Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR
暂无分享,去创建一个
[1] Elizabeth M. Smigielski,et al. dbSNP: the NCBI database of genetic variation , 2001, Nucleic Acids Res..
[2] Philip Lijnzaad,et al. The Ensembl genome database project , 2002, Nucleic Acids Res..
[3] Steven Henikoff,et al. SIFT: predicting amino acid changes that affect protein function , 2003, Nucleic Acids Res..
[4] C. Burge,et al. Prediction of Mammalian MicroRNA Targets , 2003, Cell.
[5] R. Durbin,et al. The Sequence Ontology: a tool for the unification of genome annotations , 2005, Genome Biology.
[6] D. Haussler,et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. , 2005, Genome research.
[7] David Haussler,et al. The UCSC Known Genes , 2006, Bioinform..
[8] William Stafford Noble,et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.
[9] Tatiana Tatusova,et al. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins , 2004, Nucleic Acids Res..
[10] Cole Trapnell,et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.
[11] Steven J. M. Jones,et al. Abyss: a Parallel Assembler for Short Read Sequence Data Material Supplemental Open Access , 2022 .
[12] Gonçalo R. Abecasis,et al. The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..
[13] Richard Durbin,et al. Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .
[14] P. Bork,et al. A method and server for predicting damaging missense mutations , 2010, Nature Methods.
[15] M. DePristo,et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.
[16] K. Pollard,et al. Detection of nonneutral substitution rates on mammalian phylogenies. , 2010, Genome research.
[17] H. Hakonarson,et al. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data , 2010, Nucleic acids research.
[18] P. Shannon,et al. Exome sequencing identifies the cause of a Mendelian disorder , 2009, Nature Genetics.
[19] D. Altshuler,et al. A map of human genome variation from population-scale sequencing , 2010, Nature.
[20] Daniel Rios,et al. Bioinformatics Applications Note Databases and Ontologies Deriving the Consequences of Genomic Variants with the Ensembl Api and Snp Effect Predictor , 2022 .
[21] Ian N M Day,et al. dbSNP in the detail and copy number complexities , 2010, Human mutation.
[22] Heng Li,et al. A survey of sequence alignment algorithms for next-generation sequencing , 2010, Briefings Bioinform..
[23] M. Weedon,et al. Exome sequencing identifies a DYNC1H1 mutation in a large pedigree with dominant axonal Charcot-Marie-Tooth disease. , 2011, American journal of human genetics.
[24] Gonçalo R. Abecasis,et al. The variant call format and VCFtools , 2011, Bioinform..
[25] Jie Li,et al. Regenerative phenotype in mice with a point mutation in transforming growth factor β type I receptor (TGFBR1) , 2011, Proceedings of the National Academy of Sciences.
[26] M. Gerstein,et al. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. , 2011, Genome research.
[27] Joshua S. Paul,et al. Genotype and SNP calling from next-generation sequencing data , 2011, Nature Reviews Genetics.
[28] S. Lok,et al. Increased exonic de novo mutation rate in individuals with schizophrenia , 2011, Nature Genetics.
[29] Cristina Y. González,et al. VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing , 2012, Nucleic Acids Res..
[30] Joaquín Dopazo,et al. SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants , 2011, Nucleic Acids Res..
[31] K. Shianna,et al. Using ERDS to infer copy-number variants in high-coverage genomes. , 2012, American journal of human genetics.
[32] Heng Li,et al. Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly , 2012, Bioinform..
[33] David G. Knowles,et al. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression , 2012, Genome research.
[34] Lilia M. Iakoucheva,et al. Whole-Genome Sequencing in Autism Identifies Hot Spots for De Novo Germline Mutation , 2012, Cell.
[35] Kai Wang,et al. Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress , 2012, Genome Medicine.
[36] Kenny Q. Ye,et al. An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.
[37] Pablo Cingolani,et al. © 2012 Landes Bioscience. Do not distribute. , 2022 .
[38] Vladimir Makarov,et al. AnnTools: a comprehensive and versatile annotation toolkit for genomic variants , 2012, Bioinform..
[39] Kai Wang,et al. wANNOVAR: annotating genetic variants for personal genomes via the web , 2012, Journal of Medical Genetics.
[40] Mark Gerstein,et al. VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment , 2012, Bioinform..
[41] E. Boerwinkle,et al. dbNSFP v2.0: A Database of Human Non‐synonymous SNVs and Their Functional Predictions and Annotations , 2013, Human mutation.
[42] C. Tang,et al. Whole-Exome Sequencing to Identify a Novel LMNA Gene Mutation Associated with Inherited Cardiac Conduction Disease , 2013, PloS one.
[43] Qingguo Wang,et al. Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives , 2013, BMC Bioinformatics.
[44] Aaron R. Quinlan,et al. GEMINI: Integrative Exploration of Genetic Variation and Genome Annotations , 2013, PLoS Comput. Biol..
[45] S. Gabriel,et al. Analysis of 6,515 exomes reveals a recent origin of most human protein-coding variants , 2012, Nature.
[46] Mark Yandell,et al. VAAST 2.0: Improved Variant Classification and Disease-Gene Identification Using a Conservation-Controlled Amino Acid Substitution Matrix , 2013, Genetic epidemiology.
[47] M. Pop,et al. Sequence assembly demystified , 2013, Nature Reviews Genetics.
[48] Daniel Nilsson,et al. An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge , 2014, Genome Biology.
[49] Jean-Baptiste Cazier,et al. Choice of transcripts and software has a large effect on variant annotation , 2014, Genome Medicine.
[50] August E. Woerner,et al. Strong selective sweeps associated with ampliconic regions in great ape X chromosomes , 2014, 1402.5790.
[51] David Haussler,et al. The UCSC Genome Browser database: 2014 update , 2013, Nucleic Acids Res..
[52] J. Shendure,et al. A general framework for estimating the relative pathogenicity of human genetic variants , 2014, Nature Genetics.
[53] Xun Xu,et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads , 2013, Bioinform..
[54] Gustavo Glusman,et al. A unified test of linkage analysis and rare-variant association for analysis of pedigree sequence data , 2014, Nature Biotechnology.
[55] Deanna M. Church,et al. ClinVar: public archive of relationships among sequence variation and human phenotype , 2013, Nucleic Acids Res..
[56] Hui Yang,et al. Phenolyzer: phenotype-based prioritization of candidate genes for human diseases , 2015, Nature Methods.
[57] Jack R. Collins,et al. AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes , 2015, Bioinform..
[58] R. Gibbs,et al. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. , 2015, Human molecular genetics.