-
1
-
-
84883364264
-
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor
-
Anders S., et al. Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. Nat. Protocols 2013, 8:1765-1786.
-
(2013)
Nat. Protocols
, vol.8
, pp. 1765-1786
-
-
Anders, S.1
-
2
-
-
84859885816
-
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
-
Trapnell C., et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat. Protocols 2012, 7:562-578.
-
(2012)
Nat. Protocols
, vol.7
, pp. 562-578
-
-
Trapnell, C.1
-
3
-
-
80051968181
-
Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data
-
Cooper G.M., Shendure J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nat. Rev. Genet. 2011, 12:628-640.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 628-640
-
-
Cooper, G.M.1
Shendure, J.2
-
4
-
-
79956314887
-
Genotype and SNP calling from next-generation sequencing data
-
Nielsen R., et al. Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 2011, 12:443-451.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 443-451
-
-
Nielsen, R.1
-
5
-
-
84859898660
-
A beginner's guide to eukaryotic genome annotation
-
Yandell M., Ence D. A beginner's guide to eukaryotic genome annotation. Nat. Rev. Genet. 2012, 13:329-342.
-
(2012)
Nat. Rev. Genet.
, vol.13
, pp. 329-342
-
-
Yandell, M.1
Ence, D.2
-
6
-
-
77953808473
-
Next-generation genomics: an integrative approach
-
Hawkins R.D., et al. Next-generation genomics: an integrative approach. Nat. Rev. Genet. 2010, 11:476-486.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 476-486
-
-
Hawkins, R.D.1
-
8
-
-
84862249935
-
Association testing for next-generation sequencing data using score statistics
-
Skotte L., et al. Association testing for next-generation sequencing data using score statistics. Genet. Epidemiol. 2012, 36:430-437.
-
(2012)
Genet. Epidemiol.
, vol.36
, pp. 430-437
-
-
Skotte, L.1
-
9
-
-
84887421071
-
Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation
-
Vieira F.G., et al. Estimating inbreeding coefficients from NGS data: impact on genotype calling and allele frequency estimation. Genome Res. 2013, 23:1852-1861.
-
(2013)
Genome Res.
, vol.23
, pp. 1852-1861
-
-
Vieira, F.G.1
-
10
-
-
84887092567
-
Estimating individual admixture proportions from next generation sequencing data
-
Skotte L., et al. Estimating individual admixture proportions from next generation sequencing data. Genetics 2013, 195:693-702.
-
(2013)
Genetics
, vol.195
, pp. 693-702
-
-
Skotte, L.1
-
11
-
-
84887078795
-
Quantifying population genetic differentiation from next-generation sequencing data
-
Fumagalli M., et al. Quantifying population genetic differentiation from next-generation sequencing data. Genetics 2013, 195:979-992.
-
(2013)
Genetics
, vol.195
, pp. 979-992
-
-
Fumagalli, M.1
-
12
-
-
84884735609
-
Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data
-
Korneliussen T.S., et al. Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data. BMC Bioinformatics 2013, 14:289.
-
(2013)
BMC Bioinformatics
, vol.14
, pp. 289
-
-
Korneliussen, T.S.1
-
13
-
-
79958078775
-
Estimation of allele frequency and association mapping using next-generation sequencing data
-
Kim S., et al. Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics 2011, 12:231.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 231
-
-
Kim, S.1
-
14
-
-
0031978181
-
Base-calling of automated sequencer traces using Phred. II. Error probabilities
-
Ewing B., Green P. Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Res. 1998, 8:186-194.
-
(1998)
Genome Res.
, vol.8
, pp. 186-194
-
-
Ewing, B.1
Green, P.2
-
15
-
-
0031955430
-
Estimation of errors in 'raw' DNA sequences: a validation study
-
Richterich P. Estimation of errors in 'raw' DNA sequences: a validation study. Genome Res. 1998, 8:251-259.
-
(1998)
Genome Res.
, vol.8
, pp. 251-259
-
-
Richterich, P.1
-
16
-
-
84890565382
-
The role of replicates for error mitigation in next-generation sequencing
-
Robasky K., et al. The role of replicates for error mitigation in next-generation sequencing. Nat. Rev. Genet. 2014, 15:56-62.
-
(2014)
Nat. Rev. Genet.
, vol.15
, pp. 56-62
-
-
Robasky, K.1
-
17
-
-
84875312984
-
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing
-
O'Rawe J., et al. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013, 5:28.
-
(2013)
Genome Med.
, vol.5
, pp. 28
-
-
O'Rawe, J.1
-
18
-
-
84893904007
-
A polygenic burden of rare disruptive mutations in schizophrenia
-
Purcell S.M., et al. A polygenic burden of rare disruptive mutations in schizophrenia. Nature 2014, 506:185-190.
-
(2014)
Nature
, vol.506
, pp. 185-190
-
-
Purcell, S.M.1
-
19
-
-
84864326252
-
Genomic dark matter: the reliability of short read mapping illustrated by the Genome Mappability Score
-
Lee H., Schatz M.C. Genomic dark matter: the reliability of short read mapping illustrated by the Genome Mappability Score. Bioinformatics 2012, 28:2097-2105.
-
(2012)
Bioinformatics
, vol.28
, pp. 2097-2105
-
-
Lee, H.1
Schatz, M.C.2
-
20
-
-
68549104404
-
The Sequence Alignment/Map format and SAMtools
-
Li H., et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
-
(2009)
Bioinformatics
, vol.25
, pp. 2078-2079
-
-
Li, H.1
-
21
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
DePristo M.A., et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 2011, 43:491-498.
-
(2011)
Nat. Genet.
, vol.43
, pp. 491-498
-
-
DePristo, M.A.1
-
22
-
-
0019887799
-
Identification of common molecular subsequences
-
Smith T.F., Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 1981, 147:195-197.
-
(1981)
J. Mol. Biol.
, vol.147
, pp. 195-197
-
-
Smith, T.F.1
Waterman, M.S.2
-
23
-
-
84899474340
-
Haplotype-based variant detection from short-read sequencing
-
Garrison E., Marth G. Haplotype-based variant detection from short-read sequencing. arXiv 2012, 1207:3907.
-
(2012)
arXiv
, vol.1207
, pp. 3907
-
-
Garrison, E.1
Marth, G.2
-
24
-
-
80455129691
-
SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data
-
Wei Z., et al. SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data. Nucleic Acids Res. 2011, 39:e132.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Wei, Z.1
-
25
-
-
84891543623
-
An empirical Bayes testing procedure for detecting variants in analysis of next generation sequencing data
-
Zhao Z., et al. An empirical Bayes testing procedure for detecting variants in analysis of next generation sequencing data. Ann. Appl. Stat. 2013, 7:2229-2248.
-
(2013)
Ann. Appl. Stat.
, vol.7
, pp. 2229-2248
-
-
Zhao, Z.1
-
26
-
-
84905576523
-
Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications
-
Rimmer A., et al. Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications. Nat. Genet. 2014, 46:912-918.
-
(2014)
Nat. Genet.
, vol.46
, pp. 912-918
-
-
Rimmer, A.1
-
27
-
-
84921783122
-
Accurate de novo and transmitted indel detection in exome-capture data using microassembly
-
Narzisi G., et al. Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nat. Methods 2014, 11:1033-1036.
-
(2014)
Nat. Methods
, vol.11
, pp. 1033-1036
-
-
Narzisi, G.1
-
28
-
-
84871988179
-
SOAPindel: Efficient identification of indels from short paired reads
-
Li S., et al. SOAPindel: Efficient identification of indels from short paired reads. Genome Res. 2013, 23:195-200.
-
(2013)
Genome Res.
, vol.23
, pp. 195-200
-
-
Li, S.1
-
30
-
-
84863651532
-
Hybrid error correction and de novo assembly of single-molecule sequencing reads
-
Koren S., et al. Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat. Biotechnol. 2012, 30:693-700.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 693-700
-
-
Koren, S.1
-
31
-
-
81355147147
-
Identification and correction of systematic error in high-throughput sequence data
-
Meacham F., et al. Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics 2011, 12:451.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 451
-
-
Meacham, F.1
-
37
-
-
0004293209
-
-
Prentice-Hall Englewood Cliffs
-
Moore R.E. Interval Analysis 1966, Prentice-Hall Englewood Cliffs.
-
(1966)
Interval Analysis
-
-
Moore, R.E.1
-
39
-
-
0001503499
-
Best-possible bounds for the distribution of a sum: a problem of Kolmogorov
-
Frank M.J., et al. Best-possible bounds for the distribution of a sum: a problem of Kolmogorov. Probab. Theory Rel. Fields 1987, 74:199-211.
-
(1987)
Probab. Theory Rel. Fields
, vol.74
, pp. 199-211
-
-
Frank, M.J.1
-
40
-
-
0002063018
-
Probabilistic arithmetic. I. Numerical methods for calculating convolutions and dependency bounds
-
Williamson R.C., Downs T. Probabilistic arithmetic. I. Numerical methods for calculating convolutions and dependency bounds. Int. J. Approximate Reasoning 1990, 4:89-158.
-
(1990)
Int. J. Approximate Reasoning
, vol.4
, pp. 89-158
-
-
Williamson, R.C.1
Downs, T.2
-
41
-
-
38449109462
-
Quality assurance for Monte Carlo risk assessment
-
pp. 14, 19, 17-19. IEEF
-
Ferson S. Quality assurance for Monte Carlo risk assessment. Uncertainty Modeling and Analysis, 1995, and Annual Conference of the North American Fuzzy Information Processing Society. Proceedings of ISUMA-NAFIPS'95, Third International Symposium 1995, pp. 14, 19, 17-19. IEEF http://dx.doi.org/10.1109/ISUMA.1995.527662.
-
(1995)
Uncertainty Modeling and Analysis, 1995, and Annual Conference of the North American Fuzzy Information Processing Society. Proceedings of ISUMA-NAFIPS'95, Third International Symposium
-
-
Ferson, S.1
-
42
-
-
2642539278
-
Arithmetic with uncertain numbers: rigorous and (often) best possible answers
-
Ferson S., Hajagos J.G. Arithmetic with uncertain numbers: rigorous and (often) best possible answers. Reliab. Eng. Syst. Saf. 2004, 85:135-152.
-
(2004)
Reliab. Eng. Syst. Saf.
, vol.85
, pp. 135-152
-
-
Ferson, S.1
Hajagos, J.G.2
-
45
-
-
51649134515
-
An overview of robust Bayesian analysis
-
Berger J.O., et al. An overview of robust Bayesian analysis. Test 1994, 3:5-124.
-
(1994)
Test
, vol.3
, pp. 5-124
-
-
Berger, J.O.1
-
47
-
-
84921866619
-
-
The Society for Imprecise Probability: Theories and Applications
-
Pericchi L.R. Sets of Prior Probabilities and Bayesian Robustness 1998, The Society for Imprecise Probability: Theories and Applications, http://www.sipta.org/documentation/robust/pericchi.pdf.
-
(1998)
Sets of Prior Probabilities and Bayesian Robustness
-
-
Pericchi, L.R.1
-
48
-
-
38149147568
-
Posterior robustness with more than one sampling model
-
Pericchi L.R., Pérez M.E. Posterior robustness with more than one sampling model. J. Stat. Plann. Inference 1994, 40:279-294.
-
(1994)
J. Stat. Plann. Inference
, vol.40
, pp. 279-294
-
-
Pericchi, L.R.1
Pérez, M.E.2
-
49
-
-
38249000449
-
Bayesian robustness for hierarchical ε-contamination models
-
Moreno E., Pericchi L.R. Bayesian robustness for hierarchical ε-contamination models. J. Stat. Plann. Inference 1993, 37:159-167.
-
(1993)
J. Stat. Plann. Inference
, vol.37
, pp. 159-167
-
-
Moreno, E.1
Pericchi, L.R.2
-
50
-
-
84921872479
-
Computing with confidence: imprecise posteriors and predictive distributions
-
ASCE, M. Beer (Ed.)
-
Ferson S., et al. Computing with confidence: imprecise posteriors and predictive distributions. Vulnerability, Uncertainty, and Risks: Quantification, Mitigation, and Management 2014, 895-904. ASCE http://dx.doi.org/10.1061/9780784413609.091. M. Beer (Ed.).
-
(2014)
Vulnerability, Uncertainty, and Risks: Quantification, Mitigation, and Management
, pp. 895-904
-
-
Ferson, S.1
-
51
-
-
84864453448
-
Mathematical foundations for a theory of confidence structures
-
Balch M.S. Mathematical foundations for a theory of confidence structures. Int. J. Approximate Reasoning 2012, 53:1003-1019.
-
(2012)
Int. J. Approximate Reasoning
, vol.53
, pp. 1003-1019
-
-
Balch, M.S.1
-
53
-
-
84921879990
-
-
Novocraft Novoalign 2014, Novocraft, https://www.broadinstitute.org/gatk/guide/article?id=4146.
-
(2014)
Novocraft Novoalign
-
-
-
54
-
-
84921885112
-
-
Broad Institute HaplotypeCaller
-
Broad Institute HaplotypeCaller 2014, Broad Institute, https://www.broadinstitute.org/gatk/guide/article?id=4146.
-
(2014)
-
-
-
55
-
-
84875312984
-
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing
-
O'Rawe J., et al. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 2013, 5:28.
-
(2013)
Genome Med.
, vol.5
, pp. 28
-
-
O'Rawe, J.1
-
56
-
-
84921850275
-
Reducing INDEL calling errors in whole-genome and exome sequencing data
-
Fang H., et al. Reducing INDEL calling errors in whole-genome and exome sequencing data. Genome Med. 2014, 6:89.
-
(2014)
Genome Med.
, vol.6
, pp. 89
-
-
Fang, H.1
-
57
-
-
70349873824
-
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
-
Lieberman-Aiden E., et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293.
-
(2009)
Science
, vol.326
, pp. 289-293
-
-
Lieberman-Aiden, E.1
-
58
-
-
84861095603
-
Topological domains in mammalian genomes identified by analysis of chromatin interactions
-
Dixon J.R., et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012, 485:376-380.
-
(2012)
Nature
, vol.485
, pp. 376-380
-
-
Dixon, J.R.1
-
59
-
-
84903835646
-
Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products
-
Beitel C.W., et al. Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products. PeerJ 2014, 2:e415.
-
(2014)
PeerJ
, vol.2
-
-
Beitel, C.W.1
-
60
-
-
84904548768
-
Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability Maps
-
Burton J.N., et al. Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability Maps. G3 2014, 4:1339-1346.
-
(2014)
G3
, vol.4
, pp. 1339-1346
-
-
Burton, J.N.1
-
61
-
-
84865800494
-
The long-range interaction landscape of gene promoters
-
Sanyal A., et al. The long-range interaction landscape of gene promoters. Nature 2012, 489:109-113.
-
(2012)
Nature
, vol.489
, pp. 109-113
-
-
Sanyal, A.1
-
62
-
-
84864344347
-
Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress
-
Lyon G.J., Wang K. Identifying disease mutations in genomic medicine settings: current challenges and how to accelerate progress. Genome Med. 2012, 4:58.
-
(2012)
Genome Med.
, vol.4
, pp. 58
-
-
Lyon, G.J.1
Wang, K.2
-
63
-
-
80051550297
-
Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency
-
Rope A.F., et al. Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency. Am. J. Hum. Genet. 2011, 89:28-43.
-
(2011)
Am. J. Hum. Genet.
, vol.89
, pp. 28-43
-
-
Rope, A.F.1
-
64
-
-
84864273210
-
SNP Calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data
-
Nielsen R., et al. SNP Calling, genotype calling, and sample allele frequency estimation from new-generation sequencing data. PLoS ONE 2012, 7:e37558.
-
(2012)
PLoS ONE
, vol.7
-
-
Nielsen, R.1
-
65
-
-
84896009017
-
From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline
-
John Wiley & Sons
-
Van der Auwera G.A., et al. From FastQ data to high-confidence variant calls: the genome analysis toolkit best practices pipeline. Current Protocols in Bioinformatics 2013, John Wiley & Sons.
-
(2013)
Current Protocols in Bioinformatics
-
-
Van der Auwera, G.A.1
|