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A composite framework for the statistical analysis of epidemiological DNA methylation data with the Infinium Human Methylation 450K BeadChip.

IEEE journal of biomedical and health informatics

Valavanis I, Sifakis EG, Georgiadis P, Kyrtopoulos S, Chatziioannou AA.
PMID: 24808224
IEEE J Biomed Health Inform. 2014 May;18(3):817-23. doi: 10.1109/JBHI.2014.2298351.

High-throughput DNA methylation profiling exploits microarray technologies thus providing a wealth of data, which however solicits rigorous, generic, and analytical pipelines for an efficient systems level analysis and interpretation. In this study, we utilize the Illumina's Infinium Human Methylation...

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Valavanis I, Sifakis EG, Georgiadis P, et al. A composite framework for the statistical analysis of epidemiological DNA methylation data with the Infinium Human Methylation 450K BeadChip. IEEE J Biomed Health Inform. 2014;18(3):817-23doi: 10.1109/JBHI.2014.2298351.
Valavanis, I., Sifakis, E. G., Georgiadis, P., Kyrtopoulos, S., & Chatziioannou, A. A. (2014). A composite framework for the statistical analysis of epidemiological DNA methylation data with the Infinium Human Methylation 450K BeadChip. IEEE journal of biomedical and health informatics, 18(3), 817-23. https://doi.org/10.1109/JBHI.2014.2298351
Valavanis, Ioannis, et al. "A composite framework for the statistical analysis of epidemiological DNA methylation data with the Infinium Human Methylation 450K BeadChip." IEEE journal of biomedical and health informatics vol. 18,3 (2014): 817-23. doi: https://doi.org/10.1109/JBHI.2014.2298351
Valavanis I, Sifakis EG, Georgiadis P, Kyrtopoulos S, Chatziioannou AA. A composite framework for the statistical analysis of epidemiological DNA methylation data with the Infinium Human Methylation 450K BeadChip. IEEE J Biomed Health Inform. 2014 May;18(3):817-23. doi: 10.1109/JBHI.2014.2298351. PMID: 24808224.
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Single nucleotide polymorphisms on DNA methylation microarrays: precautions against confounding.

Epigenomics

Barrow TM, Byun HM.
PMID: 25531251
Epigenomics. 2014;6(6):577-9. doi: 10.2217/epi.14.55.

No abstract available.

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Barrow TM, Byun HM. Single nucleotide polymorphisms on DNA methylation microarrays: precautions against confounding. Epigenomics. 2014;6(6):577-9doi: 10.2217/epi.14.55.
Barrow, T. M., & Byun, H. M. (2014). Single nucleotide polymorphisms on DNA methylation microarrays: precautions against confounding. Epigenomics, 6(6), 577-9. https://doi.org/10.2217/epi.14.55
Barrow, Timothy M, and Byun, Hyang-Min. "Single nucleotide polymorphisms on DNA methylation microarrays: precautions against confounding." Epigenomics vol. 6,6 (2014): 577-9. doi: https://doi.org/10.2217/epi.14.55
Barrow TM, Byun HM. Single nucleotide polymorphisms on DNA methylation microarrays: precautions against confounding. Epigenomics. 2014;6(6):577-9. doi: 10.2217/epi.14.55. PMID: 25531251.
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Identification of sample annotation errors in gene expression datasets.

Archives of toxicology

Lohr M, Hellwig B, Edlund K, Mattsson JS, Botling J, Schmidt M, Hengstler JG, Micke P, Rahnenführer J.
PMID: 26608184
Arch Toxicol. 2015 Dec;89(12):2265-72. doi: 10.1007/s00204-015-1632-4. Epub 2015 Nov 25.

The comprehensive transcriptomic analysis of clinically annotated human tissue has found widespread use in oncology, cell biology, immunology, and toxicology. In cancer research, microarray-based gene expression profiling has successfully been applied to subclassify disease entities, predict therapy response, and...

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Lohr M, Hellwig B, Edlund K, et al. Identification of sample annotation errors in gene expression datasets. Arch Toxicol. 2015;89(12):2265-72doi: 10.1007/s00204-015-1632-4.
Lohr, M., Hellwig, B., Edlund, K., Mattsson, J. S., Botling, J., Schmidt, M., Hengstler, J. G., Micke, P., & Rahnenführer, J. (2015). Identification of sample annotation errors in gene expression datasets. Archives of toxicology, 89(12), 2265-72. https://doi.org/10.1007/s00204-015-1632-4
Lohr, Miriam, et al. "Identification of sample annotation errors in gene expression datasets." Archives of toxicology vol. 89,12 (2015): 2265-72. doi: https://doi.org/10.1007/s00204-015-1632-4
Lohr M, Hellwig B, Edlund K, Mattsson JS, Botling J, Schmidt M, Hengstler JG, Micke P, Rahnenführer J. Identification of sample annotation errors in gene expression datasets. Arch Toxicol. 2015 Dec;89(12):2265-72. doi: 10.1007/s00204-015-1632-4. Epub 2015 Nov 25. PMID: 26608184; PMCID: PMC4673097.
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Bioinformatics on the cloud computing platform Azure.

PloS one

Shanahan HP, Owen AM, Harrison AP.
PMID: 25050811
PLoS One. 2014 Jul 22;9(7):e102642. doi: 10.1371/journal.pone.0102642. eCollection 2014.

We discuss the applicability of the Microsoft cloud computing platform, Azure, for bioinformatics. We focus on the usability of the resource rather than its performance. We provide an example of how R can be used on Azure to analyse...

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Shanahan HP, Owen AM, Harrison AP. Bioinformatics on the cloud computing platform Azure. PLoS One. 2014;9(7):e102642doi: 10.1371/journal.pone.0102642.
Shanahan, H. P., Owen, A. M., & Harrison, A. P. (2014). Bioinformatics on the cloud computing platform Azure. PloS one, 9(7), e102642. https://doi.org/10.1371/journal.pone.0102642
Shanahan, Hugh P, et al. "Bioinformatics on the cloud computing platform Azure." PloS one vol. 9,7 (2014): e102642. doi: https://doi.org/10.1371/journal.pone.0102642
Shanahan HP, Owen AM, Harrison AP. Bioinformatics on the cloud computing platform Azure. PLoS One. 2014 Jul 22;9(7):e102642. doi: 10.1371/journal.pone.0102642. eCollection 2014. PMID: 25050811; PMCID: PMC4106841.
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Better together: multiplexing samples to improve the preparation and reliability of gene expression studies.

Nature methods

Mortazavi A.
PMID: 25825835
Nat Methods. 2015 Apr;12(4):304-5. doi: 10.1038/nmeth.3333.

No abstract available.

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Mortazavi A. Better together: multiplexing samples to improve the preparation and reliability of gene expression studies. Nat Methods. 2015;12(4):304-5doi: 10.1038/nmeth.3333.
Mortazavi, A. (2015). Better together: multiplexing samples to improve the preparation and reliability of gene expression studies. Nature methods, 12(4), 304-5. https://doi.org/10.1038/nmeth.3333
Mortazavi, Ali. "Better together: multiplexing samples to improve the preparation and reliability of gene expression studies." Nature methods vol. 12,4 (2015): 304-5. doi: https://doi.org/10.1038/nmeth.3333
Mortazavi A. Better together: multiplexing samples to improve the preparation and reliability of gene expression studies. Nat Methods. 2015 Apr;12(4):304-5. doi: 10.1038/nmeth.3333. PMID: 25825835.
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A high-throughput microRNA expression profiling system.

Methods in molecular biology (Clifton, N.J.)

Guo Y, Mastriano S, Lu J.
PMID: 25030917
Methods Mol Biol. 2014;1176:33-44. doi: 10.1007/978-1-4939-0992-6_4.

As small noncoding RNAs, microRNAs (miRNAs) regulate diverse biological functions, including physiological and pathological processes. The expression and deregulation of miRNA levels contain rich information with diagnostic and prognostic relevance and can reflect pharmacological responses. The increasing interest in...

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Guo Y, Mastriano S, Lu J. A high-throughput microRNA expression profiling system. Methods Mol Biol. 2014;1176:33-44doi: 10.1007/978-1-4939-0992-6_4.
Guo, Y., Mastriano, S., & Lu, J. (2014). A high-throughput microRNA expression profiling system. Methods in molecular biology (Clifton, N.J.), 117633-44. https://doi.org/10.1007/978-1-4939-0992-6_4
Guo, Yanwen, et al. "A high-throughput microRNA expression profiling system." Methods in molecular biology (Clifton, N.J.) vol. 1176 (2014): 33-44. doi: https://doi.org/10.1007/978-1-4939-0992-6_4
Guo Y, Mastriano S, Lu J. A high-throughput microRNA expression profiling system. Methods Mol Biol. 2014;1176:33-44. doi: 10.1007/978-1-4939-0992-6_4. PMID: 25030917.
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Tissue microarray.

The Journal of investigative dermatology

Barrette K, van den Oord JJ, Garmyn M.
PMID: 25120151
J Invest Dermatol. 2014 Sep;134(9):1-4. doi: 10.1038/jid.2014.277.

No abstract available.

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Barrette K, van den Oord JJ, Garmyn M. Tissue microarray. J Invest Dermatol. 2014;134(9):1-4doi: 10.1038/jid.2014.277.
Barrette, K., van den Oord, J. J., & Garmyn, M. (2014). Tissue microarray. The Journal of investigative dermatology, 134(9), 1-4. https://doi.org/10.1038/jid.2014.277
Barrette, Kathleen, et al. "Tissue microarray." The Journal of investigative dermatology vol. 134,9 (2014): 1-4. doi: https://doi.org/10.1038/jid.2014.277
Barrette K, van den Oord JJ, Garmyn M. Tissue microarray. J Invest Dermatol. 2014 Sep;134(9):1-4. doi: 10.1038/jid.2014.277. PMID: 25120151.
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DNA chips and development: prospects and problems.

Genesis (New York, N.Y. : 2000)

Schwarz DG.
PMID: 11105054
Genesis. 2000 Nov-Dec;28(3):134.

No abstract available.

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Schwarz DG. DNA chips and development: prospects and problems. Genesis. 2000;28(3):134
Schwarz, D. G. (2000). DNA chips and development: prospects and problems. Genesis (New York, N.Y. : 2000), 28(3), 134.
Schwarz, D G. "DNA chips and development: prospects and problems." Genesis (New York, N.Y. : 2000) vol. 28,3 (2000): 134.
Schwarz DG. DNA chips and development: prospects and problems. Genesis. 2000 Nov-Dec;28(3):134. PMID: 11105054.
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[Biochips].

Casopis lekaru ceskych

Rajská G.
PMID: 11192761
Cas Lek Cesk. 2000 Oct 25;139(21):647-51.

A new revolution technology that may become promising for research, diagnostics and therapy enters into biology and medicine. The basic idea of the biochip technology is to convert the chemistry of life into a static form programmed to monitor...

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Rajská G. Biocipy. [Biochips]. Cas Lek Cesk. 2000;139(21):647-51
Rajská, G. (2000). Biocipy. [Biochips]. Casopis lekaru ceskych, 139(21), 647-51.
Rajská, G. "Biocipy." [Biochips]. Casopis lekaru ceskych vol. 139,21 (2000): 647-51.
Rajská G. Biocipy. [Biochips]. Cas Lek Cesk. 2000 Oct 25;139(21):647-51. Czech. PMID: 11192761.
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Free and public expression.

Nature

[No authors listed]
PMID: 11309567
Nature. 2001 Apr 19;410(6831):851. doi: 10.1038/35073755.

No abstract available.

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Free and public expression. Nature. 2001;410(6831):851doi: 10.1038/35073755.
(2001). Free and public expression. Nature, 410(6831), 851. https://doi.org/10.1038/35073755
"Free and public expression." Nature vol. 410,6831 (2001): 851. doi: https://doi.org/10.1038/35073755
Free and public expression. Nature. 2001 Apr 19;410(6831):851. doi: 10.1038/35073755. PMID: 11309567.
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Argus--a new database system for Web-based analysis of multiple microarray data sets.

Genome research

Comander J, Weber GM, Gimbrone MA, García-Cardeña G.
PMID: 11544205
Genome Res. 2001 Sep;11(9):1603-10. doi: 10.1101/gr.186601.

The ongoing revolution in microarray technology allows biologists studying gene expression to routinely collect >10(5) data points in a given experiment. Widely accessible and versatile database software is required to process this large amount of raw data into a...

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Comander J, Weber GM, Gimbrone MA, et al. Argus--a new database system for Web-based analysis of multiple microarray data sets. Genome Res. 2001;11(9):1603-10doi: 10.1101/gr.186601.
Comander, J., Weber, G. M., Gimbrone, M. A., & García-Cardeña, G. (2001). Argus--a new database system for Web-based analysis of multiple microarray data sets. Genome research, 11(9), 1603-10. https://doi.org/10.1101/gr.186601
Comander, J, et al. "Argus--a new database system for Web-based analysis of multiple microarray data sets." Genome research vol. 11,9 (2001): 1603-10. doi: https://doi.org/10.1101/gr.186601
Comander J, Weber GM, Gimbrone MA, García-Cardeña G. Argus--a new database system for Web-based analysis of multiple microarray data sets. Genome Res. 2001 Sep;11(9):1603-10. doi: 10.1101/gr.186601. PMID: 11544205; PMCID: PMC311087.
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DRAGON View: information visualization for annotated microarray data.

Bioinformatics (Oxford, England)

Bouton CM, Pevsner J.
PMID: 11847082
Bioinformatics. 2002 Feb;18(2):323-4. doi: 10.1093/bioinformatics/18.2.323.

The DRAGON View information visualization tools aid in the comprehensive analysis of large-scale gene expression data that has been annotated with biologically relevant information through the generation of three types of complementary graphical outputs.

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Bouton CM, Pevsner J. DRAGON View: information visualization for annotated microarray data. Bioinformatics. 2002;18(2):323-4doi: 10.1093/bioinformatics/18.2.323.
Bouton, C. M., & Pevsner, J. (2002). DRAGON View: information visualization for annotated microarray data. Bioinformatics (Oxford, England), 18(2), 323-4. https://doi.org/10.1093/bioinformatics/18.2.323
Bouton, Christopher M L S, and Pevsner, Jonathan. "DRAGON View: information visualization for annotated microarray data." Bioinformatics (Oxford, England) vol. 18,2 (2002): 323-4. doi: https://doi.org/10.1093/bioinformatics/18.2.323
Bouton CM, Pevsner J. DRAGON View: information visualization for annotated microarray data. Bioinformatics. 2002 Feb;18(2):323-4. doi: 10.1093/bioinformatics/18.2.323. PMID: 11847082.
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Showing 1 to 12 of 306 entries