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Social network Analysis-based classifier (SNAc): A case study on time course gene expression data.

Computer methods and programs in biomedicine

Üçer S, Koçak Y, Ozyer T, Alhajj R.
PMID: 28859830
Comput Methods Programs Biomed. 2017 Oct;150:73-84. doi: 10.1016/j.cmpb.2017.06.015. Epub 2017 Jul 24.

BACKGROUND AND OBJECTIVES: Social Network Analysis is an attractive approach to model and analyze complex networks. In recent years, several bioinformatics related networks have been modeled and analyzed thoroughly using social network analysis. The objective of this study is...

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Üçer S, Koçak Y, Ozyer T, et al. Social network Analysis-based classifier (SNAc): A case study on time course gene expression data. Comput Methods Programs Biomed. 2017;150:73-84doi: 10.1016/j.cmpb.2017.06.015.
Üçer, S., Koçak, Y., Ozyer, T., & Alhajj, R. (2017). Social network Analysis-based classifier (SNAc): A case study on time course gene expression data. Computer methods and programs in biomedicine, 15073-84. https://doi.org/10.1016/j.cmpb.2017.06.015
Üçer, Serkan, et al. "Social network Analysis-based classifier (SNAc): A case study on time course gene expression data." Computer methods and programs in biomedicine vol. 150 (2017): 73-84. doi: https://doi.org/10.1016/j.cmpb.2017.06.015
Üçer S, Koçak Y, Ozyer T, Alhajj R. Social network Analysis-based classifier (SNAc): A case study on time course gene expression data. Comput Methods Programs Biomed. 2017 Oct;150:73-84. doi: 10.1016/j.cmpb.2017.06.015. Epub 2017 Jul 24. PMID: 28859830.
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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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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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FunRich: An open access standalone functional enrichment and interaction network analysis tool.

Proteomics

Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, Mouradov D, Sieber OM, Simpson RJ, Salim A, Bacic A, Hill AF, Stroud DA, Ryan MT, Agbinya JI, Mariadason JM, Burgess AW, Mathivanan S.
PMID: 25921073
Proteomics. 2015 Aug;15(15):2597-601. doi: 10.1002/pmic.201400515. Epub 2015 Jun 17.

As high-throughput techniques including proteomics become more accessible to individual laboratories, there is an urgent need for a user-friendly bioinformatics analysis system. Here, we describe FunRich, an open access, standalone functional enrichment and network analysis tool. FunRich is designed...

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Pathan M, Keerthikumar S, Ang CS, et al. FunRich: An open access standalone functional enrichment and interaction network analysis tool. Proteomics. 2015;15(15):2597-601doi: 10.1002/pmic.201400515.
Pathan, M., Keerthikumar, S., Ang, C. S., Gangoda, L., Quek, C. Y., Williamson, N. A., Mouradov, D., Sieber, O. M., Simpson, R. J., Salim, A., Bacic, A., Hill, A. F., Stroud, D. A., Ryan, M. T., Agbinya, J. I., Mariadason, J. M., Burgess, A. W., & Mathivanan, S. (2015). FunRich: An open access standalone functional enrichment and interaction network analysis tool. Proteomics, 15(15), 2597-601. https://doi.org/10.1002/pmic.201400515
Pathan, Mohashin, et al. "FunRich: An open access standalone functional enrichment and interaction network analysis tool." Proteomics vol. 15,15 (2015): 2597-601. doi: https://doi.org/10.1002/pmic.201400515
Pathan M, Keerthikumar S, Ang CS, Gangoda L, Quek CY, Williamson NA, Mouradov D, Sieber OM, Simpson RJ, Salim A, Bacic A, Hill AF, Stroud DA, Ryan MT, Agbinya JI, Mariadason JM, Burgess AW, Mathivanan S. FunRich: An open access standalone functional enrichment and interaction network analysis tool. Proteomics. 2015 Aug;15(15):2597-601. doi: 10.1002/pmic.201400515. Epub 2015 Jun 17. PMID: 25921073.
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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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Differentiating disease subtypes by using pathway patterns constructed from gene expressions and protein networks.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference

Hung FH, Chiu HW.
PMID: 26737786
Annu Int Conf IEEE Eng Med Biol Soc. 2015;2015:6519-22. doi: 10.1109/EMBC.2015.7319886.

Gene expression profiles differ in different diseases. Even if diseases are at the same stage, such diseases exhibit different gene expressions, not to mention the different subtypes at a single lesion site. Distinguishing different disease subtypes at a single...

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Hung FH, Chiu HW. Differentiating disease subtypes by using pathway patterns constructed from gene expressions and protein networks. Annu Int Conf IEEE Eng Med Biol Soc. 2015;2015:6519-22doi: 10.1109/EMBC.2015.7319886.
Hung, F. H., & Chiu, H. W. (2015). Differentiating disease subtypes by using pathway patterns constructed from gene expressions and protein networks. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference, 20156519-22. https://doi.org/10.1109/EMBC.2015.7319886
Hung, Fei-Hung, and Chiu, Hung-Wen. "Differentiating disease subtypes by using pathway patterns constructed from gene expressions and protein networks." Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference vol. 2015 (2015): 6519-22. doi: https://doi.org/10.1109/EMBC.2015.7319886
Hung FH, Chiu HW. Differentiating disease subtypes by using pathway patterns constructed from gene expressions and protein networks. Annu Int Conf IEEE Eng Med Biol Soc. 2015;2015:6519-22. doi: 10.1109/EMBC.2015.7319886. PMID: 26737786.
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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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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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Gene expression analysis on medium-density oligonucleotide arrays.

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

Sinibaldi R, O'Connell C, Seidel C, Rodriguez H.
PMID: 11357684
Methods Mol Biol. 2001;170:211-22. doi: 10.1385/1-59259-234-1:211.

No abstract available.

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Sinibaldi R, O'Connell C, Seidel C, et al. Gene expression analysis on medium-density oligonucleotide arrays. Methods Mol Biol. 2001;170:211-22doi: 10.1385/1-59259-234-1:211.
Sinibaldi, R., O'Connell, C., Seidel, C., & Rodriguez, H. (2001). Gene expression analysis on medium-density oligonucleotide arrays. Methods in molecular biology (Clifton, N.J.), 170211-22. https://doi.org/10.1385/1-59259-234-1:211
Sinibaldi, R, et al. "Gene expression analysis on medium-density oligonucleotide arrays." Methods in molecular biology (Clifton, N.J.) vol. 170 (2001): 211-22. doi: https://doi.org/10.1385/1-59259-234-1:211
Sinibaldi R, O'Connell C, Seidel C, Rodriguez H. Gene expression analysis on medium-density oligonucleotide arrays. Methods Mol Biol. 2001;170:211-22. doi: 10.1385/1-59259-234-1:211. PMID: 11357684.
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Use of bioinformatics in arrays.

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

Kalocsai P, Shams S.
PMID: 11357685
Methods Mol Biol. 2001;170:223-36. doi: 10.1385/1-59259-234-1:223.

No abstract available.

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Kalocsai P, Shams S. Use of bioinformatics in arrays. Methods Mol Biol. 2001;170:223-36doi: 10.1385/1-59259-234-1:223.
Kalocsai, P., & Shams, S. (2001). Use of bioinformatics in arrays. Methods in molecular biology (Clifton, N.J.), 170223-36. https://doi.org/10.1385/1-59259-234-1:223
Kalocsai, P, and Shams, S. "Use of bioinformatics in arrays." Methods in molecular biology (Clifton, N.J.) vol. 170 (2001): 223-36. doi: https://doi.org/10.1385/1-59259-234-1:223
Kalocsai P, Shams S. Use of bioinformatics in arrays. Methods Mol Biol. 2001;170:223-36. doi: 10.1385/1-59259-234-1:223. PMID: 11357685.
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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 148 entries