-
1
-
-
84904818189
-
A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies
-
Aleman A, Garcia-Garcia F, Salavert F, Medina I, Dopazo J. 2014. A web-based interactive framework to assist in the prioritization of disease candidate genes in whole-exome sequencing studies. Nucleic Acids Res 42:W88-W93.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. W88-W93
-
-
Aleman, A.1
Garcia-Garcia, F.2
Salavert, F.3
Medina, I.4
Dopazo, J.5
-
2
-
-
84862929636
-
TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data
-
Asmann YW, Middha S, Hossain A, Baheti S, Li Y, Chai HS, Sun Z, Duffy PH, Hadad AA, Nair A, Liu X, Zhang Y, et al. 2012. TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. Bioinformatics 28:277-278.
-
(2012)
Bioinformatics
, vol.28
, pp. 277-278
-
-
Asmann, Y.W.1
Middha, S.2
Hossain, A.3
Baheti, S.4
Li, Y.5
Chai, H.S.6
Sun, Z.7
Duffy, P.H.8
Hadad, A.A.9
Nair, A.10
Liu, X.11
Zhang, Y.12
-
3
-
-
80054746492
-
Exome sequencing as a tool for Mendelian disease gene discovery
-
Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J. 2011. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 12:745-755.
-
(2011)
Nat Rev Genet
, vol.12
, pp. 745-755
-
-
Bamshad, M.J.1
Ng, S.B.2
Bigham, A.W.3
Tabor, H.K.4
Emond, M.J.5
Nickerson, D.A.6
Shendure, J.7
-
4
-
-
79961023788
-
Defective IL10 signaling defining a subgroup of patients with inflammatory bowel disease
-
Begue B, Verdier J, Rieux-Laucat F, Goulet O, Morali A, Canioni D, Hugot JP, Daussy C, Verkarre V, Pigneur B, Fischer A, Klein A, et al. 2011. Defective IL10 signaling defining a subgroup of patients with inflammatory bowel disease. Am J Gastroenterol 106:1544-1555.
-
(2011)
Am J Gastroenterol
, vol.106
, pp. 1544-1555
-
-
Begue, B.1
Verdier, J.2
Rieux-Laucat, F.3
Goulet, O.4
Morali, A.5
Canioni, D.6
Hugot, J.P.7
Daussy, C.8
Verkarre, V.9
Pigneur, B.10
Fischer, A.11
Klein, A.12
-
5
-
-
84878589007
-
Improving the accuracy and efficiency of identity-by-descent detection in population data
-
Browning BL, Browning SR. 2013. Improving the accuracy and efficiency of identity-by-descent detection in population data. Genetics 194:459-471.
-
(2013)
Genetics
, vol.194
, pp. 459-471
-
-
Browning, B.L.1
Browning, S.R.2
-
6
-
-
84864294140
-
wANNOVAR: annotating genetic variants for personal genomes via the web
-
Chang X, Wang K. 2012. wANNOVAR: annotating genetic variants for personal genomes via the web. J Med Genet 49:433-436.
-
(2012)
J Med Genet
, vol.49
, pp. 433-436
-
-
Chang, X.1
Wang, K.2
-
7
-
-
84871952176
-
Improved whole-chromosome phasing for disease and population genetic studies
-
Delaneau O, Zagury JF, Marchini J. 2013. Improved whole-chromosome phasing for disease and population genetic studies. Nat Methods 10:5-6.
-
(2013)
Nat Methods
, vol.10
, pp. 5-6
-
-
Delaneau, O.1
Zagury, J.F.2
Marchini, J.3
-
8
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas MA, Hanna M, McKenna A, Fennell T, et al. 2011. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491-498.
-
(2011)
Nat Genet
, vol.43
, pp. 491-498
-
-
DePristo, M.A.1
Banks, E.2
Poplin, R.3
Garimella, K.V.4
Maguire, J.R.5
Hartl, C.6
Philippakis, A.A.7
del Angel, G.8
Rivas, M.A.9
Hanna, M.10
McKenna, A.11
Fennell, T.12
-
9
-
-
84867130076
-
Exome sequencing and complex disease: practical aspects of rare variant association studies
-
Do R, Kathiresan S, Abecasis GR. 2012. Exome sequencing and complex disease: practical aspects of rare variant association studies. Hum Mol Genet 21:R1-R9.
-
(2012)
Hum Mol Genet
, vol.21
, pp. R1-R9
-
-
Do, R.1
Kathiresan, S.2
Abecasis, G.R.3
-
11
-
-
70949087383
-
Inflammatory bowel disease and mutations affecting the interleukin-10 receptor
-
Glocker EO, Kotlarz D, Boztug K, Gertz EM, Schaffer AA, Noyan F, Perro M, Diestelhorst J, Allroth A, Murugan D, Hatscher N, Pfeifer D, et al. 2009. Inflammatory bowel disease and mutations affecting the interleukin-10 receptor. New Engl J Med 361:2033-2045.
-
(2009)
New Engl J Med
, vol.361
, pp. 2033-2045
-
-
Glocker, E.O.1
Kotlarz, D.2
Boztug, K.3
Gertz, E.M.4
Schaffer, A.A.5
Noyan, F.6
Perro, M.7
Diestelhorst, J.8
Allroth, A.9
Murugan, D.10
Hatscher, N.11
Pfeifer, D.12
-
12
-
-
84865530942
-
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment
-
Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M. 2012. VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics 28:2267-2269.
-
(2012)
Bioinformatics
, vol.28
, pp. 2267-2269
-
-
Habegger, L.1
Balasubramanian, S.2
Chen, D.Z.3
Khurana, E.4
Sboner, A.5
Harmanci, A.6
Rozowsky, J.7
Clarke, D.8
Snyder, M.9
Gerstein, M.10
-
13
-
-
80053176070
-
Detecting autozygosity through runs of homozygosity: a comparison of three autozygosity detection algorithms
-
Howrigan DP, Simonson MA, Keller MC. 2011. Detecting autozygosity through runs of homozygosity: a comparison of three autozygosity detection algorithms. BMC Genomics 12:460.
-
(2011)
BMC Genomics
, vol.12
, pp. 460
-
-
Howrigan, D.P.1
Simonson, M.A.2
Keller, M.C.3
-
14
-
-
84867326768
-
GeneTalk: an expert exchange platform for assessing rare sequence variants in personal genomes
-
Kamphans T, Krawitz PM. 2012. GeneTalk: an expert exchange platform for assessing rare sequence variants in personal genomes. Bioinformatics 28:2515-2516.
-
(2012)
Bioinformatics
, vol.28
, pp. 2515-2516
-
-
Kamphans, T.1
Krawitz, P.M.2
-
15
-
-
84891771466
-
The UCSC Genome Browser database: 2014 update
-
Karolchik D, Barber GP, Casper J, Clawson H, Cline MS, Diekhans M, Dreszer TR, Fujita PA, Guruvadoo L, Haeussler M, Harte RA, Heitner S, et al. 2014. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res 42:D764-D770.
-
(2014)
Nucleic Acids Res
, vol.42
, pp. D764-D770
-
-
Karolchik, D.1
Barber, G.P.2
Casper, J.3
Clawson, H.4
Cline, M.S.5
Diekhans, M.6
Dreszer, T.R.7
Fujita, P.A.8
Guruvadoo, L.9
Haeussler, M.10
Harte, R.A.11
Heitner, S.12
-
16
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754-1760.
-
(2009)
Bioinformatics
, vol.25
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
17
-
-
84905982050
-
PMCA4 (ATP2B4) mutation in familial spastic paraplegia
-
Li M, Ho PW, Pang SY, Tse ZH, Kung MH, Sham PC, Ho SL. 2014. PMCA4 (ATP2B4) mutation in familial spastic paraplegia. PLoS One 9:e104790.
-
(2014)
PLoS One
, vol.9
, pp. e104790
-
-
Li, M.1
Ho, P.W.2
Pang, S.Y.3
Tse, Z.H.4
Kung, M.H.5
Sham, P.C.6
Ho, S.L.7
-
18
-
-
84874018379
-
Whole exome sequencing identifies a novel mutation in the transglutaminase 6 gene for spinocerebellar ataxia in a Chinese family
-
Li M, Pang SY, Song Y, Kung MH, Ho SL, Sham PC. 2013a. Whole exome sequencing identifies a novel mutation in the transglutaminase 6 gene for spinocerebellar ataxia in a Chinese family. Clin Genet 83:269-273.
-
(2013)
Clin Genet
, vol.83
, pp. 269-273
-
-
Li, M.1
Pang, S.Y.2
Song, Y.3
Kung, M.H.4
Ho, S.L.5
Sham, P.C.6
-
19
-
-
84867042205
-
Genetic variant representation, annotation and prioritization in the post-GWAS era
-
Li MJ, Sham PC, Wang J. 2012a. Genetic variant representation, annotation and prioritization in the post-GWAS era. Cell Res 22:1505-1508.
-
(2012)
Cell Res
, vol.22
, pp. 1505-1508
-
-
Li, M.J.1
Sham, P.C.2
Wang, J.3
-
20
-
-
84928204709
-
Current trend of annotating single nucleotide variation in humans-a case study on SNVrap
-
Epub ahead of print
-
Li MJ, Wang J. 2014. Current trend of annotating single nucleotide variation in humans-a case study on SNVrap. Methods. [Epub ahead of print]
-
(2014)
Methods
-
-
Li, M.J.1
Wang, J.2
-
21
-
-
84860147579
-
A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases
-
Li MX, Gui HS, Kwan JS, Bao SY, Sham PC. 2012b. A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases. Nucleic acids research 40:e53.
-
(2012)
Nucleic acids research
, vol.40
, pp. e53
-
-
Li, M.X.1
Gui, H.S.2
Kwan, J.S.3
Bao, S.Y.4
Sham, P.C.5
-
22
-
-
84873486397
-
Predicting mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies
-
Li MX, Kwan JS, Bao SY, Yang W, Ho SL, Song YQ, Sham PC. 2013b. Predicting mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies. PLoS Genet 9:e1003143.
-
(2013)
PLoS Genet
, vol.9
, pp. e1003143
-
-
Li, M.X.1
Kwan, J.S.2
Bao, S.Y.3
Yang, W.4
Ho, S.L.5
Song, Y.Q.6
Sham, P.C.7
-
23
-
-
84864118162
-
Exome sequencing identifies novel compound heterozygous mutations of IL-10 receptor 1 in neonatal-onset Crohn's disease
-
Mao H, Yang W, Lee PP, Ho MH, Yang J, Zeng S, Chong CY, Lee TL, Tu W, Lau YL. 2012. Exome sequencing identifies novel compound heterozygous mutations of IL-10 receptor 1 in neonatal-onset Crohn's disease. Genes Immun 13:437-442.
-
(2012)
Genes Immun
, vol.13
, pp. 437-442
-
-
Mao, H.1
Yang, W.2
Lee, P.P.3
Ho, M.H.4
Yang, J.5
Zeng, S.6
Chong, C.Y.7
Lee, T.L.8
Tu, W.9
Lau, Y.L.10
-
24
-
-
84898047240
-
exomeSuite: Whole exome sequence variant filtering tool for rapid identification of putative disease causing SNVs/indels
-
Maranhao B, Biswas P, Duncan JL, Branham KE, Silva GA, Naeem MA, Khan SN, Riazuddin S, Hejtmancik JF, Heckenlively JR, Riazuddin SA, Lee PL, Ayyagari R. 2014. exomeSuite: Whole exome sequence variant filtering tool for rapid identification of putative disease causing SNVs/indels. Genomics 103:169-176.
-
(2014)
Genomics
, vol.103
, pp. 169-176
-
-
Maranhao, B.1
Biswas, P.2
Duncan, J.L.3
Branham, K.E.4
Silva, G.A.5
Naeem, M.A.6
Khan, S.N.7
Riazuddin, S.8
Hejtmancik, J.F.9
Heckenlively, J.R.10
Riazuddin, S.A.11
Lee, P.L.12
Ayyagari, R.13
-
25
-
-
84901410645
-
Choice of transcripts and software has a large effect on variant annotation
-
McCarthy DJ, Humburg P, Kanapin A, Rivas MA, Gaulton K, Cazier JB, Donnelly P. 2014. Choice of transcripts and software has a large effect on variant annotation. Genome Med 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
Donnelly, P.7
-
26
-
-
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. 2010. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26:2069-2070.
-
(2010)
Bioinformatics
, vol.26
, pp. 2069-2070
-
-
McLaren, W.1
Pritchard, B.2
Rios, D.3
Chen, Y.4
Flicek, P.5
Cunningham, F.6
-
27
-
-
84878582216
-
Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements
-
Paulsen J, Lien TG, Sandve GK, Holden L, Borgan O, Glad IK, Hovig E. 2013. Handling realistic assumptions in hypothesis testing of 3D co-localization of genomic elements. Nucleic Acids Res 41:5164-5174.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. 5164-5174
-
-
Paulsen, J.1
Lien, T.G.2
Sandve, G.K.3
Holden, L.4
Borgan, O.5
Glad, I.K.6
Hovig, E.7
-
28
-
-
84875217898
-
Disease-targeted sequencing: a cornerstone in the clinic
-
Rehm HL. 2013. Disease-targeted sequencing: a cornerstone in the clinic. Nat Rev Genet 14:295-300.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 295-300
-
-
Rehm, H.L.1
-
29
-
-
79960266560
-
Strategies for exome and genome sequence data analysis in disease-gene discovery projects
-
Robinson PN, Krawitz P, Mundlos S. 2011. Strategies for exome and genome sequence data analysis in disease-gene discovery projects. Clin Genet 80:127-132.
-
(2011)
Clin Genet
, vol.80
, pp. 127-132
-
-
Robinson, P.N.1
Krawitz, P.2
Mundlos, S.3
-
30
-
-
80051550297
-
Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency
-
Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen JJ, Johnson WE, Moore B, Huff CD, Bird LM, Carey JC, Opitz JM, et al. 2011. Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am J Hum Genet 89:28-43.
-
(2011)
Am J Hum Genet
, vol.89
, pp. 28-43
-
-
Rope, A.F.1
Wang, K.2
Evjenth, R.3
Xing, J.4
Johnston, J.J.5
Swensen, J.J.6
Johnson, W.E.7
Moore, B.8
Huff, C.D.9
Bird, L.M.10
Carey, J.C.11
Opitz, J.M.12
-
31
-
-
84875964664
-
The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency
-
Rubinstein WS, Maglott DR, Lee JM, Kattman BL, Malheiro AJ, Ovetsky M, Hem V, Gorelenkov V, Song G, Wallin C, Husain N, Chitipiralla S, et al. 2013. The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency. Nucleic Acids Res 41:D925-D935.
-
(2013)
Nucleic Acids Res
, vol.41
, pp. D925-D935
-
-
Rubinstein, W.S.1
Maglott, D.R.2
Lee, J.M.3
Kattman, B.L.4
Malheiro, A.J.5
Ovetsky, M.6
Hem, V.7
Gorelenkov, V.8
Song, G.9
Wallin, C.10
Husain, N.11
Chitipiralla, S.12
-
32
-
-
78649890408
-
TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing
-
Wang JL, Yang X, Xia K, Hu ZM, Weng L, Jin X, Jiang H, Zhang P, Shen L, Guo JF, Li N, Li YR, et al. 2010. TGM6 identified as a novel causative gene of spinocerebellar ataxias using exome sequencing. Brain 133:3510-3518.
-
(2010)
Brain
, vol.133
, pp. 3510-3518
-
-
Wang, J.L.1
Yang, X.2
Xia, K.3
Hu, Z.M.4
Weng, L.5
Jin, X.6
Jiang, H.7
Zhang, P.8
Shen, L.9
Guo, J.F.10
Li, N.11
Li, Y.R.12
-
33
-
-
77956534324
-
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
-
Wang K, Li M, Hakonarson H. 2010b. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38:e164.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. e164
-
-
Wang, K.1
Li, M.2
Hakonarson, H.3
-
34
-
-
84871730851
-
PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data
-
Zhang L, Zhang J, Yang J, Ying D, Lau YL, Yang W. 2013. PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data. Bioinformatics 29:124-125.
-
(2013)
Bioinformatics
, vol.29
, pp. 124-125
-
-
Zhang, L.1
Zhang, J.2
Yang, J.3
Ying, D.4
Lau, Y.L.5
Yang, W.6
|