-
1
-
-
84907262675
-
Personalized medicine: Special treatment
-
Eisenstein M. Personalized medicine: Special treatment. Nature. 2014;513:S8-9.
-
(2014)
Nature.
, vol.513
, pp. S8-S9
-
-
Eisenstein, M.1
-
2
-
-
79551587725
-
PARP inhibitor treatment in ovarian and breast cancer
-
Weil MK, Chen A. PARP inhibitor treatment in ovarian and breast cancer. Curr Probl Cancer. 2011;35:7-50.
-
(2011)
Curr Probl Cancer.
, vol.35
, pp. 7-50
-
-
Weil, M.K.1
Chen, A.2
-
3
-
-
84924666082
-
Large-scale discovery of novel genetic causes of developmental disorders
-
The Deciphering Developmental Disorders Study. Large-scale discovery of novel genetic causes of developmental disorders. Nature. 2015;519:223-8.
-
(2015)
Nature
, vol.519
, pp. 223-228
-
-
-
4
-
-
84865346397
-
Non-communicable diseases: fact sheet
-
Jan Accessed 17 Mar 2016
-
World Health Organisation. Non-communicable diseases: fact sheet. Jan 2015. http://www.who.int/mediacentre/factsheets/fs355/en/. Accessed 17 Mar 2016.
-
(2015)
-
-
-
6
-
-
84920476665
-
How important are rare variants in common disease?
-
Saint Pierre A, Génin E. How important are rare variants in common disease? Brief Funct Genomics. 2014;13:353-61.
-
(2014)
Brief Funct Genomics
, vol.13
, pp. 353-361
-
-
Saint Pierre, A.1
Génin, E.2
-
7
-
-
84893378179
-
Searching for missing heritability: designing rare variant association studies
-
Zuk O, Schaffner SF, Samocha K, Do R, Hechter E, Kathiresan S, et al. Searching for missing heritability: designing rare variant association studies. Proc Natl Acad Sci U S A. 2014;111:E455-64.
-
(2014)
Proc Natl Acad Sci U S A.
, vol.111
, pp. E455-E464
-
-
Zuk, O.1
Schaffner, S.F.2
Samocha, K.3
Do, R.4
Hechter, E.5
Kathiresan, S.6
-
8
-
-
67249117049
-
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits
-
Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A. 2009;106:9362-7.
-
(2009)
Proc Natl Acad Sci U S A.
, vol.106
, pp. 9362-9367
-
-
Hindorff, L.A.1
Sethupathy, P.2
Junkins, H.A.3
Ramos, E.M.4
Mehta, J.P.5
Collins, F.S.6
-
9
-
-
84945248976
-
Non-coding recurrent mutations in chronic lymphocytic leukaemia
-
Puente XS, Beà S, Valdés-Mas R, Villamor N, Gutiérrez-Abril J, Martín-Subero JI, et al. Non-coding recurrent mutations in chronic lymphocytic leukaemia. Nature. 2015;526:519-24.
-
(2015)
Nature.
, vol.526
, pp. 519-524
-
-
Puente, X.S.1
Beà, S.2
Valdés-Mas, R.3
Villamor, N.4
Gutiérrez-Abril, J.5
Martín-Subero, J.I.6
-
10
-
-
84929132687
-
Large-scale whole-genome sequencing of the Icelandic population
-
Gudbjartsson DF, Helgason H, Gudjonsson SA, Zink F, Oddson A, Gylfason A, et al. Large-scale whole-genome sequencing of the Icelandic population. Nat Genet. 2015;47:435-44.
-
(2015)
Nat Genet.
, vol.47
, pp. 435-444
-
-
Gudbjartsson, D.F.1
Helgason, H.2
Gudjonsson, S.A.3
Zink, F.4
Oddson, A.5
Gylfason, A.6
-
11
-
-
84973362927
-
NHS set to deliver world-leading genomics project in fight against cancer and rare diseases
-
Accessed 17 Mar
-
NHS. NHS set to deliver world-leading genomics project in fight against cancer and rare diseases. http://www.england.nhs.uk/2014/12/22/genomics-project/. Accessed 17 Mar 2016.
-
(2016)
-
-
-
12
-
-
84923762812
-
A new initiative on precision medicine
-
Collins FS, Varmus H. A new initiative on precision medicine. N Engl J Med. 2015;372:793-5.
-
(2015)
N Engl J Med.
, vol.372
, pp. 793-795
-
-
Collins, F.S.1
Varmus, H.2
-
14
-
-
80053384429
-
Whole-genome sequencing of multiple Arabidopsis thaliana populations
-
Cao J, Schneeberger K, Ossowski S, Günther T, Bender S, Fitz J, et al. Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet. 2011;43:956-63.
-
(2011)
Nat Genet.
, vol.43
, pp. 956-963
-
-
Cao, J.1
Schneeberger, K.2
Ossowski, S.3
Günther, T.4
Bender, S.5
Fitz, J.6
-
15
-
-
84905483050
-
Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle
-
Daetwyler HD, Capitan A, Pausch H, Stothard P, van Binsbergen R, Brøndum RF, et al. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet. 2014;46:858-65.
-
(2014)
Nat Genet.
, vol.46
, pp. 858-865
-
-
Daetwyler, H.D.1
Capitan, A.2
Pausch, H.3
Stothard, P.4
Binsbergen, R.5
Brøndum, R.F.6
-
17
-
-
84865760395
-
GENCODE: the reference human genome annotation for the ENCODE Project
-
Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, et al. GENCODE: the reference human genome annotation for the ENCODE Project. Genome Res. 2012;22:1760-74.
-
(2012)
Genome Res.
, vol.22
, pp. 1760-1774
-
-
Harrow, J.1
Frankish, A.2
Gonzalez, J.M.3
Tapanari, E.4
Diekhans, M.5
Kokocinski, F.6
-
18
-
-
84891767394
-
RefSeq: an update on mammalian reference sequences
-
Pruitt KD, Brown GR, Hiatt SM, Thibaud-Nissen F, Astashyn A, Ermolaeva O, et al. RefSeq: an update on mammalian reference sequences. Nucleic Acids Res. 2014;42:D756-63.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D756-D763
-
-
Pruitt, K.D.1
Brown, G.R.2
Hiatt, S.M.3
Thibaud-Nissen, F.4
Astashyn, A.5
Ermolaeva, O.6
-
19
-
-
77954314621
-
Locus Reference Genomic sequences: an improved basis for describing human DNA variants
-
Dalgleish R, Flicek P, Cunningham F, Astashyn A, Tully RE, Proctor G, et al. Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Med. 2010;2:24.
-
(2010)
Genome Med.
, vol.2
, pp. 24
-
-
Dalgleish, R.1
Flicek, P.2
Cunningham, F.3
Astashyn, A.4
Tully, R.E.5
Proctor, G.6
-
20
-
-
84946037477
-
Ensembl 2015
-
Cunningham F, Amode MR, Barrell D, Beal K, Billis K, Brent S, et al. Ensembl 2015. Nucleic Acids Res. 2015;43:D662-9.
-
(2015)
Nucleic Acids Res.
, vol.43
, pp. D662-D669
-
-
Cunningham, F.1
Amode, M.R.2
Barrell, D.3
Beal, K.4
Billis, K.5
Brent, S.6
-
21
-
-
84973295973
-
Ensembl Variant Effect Predictor web interface
-
Accessed 17 Mar
-
Ensembl Variant Effect Predictor web interface. http://www.ensembl.org/vep. Accessed 17 Mar 2016.
-
(2016)
-
-
-
22
-
-
84896448861
-
A survey of tools for variant analysis of next-generation genome sequencing data
-
Pabinger S, Dander A, Fischer M, Snajder R, Sperk M, Efremova M, et al. A survey of tools for variant analysis of next-generation genome sequencing data. Brief Bioinform. 2014;15:256-78.
-
(2014)
Brief Bioinform.
, vol.15
, pp. 256-278
-
-
Pabinger, S.1
Dander, A.2
Fischer, M.3
Snajder, R.4
Sperk, M.5
Efremova, M.6
-
23
-
-
77955405475
-
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor
-
McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinforma Oxf Engl. 2010;26:2069-70.
-
(2010)
Bioinforma Oxf Engl.
, vol.26
, pp. 2069-2070
-
-
McLaren, W.1
Pritchard, B.2
Rios, D.3
Chen, Y.4
Flicek, P.5
Cunningham, F.6
-
24
-
-
84907297224
-
Fine mapping QTL for female fertility on BTA04 and BTA13 in dairy cattle using HD SNP and sequence data
-
Höglund JK, Sahana G, Brøndum RF, Guldbrandtsen B, Buitenhuis B, Lund MS. Fine mapping QTL for female fertility on BTA04 and BTA13 in dairy cattle using HD SNP and sequence data. BMC Genomics. 2014;15:790.
-
(2014)
BMC Genomics.
, vol.15
, pp. 790
-
-
Höglund, J.K.1
Sahana, G.2
Brøndum, R.F.3
Guldbrandtsen, B.4
Buitenhuis, B.5
Lund, M.S.6
-
25
-
-
84924573875
-
SNP and INDEL detection in a QTL region on chicken chromosome 2 associated with muscle deposition
-
Godoy TF, Moreira GCM, Boschiero C, Gheyas AA, Gasparin G, Paduan M, et al. SNP and INDEL detection in a QTL region on chicken chromosome 2 associated with muscle deposition. Anim Genet. 2015;46:158-63.
-
(2015)
Anim Genet.
, vol.46
, pp. 158-163
-
-
Godoy, T.F.1
Moreira, G.C.M.2
Boschiero, C.3
Gheyas, A.A.4
Gasparin, G.5
Paduan, M.6
-
26
-
-
84924238819
-
Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci
-
Leslie EJ, Taub MA, Liu H, Steinberg KM, Koboldt DC, Zhang Q, et al. Identification of functional variants for cleft lip with or without cleft palate in or near PAX7, FGFR2, and NOG by targeted sequencing of GWAS loci. Am J Hum Genet. 2015;96:397-411.
-
(2015)
Am J Hum Genet.
, vol.96
, pp. 397-411
-
-
Leslie, E.J.1
Taub, M.A.2
Liu, H.3
Steinberg, K.M.4
Koboldt, D.C.5
Zhang, Q.6
-
27
-
-
84892385595
-
A review of post-GWAS prioritization approaches
-
Hou L, Zhao H. A review of post-GWAS prioritization approaches. Front Genet. 2013;4:280.
-
(2013)
Front Genet.
, vol.4
, pp. 280
-
-
Hou, L.1
Zhao, H.2
-
28
-
-
84887058596
-
Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis
-
International Multiple Sclerosis Genetics Consortium. Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat Genet. 2013;45:1353-60.
-
(2013)
Nat Genet
, vol.45
, pp. 1353-1360
-
-
-
29
-
-
84867214350
-
Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units
-
Saunders CJ, Miller NA, Soden SE, Dinwiddie DL, Noll A, Alnadi NA, et al. Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci Transl Med. 2012;4:154-135.
-
(2012)
Sci Transl Med
, vol.4
, pp. 135-154
-
-
Saunders, C.J.1
Miller, N.A.2
Soden, S.E.3
Dinwiddie, D.L.4
Noll, A.5
Alnadi, N.A.6
-
30
-
-
84926522440
-
Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data
-
Wright CF, Fitzgerald TW, Jones WD, Clayton S, McRae JF, van Kogelenberg M, et al. Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data. Lancet. 2015;385:1305-14.
-
(2015)
Lancet.
, vol.385
, pp. 1305-1314
-
-
Wright, C.F.1
Fitzgerald, T.W.2
Jones, W.D.3
Clayton, S.4
McRae, J.F.5
Kogelenberg, M.6
-
31
-
-
84975795680
-
An integrated map of genetic variation from 1,092 human genomes
-
McVean GA, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491:56-65.
-
(2012)
Nature.
, vol.491
, pp. 56-65
-
-
McVean, G.A.1
Auton, A.2
Brooks, L.D.3
DePristo, M.A.4
Durbin, R.M.5
Handsaker, R.E.6
-
32
-
-
84973392787
-
-
Accessed 17 Mar
-
Exome Aggregation Consortium (ExAC). http://exac.broadinstitute.org. Accessed 17 Mar 2016.
-
(2016)
-
-
-
34
-
-
84891822189
-
Ensembl Genomes 2013: scaling up access to genome-wide data
-
Kersey PJ, Allen JE, Christensen M, Davis P, Falin LJ, Grabmueller C, et al. Ensembl Genomes 2013: scaling up access to genome-wide data. Nucleic Acids Res. 2014;42:D546-52.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D546-D552
-
-
Kersey, P.J.1
Allen, J.E.2
Christensen, M.3
Davis, P.4
Falin, L.J.5
Grabmueller, C.6
-
35
-
-
84973291624
-
Developers mailing list
-
Accessed 17 Mar
-
Developers mailing list. http://lists.ensembl.org/mailman/listinfo/dev. Accessed 17 Mar 2016.
-
(2016)
-
-
-
36
-
-
84964425617
-
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction
-
Frankish A, Uszczynska B, Ritchie GR, Gonzalez JM, Pervouchine D, Petryszak R, et al. Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction. BMC Genomics. 2015;16(8):S2.
-
(2015)
BMC Genomics
, vol.16
, Issue.8
, pp. S2
-
-
Frankish, A.1
Uszczynska, B.2
Ritchie, G.R.3
Gonzalez, J.M.4
Pervouchine, D.5
Petryszak, R.6
-
37
-
-
84973392774
-
-
Accessed 17 Mar
-
Transcript Supporting Level (TSL). http://www.ensembl.org/Help/Glossary?id=492. Accessed 17 Mar 2016.
-
(2016)
-
-
-
38
-
-
84876513019
-
APPRIS: annotation of principal and alternative splice isoforms
-
Rodriguez JM, Maietta P, Ezkurdia I, Pietrelli A, Wesselink J-J, Lopez G, et al. APPRIS: annotation of principal and alternative splice isoforms. Nucleic Acids Res. 2013;41:D110-7.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. D110-D117
-
-
Rodriguez, J.M.1
Maietta, P.2
Ezkurdia, I.3
Pietrelli, A.4
Wesselink, J.-J.5
Lopez, G.6
-
39
-
-
84891768855
-
Expression Atlas update-a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments
-
Petryszak R, Burdett T, Fiorelli B, Fonseca NA, Gonzalez-Porta M, Hastings E, et al. Expression Atlas update-a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments. Nucleic Acids Res. 2014;42:D926-32.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D926-D932
-
-
Petryszak, R.1
Burdett, T.2
Fiorelli, B.3
Fonseca, N.A.4
Gonzalez-Porta, M.5
Hastings, E.6
-
40
-
-
68149165614
-
Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm
-
Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4:1073-81.
-
(2009)
Nat Protoc.
, vol.4
, pp. 1073-1081
-
-
Kumar, P.1
Henikoff, S.2
Ng, P.C.3
-
41
-
-
77951640946
-
A method and server for predicting damaging missense mutations
-
Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P, et al. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7:248-9.
-
(2010)
Nat Methods.
, vol.7
, pp. 248-249
-
-
Adzhubei, I.A.1
Schmidt, S.2
Peshkin, L.3
Ramensky, V.E.4
Gerasimova, A.5
Bork, P.6
-
42
-
-
84869873569
-
Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation
-
Gonzalez-Perez A, Deu-Pons J, Lopez-Bigas N. Improving the prediction of the functional impact of cancer mutations by baseline tolerance transformation. Genome Med. 2012;4:89.
-
(2012)
Genome Med.
, vol.4
, pp. 89
-
-
Gonzalez-Perez, A.1
Deu-Pons, J.2
Lopez-Bigas, N.3
-
43
-
-
84871578629
-
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models
-
Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GLA, Edwards KJ, et al. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Hum Mutat. 2013;34:57-65.
-
(2013)
Hum Mutat.
, vol.34
, pp. 57-65
-
-
Shihab, H.A.1
Gough, J.2
Cooper, D.N.3
Stenson, P.D.4
Barker, G.L.A.5
Edwards, K.J.6
-
45
-
-
84869436774
-
Interpreting noncoding genetic variation in complex traits and human disease
-
Ward LD, Kellis M. Interpreting noncoding genetic variation in complex traits and human disease. Nat Biotechnol. 2012;30:1095-106.
-
(2012)
Nat Biotechnol.
, vol.30
, pp. 1095-1106
-
-
Ward, L.D.1
Kellis, M.2
-
46
-
-
84939123947
-
The Ensembl Regulatory Build
-
Zerbino DR, Wilder SP, Johnson N, Juettemann T, Flicek PR. The Ensembl Regulatory Build. Genome Biol. 2015;16:56.
-
(2015)
Genome Biol.
, vol.16
, pp. 56
-
-
Zerbino, D.R.1
Wilder, S.P.2
Johnson, N.3
Juettemann, T.4
Flicek, P.R.5
-
47
-
-
84865790047
-
An integrated encyclopedia of DNA elements in the human genome
-
The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57-74.
-
(2012)
Nature
, vol.489
, pp. 57-74
-
-
-
48
-
-
84857980747
-
BLUEPRINT to decode the epigenetic signature written in blood
-
Adams D, Altucci L, Antonarakis SE, Ballesteros J, Beck S, Bird A, et al. BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol. 2012;30:224-6.
-
(2012)
Nat Biotechnol.
, vol.30
, pp. 224-226
-
-
Adams, D.1
Altucci, L.2
Antonarakis, S.E.3
Ballesteros, J.4
Beck, S.5
Bird, A.6
-
49
-
-
84925230058
-
Epigenomics: Roadmap for regulation
-
Romanoski CE, Glass CK, Stunnenberg HG, Wilson L, Almouzni G. Epigenomics: Roadmap for regulation. Nature. 2015;518:314-6.
-
(2015)
Nature.
, vol.518
, pp. 314-316
-
-
Romanoski, C.E.1
Glass, C.K.2
Stunnenberg, H.G.3
Wilson, L.4
Almouzni, G.5
-
50
-
-
22244452677
-
Distribution and intensity of constraint in mammalian genomic sequence
-
Cooper GM, Stone EA, Asimenos G, Green ED, Batzoglou S, Sidow A. Distribution and intensity of constraint in mammalian genomic sequence. Genome Res. 2005;15:901-13.
-
(2005)
Genome Res.
, vol.15
, pp. 901-913
-
-
Cooper, G.M.1
Stone, E.A.2
Asimenos, G.3
Green, E.D.4
Batzoglou, S.5
Sidow, A.6
-
52
-
-
84895858942
-
A general framework for estimating the relative pathogenicity of human genetic variants
-
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014;46:310-5.
-
(2014)
Nat Genet.
, vol.46
, pp. 310-315
-
-
Kircher, M.1
Witten, D.M.2
Jain, P.3
O'Roak, B.J.4
Cooper, G.M.5
Shendure, J.6
-
53
-
-
84906926068
-
Ranking non-synonymous single nucleotide polymorphisms based on disease concepts
-
Shihab HA, Gough J, Mort M, Cooper DN, Day INM, Gaunt TR. Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. Hum Genomics. 2014;8:11.
-
(2014)
Hum Genomics.
, vol.8
, pp. 11
-
-
Shihab, H.A.1
Gough, J.2
Mort, M.3
Cooper, D.N.4
Day, I.N.M.5
Gaunt, T.R.6
-
54
-
-
77951943748
-
Ensembl variation resources
-
Chen Y, Cunningham F, Rios D, McLaren WM, Smith J, Pritchard B, et al. Ensembl variation resources. BMC Genomics. 2010;11:293.
-
(2010)
BMC Genomics.
, vol.11
, pp. 293
-
-
Chen, Y.1
Cunningham, F.2
Rios, D.3
McLaren, W.M.4
Smith, J.5
Pritchard, B.6
-
55
-
-
77951967863
-
A database and API for variation, dense genotyping and resequencing data
-
Rios D, McLaren WM, Chen Y, Birney E, Stabenau A, Flicek P, et al. A database and API for variation, dense genotyping and resequencing data. BMC Bioinformatics. 2010;11:238.
-
(2010)
BMC Bioinformatics.
, vol.11
, pp. 238
-
-
Rios, D.1
McLaren, W.M.2
Chen, Y.3
Birney, E.4
Stabenau, A.5
Flicek, P.6
-
56
-
-
0035173378
-
dbSNP: the NCBI database of genetic variation
-
Sherry ST, Ward MH, Kholodov M, Baker J, Phan L, Smigielski EM, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001;29:308-11.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 308-311
-
-
Sherry, S.T.1
Ward, M.H.2
Kholodov, M.3
Baker, J.4
Phan, L.5
Smigielski, E.M.6
-
57
-
-
78651330430
-
COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
-
Forbes SA, Bindal N, Bamford S, Cole C, Kok CY, Beare D, et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 2011;39:D945-50.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. D945-D950
-
-
Forbes, S.A.1
Bindal, N.2
Bamford, S.3
Cole, C.4
Kok, C.Y.5
Beare, D.6
-
58
-
-
84868343901
-
The Human Gene Mutation Database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution
-
Chapter 1:Unit1.13
-
Stenson PD, Ball EV, Mort M, Phillips AD, Shaw K, Cooper DN. The Human Gene Mutation Database (HGMD) and its exploitation in the fields of personalized genomics and molecular evolution. Curr. Protoc. Bioinformatics. 2012;Chapter 1:Unit1.13.
-
(2012)
Curr. Protoc. Bioinformatics.
-
-
Stenson, P.D.1
Ball, E.V.2
Mort, M.3
Phillips, A.D.4
Shaw, K.5
Cooper, D.N.6
-
59
-
-
84876527890
-
dbVar and DGVa: public archives for genomic structural variation
-
Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, et al. dbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res. 2013;41:D936-41.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D936-D941
-
-
Lappalainen, I.1
Lopez, J.2
Skipper, L.3
Hefferon, T.4
Spalding, J.D.5
Garner, J.6
-
60
-
-
84973291584
-
-
Accessed 17 Mar
-
NHLBI exome sequencing. http://evs.gs.washington.edu/EVS/. Accessed 17 Mar 2016.
-
(2016)
-
-
-
61
-
-
84973291587
-
-
Accessed 17 Mar
-
OMIM. http://omim.org/. Accessed 17 Mar 2016.
-
(2016)
-
-
-
62
-
-
84973296002
-
-
Orphanet. Accessed 17 Mar
-
Orphanet. http://www.orpha.net/. Accessed 17 Mar 2016.
-
(2016)
-
-
-
63
-
-
84891790401
-
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations
-
Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 2013;42:D1001-6.
-
(2013)
Nucleic Acids Res.
, vol.42
, pp. D1001-D1006
-
-
Welter, D.1
MacArthur, J.2
Morales, J.3
Burdett, T.4
Hall, P.5
Junkins, H.6
-
64
-
-
84973316671
-
Ensembl Variation sources of phenotype data
-
Accessed 17 Mar
-
Ensembl Variation sources of phenotype data. http://www.ensembl.org/info/genome/variation/sources_phenotype_documentation.html. Accessed 17 Mar 2016.
-
(2016)
-
-
-
65
-
-
84891809093
-
ClinVar: public archive of relationships among sequence variation and human phenotype
-
Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, et al. ClinVar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014;42:D980-5.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D980-D985
-
-
Landrum, M.J.1
Lee, J.M.2
Riley, G.R.3
Jang, W.4
Rubinstein, W.S.5
Church, D.M.6
-
66
-
-
84862506964
-
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
-
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. 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 (Austin). 2012;6:80-92.
-
(2012)
Fly (Austin)
, vol.6
, pp. 80-92
-
-
Cingolani, P.1
Platts, A.2
Wang, L.L.3
Coon, M.4
Nguyen, T.5
Wang, L.6
-
67
-
-
84973341658
-
Sequence Ontology terms for describing variant consequences
-
Accessed 17 Mar
-
Sequence Ontology terms for describing variant consequences. http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences. Accessed 17 Mar 2016.
-
(2016)
-
-
-
68
-
-
84938078941
-
Improving the Sequence Ontology terminology for genomic variant annotation
-
Cunningham F, Moore B, Ruiz-Schultz N, Ritchie GR, Eilbeck K. Improving the Sequence Ontology terminology for genomic variant annotation. J Biomed Semant. 2015;6:32.
-
(2015)
J Biomed Semant.
, vol.6
, pp. 32
-
-
Cunningham, F.1
Moore, B.2
Ruiz-Schultz, N.3
Ritchie, G.R.4
Eilbeck, K.5
-
69
-
-
84946100079
-
The UCSC Genome Browser database: 2015 update
-
gku1177
-
Rosenbloom KR, Armstrong J, Barber GP, Casper J, Clawson H, Diekhans M, et al. The UCSC Genome Browser database: 2015 update. Nucleic Acids Res. 2014;gku1177.
-
(2014)
Nucleic Acids Res.
-
-
Rosenbloom, K.R.1
Armstrong, J.2
Barber, G.P.3
Casper, J.4
Clawson, H.5
Diekhans, M.6
-
70
-
-
84860373866
-
The 1000 Genomes Project: data management and community access
-
Clarke L, Zheng-Bradley X, Smith R, Kulesha E, Xiao C, Toneva I, et al. The 1000 Genomes Project: data management and community access. Nat Methods. 2012;9:459-62.
-
(2012)
Nat Methods.
, vol.9
, pp. 459-462
-
-
Clarke, L.1
Zheng-Bradley, X.2
Smith, R.3
Kulesha, E.4
Xiao, C.5
Toneva, I.6
-
71
-
-
84881396090
-
Computational approaches to identify functional genetic variants in cancer genomes
-
The International Cancer Genome Consortium Mutation Pathways and Consequences Subgroup of the Bioinformatics Analyses Working Group. Computational approaches to identify functional genetic variants in cancer genomes. Nat Methods. 2013;10:723-9.
-
(2013)
Nat Methods
, vol.10
, pp. 723-729
-
-
-
72
-
-
84946100094
-
The Ensembl REST API: Ensembl Data for Any Language
-
btu613
-
Yates A, Beal K, Keenan S, McLaren W, Pignatelli M, Ritchie GRS, et al. The Ensembl REST API: Ensembl Data for Any Language. Bioinformatics. 2014;btu613.
-
(2014)
Bioinformatics.
-
-
Yates, A.1
Beal, K.2
Keenan, S.3
McLaren, W.4
Pignatelli, M.5
Ritchie, G.R.S.6
-
73
-
-
84973362873
-
-
Accessed 17 Mar
-
Travis CI. https://travis-ci.org/. Accessed 17 Mar 2016.
-
(2016)
-
-
Travis, C.I.1
-
74
-
-
84973362823
-
Ensembl Variant Effect Predictor script
-
Accessed 17 Mar
-
Ensembl Variant Effect Predictor script. http://www.ensembl.org/info/docs/tools/vep/script/index.html. Accessed 17 Mar 2016.
-
(2016)
-
-
-
75
-
-
84975311524
-
Vcfanno: fast, flexible annotation of genetic variants
-
Pedersen BS, Layer RM, Quinlan AR. Vcfanno: fast, flexible annotation of genetic variants. Genome Biol. 2016; 17:118
-
(2016)
Genome Biol.
, vol.17
, pp. 118
-
-
Pedersen, B.S.1
Layer, R.M.2
Quinlan, A.R.3
-
76
-
-
84973362823
-
Ensembl Variant Effect Predictor plugins
-
Accessed 17 Mar
-
Ensembl Variant Effect Predictor plugins. https://github.com/ensembl-variation/VEP_plugins. Accessed 17 Mar 2016.
-
(2016)
-
-
-
77
-
-
84930865093
-
Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins
-
bbu008
-
Yourshaw M, Taylor SP, Rao AR, Martín MG, Nelson SF. Rich annotation of DNA sequencing variants by leveraging the Ensembl Variant Effect Predictor with plugins. Brief Bioinform. 2014;bbu008.
-
(2014)
Brief Bioinform.
-
-
Yourshaw, M.1
Taylor, S.P.2
Rao, A.R.3
Martín, M.G.4
Nelson, S.F.5
-
78
-
-
84891779149
-
DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation
-
Bragin E, Chatzimichali EA, Wright CF, Hurles ME, Firth HV, Bevan AP, et al. DECIPHER: database for the interpretation of phenotype-linked plausibly pathogenic sequence and copy-number variation. Nucleic Acids Res. 2014;42:D993-1000.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. D993-1000
-
-
Bragin, E.1
Chatzimichali, E.A.2
Wright, C.F.3
Hurles, M.E.4
Firth, H.V.5
Bevan, A.P.6
-
79
-
-
84973362903
-
-
Accessed 17 Mar
-
Ensembl Variant Effect Predictor REST API documentation. http://rest.ensembl.org/#VEP. Accessed 17 Mar 2016.
-
(2016)
-
-
-
80
-
-
84973341589
-
Illumina's Platinum Genomes set
-
Accessed 17 Mar
-
Illumina's Platinum Genomes set. ftp://ussd-ftp.illumina.com/hg19/2.0.1/NA12878/. Accessed 17 Mar 2016.
-
(2016)
-
-
-
81
-
-
84973318994
-
Differences between compiled and interpreted languages
-
Accessed 17 Mar
-
Differences between compiled and interpreted languages. http://www.codeproject.com/Articles/696764/Differences-between-compiled-and-Interpreted-Langu. Accessed 17 Mar 2016.
-
(2016)
-
-
-
82
-
-
84901410645
-
Choice of transcripts and software has a large effect on variant annotation
-
McCarthy DJ, Humburg P, Kanapin A, Rivas MA, Gaulton K, Cazier J-B, et al. Choice of transcripts and software has a large effect on variant annotation. Genome Med. 2014;6:26.
-
(2014)
Genome Med.
, vol.6
, pp. 26
-
-
McCarthy, D.J.1
Humburg, P.2
Kanapin, A.3
Rivas, M.A.4
Gaulton, K.5
Cazier, J.-B.6
-
83
-
-
84973318998
-
-
Accessed 17 Mar
-
Global Alliance for Genomic Health (GA4GH) Beacon project. https://beacon-network.org/. Accessed 17 Mar 2016.
-
(2016)
-
-
-
84
-
-
84929001104
-
The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
-
GTEx Consortium T, Ardlie KG, Deluca DS, Segrè AV, Sullivan TJ, Young TR, et al. The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans. Science. 2015;348:648-60.
-
(2015)
Science.
, vol.348
, pp. 648-660
-
-
Ardlie, K.G.1
Deluca, D.S.2
Segrè, A.V.3
Sullivan, T.J.4
Young, T.R.5
-
85
-
-
84973341560
-
Ensembl Variant Effect Predictor historical release notes
-
Accessed 17 Mar
-
Ensembl Variant Effect Predictor historical release notes. http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#history. Accessed 17 Mar 2016.
-
(2016)
-
-
-
86
-
-
84973318235
-
-
XS framework. Accessed 17 Mar
-
XS framework. http://perldoc.perl.org/perlxs.html. Accessed 17 Mar 2016.
-
(2016)
-
-
-
87
-
-
18644368714
-
The Bioperl toolkit: Perl modules for the life sciences
-
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, et al. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002;12:1611-8.
-
(2002)
Genome Res.
, vol.12
, pp. 1611-1618
-
-
Stajich, J.E.1
Block, D.2
Boulez, K.3
Brenner, S.E.4
Chervitz, S.A.5
Dagdigian, C.6
-
89
-
-
84973362881
-
-
Perl's Storable framework. Accessed 17 Mar
-
Perl's Storable framework. http://perldoc.perl.org/Storable.html. Accessed 17 Mar 2016.
-
(2016)
-
-
-
90
-
-
0033987736
-
Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion
-
den Dunnen JT, Antonarakis SE. Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion. Hum Mutat. 2000;15:7-12.
-
(2000)
Hum Mutat.
, vol.15
, pp. 7-12
-
-
Dunnen, J.T.1
Antonarakis, S.E.2
-
91
-
-
84973326449
-
-
Ensembl's FTP archive site. Accessed 17 Mar
-
Ensembl's FTP archive site. ftp://ftp.ensembl.org/pub/. Accessed 17 Mar 2016.
-
(2016)
-
-
-
92
-
-
84973392370
-
-
htslib-based indexer. Accessed 17 Mar
-
htslib-based indexer. http://www.htslib.org/. Accessed 17 Mar 2016.
-
(2016)
-
-
-
93
-
-
84973341589
-
-
Accessed 17 Mar
-
Illumina's Platinum Genomes. http://www.illumina.com/platinumgenomes/. Accessed 17 Mar 2016.
-
(2016)
Illumina's Platinum Genomes
-
-
-
94
-
-
84973362822
-
Prebuilt Variant Effect Predictor datasets
-
Accessed 17 Mar
-
Prebuilt Variant Effect Predictor datasets. ftp://ftp.ensembl.org/pub/current_variation/VEP/. Accessed 17 Mar 2016.
-
(2016)
-
-
-
95
-
-
77956534324
-
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
-
Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
-
(2010)
Nucleic Acids Res.
, vol.38
-
-
Wang, K.1
Li, M.2
Hakonarson, H.3
-
96
-
-
84881613239
-
dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations
-
Liu X, Jian X, Boerwinkle E. dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. Hum Mutat. 2013;34:E2393-402.
-
(2013)
Hum Mutat
, vol.34
, pp. E2393-E2402
-
-
Liu, X.1
Jian, X.2
Boerwinkle, E.3
-
97
-
-
84926503617
-
In silico prediction of splice-altering single nucleotide variants in the human genome
-
Jian X, Boerwinkle E, Liu X. In silico prediction of splice-altering single nucleotide variants in the human genome. Nucleic Acids Res. 2014;42:13534-44.
-
(2014)
Nucleic Acids Res.
, vol.42
, pp. 13534-13544
-
-
Jian, X.1
Boerwinkle, E.2
Liu, X.3
|