Scripps Genome ADVISER | Annotation and Distributed Variant Interpretation Server
Scripps Genome ADVISER | Annotation and Distributed Variant Interpretation Server


If you use SG-ADVISER in your research please cite [Manuscript Under Review]

References for tools and knowledgebases implemented in SG-ADVISER:

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  • Andersen MC, et al. In silico detection of sequence variations modifying transcriptional regulation. PLoS Comput Biol. 2008 Jan;4(1):e5.
  • Ashburner M, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25-9.
  • Bamford S, et al. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br J Cancer. 2004 Jul 19;91(2):355-8.
  • Becker KG, et al. The genetic association database. Nat Genet. 2004 May;36(5):431-2.
  • Bernhart SH, et al. Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol. 2006 Mar 16;1(1):3.
  • Clifford RJ, et al. Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms. Bioinformatics. 2004 May 1;20(7):1006-14.
  • Eddy SR. A new generation of homology search tools based on probabilistic inference. Genome Inform. 2009 Oct;23(1):205-11.
  • Finn RD, et al. The Pfam protein families database. Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8.
  • Futreal PA, et al. A census of human cancer genes. Nat Rev Cancer. 2004 Mar;4(3):177-83.
  • Griffiths-Jones S, et al. miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D140-4.
  • Gibbs JR, et al. Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet. 2010 May 13;6(5):e1000952.
  • González-Pérez A, López-Bigas N. Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel. Am J Hum Genet. 2011 Apr 8;88(4):440-9.
  • Higgins ME, et al. CancerGenes: a gene selection resource for cancer genome projects. Nucleic Acids Res. 2007 Jan;35(Database issue):D721-6.
  • Hofacker IL, Stadler PF. Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics. 2006 May 15;22(10):1172-6.
  • Hu J, Ng PC. Predicting the effects of frameshifting indels. Genome Biol. 2012 Feb 9;13(2):R9.
  • International HapMap Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007 Oct 18;449(7164):851-61.
  • Joshi-Tope G, et al. Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D428-32.
  • Korhonen J, et al. MOODS: fast search for position weight matrix matches in DNA sequences. Bioinformatics. 2009 Dec 1;25(23):3181-2.
  • Krawczak M, et al. Human gene mutation database-a biomedical information and research resource. Hum Mutat. 2000;15(1):45-51.
  • Kumar P, et al. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4(7):1073-81.
  • Lewis BP, et al. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005 Jan 14;120(1):15-20.
  • McKusick VA. Mendelian Inheritance in Man. A Catalog of Human Genes and Genetic Disorders. Baltimore: Johns Hopkins University Press, 1998 (12th edition).
  • Meyer LR, et al. The UCSC Genome Browser database: extensions and updates 2013. Nucleic Acids Res. 2013 Jan 1;41(D1):D64-9.
  • Montgomery SB, et al. Transcriptome genetics using second generation sequencing in a Caucasian population. Nature. 2010 Apr 1;464(7289):773-7.
  • Osborne JD, et al. Annotating the human genome with Disease Ontology. BMC Genomics. 2009 Jul 7;10 Suppl 1:S6.
  • Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010 Jan;20(1):110-21.
  • Richards CS, et al. Molecular Subcommittee of the ACMG Laboratory Quality Assurance Committee. ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. Genet Med. 2008 Apr;10(4):294-300.
  • Schadt EE, et al. Mapping the genetic architecture of gene expression in human liver. PLoS Biol. 2008 May 6;6(5):e107.
  • Sherry ST, et al. dbSNP-database for single nucleotide polymorphisms and other classes of minor genetic variation. Genome Res. 1999 Aug;9(8):677-9.
  • Siepel A, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50.
  • Stadler MB, et al. Inference of splicing regulatory activities by sequence neighborhood analysis. PLoS Genet. 2006 Nov 24;2(11):e191.
  • Stormo GD. DNA binding sites: representation and discovery. Bioinformatics. 2000 Jan;16(1):16-23.
  • Stranger BE, et al. Population genomics of human gene expression. Nat Genet. 2007 Oct;39(10):1217-24.
  • Thorn CF, et al. Pharmacogenomics and bioinformatics: PharmGKB. Pharmacogenomics. 2010 Apr;11(4):501-5.
  • Wasserman WW, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nat Rev Genet. 2004 Apr;5(4):276-87.
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  • Wishart DS, et al.. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D668-72.
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  • Zdobnov EM, Apweiler R. InterProScan--an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001 Sep;17(9):847-8.
Scripps Genome ADVISER | Annotation and Distributed Variant Interpretation Server