-
1
-
-
55549097836
-
Mapping short DNA sequencing reads and calling variants using mapping quality scores
-
Li H., Ruan J., Durbin R., Mapping short DNA sequencing reads and calling variants using mapping quality scores Genome Research 2008 18 11 1851 1858
-
(2008)
Genome Research
, vol.18
, Issue.11
, pp. 1851-1858
-
-
Li, H.1
Ruan, J.2
Durbin, R.3
-
2
-
-
67649884743
-
Fast and accurate short read alignment with Burrows-Wheeler transform
-
Li H., Durbin R., Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 2009 25 14 1754 1760
-
(2009)
Bioinformatics
, vol.25
, Issue.14
, pp. 1754-1760
-
-
Li, H.1
Durbin, R.2
-
3
-
-
62349130698
-
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
-
ARTICLE R25
-
Langmead B., Trapnell C., Pop M., Salzberg S. L., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biology 2009 10 3, article R25
-
(2009)
Genome Biology
, vol.10
, Issue.3
-
-
Langmead, B.1
Trapnell, C.2
Pop, M.3
Salzberg, S.L.4
-
4
-
-
77954346055
-
Local alignment of generalized k-base encoded DNA sequence
-
article 347
-
Homer N., Nelson S. F., Merriman B., Local alignment of generalized k-base encoded DNA sequence BMC Bioinformatics 2010 11, article 347
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Homer, N.1
Nelson, S.F.2
Merriman, B.3
-
5
-
-
33846101990
-
Variation resources at UC Santa Cruz
-
DOI 10.1093/nar/gkl953
-
Thomas D. J., Trumbower H., Kern A. D., Rhead B. L., Kuhn R. M., Haussler D., Kent J. W., Variation resources at UC Santa Cruz Nucleic Acids Research 2007 35 1 D716 D720 (Pubitemid 46061034)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Thomas, D.J.1
Trumbower, H.2
Kern, A.D.3
Rhead, B.L.4
Kuhn, R.M.5
Haussler, D.6
Kent, J.W.7
-
6
-
-
75549089335
-
Ensembl's 10th year
-
Flicek P., Aken B. L., Ballester B., Beal K., Bragin E., Brent S., Chen Y., Clapham P., Coates G., Fairley S., Fitzgerald S., Fernandez-Banet J., Gordon L., Grf S., Haider S., Hammond M., Howe K., Jenkinson A., Johnson N., Khri A., Keefe D., Keenan S., Kinsella R., Kokocinski F., Koscielny G., Kulesha E., Lawson D., Longden I., Massingham T., Mclaren W., Megy K., Overduin B., Pritchard B., Rios D., Ruffier M., Schuster M., Slater G., Smedley D., Spudich G., Tang Y. A., Trevanion S., Vilella A., Vogel J., White S., Wilder S. P., Zadissa A., Birney E., Cunningham F., Dunham I., Durbin R., Fernndez-Suarez X. M., Herrero J., Hubbard T. J. P., Parker A., Proctor G., Smith J., Searle S. M. J., Ensembl's 10th year Nucleic Acids Research 2009 38 1 D557 D562
-
(2009)
Nucleic Acids Research
, vol.38
, Issue.1
-
-
Flicek, P.1
Aken, B.L.2
Ballester, B.3
Beal, K.4
Bragin, E.5
Brent, S.6
Chen, Y.7
Clapham, P.8
Coates, G.9
Fairley, S.10
Fitzgerald, S.11
Fernandez-Banet, J.12
Gordon, L.13
Grf, S.14
Haider, S.15
Hammond, M.16
Howe, K.17
Jenkinson, A.18
Johnson, N.19
Khri, A.20
Keefe, D.21
Keenan, S.22
Kinsella, R.23
Kokocinski, F.24
Koscielny, G.25
Kulesha, E.26
Lawson, D.27
Longden, I.28
Massingham, T.29
McLaren, W.30
Megy, K.31
Overduin, B.32
Pritchard, B.33
Rios, D.34
Ruffier, M.35
Schuster, M.36
Slater, G.37
Smedley, D.38
Spudich, G.39
Tang, Y.A.40
Trevanion, S.41
Vilella, A.42
Vogel, J.43
White, S.44
Wilder, S.P.45
Zadissa, A.46
Birney, E.47
Cunningham, F.48
Dunham, I.49
Durbin, R.50
Fernndez-Suarez, X.M.51
Herrero, J.52
Hubbard, T.J.P.53
Parker, A.54
Proctor, G.55
Smith, J.56
Searle, S.M.J.57
more..
-
7
-
-
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 Bioinformatics 2010 26 16 2069 2070
-
(2010)
Bioinformatics
, vol.26
, Issue.16
, pp. 2069-2070
-
-
McLaren, W.1
Pritchard, B.2
Rios, D.3
Chen, Y.4
Flicek, P.5
Cunningham, F.6
-
8
-
-
33750920085
-
SNPSplicer: Systematic analysis of SNP-dependent splicing in genotyped cDNAs
-
DOI 10.1002/humu.20377
-
ElSharawy A., Manaster C., Teuber M., Rosenstiel P., Kwiatkowski R., Huse K., Platzer M., Becker A., Nrnberg P., Schreiber S., Hampe J., SNPSplicer: systematic analysis of SNP-dependent splicing in genotyped cDNAs Human Mutation 2006 27 11 1129 1134 (Pubitemid 44730508)
-
(2006)
Human Mutation
, vol.27
, Issue.11
, pp. 1129-1134
-
-
ElSharawy, A.1
Manaster, C.2
Teuber, M.3
Rosenstiel, P.4
Kwiatkowski, R.5
Huse, K.6
Platzer, M.7
Becker, A.8
Nurnberg, P.9
Schreiber, S.10
Hampe, J.11
-
10
-
-
68349104949
-
MAQGene: Software to facilitate C. elegans mutant genome sequence analysis
-
Bigelow H., Doitsidou M., Sarin S., Hobert O., MAQGene: software to facilitate C. elegans mutant genome sequence analysis Nature Methods 2009 6 8 549
-
(2009)
Nature Methods
, vol.6
, Issue.8
, pp. 549
-
-
Bigelow, H.1
Doitsidou, M.2
Sarin, S.3
Hobert, O.4
-
11
-
-
77953206138
-
FunctSNP: An R package to link SNPs to functional knowledge and dbAutoMaker: A suite of Perl scripts to build SNP databases
-
article 113
-
Goodswen S. J., Gondro C., Watson-Haigh N. S., Kadarmideen H. N., FunctSNP: an R package to link SNPs to functional knowledge and dbAutoMaker: a suite of Perl scripts to build SNP databases BMC Bioinformatics 2010 11, article 311
-
(2010)
BMC Bioinformatics
, vol.11
-
-
Goodswen, S.J.1
Gondro, C.2
Watson-Haigh, N.S.3
Kadarmideen, H.N.4
-
12
-
-
57649193091
-
Functional analysis of novel SNPs and mutations in human and mouse genomes
-
article S10
-
Liu C. K., Chen Y. H., Tang C. Y., Chang S. C., Lin Y. J., Tsai M. F., Chen Y. T., Yao A., Functional analysis of novel SNPs and mutations in human and mouse genomes BMC Bioinformatics 2008 9 supplement 12, article S10
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.SUPPL. 12
-
-
Liu, C.K.1
Chen, Y.H.2
Tang, C.Y.3
Chang, S.C.4
Lin, Y.J.5
Tsai, M.F.6
Chen, Y.T.7
Yao, A.8
-
13
-
-
75549088687
-
Database resources of the National Center for Biotechnology Information
-
Sayers E. W., Barrett T., Benson D. A., Bolton E., Bryant S. H., Canese K., Chetvernin V., Church D. M., Dicuccio M., Federhen S., Feolo M., Geer L. Y., Helmberg W., Kapustin Y., Landsman D., Lipman D. J., Lu Z., Madden T. L., Madej T., Maglott D. R., Marchler-Bauer A., Miller V., Mizrachi I., Ostell J., Panchenko A., Pruitt K. D., Schuler G. D., Sequeira E., Sherry S. T., Shumway M., Sirotkin K., Slotta D., Souvorov A., Starchenko G., Tatusova T. A., Wagner L., Wang Y., John Wilbur W., Yaschenko E., Ye J., Database resources of the National Center for Biotechnology Information Nucleic Acids Research 2010 38 1 D5 D16
-
(2010)
Nucleic Acids Research
, vol.38
, Issue.1
-
-
Sayers, E.W.1
Barrett, T.2
Benson, D.A.3
Bolton, E.4
Bryant, S.H.5
Canese, K.6
Chetvernin, V.7
Church, D.M.8
Dicuccio, M.9
Federhen, S.10
Feolo, M.11
Geer, L.Y.12
Helmberg, W.13
Kapustin, Y.14
Landsman, D.15
Lipman, D.J.16
Lu, Z.17
Madden, T.L.18
Madej, T.19
Maglott, D.R.20
Marchler-Bauer, A.21
Miller, V.22
Mizrachi, I.23
Ostell, J.24
Panchenko, A.25
Pruitt, K.D.26
Schuler, G.D.27
Sequeira, E.28
Sherry, S.T.29
Shumway, M.30
Sirotkin, K.31
Slotta, D.32
Souvorov, A.33
Starchenko, G.34
Tatusova, T.A.35
Wagner, L.36
Wang, Y.37
John Wilbur, W.38
Yaschenko, E.39
Ye, J.40
more..
-
14
-
-
61449107734
-
SNPnexus: A web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms
-
Chelala C., Khan A., Lemoine N. R., SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms Bioinformatics 2009 25 5 655 661
-
(2009)
Bioinformatics
, vol.25
, Issue.5
, pp. 655-661
-
-
Chelala, C.1
Khan, A.2
Lemoine, N.R.3
-
15
-
-
58149189858
-
VarySysDB: A human genetic polymorphism database based on all H-InvDB transcripts
-
Shimada M. K., Matsumoto R., Hayakawa Y., Sanbonmatsu R., Gough C., Yamaguchi-Kabata Y., Yamasaki C., Imanishi T., Gojobori T., VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts Nucleic Acids Research 2009 37 1 D810 D815
-
(2009)
Nucleic Acids Research
, vol.37
, Issue.1
-
-
Shimada, M.K.1
Matsumoto, R.2
Hayakawa, Y.3
Sanbonmatsu, R.4
Gough, C.5
Yamaguchi-Kabata, Y.6
Yamasaki, C.7
Imanishi, T.8
Gojobori, T.9
-
16
-
-
77951943748
-
Ensembl variation resources
-
ARTICLE 293
-
Chen Y., Cunningham F., Rios D., McLaren W. M., Smith J., Pritchard B., Spudich G. M., Brent S., Kulesha E., Marin-Garcia P., Smedley D., Birney E., Flicek P., Ensembl variation resources BMC Genomics 2010 11 1, article 293
-
(2010)
BMC Genomics
, vol.11
, Issue.1
-
-
Chen, Y.1
Cunningham, F.2
Rios, D.3
McLaren, W.M.4
Smith, J.5
Pritchard, B.6
Spudich, G.M.7
Brent, S.8
Kulesha, E.9
Marin-Garcia, P.10
Smedley, D.11
Birney, E.12
Flicek, P.13
-
17
-
-
84855328594
-
1000 Genomes project
-
January
-
VCF (Variant Call Format) Specification, 1000 Genomes project. January 2009, http://vcftools.sourceforge.net/specs.html
-
(2009)
Vcf (Variant Call Format) Specification
-
-
-
18
-
-
84855314860
-
Personal Genome Snp format
-
Personal Genome SNP format, UCSC Genome Bioinformatics. http://genome.ucsc.edu/FAQ/FAQformat.html
-
UCSC Genome Bioinformatics
-
-
-
19
-
-
84855314859
-
Bed File format
-
BED file format, UCSC Genome Bioinformatics. http://genome.ucsc.edu/FAQ/ FAQformat.html
-
UCSC Genome Bioinformatics
-
-
-
21
-
-
70149113077
-
-
Development Core Team R. Vienna, Austria R Foundation for Statistical Computing
-
Development Core Team R., R: A Language and Environment for Statistical Computing 2009 Vienna, Austria R Foundation for Statistical Computing
-
(2009)
R: A Language and Environment for Statistical Computing
-
-
-
22
-
-
0033635022
-
Artemis: Sequence visualization and annotation
-
Rutherford K., Parkhill J., Crook J., Horsnell T., Rice P., Rajandream M. A., Barrell B., Artemis: sequence visualization and annotation Bioinformatics 2000 16 10 944 945
-
(2000)
Bioinformatics
, vol.16
, Issue.10
, pp. 944-945
-
-
Rutherford, K.1
Parkhill, J.2
Crook, J.3
Horsnell, T.4
Rice, P.5
Rajandream, M.A.6
Barrell, B.7
-
23
-
-
70349739736
-
The Integrated Genome Browser: Free software for distribution and exploration of genome-scale datasets
-
Nicol J. W., Helt G. A., Blanchard J. S. G., Raja A., Loraine A. E., The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets Bioinformatics 2009 25 20 2730 2731
-
(2009)
Bioinformatics
, vol.25
, Issue.20
, pp. 2730-2731
-
-
Nicol, J.W.1
Helt, G.A.2
Blanchard, J.S.G.3
Raja, A.4
Loraine, A.E.5
-
24
-
-
0024470037
-
Transcription and reverse transcription of retrotransposons
-
Boeke J. D., Corces V. G., Transcription and reverse transcription of retrotransposons Annual Review of Microbiology 1989 43 403 434 (Pubitemid 19250053)
-
(1989)
Annual Review of Microbiology
, vol.43
, pp. 403-434
-
-
Boeke, J.D.1
Corces, V.G.2
-
25
-
-
84871979029
-
SNP@Promoter: A database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions
-
article S2
-
Kim B. C., Kim W. Y., Park D., Chung W. H., Shin K. S., Bhak J., SNP@Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions BMC Bioinformatics 2008 9, article S2 supplement 1
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.SUPPL. 1
-
-
Kim, B.C.1
Kim, W.Y.2
Park, D.3
Chung, W.H.4
Shin, K.S.5
Bhak, J.6
-
26
-
-
75549090603
-
The Pfam protein families database
-
Finn R. D., Mistry J., Tate J., Coggill P., Heger A., Pollington J. E., Gavin O. L., Gunasekaran P., Ceric G., Forslund K., Holm L., Sonnhammer E. L. L., Eddy S. R., Bateman A., The Pfam protein families database Nucleic Acids Research 2010 38 1 D211 D222
-
(2010)
Nucleic Acids Research
, vol.38
, Issue.1
-
-
Finn, R.D.1
Mistry, J.2
Tate, J.3
Coggill, P.4
Heger, A.5
Pollington, J.E.6
Gavin, O.L.7
Gunasekaran, P.8
Ceric, G.9
Forslund, K.10
Holm, L.11
Sonnhammer, E.L.L.12
Eddy, S.R.13
Bateman, A.14
-
27
-
-
22244452677
-
Distribution and intensity of constraint in mammalian genomic sequence
-
DOI 10.1101/gr.3577405
-
Cooper G. M., Stone E. A., Asimenos G., Green E. D., Batzoglou S., Sidow A., Distribution and intensity of constraint in mammalian genomic sequence Genome Research 2005 15 7 901 913 (Pubitemid 40994210)
-
(2005)
Genome Research
, vol.15
, Issue.7
, pp. 901-913
-
-
Cooper, G.M.1
Stone, E.A.2
Asimenos, G.3
Green, E.D.4
Batzoglou, S.5
Sidow, A.6
-
28
-
-
70350002071
-
Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery
-
Eck S. H., Benet-Pag A., Flisikowski K., Meitinger T., Fries R., Strom T. M., Whole genome sequencing of a single Bos taurus animal for single nucleotide polymorphism discovery Genome Biology 2009 10 8 R82
-
(2009)
Genome Biology
, vol.10
, Issue.8
, pp. 82
-
-
Eck, S.H.1
Benet-Pag, A.2
Flisikowski, K.3
Meitinger, T.4
Fries, R.5
Strom, T.M.6
-
29
-
-
66049157839
-
Initiation codon mutation in B1-crystallin (CRYBB1) associated with autosomal recessive nuclear pulverulent cataract
-
Meyer E., Rahman F., Owens J., Pasha S., Morgan N. V., Trembath R. C., Stone E. M., Moore A. T., Maher E. R., Initiation codon mutation in B1-crystallin (CRYBB1) associated with autosomal recessive nuclear pulverulent cataract Molecular Vision 2009 15 1014 1019
-
(2009)
Molecular Vision
, vol.15
, pp. 1014-1019
-
-
Meyer, E.1
Rahman, F.2
Owens, J.3
Pasha, S.4
Morgan, N.V.5
Trembath, R.C.6
Stone, E.M.7
Moore, A.T.8
Maher, E.R.9
-
30
-
-
23044470239
-
The role of alternative translation start sites in the generation of human protein diversity
-
DOI 10.1007/s00438-005-1152-7
-
Kochetov A. V., Sarai A., Rogozin I. B., Shumny V. K., Kolchanov N. A., The role of alternative translation start sites in the generation of human protein diversity Molecular Genetics and Genomics 2005 273 6 491 496 (Pubitemid 41073969)
-
(2005)
Molecular Genetics and Genomics
, vol.273
, Issue.6
, pp. 491-496
-
-
Kochetov, A.V.1
Sarai, A.2
Rogozin, I.B.3
Shumny, V.K.4
Kolchanov, N.A.5
-
31
-
-
73649118537
-
Functional effects of polymorphisms in the human gene encoding 11 betahydroxysteroid dehydrogenase type 1 (11 beta-HSD1): A sequence variant at the translation start of 11 beta-HSD1 alters enzyme levels
-
Malavasi E. L., Kelly V., Nath N., Functional effects of polymorphisms in the human gene encoding 11 betahydroxysteroid dehydrogenase type 1 (11 beta-HSD1): a sequence variant at the translation start of 11 beta-HSD1 alters enzyme levels Endocrinology 2010 151 195 202
-
(2010)
Endocrinology
, vol.151
, pp. 195-202
-
-
Malavasi, E.L.1
Kelly, V.2
Nath, N.3
-
33
-
-
0026574207
-
Recent evidence for evolution of the genetic code
-
Osawa S., Jukes T. H., Watanabe K., Muto A., Recent evidence for evolution of the genetic code Microbiological Reviews 1992 56 1 229 264
-
(1992)
Microbiological Reviews
, vol.56
, Issue.1
, pp. 229-264
-
-
Osawa, S.1
Jukes, T.H.2
Watanabe, K.3
Muto, A.4
-
35
-
-
40949152971
-
Evolving genetic code
-
DOI 10.2183/pjab.84.58
-
Ohama T., Inagaki Y., Bessho Y., Osawa S., Evolving genetic code Proceedings of the Japan Academy Series B 2008 84 2 58 74 (Pubitemid 351413771)
-
(2008)
Proceedings of the Japan Academy Series B: Physical and Biological Sciences
, vol.84
, Issue.2
, pp. 58-74
-
-
Ohama, T.1
Inagaki, Y.2
Bessho, Y.3
Osawa, S.4
-
36
-
-
77958086579
-
A NADH dehydrogenase ubiquinone flavoprotein is decreased in patients with dilated cardiomyopathy
-
Ono H., Nakamura H., Matsuzaki M., A NADH dehydrogenase ubiquinone flavoprotein is decreased in patients with dilated cardiomyopathy Internal Medicine 2010 49 19 2039 2042
-
(2010)
Internal Medicine
, vol.49
, Issue.19
, pp. 2039-2042
-
-
Ono, H.1
Nakamura, H.2
Matsuzaki, M.3
-
37
-
-
69949174405
-
FancyGene: Dynamic visualization of gene structures and protein domain architectures on genomic loci
-
Rambaldi D., Ciccarelli F. D., FancyGene: dynamic visualization of gene structures and protein domain architectures on genomic loci Bioinformatics 2009 25 17 2281 2282
-
(2009)
Bioinformatics
, vol.25
, Issue.17
, pp. 2281-2282
-
-
Rambaldi, D.1
Ciccarelli, F.D.2
-
38
-
-
77955486655
-
Analysis of multiple ethyl methanesulfonate-mutagenized Caenorhabditis elegans strains by whole-genome sequencing
-
Sarin S., Bertrand V., Bigelow H., Boyanov A., Doitsidou M., Poole R. J., Narula S., Hobert O., Analysis of multiple ethyl methanesulfonate-mutagenized Caenorhabditis elegans strains by whole-genome sequencing Genetics 2010 185 2 417 430
-
(2010)
Genetics
, vol.185
, Issue.2
, pp. 417-430
-
-
Sarin, S.1
Bertrand, V.2
Bigelow, H.3
Boyanov, A.4
Doitsidou, M.5
Poole, R.J.6
Narula, S.7
Hobert, O.8
-
39
-
-
77958014643
-
Single nucleotide polymorphisms in the human Na + -dicarboxylate cotransporter affect transport activity and protein expression
-
Pajor A. M., Sun N. N., Single nucleotide polymorphisms in the human Na + -dicarboxylate cotransporter affect transport activity and protein expression American Journal of Physiology 2010 299 4 F704 F711
-
(2010)
American Journal of Physiology
, vol.299
, Issue.4
-
-
Pajor, A.M.1
Sun, N.N.2
|