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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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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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Jets: a modification to speed flexible oligonucleotide array construction.

The pharmacogenomics journal

Yoder B, Sell SM.
PMID: 11908749
Pharmacogenomics J. 2001;1(3):163-5. doi: 10.1038/sj.tpj.6500032.

No abstract available.

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Yoder B, Sell SM. Jets: a modification to speed flexible oligonucleotide array construction. Pharmacogenomics J. 2001;1(3):163-5doi: 10.1038/sj.tpj.6500032.
Yoder, B., & Sell, S. M. (2001). Jets: a modification to speed flexible oligonucleotide array construction. The pharmacogenomics journal, 1(3), 163-5. https://doi.org/10.1038/sj.tpj.6500032
Yoder, B, and Sell, S M. "Jets: a modification to speed flexible oligonucleotide array construction." The pharmacogenomics journal vol. 1,3 (2001): 163-5. doi: https://doi.org/10.1038/sj.tpj.6500032
Yoder B, Sell SM. Jets: a modification to speed flexible oligonucleotide array construction. Pharmacogenomics J. 2001;1(3):163-5. doi: 10.1038/sj.tpj.6500032. PMID: 11908749.
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Application of microarrays to the analysis of gene expression in cancer.

Clinical chemistry

Macgregor PF, Squire JA.
PMID: 12142369
Clin Chem. 2002 Aug;48(8):1170-7.

Molecular diagnostics is a rapidly advancing field in which insights into disease mechanisms are being elucidated by use of new gene-based biomarkers. Until recently, diagnostic and prognostic assessment of diseased tissues and tumors relied heavily on indirect indicators that...

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Macgregor PF, Squire JA. Application of microarrays to the analysis of gene expression in cancer. Clin Chem. 2002;48(8):1170-7
Macgregor, P. F., & Squire, J. A. (2002). Application of microarrays to the analysis of gene expression in cancer. Clinical chemistry, 48(8), 1170-7.
Macgregor, Pascale F, and Squire, Jeremy A. "Application of microarrays to the analysis of gene expression in cancer." Clinical chemistry vol. 48,8 (2002): 1170-7.
Macgregor PF, Squire JA. Application of microarrays to the analysis of gene expression in cancer. Clin Chem. 2002 Aug;48(8):1170-7. PMID: 12142369.
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An accelerated procedure for recursive feature ranking on microarray data.

Neural networks : the official journal of the International Neural Network Society

Furlanello C, Serafini M, Merler S, Jurman G.
PMID: 12850018
Neural Netw. 2003 Jun-Jul;16(5):641-8. doi: 10.1016/S0893-6080(03)00103-5.

We describe a new wrapper algorithm for fast feature ranking in classification problems. The Entropy-based Recursive Feature Elimination (E-RFE) method eliminates chunks of uninteresting features according to the entropy of the weights distribution of a SVM classifier. With specific...

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Furlanello C, Serafini M, Merler S, et al. An accelerated procedure for recursive feature ranking on microarray data. Neural Netw. 2003;16(5):641-8doi: 10.1016/S0893-6080(03)00103-5.
Furlanello, C., Serafini, M., Merler, S., & Jurman, G. (2003). An accelerated procedure for recursive feature ranking on microarray data. Neural networks : the official journal of the International Neural Network Society, 16(5), 641-8. https://doi.org/10.1016/S0893-6080(03)00103-5
Furlanello, C, et al. "An accelerated procedure for recursive feature ranking on microarray data." Neural networks : the official journal of the International Neural Network Society vol. 16,5 (2003): 641-8. doi: https://doi.org/10.1016/S0893-6080(03)00103-5
Furlanello C, Serafini M, Merler S, Jurman G. An accelerated procedure for recursive feature ranking on microarray data. Neural Netw. 2003 Jun-Jul;16(5):641-8. doi: 10.1016/S0893-6080(03)00103-5. PMID: 12850018.
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Statistical methods for identifying differentially expressed genes in DNA microarrays.

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

Storey JD, Tibshirani R.
PMID: 12710672
Methods Mol Biol. 2003;224:149-57. doi: 10.1385/1-59259-364-X:149.

No abstract available.

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Storey JD, Tibshirani R. Statistical methods for identifying differentially expressed genes in DNA microarrays. Methods Mol Biol. 2003;224:149-57doi: 10.1385/1-59259-364-X:149.
Storey, J. D., & Tibshirani, R. (2003). Statistical methods for identifying differentially expressed genes in DNA microarrays. Methods in molecular biology (Clifton, N.J.), 224149-57. https://doi.org/10.1385/1-59259-364-X:149
Storey, John D, and Tibshirani, Robert. "Statistical methods for identifying differentially expressed genes in DNA microarrays." Methods in molecular biology (Clifton, N.J.) vol. 224 (2003): 149-57. doi: https://doi.org/10.1385/1-59259-364-X:149
Storey JD, Tibshirani R. Statistical methods for identifying differentially expressed genes in DNA microarrays. Methods Mol Biol. 2003;224:149-57. doi: 10.1385/1-59259-364-X:149. PMID: 12710672.
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Microarray analysis: the evolving story of oral polio vaccines.

Heredity

Breuer J.
PMID: 14603348
Heredity (Edinb). 2004 Jan;92(1):3-4. doi: 10.1038/sj.hdy.6800373.

No abstract available.

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Breuer J. Microarray analysis: the evolving story of oral polio vaccines. Heredity (Edinb). 2004;92(1):3-4doi: 10.1038/sj.hdy.6800373.
Breuer, J. (2004). Microarray analysis: the evolving story of oral polio vaccines. Heredity, 92(1), 3-4. https://doi.org/10.1038/sj.hdy.6800373
Breuer, J. "Microarray analysis: the evolving story of oral polio vaccines." Heredity vol. 92,1 (2004): 3-4. doi: https://doi.org/10.1038/sj.hdy.6800373
Breuer J. Microarray analysis: the evolving story of oral polio vaccines. Heredity (Edinb). 2004 Jan;92(1):3-4. doi: 10.1038/sj.hdy.6800373. PMID: 14603348.
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Critical assessment of microarray data analysis: the 2001 challenge.

Bioinformatics (Oxford, England)

Johnson KF, Lin SM.
PMID: 11590109
Bioinformatics. 2001 Sep;17(9):857-8. doi: 10.1093/bioinformatics/17.9.857.

UNLABELLED: We initiated the Critical Assessment of Microarray Data Analysis (CAMDA) conference to stimulate and evaluate the development of advanced data analysis techniques for microarrays. A standard data set has been released for this data analysis challenge. The goal...

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Johnson KF, Lin SM. Critical assessment of microarray data analysis: the 2001 challenge. Bioinformatics. 2001;17(9):857-8doi: 10.1093/bioinformatics/17.9.857.
Johnson, K. F., & Lin, S. M. (2001). Critical assessment of microarray data analysis: the 2001 challenge. Bioinformatics (Oxford, England), 17(9), 857-8. https://doi.org/10.1093/bioinformatics/17.9.857
Johnson, K F, and Lin, S M. "Critical assessment of microarray data analysis: the 2001 challenge." Bioinformatics (Oxford, England) vol. 17,9 (2001): 857-8. doi: https://doi.org/10.1093/bioinformatics/17.9.857
Johnson KF, Lin SM. Critical assessment of microarray data analysis: the 2001 challenge. Bioinformatics. 2001 Sep;17(9):857-8. doi: 10.1093/bioinformatics/17.9.857. PMID: 11590109.
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PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways.

Nucleic acids research

Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z.
PMID: 15980551
Nucleic Acids Res. 2005 Jul 01;33:W633-7. doi: 10.1093/nar/gki391.

While generation of high-throughput expression data is becoming routine, the fast, easy, and systematic presentation and analysis of these data in a biological context is still an obstacle. To address this need, we have developed PathwayExplorer, which maps expression...

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Mlecnik B, Scheideler M, Hackl H, et al. PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways. Nucleic Acids Res. 2005;33:W633-7doi: 10.1093/nar/gki391.
Mlecnik, B., Scheideler, M., Hackl, H., Hartler, J., Sanchez-Cabo, F., & Trajanoski, Z. (2005). PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways. Nucleic acids research, 33W633-7. https://doi.org/10.1093/nar/gki391
Mlecnik, Bernhard, et al. "PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways." Nucleic acids research vol. 33 (2005): W633-7. doi: https://doi.org/10.1093/nar/gki391
Mlecnik B, Scheideler M, Hackl H, Hartler J, Sanchez-Cabo F, Trajanoski Z. PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways. Nucleic Acids Res. 2005 Jul 01;33:W633-7. doi: 10.1093/nar/gki391. PMID: 15980551; PMCID: PMC1160152.
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Showing 1 to 12 of 133 entries