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ONCOMINE: a cancer microarray database and integrated data-mining platform.

Neoplasia (New York, N.Y.)

Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM.
PMID: 15068665
Neoplasia. 2004 Jan-Feb;6(1):1-6. doi: 10.1016/s1476-5586(04)80047-2.

DNA microarray technology has led to an explosion of oncogenomic analyses, generating a wealth of data and uncovering the complex gene expression patterns of cancer. Unfortunately, due to the lack of a unifying bioinformatic resource, the majority of these...

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Rhodes DR, Yu J, Shanker K, et al. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia. 2004;6(1):1-6doi: 10.1016/s1476-5586(04)80047-2.
Rhodes, D. R., Yu, J., Shanker, K., Deshpande, N., Varambally, R., Ghosh, D., Barrette, T., Pandey, A., & Chinnaiyan, A. M. (2004). ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia (New York, N.Y.), 6(1), 1-6. https://doi.org/10.1016/s1476-5586(04)80047-2
Rhodes, Daniel R, et al. "ONCOMINE: a cancer microarray database and integrated data-mining platform." Neoplasia (New York, N.Y.) vol. 6,1 (2004): 1-6. doi: https://doi.org/10.1016/s1476-5586(04)80047-2
Rhodes DR, Yu J, Shanker K, Deshpande N, Varambally R, Ghosh D, Barrette T, Pandey A, Chinnaiyan AM. ONCOMINE: a cancer microarray database and integrated data-mining platform. Neoplasia. 2004 Jan-Feb;6(1):1-6. doi: 10.1016/s1476-5586(04)80047-2. PMID: 15068665; PMCID: PMC1635162.
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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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Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers.

Omics : a journal of integrative biology

Van Brabant B, Gray T, Verslyppe B, Kyrpides N, Dietrich K, Glöckner FO, Cole J, Farris R, Schriml LM, De Vos P, De Baets B, Field D, Dawyndt P.
PMID: 18479205
OMICS. 2008 Jun;12(2):123-7. doi: 10.1089/omi.2008.0020.

Given the growing wealth of downstream information, the integration of molecular and non-molecular data on a given organism has become a major challenge. For micro-organisms, this information now includes a growing collection of sequenced genes and complete genomes, and...

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Van Brabant B, Gray T, Verslyppe B, et al. Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers. OMICS. 2008;12(2):123-7doi: 10.1089/omi.2008.0020.
Van Brabant, B., Gray, T., Verslyppe, B., Kyrpides, N., Dietrich, K., Glöckner, F. O., Cole, J., Farris, R., Schriml, L. M., De Vos, P., De Baets, B., Field, D., Dawyndt, P. (2008). Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers. Omics : a journal of integrative biology, 12(2), 123-7. https://doi.org/10.1089/omi.2008.0020
Van Brabant, Bart, et al. "Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers." Omics : a journal of integrative biology vol. 12,2 (2008): 123-7. doi: https://doi.org/10.1089/omi.2008.0020
Van Brabant B, Gray T, Verslyppe B, Kyrpides N, Dietrich K, Glöckner FO, Cole J, Farris R, Schriml LM, De Vos P, De Baets B, Field D, Dawyndt P. Laying the foundation for a Genomic Rosetta Stone: creating information hubs through the use of consensus identifiers. OMICS. 2008 Jun;12(2):123-7. doi: 10.1089/omi.2008.0020. PMID: 18479205.
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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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The emperor's new clothes revisited.

Trends in genetics : TIG

Shields R.
PMID: 16859804
Trends Genet. 2006 Sep;22(9):463. doi: 10.1016/j.tig.2006.07.004. Epub 2006 Jul 21.

No abstract available.

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Shields R. The emperor's new clothes revisited. Trends Genet. 2006;22(9):463doi: 10.1016/j.tig.2006.07.004.
Shields, R. (2006). The emperor's new clothes revisited. Trends in genetics : TIG, 22(9), 463. https://doi.org/10.1016/j.tig.2006.07.004
Shields, Robert. "The emperor's new clothes revisited." Trends in genetics : TIG vol. 22,9 (2006): 463. doi: https://doi.org/10.1016/j.tig.2006.07.004
Shields R. The emperor's new clothes revisited. Trends Genet. 2006 Sep;22(9):463. doi: 10.1016/j.tig.2006.07.004. Epub 2006 Jul 21. PMID: 16859804.
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Self-incompatibility studies in guayule; inheritance.

Genetics

GERSTEL DU.
PMID: 15427838
Genetics. 1950 Jul;35(4):482-506. doi: 10.1093/genetics/35.4.482.

No abstract available.

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GERSTEL DU. Self-incompatibility studies in guayule; inheritance. Genetics. 1950;35(4):482-506doi: 10.1093/genetics/35.4.482.
GERSTEL, D. U. (1950). Self-incompatibility studies in guayule; inheritance. Genetics, 35(4), 482-506. https://doi.org/10.1093/genetics/35.4.482
GERSTEL, D U. "Self-incompatibility studies in guayule; inheritance." Genetics vol. 35,4 (1950): 482-506. doi: https://doi.org/10.1093/genetics/35.4.482
GERSTEL DU. Self-incompatibility studies in guayule; inheritance. Genetics. 1950 Jul;35(4):482-506. doi: 10.1093/genetics/35.4.482. PMID: 15427838; PMCID: PMC1209496.
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[General review of inheritance in ophthalmology].

Archivos de la Sociedad Oftalmologica Hispano-Americana

DEL RIO CABANAS JL.
PMID: 14811784
Archivos Soc Oftalmol Hisp Am. 1950 Nov;10(11):1176-1218.

No abstract available.

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DEL RIO CABANAS JL. Revisión de conjunto sobre herencia en oftalmologäa. [General review of inheritance in ophthalmology]. Archivos Soc Oftalmol Hisp Am. 1950;10(11):1176-1218
DEL RIO CABANAS, J. L. (1950). Revisión de conjunto sobre herencia en oftalmologäa. [General review of inheritance in ophthalmology]. Archivos de la Sociedad Oftalmologica Hispano-Americana, 10(11), 1176-1218.
DEL RIO CABANAS, J L. "Revisión de conjunto sobre herencia en oftalmologäa." [General review of inheritance in ophthalmology]. Archivos de la Sociedad Oftalmologica Hispano-Americana vol. 10,11 (1950): 1176-1218.
DEL RIO CABANAS JL. Revisión de conjunto sobre herencia en oftalmologäa. [General review of inheritance in ophthalmology]. Archivos Soc Oftalmol Hisp Am. 1950 Nov;10(11):1176-1218. Undetermined. PMID: 14811784.
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Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. Introduction.

BMC bioinformatics

Wren JD, Gusev Y, Ptitsyn A, Winters-Hilt S.
PMID: 17118130
BMC Bioinformatics. 2006 Sep 06;7:S1. doi: 10.1186/1471-2105-7-S2-S1.

No abstract available.

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Wren JD, Gusev Y, Ptitsyn A, et al. Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. Introduction. BMC Bioinformatics. 2006;7:S1doi: 10.1186/1471-2105-7-S2-S1.
Wren, J. D., Gusev, Y., Ptitsyn, A., & Winters-Hilt, S. (2006). Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. Introduction. BMC bioinformatics, 7S1. https://doi.org/10.1186/1471-2105-7-S2-S1
Wren, Jonathan D, et al. "Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. Introduction." BMC bioinformatics vol. 7 (2006): S1. doi: https://doi.org/10.1186/1471-2105-7-S2-S1
Wren JD, Gusev Y, Ptitsyn A, Winters-Hilt S. Proceedings of the Third Annual Conference of the MidSouth Computational Biology and Bioinformatics Society. Introduction. BMC Bioinformatics. 2006 Sep 06;7:S1. doi: 10.1186/1471-2105-7-S2-S1. PMID: 17118130; PMCID: PMC1683579.
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Network medicine: a network-based approach to human disease.

Nature reviews. Genetics

Barabási AL, Gulbahce N, Loscalzo J.
PMID: 21164525
Nat Rev Genet. 2011 Jan;12(1):56-68. doi: 10.1038/nrg2918.

Given the functional interdependencies between the molecular components in a human cell, a disease is rarely a consequence of an abnormality in a single gene, but reflects the perturbations of the complex intracellular and intercellular network that links tissue...

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Barabási AL, Gulbahce N, Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet. 2011;12(1):56-68doi: 10.1038/nrg2918.
Barabási, A. L., Gulbahce, N., & Loscalzo, J. (2011). Network medicine: a network-based approach to human disease. Nature reviews. Genetics, 12(1), 56-68. https://doi.org/10.1038/nrg2918
Barabási, Albert-László, et al. "Network medicine: a network-based approach to human disease." Nature reviews. Genetics vol. 12,1 (2011): 56-68. doi: https://doi.org/10.1038/nrg2918
Barabási AL, Gulbahce N, Loscalzo J. Network medicine: a network-based approach to human disease. Nat Rev Genet. 2011 Jan;12(1):56-68. doi: 10.1038/nrg2918. PMID: 21164525; PMCID: PMC3140052.
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Integration of diverse microarray data types.

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

Salari K, Pollack JR.
PMID: 19488881
Methods Mol Biol. 2009;556:205-16. doi: 10.1007/978-1-60327-192-9_15.

Over the past decade, DNA microarrays have proven to be a powerful tool in biological research for the molecular surveillance of cells and tissues. The expansive utility of DNA microarrays owes its nascence to the development of a multitude...

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Salari K, Pollack JR. Integration of diverse microarray data types. Methods Mol Biol. 2009;556:205-16doi: 10.1007/978-1-60327-192-9_15.
Salari, K., & Pollack, J. R. (2009). Integration of diverse microarray data types. Methods in molecular biology (Clifton, N.J.), 556205-16. https://doi.org/10.1007/978-1-60327-192-9_15
Salari, Keyan, and Pollack, Jonathan R. "Integration of diverse microarray data types." Methods in molecular biology (Clifton, N.J.) vol. 556 (2009): 205-16. doi: https://doi.org/10.1007/978-1-60327-192-9_15
Salari K, Pollack JR. Integration of diverse microarray data types. Methods Mol Biol. 2009;556:205-16. doi: 10.1007/978-1-60327-192-9_15. PMID: 19488881.
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Graph kernels for disease outcome prediction from protein-protein interaction networks.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing

Borgwardt KM, Kriegel HP, Vishwanathan SV, Schraudolph NN.
PMID: 17992741
Pac Symp Biocomput. 2007;4-15.

It is widely believed that comparing discrepancies in the protein-protein interaction (PPI) networks of individuals will become an important tool in understanding and preventing diseases. Currently PPI networks for individuals are not available, but gene expression data is becoming...

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Borgwardt KM, Kriegel HP, Vishwanathan SV, et al. Graph kernels for disease outcome prediction from protein-protein interaction networks. Pac Symp Biocomput. 2007;4-15
Borgwardt, K. M., Kriegel, H. P., Vishwanathan, S. V., & Schraudolph, N. N. (2007). Graph kernels for disease outcome prediction from protein-protein interaction networks. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 4-15.
Borgwardt, Karsten M, et al. "Graph kernels for disease outcome prediction from protein-protein interaction networks." Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing vol. (2007): 4-15.
Borgwardt KM, Kriegel HP, Vishwanathan SV, Schraudolph NN. Graph kernels for disease outcome prediction from protein-protein interaction networks. Pac Symp Biocomput. 2007;4-15. PMID: 17992741.
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Developing an ontology.

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

Harris MA.
PMID: 18563371
Methods Mol Biol. 2008;452:111-24. doi: 10.1007/978-1-60327-159-2_5.

In recent years, biological ontologies have emerged as a means of representing and organizing biological concepts, enabling biologists, bioinformaticians, and others to derive meaning from large datasets.This chapter provides an overview of formal principles and practical considerations of ontology...

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Harris MA. Developing an ontology. Methods Mol Biol. 2008;452:111-24doi: 10.1007/978-1-60327-159-2_5.
Harris, M. A. (2008). Developing an ontology. Methods in molecular biology (Clifton, N.J.), 452111-24. https://doi.org/10.1007/978-1-60327-159-2_5
Harris, Midori A. "Developing an ontology." Methods in molecular biology (Clifton, N.J.) vol. 452 (2008): 111-24. doi: https://doi.org/10.1007/978-1-60327-159-2_5
Harris MA. Developing an ontology. Methods Mol Biol. 2008;452:111-24. doi: 10.1007/978-1-60327-159-2_5. PMID: 18563371.
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