{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T07:36:48Z","timestamp":1762673808797},"reference-count":74,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The past decade has seen the introduction of fast and relatively inexpensive methods to detect genetic variation across the genome and exponential growth in the number of known single nucleotide variants (SNVs). There is increasing interest in bioinformatics approaches to identify variants that are functionally important from millions of candidate variants. Here, we describe the essential components of bionformatics tools that predict functional SNVs.<\/jats:p>\n               <jats:p>Results: Bioinformatics tools have great potential to identify functional SNVs, but the black box nature of many tools can be a pitfall for researchers. Understanding the underlying methods, assumptions and biases of these tools is essential to their intelligent application.<\/jats:p>\n               <jats:p>Contact: \u00a0karchin@jhu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq695","type":"journal-article","created":{"date-parts":[[2010,12,16]],"date-time":"2010-12-16T01:15:18Z","timestamp":1292462118000},"page":"441-448","source":"Crossref","is-referenced-by-count":74,"title":["Using bioinformatics to predict the functional impact of SNVs"],"prefix":"10.1093","volume":"27","author":[{"given":"Melissa S.","family":"Cline","sequence":"first","affiliation":[{"name":"1 Department of Molecular Cell and Developmental Biology and Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA and 2Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, USA"}]},{"given":"Rachel","family":"Karchin","sequence":"additional","affiliation":[{"name":"1 Department of Molecular Cell and Developmental Biology and Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA and 2Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, USA"}]}],"member":"286","published-online":{"date-parts":[[2010,12,14]]},"reference":[{"key":"2023012511563839800_B1","doi-asserted-by":"crossref","first-page":"1622","DOI":"10.1101\/gr.092197.109","article-title":"The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group","volume":"19","author":"Ahn","year":"2009","journal-title":"Genome Res."},{"key":"2023012511563839800_B2","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1126\/science.1156409","article-title":"Genetic mapping in human disease","volume":"322","author":"Altshuler","year":"2008","journal-title":"Science"},{"key":"2023012511563839800_B3","doi-asserted-by":"crossref","first-page":"D154","DOI":"10.1093\/nar\/gki070","article-title":"The Universal Protein Resource (UniProt)","volume":"33","author":"Bairoch","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2023012511563839800_B4","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/nature05915","article-title":"The complex language of chromatin regulation during transcription","volume":"447","author":"Berger","year":"2007","journal-title":"Nature"},{"key":"2023012511563839800_B5","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1002\/pmic.200300771","article-title":"Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence","volume":"4","author":"Blom","year":"2004","journal-title":"Proteomics"},{"key":"2023012511563839800_B6","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1038\/ng1090","article-title":"Discovering genotypes underlying human phenotypes: past successes for mendelian disease, future approaches for complex disease","volume":"33","author":"Botstein","year":"2003","journal-title":"Nat. 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