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A scaling normalization method for differential expression analysis of RNA-seq data.
Robinson MD, Oshlack A. Robinson MD, et al. Among authors: oshlack a. Genome Biol. 2010;11(3):R25. doi: 10.1186/gb-2010-11-3-r25. Epub 2010 Mar 2. Genome Biol. 2010. PMID: 20196867 Free PMC article.
We outline a simple and effective method for performing normalization and show dramatically improved results for inferring differential expression in simulated and publicly available data sets....
We outline a simple and effective method for performing normalization and show dramatically improved results for inferring differenti …
The role of cardiac transcription factor NKX2-5 in regulating the human cardiac miRNAome.
Arasaratnam D, Bell KM, Sim CB, Koutsis K, Anderson DJ, Qian EL, Stanley EG, Elefanty AG, Cheung MM, Oshlack A, White AJ, Abi Khalil C, Hudson JE, Porrello ER, Elliott DA. Arasaratnam D, et al. Among authors: oshlack a. Sci Rep. 2019 Nov 4;9(1):15928. doi: 10.1038/s41598-019-52280-9. Sci Rep. 2019. PMID: 31685864 Free PMC article.
Statistical analysis of an RNA titration series evaluates microarray precision and sensitivity on a whole-array basis.
Holloway AJ, Oshlack A, Diyagama DS, Bowtell DD, Smyth GK. Holloway AJ, et al. Among authors: oshlack a. BMC Bioinformatics. 2006 Nov 22;7:511. doi: 10.1186/1471-2105-7-511. BMC Bioinformatics. 2006. PMID: 17118209 Free PMC article.
RESULTS: A methodology is described for evaluating the precision and sensitivity of whole-genome gene expression technologies such as microarrays. ...The method evaluates the precision and responsiveness of each microarray platform on a whole-array basis, i.e., usin …
RESULTS: A methodology is described for evaluating the precision and sensitivity of whole-genome gene expression technologies such as …
Normalization of boutique two-color microarrays with a high proportion of differentially expressed probes.
Oshlack A, Emslie D, Corcoran LM, Smyth GK. Oshlack A, et al. Genome Biol. 2007;8(1):R2. doi: 10.1186/gb-2007-8-1-r2. Genome Biol. 2007. PMID: 17204140 Free PMC article.
Here we outline a normalization method for use when the assumptions of lowess normalization fail. Specifically, this can occur when specialized boutique arrays are constructed that contain a subset of genes selected to test particular biological functions....
Here we outline a normalization method for use when the assumptions of lowess normalization fail. Specifically, this can occur when s …
Using DNA microarrays to study gene expression in closely related species.
Oshlack A, Chabot AE, Smyth GK, Gilad Y. Oshlack A, et al. Bioinformatics. 2007 May 15;23(10):1235-42. doi: 10.1093/bioinformatics/btm111. Epub 2007 Mar 23. Bioinformatics. 2007. PMID: 17384014
DNA microarrays are a key technology that enables these studies. Currently, however, microarrays are only available for a small number of species. ...We also demonstrate that within-species expression differences can be estimated using a microarray for a
DNA microarrays are a key technology that enables these studies. Currently, however, microarrays are only available for a smal …
Segmental duplications contribute to gene expression differences between humans and chimpanzees.
Blekhman R, Oshlack A, Gilad Y. Blekhman R, et al. Among authors: oshlack a. Genetics. 2009 Jun;182(2):627-30. doi: 10.1534/genetics.108.099960. Epub 2009 Mar 30. Genetics. 2009. PMID: 19332884 Free PMC article.
In addition to specific changes in cis- and trans-regulatory elements, structural changes in the genome are hypothesized to underlie a large number of differences in gene expression between species. ...
In addition to specific changes in cis- and trans-regulatory elements, structural changes in the genome are hypothesized to underlie a
Transcript length bias in RNA-seq data confounds systems biology.
Oshlack A, Wakefield MJ. Oshlack A, et al. Biol Direct. 2009 Apr 16;4:14. doi: 10.1186/1745-6150-4-14. Biol Direct. 2009. PMID: 19371405 Free PMC article.
As yet, a rigorous analysis methodology has not been developed and we are still in the stages of exploring the features of the data. ...CONCLUSION: Transcript length bias for calling differentially expressed genes is a general feature of current protocols for RNA-se …
As yet, a rigorous analysis methodology has not been developed and we are still in the stages of exploring the features of the data. …
Gene ontology analysis for RNA-seq: accounting for selection bias.
Young MD, Wakefield MJ, Smyth GK, Oshlack A. Young MD, et al. Among authors: oshlack a. Genome Biol. 2010;11(2):R14. doi: 10.1186/gb-2010-11-2-r14. Epub 2010 Feb 4. Genome Biol. 2010. PMID: 20132535 Free PMC article.
Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more consistent with the known biology....
Application of GOseq to a prostate cancer data set shows that GOseq dramatically changes the results, highlighting categories more co …
Optimizing the noise versus bias trade-off for Illumina whole genome expression BeadChips.
Shi W, Oshlack A, Smyth GK. Shi W, et al. Among authors: oshlack a. Nucleic Acids Res. 2010 Dec;38(22):e204. doi: 10.1093/nar/gkq871. Epub 2010 Oct 6. Nucleic Acids Res. 2010. PMID: 20929874 Free PMC article.
The strategies include a popular variance stabilizing transformation and model-based background corrections that either use or ignore the control probes. ...The use of control probes as part of the background correction and normalization strategy is shown to achieve the lo …
The strategies include a popular variance stabilizing transformation and model-based background corrections that either use or ignore …
From RNA-seq reads to differential expression results.
Oshlack A, Robinson MD, Young MD. Oshlack A, et al. Genome Biol. 2010;11(12):220. doi: 10.1186/gb-2010-11-12-220. Epub 2010 Dec 22. Genome Biol. 2010. PMID: 21176179 Free PMC article. Review.
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