discovery
inferredcites →https://doi.org/10.1186/s13073-017-0494-1openalex-snapshot
Copy number variation meta-analysis reveals a novel duplication at 9p24 associated with multiple neurodevelopmental disorders
inferredcites →https://doi.org/10.1371/journal.pcbi.1001025openalex-snapshot
Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++
inferredcites →https://doi.org/10.1371/journal.pcbi.1004572openalex-snapshot
Wham: Identifying Structural Variants of Biological Consequence
inferredcites →https://doi.org/10.1371/journal.pgen.0030161openalex-snapshot
Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis
inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1038/s41436-020-00974-1openalex-snapshot
Interpreting the impact of noncoding structural variation in neurodevelopmental disorders
inferred← citeshttps://doi.org/10.1038/s41525-023-00371-yopenalex-snapshot
Structural variation of the coding and non-coding human pharmacogenome
inferred← citeshttps://doi.org/10.1038/s41576-021-00367-3openalex-snapshot
Towards population-scale long-read sequencing
inferred← citeshttps://doi.org/10.1038/s41576-024-00808-9openalex-snapshot
Diversity and consequences of structural variation in the human genome
inferred← citeshttps://doi.org/10.1038/s41593-022-01031-7openalex-snapshot
Integrating whole-genome sequencing with multi-omic data reveals the impact of structural variants on gene regulation in the human brain
inferred← citeshttps://doi.org/10.1101/2021.05.17.444424openalex-snapshot
Genomic variations and epigenomic landscape of the Medaka Inbred Kiyosu-Karlsruhe (MIKK) panel
inferred← citeshttps://doi.org/10.1101/2022.06.23.22276396openalex-snapshot
CNVscore calculates pathogenicity scores for copy number variants together with uncertainty estimates accounting for learning biases in reference Mendelian disorder datasets
inferred← citeshttps://doi.org/10.1101/2024.12.16.628723openalex-snapshot
Haplotype-Resolved Long-Read Sequencing in Hundreds of Diverse Brains Identifies Structural Variant Impacts on Expression and Allele-Specific Methylation
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