Restricted accessOtherFirst published online 2017-8
Discussion on ‘Statistical contributions to bioinformatics: Design,modelling,structure learning and integration’ by Jeffrey S. Morris and Veerabhadran Baladandayuthapani
AltschulSFGishW (1996) Local alignment statistics. Methods in Enzymology, 266, 460–80. PubMed PMID: 8743700.
2.
BartelJKrumsiekJTheisFJ (2013) Statistical methods for the analysis of high-throughput metabolomics data. Computational and Structural Biotechnology Journal, 4:e201301009. doi: 10.5936/csbj.201301009. PubMed PMID: 24688690; PMCID: PMC 3962125.
3.
BenjaminiYHochbergY (1995) Controlling the false discovery rate—A practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, 57, 289–300. PubMed PMID: WOS:A1995QE45300017.
4.
DawsonJAKendziorskiC (2012) An empirical Bayesian approach for identifying differential coexpression in high-throughput experiments. Biometrics, 68, 455–65.
5.
DawsonJAYeSKendziorskiC (2012) R/EBcoexpress: An empirical Bayesian framework for discovering differential co-expression. Bioinformatics, 28, 1939–40.
6.
FelsensteinJ (1973) Maximum-likelihood estimation of evolutionary trees from continuous characters. The American Journal of Human Genetics, 25, 471–92. PubMed PMID: 4741844; PMCID: PMC1762641.
7.
FelsensteinJ (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. Journal of Molecular Evolution, 17, 368–76. PubMed PMID: 7288891.
8.
FelsensteinJ (1985) Confidence-limits on phylogenies—An approach using the bootstrap. Evolution, 39, 783–91. doi: Doi 10.2307/2408678. PubMed PMID: WOS:A1985APJ8100007.
9.
HasegawaMKishinoHYanoT (1985) Dating of the human—ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22, 160–74. PubMed PMID: 3934395.
10.
HensleyP (2013) SOMAmers and SOMAscan—A protein biomarker discovery platform for rapid analysis of sample collections from bench top to the clinic. Journal of Biomolecular Techniques, 24, (Suppl.), S5. PubMed PMID: PMC3635296.
11.
IrizarryRAHobbsBCollinFBeazer-BarclayYDAntonellisKJScherfUSpeedTP (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249–64. doi: 10.1093/biostatistics/4.2.249. PubMed PMID: 12925520.
12.
JohnsonWELiCRabinovicA (2007) Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics, 8, 118–27. doi: 10.1093/biostatistics/kxj037. PubMed PMID: 16632515.
13.
JukesTCantorC (1969) Evolution of protein molecules. In MunroHN, ed. Mammalian Protein Metabolism, pages 21–32. New York, NY: Academic Press.
14.
KarlinSAltschulSF (1990) Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proceedings of the National Academy of Sciencesof the United States of America, 87, 2264–68. PubMed PMID: 2315319; PMCID: PMC53667.
15.
KarlinSDemboAKawabataT (1990) Statistical composition of high-scoring segments from molecular sequences. Annals of Statistics, 18, 571–81. doi: DOI 10.1214/aos/1176347616. PubMed PMID: WOS:A1990DP71200015.
16.
KimuraM (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111–20. PubMed PMID: 7463489.
17.
LiangFMSongQFYuK (2013) Bayesian subset modeling for high-dimensional generalized linear models. Journal of the American Statistical Association, 108, 589–606. doi: 10.1080/01621459.2012.761942. PubMed PMID: WOS:000321727700019.
18.
ObergALMahoneyDW (2012) Statistical methods for quantitative mass spectrometry proteomic experiments with labeling. BMC Bioinformatics, 13, (Suppl. 16), S7. doi:10.1186/1471-2105-13-S16-S7. PubMed PMID: 23176383; PMCID: PMC3489540.
19.
RobinsonMDMcCarthyDJSmythGK (2010) edgeR: A bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics, 26, 139–40. doi: 10.1093/bioinformatics/btp616. PubMed PMID: 19910308; PMCID: PMC2796818.
20.
ShendureJLieberman AidenE (2012) The expanding scope of DNA sequencing. Nature Biotechnology, 30, 1084–94. doi: 10.1038/nbt.2421. PubMed PMID: 23138308; PMCID: PMC4149750.
21.
SmithTFWatermanMSBurksC (1985) The statistical distribution of nucleic acid similarities. Nucleic Acids Research, 13, 645–56. PubMed PMID: 3871073; PMCID: PMC341021.
22.
SmythGK (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, 3, Article 3. doi: 10.2202/1544-6115.1027. PubMed PMID: 16646809.
23.
SmythGK (2005) Limma: Linear models for microarray data. In GentlemanRCareyVJHuberWIrizarryRADudoitS, eds. Bioinformatics and Computational Biology Solutions Using R and Bioconductor, pages 397–420. New York, NY: Springer.
24.
SuchardMAWangQLChanCFrelingerJCronAWestM (2010) Understanding GPU programming for statistical computation: Studies in massively parallel massive mixtures. Journal of Computational and Graphical Statistics, 19, 419–38. doi: 10.1198/jcgs.2010.10016. PubMed PMID: WOS:000279183700010.
25.
TrafimowDMarksM (2015) Editorial. Basic and Applied Social Psychology, 37, 1–2. doi: 10.1080/01973533.2015.1012991.
26.
WainwrightMJJordanMI (2008) Graphical models, exponential families, and variational inference. Foundations and Trends® in Machine Learning, 1, 1–305. doi: 10.1561/2200000001.
