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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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Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science.

Briefings in functional genomics

Smith DR.
PMID: 27339634
Brief Funct Genomics. 2017 May 01;16(3):156-162. doi: 10.1093/bfgp/elw026.

Next-generation sequencing technologies have revolutionized genomics and altered the scientific publication landscape. Life-science journals abound with genome papers-peer-reviewed descriptions of newly sequenced chromosomes. Although they once filled the pages of Nature and Science, genome papers are now mostly relegated...

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Smith DR. Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science. Brief Funct Genomics. 2017;16(3):156-162doi: 10.1093/bfgp/elw026.
Smith, D. R. (2017). Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science. Briefings in functional genomics, 16(3), 156-162. https://doi.org/10.1093/bfgp/elw026
Smith, David Roy. "Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science." Briefings in functional genomics vol. 16,3 (2017): 156-162. doi: https://doi.org/10.1093/bfgp/elw026
Smith DR. Goodbye genome paper, hello genome report: the increasing popularity of 'genome announcements' and their impact on science. Brief Funct Genomics. 2017 May 01;16(3):156-162. doi: 10.1093/bfgp/elw026. PMID: 27339634; PMCID: PMC5439286.
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OMICS-based personalized oncology: if it is worth doing, it is worth doing well!.

BMC medicine

Hayes DF.
PMID: 24228698
BMC Med. 2013 Oct 17;11:221. doi: 10.1186/1741-7015-11-221.

The era of Personalized Medicine implies getting the right treatment to the right patient at the right schedule and dose at the right time. Tumor biomarker tests are keys to accomplishing this goal successfully. However, much of the translational...

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Hayes DF. OMICS-based personalized oncology: if it is worth doing, it is worth doing well!. BMC Med. 2013;11:221doi: 10.1186/1741-7015-11-221.
Hayes, D. F. (2013). OMICS-based personalized oncology: if it is worth doing, it is worth doing well!. BMC medicine, 11221. https://doi.org/10.1186/1741-7015-11-221
Hayes, Daniel F. "OMICS-based personalized oncology: if it is worth doing, it is worth doing well!." BMC medicine vol. 11 (2013): 221. doi: https://doi.org/10.1186/1741-7015-11-221
Hayes DF. OMICS-based personalized oncology: if it is worth doing, it is worth doing well!. BMC Med. 2013 Oct 17;11:221. doi: 10.1186/1741-7015-11-221. PMID: 24228698; PMCID: PMC3876724.
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The common ground of genomics and systems biology.

BMC systems biology

Conesa A, Mortazavi A.
PMID: 25033072
BMC Syst Biol. 2014;8:S1. doi: 10.1186/1752-0509-8-S2-S1. Epub 2014 Mar 13.

The rise of systems biology is intertwined with that of genomics, yet their primordial relationship to one another is ill-defined. We discuss how the growth of genomics provided a critical boost to the popularity of systems biology. We describe...

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Conesa A, Mortazavi A. The common ground of genomics and systems biology. BMC Syst Biol. 2014;8:S1doi: 10.1186/1752-0509-8-S2-S1.
Conesa, A., & Mortazavi, A. (2014). The common ground of genomics and systems biology. BMC systems biology, 8S1. https://doi.org/10.1186/1752-0509-8-S2-S1
Conesa, Ana, and Mortazavi, Ali. "The common ground of genomics and systems biology." BMC systems biology vol. 8 (2014): S1. doi: https://doi.org/10.1186/1752-0509-8-S2-S1
Conesa A, Mortazavi A. The common ground of genomics and systems biology. BMC Syst Biol. 2014;8:S1. doi: 10.1186/1752-0509-8-S2-S1. Epub 2014 Mar 13. PMID: 25033072; PMCID: PMC4101703.
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Gene-environment interactions--the BioBank UK study.

The pharmacogenomics journal

Wright AF, Carothers AD, Campbell H.
PMID: 12049178
Pharmacogenomics J. 2002;2(2):75-82. doi: 10.1038/sj.tpj.6500085.

No abstract available.

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Wright AF, Carothers AD, Campbell H. Gene-environment interactions--the BioBank UK study. Pharmacogenomics J. 2002;2(2):75-82doi: 10.1038/sj.tpj.6500085.
Wright, A. F., Carothers, A. D., & Campbell, H. (2002). Gene-environment interactions--the BioBank UK study. The pharmacogenomics journal, 2(2), 75-82. https://doi.org/10.1038/sj.tpj.6500085
Wright, A F, et al. "Gene-environment interactions--the BioBank UK study." The pharmacogenomics journal vol. 2,2 (2002): 75-82. doi: https://doi.org/10.1038/sj.tpj.6500085
Wright AF, Carothers AD, Campbell H. Gene-environment interactions--the BioBank UK study. Pharmacogenomics J. 2002;2(2):75-82. doi: 10.1038/sj.tpj.6500085. PMID: 12049178.
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Kudos, not cash, is the real X-factor.

Nature

Ledford H.
PMID: 17051173
Nature. 2006 Oct 19;443(7113):733. doi: 10.1038/443733a.

No abstract available.

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Ledford H. Kudos, not cash, is the real X-factor. Nature. 2006;443(7113):733doi: 10.1038/443733a.
Ledford, H. (2006). Kudos, not cash, is the real X-factor. Nature, 443(7113), 733. https://doi.org/10.1038/443733a
Ledford, Heidi. "Kudos, not cash, is the real X-factor." Nature vol. 443,7113 (2006): 733. doi: https://doi.org/10.1038/443733a
Ledford H. Kudos, not cash, is the real X-factor. Nature. 2006 Oct 19;443(7113):733. doi: 10.1038/443733a. PMID: 17051173.
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Metabolomics: The greatest omics of them all?.

Analytical chemistry

Ryan D, Robards K.
PMID: 17134127
Anal Chem. 2006 Dec 01;78(23):7954-8. doi: 10.1021/ac0614341.

No abstract available.

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Ryan D, Robards K. Metabolomics: The greatest omics of them all?. Anal Chem. 2006;78(23):7954-8doi: 10.1021/ac0614341.
Ryan, D., & Robards, K. (2006). Metabolomics: The greatest omics of them all?. Analytical chemistry, 78(23), 7954-8. https://doi.org/10.1021/ac0614341
Ryan, Danielle, and Robards, Kevin. "Metabolomics: The greatest omics of them all?." Analytical chemistry vol. 78,23 (2006): 7954-8. doi: https://doi.org/10.1021/ac0614341
Ryan D, Robards K. Metabolomics: The greatest omics of them all?. Anal Chem. 2006 Dec 01;78(23):7954-8. doi: 10.1021/ac0614341. PMID: 17134127.
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Designing physiogenomic studies.

Pharmacogenomics

Holford TR, Windemuth A, Ruaño G.
PMID: 16515394
Pharmacogenomics. 2006 Mar;7(2):157-8. doi: 10.2217/14622416.7.2.157.

No abstract available.

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Holford TR, Windemuth A, Ruaño G. Designing physiogenomic studies. Pharmacogenomics. 2006;7(2):157-8doi: 10.2217/14622416.7.2.157.
Holford, T. R., Windemuth, A., & Ruaño, G. (2006). Designing physiogenomic studies. Pharmacogenomics, 7(2), 157-8. https://doi.org/10.2217/14622416.7.2.157
Holford, Theodore R, et al. "Designing physiogenomic studies." Pharmacogenomics vol. 7,2 (2006): 157-8. doi: https://doi.org/10.2217/14622416.7.2.157
Holford TR, Windemuth A, Ruaño G. Designing physiogenomic studies. Pharmacogenomics. 2006 Mar;7(2):157-8. doi: 10.2217/14622416.7.2.157. PMID: 16515394.
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Bioinformatic methods for integrating whole-genome expression results into cellular networks.

Drug discovery today

Cavalieri D, De Filippo C.
PMID: 15896686
Drug Discov Today. 2005 May 15;10(10):727-34. doi: 10.1016/S1359-6446(05)03433-1.

Extracting a comprehensive overview from the huge amount of information arising from whole-genome analyses is a significant challenge. This review critically surveys the state of the art methods that are used to connect information from functional genomic studies to...

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Cavalieri D, De Filippo C. Bioinformatic methods for integrating whole-genome expression results into cellular networks. Drug Discov Today. 2005;10(10):727-34doi: 10.1016/S1359-6446(05)03433-1.
Cavalieri, D., & De Filippo, C. (2005). Bioinformatic methods for integrating whole-genome expression results into cellular networks. Drug discovery today, 10(10), 727-34. https://doi.org/10.1016/S1359-6446(05)03433-1
Cavalieri, Duccio, and De Filippo, Carlotta. "Bioinformatic methods for integrating whole-genome expression results into cellular networks." Drug discovery today vol. 10,10 (2005): 727-34. doi: https://doi.org/10.1016/S1359-6446(05)03433-1
Cavalieri D, De Filippo C. Bioinformatic methods for integrating whole-genome expression results into cellular networks. Drug Discov Today. 2005 May 15;10(10):727-34. doi: 10.1016/S1359-6446(05)03433-1. PMID: 15896686.
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An audience with Claire M. Fraser.

Nature reviews. Drug discovery

Fraser CM.
PMID: 15645604
Nat Rev Drug Discov. 2004 Dec;3(12):992. doi: 10.1038/nrd1598.

No abstract available.

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Fraser CM. An audience with Claire M. Fraser. Nat Rev Drug Discov. 2004;3(12):992doi: 10.1038/nrd1598.
Fraser, C. M. (2004). An audience with Claire M. Fraser. Nature reviews. Drug discovery, 3(12), 992. https://doi.org/10.1038/nrd1598
Fraser, Claire M. "An audience with Claire M. Fraser." Nature reviews. Drug discovery vol. 3,12 (2004): 992. doi: https://doi.org/10.1038/nrd1598
Fraser CM. An audience with Claire M. Fraser. Nat Rev Drug Discov. 2004 Dec;3(12):992. doi: 10.1038/nrd1598. PMID: 15645604.
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Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies.

Bioinformatics (Oxford, England)

Yang TP, Beazley C, Montgomery SB, Dimas AS, Gutierrez-Arcelus M, Stranger BE, Deloukas P, Dermitzakis ET.
PMID: 20702402
Bioinformatics. 2010 Oct 01;26(19):2474-6. doi: 10.1093/bioinformatics/btq452. Epub 2010 Aug 10.

UNLABELLED: Genevar (GENe Expression VARiation) is a database and Java tool designed to integrate multiple datasets, and provides analysis and visualization of associations between sequence variation and gene expression. Genevar allows researchers to investigate expression quantitative trait loci (eQTL)...

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Yang TP, Beazley C, Montgomery SB, et al. Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. Bioinformatics. 2010;26(19):2474-6doi: 10.1093/bioinformatics/btq452.
Yang, T. P., Beazley, C., Montgomery, S. B., Dimas, A. S., Gutierrez-Arcelus, M., Stranger, B. E., Deloukas, P., & Dermitzakis, E. T. (2010). Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. Bioinformatics (Oxford, England), 26(19), 2474-6. https://doi.org/10.1093/bioinformatics/btq452
Yang, Tsun-Po, et al. "Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies." Bioinformatics (Oxford, England) vol. 26,19 (2010): 2474-6. doi: https://doi.org/10.1093/bioinformatics/btq452
Yang TP, Beazley C, Montgomery SB, Dimas AS, Gutierrez-Arcelus M, Stranger BE, Deloukas P, Dermitzakis ET. Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. Bioinformatics. 2010 Oct 01;26(19):2474-6. doi: 10.1093/bioinformatics/btq452. Epub 2010 Aug 10. PMID: 20702402; PMCID: PMC2944204.
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BioNet: an R-Package for the functional analysis of biological networks.

Bioinformatics (Oxford, England)

Beisser D, Klau GW, Dandekar T, Müller T, Dittrich MT.
PMID: 20189939
Bioinformatics. 2010 Apr 15;26(8):1129-30. doi: 10.1093/bioinformatics/btq089. Epub 2010 Feb 25.

MOTIVATION: Increasing quantity and quality of data in transcriptomics and interactomics create the need for integrative approaches to network analysis. Here, we present a comprehensive R-package for the analysis of biological networks including an exact and a heuristic approach...

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Beisser D, Klau GW, Dandekar T, et al. BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics. 2010;26(8):1129-30doi: 10.1093/bioinformatics/btq089.
Beisser, D., Klau, G. W., Dandekar, T., Müller, T., & Dittrich, M. T. (2010). BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics (Oxford, England), 26(8), 1129-30. https://doi.org/10.1093/bioinformatics/btq089
Beisser, Daniela, et al. "BioNet: an R-Package for the functional analysis of biological networks." Bioinformatics (Oxford, England) vol. 26,8 (2010): 1129-30. doi: https://doi.org/10.1093/bioinformatics/btq089
Beisser D, Klau GW, Dandekar T, Müller T, Dittrich MT. BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics. 2010 Apr 15;26(8):1129-30. doi: 10.1093/bioinformatics/btq089. Epub 2010 Feb 25. PMID: 20189939.
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Showing 13 to 24 of 382 entries