SNP annotation (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "SNP annotation" in English language version.

refsWebsite

Global rank English rank

99nih.gov

4^th place

55doi.org

2^nd place

8semanticscholar.org

11^th place

8^th place

2wikipedia.org

low place

2harvard.edu

18^th place

17^th place

1github.com

383^rd place

320^th place

1washington.edu

1,067^th place

749^th place

doi.org

Aubourg S, Rouzé P (2001). "Genome annotation". Plant Physiol. Biochem. 29 (3–4): 181–193. doi:10.1016/S0981-9428(01)01242-6.
Karchin R (January 2009). "Next generation tools for the annotation of human SNPs". Briefings in Bioinformatics. 10 (1): 35–52. doi:10.1093/bib/bbn047. PMC 2638621. PMID 19181721.
Shen TH, Carlson CS, Tarczy-Hornoch P (August 2009). "SNPit: a federated data integration system for the purpose of functional SNP annotation". Computer Methods and Programs in Biomedicine. 95 (2): 181–189. doi:10.1016/j.cmpb.2009.02.010. PMC 2680224. PMID 19327864.
Capriotti E, Nehrt NL, Kann MG, Bromberg Y (July 2012). "Bioinformatics for personal genome interpretation". Briefings in Bioinformatics. 13 (4): 495–512. doi:10.1093/bib/bbr070. PMC 3404395. PMID 22247263.
Wang Z, Gerstein M, Snyder M (January 2009). "RNA-Seq: a revolutionary tool for transcriptomics". Nature Reviews. Genetics. 10 (1): 57–63. doi:10.1038/nrg2484. PMC 2949280. PMID 19015660.
Halvorsen M, Martin JS, Broadaway S, Laederach A (August 2010). "Disease-associated mutations that alter the RNA structural ensemble". PLOS Genetics. 6 (8): e1001074. doi:10.1371/journal.pgen.1001074. PMC 2924325. PMID 20808897.
Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, et al. (January 2014). "Landscape and variation of RNA secondary structure across the human transcriptome". Nature. 505 (7485): 706–709. Bibcode:2014Natur.505..706W. doi:10.1038/nature12946. PMC 3973747. PMID 24476892.
Sauna ZE, Kimchi-Sarfaty C (August 2011). "Understanding the contribution of synonymous mutations to human disease". Nature Reviews. Genetics. 12 (10): 683–691. doi:10.1038/nrg3051. PMID 21878961. S2CID 8358824.
Li MJ, Yan B, Sham PC, Wang J (May 2015). "Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression". Briefings in Bioinformatics. 16 (3): 393–412. doi:10.1093/bib/bbu018. PMID 24916300.
French JD, Ghoussaini M, Edwards SL, Meyer KB, Michailidou K, Ahmed S, et al. (April 2013). "Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers". American Journal of Human Genetics. 92 (4): 489–503. doi:10.1016/j.ajhg.2013.01.002. PMC 3617380. PMID 23540573.
Faber K, Glatting KH, Mueller PJ, Risch A, Hotz-Wagenblatt A (2011). "Genome-wide prediction of splice-modifying SNPs in human genes using a new analysis pipeline called AASsites". BMC Bioinformatics. 12 (Suppl 4): S2. doi:10.1186/1471-2105-12-s4-s2. PMC 3194194. PMID 21992029.
Kumar V, Westra HJ, Karjalainen J, Zhernakova DV, Esko T, Hrdlickova B, et al. (2013). "Human disease-associated genetic variation impacts large intergenic non-coding RNA expression". PLOS Genetics. 9 (1): e1003201. doi:10.1371/journal.pgen.1003201. PMC 3547830. PMID 23341781.
Sim NL, Kumar P, Hu J, Henikoff S, Schneider G, Ng PC (July 2012). "SIFT web server: predicting effects of amino acid substitutions on proteins". Nucleic Acids Research. 40 (Web Server issue): W452–W457. doi:10.1093/nar/gks539. PMC 3394338. PMID 22689647.
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. (April 2010). "A method and server for predicting damaging missense mutations". Nature Methods. 7 (4): 248–249. doi:10.1038/nmeth0410-248. PMC 2855889. PMID 20354512.
Schwarz JM, Rödelsperger C, Schuelke M, Seelow D (August 2010). "MutationTaster evaluates disease-causing potential of sequence alterations". Nature Methods. 7 (8): 575–576. doi:10.1038/nmeth0810-575. PMID 20676075. S2CID 26892938.
Zhang P, Bigio B, Rapaport F, Zhang SY, Casanova JL, Abel L, et al. (December 2018). "PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations". Bioinformatics. 34 (24): 4307–4309. doi:10.1093/bioinformatics/bty536. PMC 6289133. PMID 30535305.
Ofoegbu TC, David A, Kelley LA, Mezulis S, Islam SA, Mersmann SF, et al. (June 2019). "PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants". Journal of Molecular Biology. 431 (13): 2460–2466. doi:10.1016/j.jmb.2019.04.043. PMC 6597944. PMID 31075275.
Ittisoponpisan S, Islam SA, Khanna T, Alhuzimi E, David A, Sternberg MJ (May 2019). "Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated?". Journal of Molecular Biology. 431 (11): 2197–2212. doi:10.1016/j.jmb.2019.04.009. PMC 6544567. PMID 30995449.
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. (2012). "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3". Fly. 6 (2): 80–92. doi:10.4161/fly.19695. PMC 3679285. PMID 22728672.
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, et al. (June 2016). "The Ensembl Variant Effect Predictor". Genome Biology. 17 (1): 122. doi:10.1186/s13059-016-0974-4. PMC 4893825. PMID 27268795.
Wang K, Li M, Hakonarson H (September 2010). "ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data". Nucleic Acids Research. 38 (16): e164. doi:10.1093/nar/gkq603. PMC 2938201. PMID 20601685.
Jäger M, Wang K, Bauer S, Smedley D, Krawitz P, Robinson PN (May 2014). "Jannovar: a java library for exome annotation". Human Mutation. 35 (5): 548–555. doi:10.1002/humu.22531. PMID 24677618. S2CID 10822001.
Capriotti E, Calabrese R, Casadio R (November 2006). "Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information". Bioinformatics. 22 (22): 2729–2734. doi:10.1093/bioinformatics/btl423. PMID 16895930.
Adzhubei I, Jordan DM, Sunyaev SR (January 2013). "Predicting functional effect of human missense mutations using PolyPhen-2". Current Protocols in Human Genetics. Chapter 7: Unit7.20. doi:10.1002/0471142905.hg0720s76. PMC 4480630. PMID 23315928.
Schwarz JM, Rödelsperger C, Schuelke M, Seelow D (August 2010). "MutationTaster evaluates disease-causing potential of sequence alterations". Nature Methods. 7 (8): 575–576. doi:10.1038/nmeth0810-575. PMID 20676075. S2CID 26892938.
Yates CM, Filippis I, Kelley LA, Sternberg MJ (July 2014). "SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features". Journal of Molecular Biology. 426 (14): 2692–2701. doi:10.1016/j.jmb.2014.04.026. PMC 4087249. PMID 24810707.
Lee PH, Shatkay H (January 2008). "F-SNP: computationally predicted functional SNPs for disease association studies". Nucleic Acids Research. 36 (Database issue): D820–D824. doi:10.1093/nar/gkm904. PMC 2238878. PMID 17986460.
Makarov V, O'Grady T, Cai G, Lihm J, Buxbaum JD, Yoon S (March 2012). "AnnTools: a comprehensive and versatile annotation toolkit for genomic variants". Bioinformatics. 28 (5): 724–725. doi:10.1093/bioinformatics/bts032. PMC 3289923. PMID 22257670.
Shen TH, Carlson CS, Tarczy-Hornoch P (August 2009). "SNPit: a federated data integration system for the purpose of functional SNP annotation". Computer Methods and Programs in Biomedicine. 95 (2): 181–189. doi:10.1016/j.cmpb.2009.02.010. PMC 2680224. PMID 19327864.
Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, Nicolae DL, et al. (January 2010). "SCAN: SNP and copy number annotation". Bioinformatics. 26 (2): 259–262. doi:10.1093/bioinformatics/btp644. PMC 2852202. PMID 19933162.
Bromberg Y, Rost B (2007). "SNAP: predict effect of non-synonymous polymorphisms on function". Nucleic Acids Research. 35 (11): 3823–3835. doi:10.1093/nar/gkm238. PMC 1920242. PMID 17526529.
Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R (August 2009). "Functional annotations improve the predictive score of human disease-related mutations in proteins". Human Mutation. 30 (8): 1237–1244. doi:10.1002/humu.21047. PMID 19514061. S2CID 33900765.
Karchin R, Diekhans M, Kelly L, Thomas DJ, Pieper U, Eswar N, et al. (June 2005). "LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources". Bioinformatics. 21 (12): 2814–2820. doi:10.1093/bioinformatics/bti442. PMID 15827081.
Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, et al. (January 2012). "TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data". Bioinformatics. 28 (2): 277–278. doi:10.1093/bioinformatics/btr612. PMC 3259432. PMID 22088845.
Doran AG, Creevey CJ (February 2013). "Snpdat: easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms". BMC Bioinformatics. 14: 45. doi:10.1186/1471-2105-14-45. PMC 3574845. PMID 23390980.
Grant JR, Arantes AS, Liao X, Stothard P (August 2011). "In-depth annotation of SNPs arising from resequencing projects using NGS-SNP". Bioinformatics. 27 (16): 2300–2301. doi:10.1093/bioinformatics/btr372. PMC 3150039. PMID 21697123.
Ge D, Ruzzo EK, Shianna KV, He M, Pelak K, Heinzen EL, et al. (July 2011). "SVA: software for annotating and visualizing sequenced human genomes". Bioinformatics. 27 (14): 1998–2000. doi:10.1093/bioinformatics/btr317. PMC 3129530. PMID 21624899.
Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J (July 2012). "VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing". Nucleic Acids Research. 40 (Web Server issue): W54–W58. doi:10.1093/nar/gks572. PMC 3394276. PMID 22693211.
Ng PC, Henikoff S (July 2003). "SIFT: Predicting amino acid changes that affect protein function". Nucleic Acids Research. 31 (13): 3812–3814. doi:10.1093/nar/gkg509. PMC 168916. PMID 12824425.
Malhis N, Jones SJ, Gsponer J (April 2019). "Improved measures for evolutionary conservation that exploit taxonomy distances". Nature Communications. 10 (1): 1556. Bibcode:2019NatCo..10.1556M. doi:10.1038/s41467-019-09583-2. PMC 6450959. PMID 30952844.
Malhis N, Jacobson M, Jones SJ, Gsponer J (July 2020). "LIST-S2: taxonomy based sorting of deleterious missense mutations across species". Nucleic Acids Research. 48 (W1): W154–W161. doi:10.1093/nar/gkaa288. PMC 7319545. PMID 32352516.
Yuan HY, Chiou JJ, Tseng WH, Liu CH, Liu CK, Lin YJ, et al. (July 2006). "FASTSNP: an always up-to-date and extendable service for SNP function analysis and prioritization". Nucleic Acids Research. 34 (Web Server issue): W635–W641. doi:10.1093/nar/gkl236. PMC 1538865. PMID 16845089.
Mi H, Guo N, Kejariwal A, Thomas PD (January 2007). "PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways". Nucleic Acids Research. 35 (Database issue): D247–D252. doi:10.1093/nar/gkl869. PMC 1716723. PMID 17130144.
Capriotti E, Altman RB, Bromberg Y (2013). "Collective judgment predicts disease-associated single nucleotide variants". BMC Genomics. 14 (Suppl 3): S2. doi:10.1186/1471-2164-14-S3-S2. PMC 3839641. PMID 23819846.
Wang K, Li M, Hakonarson H (September 2010). "ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data". Nucleic Acids Research. 38 (16): e164. doi:10.1093/nar/gkq603. PMC 2938201. PMID 20601685.
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, et al. (June 2016). "The Ensembl Variant Effect Predictor". Genome Biology. 17 (1): 122. doi:10.1186/s13059-016-0974-4. PMC 4893825. PMID 27268795.
Makarov V, O'Grady T, Cai G, Lihm J, Buxbaum JD, Yoon S (March 2012). "AnnTools: a comprehensive and versatile annotation toolkit for genomic variants". Bioinformatics. 28 (5): 724–725. doi:10.1093/bioinformatics/bts032. PMC 3289923. PMID 22257670.
Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J (July 2012). "VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing". Nucleic Acids Research. 40 (Web Server issue): W54–W58. doi:10.1093/nar/gks572. PMC 3394276. PMID 22693211.
Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, et al. (March 2014). "A survey of tools for variant analysis of next-generation genome sequencing data". Briefings in Bioinformatics. 15 (2): 256–278. doi:10.1093/bib/bbs086. PMC 3956068. PMID 23341494.
Lee PH, Lee C, Li X, Wee B, Dwivedi T, Daly M (January 2018). "Principles and methods of in-silico prioritization of non-coding regulatory variants". Human Genetics. 137 (1): 15–30. doi:10.1007/s00439-017-1861-0. PMC 5892192. PMID 29288389.
Li X, Li Z, Zhou H, Gaynor SM, Liu Y, Chen H, et al. (September 2020). "Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale". Nature Genetics. 52 (9): 969–983. doi:10.1038/s41588-020-0676-4. PMC 7483769. PMID 32839606.
Watanabe K, Taskesen E, van Bochoven A, Posthuma D (November 2017). "Functional mapping and annotation of genetic associations with FUMA". Nature Communications. 8 (1): 1826. doi:10.1038/s41467-017-01261-5. PMC 5705698. PMID 29184056.
Li Z, Li X, Zhou H, Gaynor SM, Selvaraj MS, Arapoglou T, et al. (December 2022). "A framework for detecting noncoding rare-variant associations of large-scale whole-genome sequencing studies". Nature Methods. 19 (12): 1599–1611. doi:10.1038/s41592-022-01640-x. PMC 10008172. PMID 36303018. S2CID 243873361.
"STAARpipeline: an all-in-one rare-variant tool for biobank-scale whole-genome sequencing data". Nature Methods. 19 (12): 1532–1533. December 2022. doi:10.1038/s41592-022-01641-w. PMID 36316564. S2CID 253246835.
Li, Xihao; Quick, Corbin; Zhou, Hufeng; Gaynor, Sheila M.; Liu, Yaowu; Chen, Han; Selvaraj, Margaret Sunitha; Sun, Ryan; Dey, Rounak; Arnett, Donna K.; Bielak, Lawrence F.; Bis, Joshua C.; Blangero, John; Boerwinkle, Eric; Bowden, Donald W.; Brody, Jennifer A.; Cade, Brian E.; Correa, Adolfo; Cupples, L. Adrienne; Curran, Joanne E.; de Vries, Paul S.; Duggirala, Ravindranath; Freedman, Barry I.; Göring, Harald H. H.; Guo, Xiuqing; Haessler, Jeffrey; Kalyani, Rita R.; Kooperberg, Charles; Kral, Brian G.; Lange, Leslie A.; Manichaikul, Ani; Martin, Lisa W.; McGarvey, Stephen T.; Mitchell, Braxton D.; Montasser, May E.; Morrison, Alanna C.; Naseri, Take; O’Connell, Jeffrey R.; Palmer, Nicholette D.; Peyser, Patricia A.; Psaty, Bruce M.; Raffield, Laura M.; Redline, Susan; Reiner, Alexander P.; Reupena, Muagututi’a Sefuiva; Rice, Kenneth M.; Rich, Stephen S.; Sitlani, Colleen M.; Smith, Jennifer A.; Taylor, Kent D.; Vasan, Ramachandran S.; Willer, Cristen J.; Wilson, James G.; Yanek, Lisa R.; Zhao, Wei; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lipids Working Group; Rotter, Jerome I.; Natarajan, Pradeep; Peloso, Gina M.; Li, Zilin; Lin, Xihong (January 2023). "Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies". Nature Genetics. 55 (1): 154–164. doi:10.1038/s41588-022-01225-6. PMC 10084891. PMID 36564505. S2CID 255084231.

github.com

"charite/jannovar". GitHub. Retrieved 2016-09-25.

harvard.edu

ui.adsabs.harvard.edu

Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, et al. (January 2014). "Landscape and variation of RNA secondary structure across the human transcriptome". Nature. 505 (7485): 706–709. Bibcode:2014Natur.505..706W. doi:10.1038/nature12946. PMC 3973747. PMID 24476892.
Malhis N, Jones SJ, Gsponer J (April 2019). "Improved measures for evolutionary conservation that exploit taxonomy distances". Nature Communications. 10 (1): 1556. Bibcode:2019NatCo..10.1556M. doi:10.1038/s41467-019-09583-2. PMC 6450959. PMID 30952844.

nih.gov

pubmed.ncbi.nlm.nih.gov

Karchin R (January 2009). "Next generation tools for the annotation of human SNPs". Briefings in Bioinformatics. 10 (1): 35–52. doi:10.1093/bib/bbn047. PMC 2638621. PMID 19181721.
Shen TH, Carlson CS, Tarczy-Hornoch P (August 2009). "SNPit: a federated data integration system for the purpose of functional SNP annotation". Computer Methods and Programs in Biomedicine. 95 (2): 181–189. doi:10.1016/j.cmpb.2009.02.010. PMC 2680224. PMID 19327864.
Capriotti E, Nehrt NL, Kann MG, Bromberg Y (July 2012). "Bioinformatics for personal genome interpretation". Briefings in Bioinformatics. 13 (4): 495–512. doi:10.1093/bib/bbr070. PMC 3404395. PMID 22247263.
Wang Z, Gerstein M, Snyder M (January 2009). "RNA-Seq: a revolutionary tool for transcriptomics". Nature Reviews. Genetics. 10 (1): 57–63. doi:10.1038/nrg2484. PMC 2949280. PMID 19015660.
Halvorsen M, Martin JS, Broadaway S, Laederach A (August 2010). "Disease-associated mutations that alter the RNA structural ensemble". PLOS Genetics. 6 (8): e1001074. doi:10.1371/journal.pgen.1001074. PMC 2924325. PMID 20808897.
Wan Y, Qu K, Zhang QC, Flynn RA, Manor O, Ouyang Z, et al. (January 2014). "Landscape and variation of RNA secondary structure across the human transcriptome". Nature. 505 (7485): 706–709. Bibcode:2014Natur.505..706W. doi:10.1038/nature12946. PMC 3973747. PMID 24476892.
Sauna ZE, Kimchi-Sarfaty C (August 2011). "Understanding the contribution of synonymous mutations to human disease". Nature Reviews. Genetics. 12 (10): 683–691. doi:10.1038/nrg3051. PMID 21878961. S2CID 8358824.
Li MJ, Yan B, Sham PC, Wang J (May 2015). "Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression". Briefings in Bioinformatics. 16 (3): 393–412. doi:10.1093/bib/bbu018. PMID 24916300.
French JD, Ghoussaini M, Edwards SL, Meyer KB, Michailidou K, Ahmed S, et al. (April 2013). "Functional variants at the 11q13 risk locus for breast cancer regulate cyclin D1 expression through long-range enhancers". American Journal of Human Genetics. 92 (4): 489–503. doi:10.1016/j.ajhg.2013.01.002. PMC 3617380. PMID 23540573.
Faber K, Glatting KH, Mueller PJ, Risch A, Hotz-Wagenblatt A (2011). "Genome-wide prediction of splice-modifying SNPs in human genes using a new analysis pipeline called AASsites". BMC Bioinformatics. 12 (Suppl 4): S2. doi:10.1186/1471-2105-12-s4-s2. PMC 3194194. PMID 21992029.
Kumar V, Westra HJ, Karjalainen J, Zhernakova DV, Esko T, Hrdlickova B, et al. (2013). "Human disease-associated genetic variation impacts large intergenic non-coding RNA expression". PLOS Genetics. 9 (1): e1003201. doi:10.1371/journal.pgen.1003201. PMC 3547830. PMID 23341781.
Sim NL, Kumar P, Hu J, Henikoff S, Schneider G, Ng PC (July 2012). "SIFT web server: predicting effects of amino acid substitutions on proteins". Nucleic Acids Research. 40 (Web Server issue): W452–W457. doi:10.1093/nar/gks539. PMC 3394338. PMID 22689647.
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. (April 2010). "A method and server for predicting damaging missense mutations". Nature Methods. 7 (4): 248–249. doi:10.1038/nmeth0410-248. PMC 2855889. PMID 20354512.
Schwarz JM, Rödelsperger C, Schuelke M, Seelow D (August 2010). "MutationTaster evaluates disease-causing potential of sequence alterations". Nature Methods. 7 (8): 575–576. doi:10.1038/nmeth0810-575. PMID 20676075. S2CID 26892938.
Zhang P, Bigio B, Rapaport F, Zhang SY, Casanova JL, Abel L, et al. (December 2018). "PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations". Bioinformatics. 34 (24): 4307–4309. doi:10.1093/bioinformatics/bty536. PMC 6289133. PMID 30535305.
Ofoegbu TC, David A, Kelley LA, Mezulis S, Islam SA, Mersmann SF, et al. (June 2019). "PhyreRisk: A Dynamic Web Application to Bridge Genomics, Proteomics and 3D Structural Data to Guide Interpretation of Human Genetic Variants". Journal of Molecular Biology. 431 (13): 2460–2466. doi:10.1016/j.jmb.2019.04.043. PMC 6597944. PMID 31075275.
Ittisoponpisan S, Islam SA, Khanna T, Alhuzimi E, David A, Sternberg MJ (May 2019). "Can Predicted Protein 3D Structures Provide Reliable Insights into whether Missense Variants Are Disease Associated?". Journal of Molecular Biology. 431 (11): 2197–2212. doi:10.1016/j.jmb.2019.04.009. PMC 6544567. PMID 30995449.
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. (2012). "A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3". Fly. 6 (2): 80–92. doi:10.4161/fly.19695. PMC 3679285. PMID 22728672.
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, et al. (June 2016). "The Ensembl Variant Effect Predictor". Genome Biology. 17 (1): 122. doi:10.1186/s13059-016-0974-4. PMC 4893825. PMID 27268795.
Wang K, Li M, Hakonarson H (September 2010). "ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data". Nucleic Acids Research. 38 (16): e164. doi:10.1093/nar/gkq603. PMC 2938201. PMID 20601685.
Jäger M, Wang K, Bauer S, Smedley D, Krawitz P, Robinson PN (May 2014). "Jannovar: a java library for exome annotation". Human Mutation. 35 (5): 548–555. doi:10.1002/humu.22531. PMID 24677618. S2CID 10822001.
Capriotti E, Calabrese R, Casadio R (November 2006). "Predicting the insurgence of human genetic diseases associated to single point protein mutations with support vector machines and evolutionary information". Bioinformatics. 22 (22): 2729–2734. doi:10.1093/bioinformatics/btl423. PMID 16895930.
Adzhubei I, Jordan DM, Sunyaev SR (January 2013). "Predicting functional effect of human missense mutations using PolyPhen-2". Current Protocols in Human Genetics. Chapter 7: Unit7.20. doi:10.1002/0471142905.hg0720s76. PMC 4480630. PMID 23315928.
Schwarz JM, Rödelsperger C, Schuelke M, Seelow D (August 2010). "MutationTaster evaluates disease-causing potential of sequence alterations". Nature Methods. 7 (8): 575–576. doi:10.1038/nmeth0810-575. PMID 20676075. S2CID 26892938.
Yates CM, Filippis I, Kelley LA, Sternberg MJ (July 2014). "SuSPect: enhanced prediction of single amino acid variant (SAV) phenotype using network features". Journal of Molecular Biology. 426 (14): 2692–2701. doi:10.1016/j.jmb.2014.04.026. PMC 4087249. PMID 24810707.
Lee PH, Shatkay H (January 2008). "F-SNP: computationally predicted functional SNPs for disease association studies". Nucleic Acids Research. 36 (Database issue): D820–D824. doi:10.1093/nar/gkm904. PMC 2238878. PMID 17986460.
Makarov V, O'Grady T, Cai G, Lihm J, Buxbaum JD, Yoon S (March 2012). "AnnTools: a comprehensive and versatile annotation toolkit for genomic variants". Bioinformatics. 28 (5): 724–725. doi:10.1093/bioinformatics/bts032. PMC 3289923. PMID 22257670.
Shen TH, Carlson CS, Tarczy-Hornoch P (August 2009). "SNPit: a federated data integration system for the purpose of functional SNP annotation". Computer Methods and Programs in Biomedicine. 95 (2): 181–189. doi:10.1016/j.cmpb.2009.02.010. PMC 2680224. PMID 19327864.
Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, Nicolae DL, et al. (January 2010). "SCAN: SNP and copy number annotation". Bioinformatics. 26 (2): 259–262. doi:10.1093/bioinformatics/btp644. PMC 2852202. PMID 19933162.
Bromberg Y, Rost B (2007). "SNAP: predict effect of non-synonymous polymorphisms on function". Nucleic Acids Research. 35 (11): 3823–3835. doi:10.1093/nar/gkm238. PMC 1920242. PMID 17526529.
Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R (August 2009). "Functional annotations improve the predictive score of human disease-related mutations in proteins". Human Mutation. 30 (8): 1237–1244. doi:10.1002/humu.21047. PMID 19514061. S2CID 33900765.
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Li, Xihao; Quick, Corbin; Zhou, Hufeng; Gaynor, Sheila M.; Liu, Yaowu; Chen, Han; Selvaraj, Margaret Sunitha; Sun, Ryan; Dey, Rounak; Arnett, Donna K.; Bielak, Lawrence F.; Bis, Joshua C.; Blangero, John; Boerwinkle, Eric; Bowden, Donald W.; Brody, Jennifer A.; Cade, Brian E.; Correa, Adolfo; Cupples, L. Adrienne; Curran, Joanne E.; de Vries, Paul S.; Duggirala, Ravindranath; Freedman, Barry I.; Göring, Harald H. H.; Guo, Xiuqing; Haessler, Jeffrey; Kalyani, Rita R.; Kooperberg, Charles; Kral, Brian G.; Lange, Leslie A.; Manichaikul, Ani; Martin, Lisa W.; McGarvey, Stephen T.; Mitchell, Braxton D.; Montasser, May E.; Morrison, Alanna C.; Naseri, Take; O’Connell, Jeffrey R.; Palmer, Nicholette D.; Peyser, Patricia A.; Psaty, Bruce M.; Raffield, Laura M.; Redline, Susan; Reiner, Alexander P.; Reupena, Muagututi’a Sefuiva; Rice, Kenneth M.; Rich, Stephen S.; Sitlani, Colleen M.; Smith, Jennifer A.; Taylor, Kent D.; Vasan, Ramachandran S.; Willer, Cristen J.; Wilson, James G.; Yanek, Lisa R.; Zhao, Wei; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lipids Working Group; Rotter, Jerome I.; Natarajan, Pradeep; Peloso, Gina M.; Li, Zilin; Lin, Xihong (January 2023). "Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies". Nature Genetics. 55 (1): 154–164. doi:10.1038/s41588-022-01225-6. PMC 10084891. PMID 36564505. S2CID 255084231.

semanticscholar.org

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Li, Xihao; Quick, Corbin; Zhou, Hufeng; Gaynor, Sheila M.; Liu, Yaowu; Chen, Han; Selvaraj, Margaret Sunitha; Sun, Ryan; Dey, Rounak; Arnett, Donna K.; Bielak, Lawrence F.; Bis, Joshua C.; Blangero, John; Boerwinkle, Eric; Bowden, Donald W.; Brody, Jennifer A.; Cade, Brian E.; Correa, Adolfo; Cupples, L. Adrienne; Curran, Joanne E.; de Vries, Paul S.; Duggirala, Ravindranath; Freedman, Barry I.; Göring, Harald H. H.; Guo, Xiuqing; Haessler, Jeffrey; Kalyani, Rita R.; Kooperberg, Charles; Kral, Brian G.; Lange, Leslie A.; Manichaikul, Ani; Martin, Lisa W.; McGarvey, Stephen T.; Mitchell, Braxton D.; Montasser, May E.; Morrison, Alanna C.; Naseri, Take; O’Connell, Jeffrey R.; Palmer, Nicholette D.; Peyser, Patricia A.; Psaty, Bruce M.; Raffield, Laura M.; Redline, Susan; Reiner, Alexander P.; Reupena, Muagututi’a Sefuiva; Rice, Kenneth M.; Rich, Stephen S.; Sitlani, Colleen M.; Smith, Jennifer A.; Taylor, Kent D.; Vasan, Ramachandran S.; Willer, Cristen J.; Wilson, James G.; Yanek, Lisa R.; Zhao, Wei; NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium; TOPMed Lipids Working Group; Rotter, Jerome I.; Natarajan, Pradeep; Peloso, Gina M.; Li, Zilin; Lin, Xihong (January 2023). "Powerful, scalable and resource-efficient meta-analysis of rare variant associations in large whole genome sequencing studies". Nature Genetics. 55 (1): 154–164. doi:10.1038/s41588-022-01225-6. PMC 10084891. PMID 36564505. S2CID 255084231.