GeneMerge Usage Information

One indication of a software's usefulness is the extent to which it is used by the scientific community and how often such use leads to publishable results. Below is information on this topic concerning GeneMerge.

Usage and Downloads

As of April 7, 2007:
  • Over 22,000 GeneMerge analyses have been carried out over the web server.

  • Over 2,060 copies of GeneMerge have been downloaded.

Publications

The following publications used GeneMerge in their analyses.

  • Polo, J. M., P. Juszczynski, S. Monti, et al. 2007. Transcriptional signature with differential expression of BCL6 target genes accurately identifies BCL6-dependent diffuse large B cell lymphomas. Proceedings of the National Academy of Sciences, USA. 104(9): 3207-3212.

  • Reuveni, E., V. E. Ramensky, C. Gross. 2007. Mouse SNP miner: An annotated database of mouse functional single nucleotide polymorphisms BMC Genomics. 8: Art. No. 24.

  • Kobayashi S.,T. Shimamura, S. Monti, et al. 2006. Transcriptional profiling identifies cyclin D1 as a critical downstream effector of mutant epidermal growth factor receptor signaling. Cancer Research. 66(23):11389-11398.

  • Sironi M., G. Menozzi, G. P. Comi, et al. 2006. Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns. Genome Biology. 7(12): Art. No. R120

  • Sinha S., X. Ling, C. W. Whitfield, et al. 2006. Genome scan for cis-regulatory DNA motifs associated with social behavior in honey bees. Proceedings of the National Academy of Sciences, USA. 103(44):16352-16357.

  • Gustafson A. M., E. S. Snitkin, S. C. J. Parker, et al. 2006. Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics. No. 265.

  • Metta, M., R. Gudavalli, J. M. Gibert, et al. 2006. No accelerated rate of protein evolution in male-biased Drosophila pseudoobscura genes. Genetics. 174(1):411-420.

  • Wang, J. W., S. L. Zhang, R. M. Schultz, et al. 2006. Search for basonuclin target genes. Biochemical and Biophysical Research Communications. 348(4): 1261-1271.

  • Chain, F. J. J., B. J. Evans. 2006. Multiple mechanisms promote the retained expression of gene duplicates in the tetraploid frog Xenopus laevis. PLoS Genetics. 2(4):478-490.

  • Balasubramanian, S., S. Sureshkumar, J. Lempe, et al. 2006. Potent induction of Arabidopsis thaliana flowering by elevated growth temperature. PLoS Genetics. 2(7):980-989.

  • Li, S. J., D. W. Ehrhardt, S. Y. Rhee. 2006. Systematic analysis of Arabidopsis organelles and a protein localization database for facilitating fluorescent tagging of full-length Arabidopsis proteins. Plant Physiology. 141(2): 527-539.

  • Landry, C. R., J. P. Townsend, D. L. Hartl, D. Cavalieri. 2006. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular Ecology. 15(3): 575-591.

  • Landry, C. R., J. Oh, D. L. Hartl, et al. 2006. Genome-wide scan reveals that genetic variation for transcriptional plasticity in yeast is biased towards multi-copy and dispensable genes. Gene. 366(2):343-351.

  • Lall, S., D. Grun, A. Krek, et al. 2006. A genome-wide map of conserved microRNA targets in C. elegans. Current Biology. 16(5):460-471.

  • Booms P., A. Ney, F. Barthel, et al. 2006. A fibrillin-1-fragment containing the elastin-binding-protein GxxPG consensus sequence upregulates matrix metalloproteinase-1: biochemical and computational analysis. Journal of Molecular and Cellular Cardiology. 40(2):234-246.

  • Ma, P., C. I. Castillo-Davis, W. Zhong, J. S. Liu. 2006. A data-driven clustering method for time course gene expression data. Nucleic Acids Research. 34(4):1261-1269.

  • Sironi, M., G. Menozzi, G. P. Comi, R. Cagliani, N. Bresolin,U. Pozzoli. 2005. Analysis of intronic conserved elements indicates that functional complexity might represent a major source of negative selection on non-coding sequences. Human Molecular Genetics. 14(17):2533-46.

  • Jensen, S. T., L. Shen, J. S. Liu. 2005. Combining phylogenetic motif discovery and motif clustering to predict co-regulated genes. Bioinformatics 21(20):3832-3839.

  • Zhong W., P. Zeng, P. Ma, J. S. Liu, Y. Zhu. 2005. RSIR: regularized sliced inverse regression for motif discovery. Bioinformatics 21(22):4169-4175.

  • Grun, D., Y. Wang, D. Langenberger, K. C. Gunsalus, N. Rajewsky, et al. 2005. microRNA Target Predictions across Seven Drosophila Species and Comparison to Mammalian Targets. PLoS Computational Biology. 1(1): e13.

  • Birch-Machin, I. S. Gao, D. Huen, R. McGirr1, R. A. H. White, S. Russell. 2005. Genomic analysis of heat-shock factor targets in Drosophila. Genome Biology. 6:R63.

  • Conlon, E. M., P. Eichenberger, J. S. Liu. 2004. Determining and analyzing differentially expressed genes from cDNA microarray experiments with complementary designs. Journal of Multivariate Analysis. 90(1):1-18.

  • Castillo-Davis, C. I., R. J. Kulathinal, F. A. Kondrashov, D. L. Hartl. 2004. The functional genomic distribution of protein divergence in two animal phyla: co-evolution, genomic conflict, and constraint. Genome Research. 14(5):802-11

  • Ranz J. M., K. Namgyal, G. Gibson, D. L. Hartl. 2004. Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans. Genome Research. 14:373-379.

  • Ranz, J. M., C. I. Castillo-Davis, C. D. Meiklejohn, D. L. Hartl. 2003. Sex-dependent gene expression and the evolution of the Drosophila transcriptome. Science. 300(5626): 1742-1745.

  • Castillo-Davis, C. I., S. L. Mekhedov, D. L. Hartl, E. V. Koonin and F. A. Kondrashov. 2002. Selection for short introns in highly expressed genes. Nature Genetics. 31: 415-418.


Public Software

GeneMerge is being used by the Non-Profit Sugarcane Technological Center of Brazil (Centro de Tecnologia Cavieira) to help develop new technologies related to sugarcane crops.

GeneMerge has been incorporated into Bioconductor as part of the microarray analysis package genArise.

GeneMerge has been incorporated into the Gene Expression Data Analysis Tool at the University of Pittsburgh Cancer Institute Center for Oncology Informatics to add to post-genomic functionality to this web-based microarray tool.

GeneMerge has been incorporated into the genomics and proteomics tool FACT.


Other publications that cite GeneMerge

  • Prufer K, Muetzel B, Do HH, et al. 2007. FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics 8: Art. No. 41.

  • Rivals I, Personnaz L, Taing L, et al. 2007. Enrichment or depletion of a GO category within a class of genes: which test? Bioinformatics 23(4): 401-407.

  • Alibes A, Yankilevich P, Canada A, et al. 2007. IDconverter and IDClight: Conversion and annotation of gene and protein IDs. BMC Bioinformatics 8: Art. No. 9

  • Dopazo, J. Functional interpretation of microarray experiments. 2006. Omics10(3):398-410.

  • Schmidt, T., D. Frishman. 2006. PROMPT: a protein mapping and comparison tool. BMC Bioinformatics 7: No. 331.

  • Data Analysis and Visualization in Genomics and Proteomics. 2005. Editors: Francisco Azuaje, Joaquin Dopazo. John Wiley & Sons, Ltd.

  • Khatri, P., S. Draghici. 2005. Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics. 21(18): 3587-3595. GeneMerge recognized as one of the "top three tools" and rated second fastest of 14 different applications.

  • Kokocinski F., N. Delhomme, G. Wrobel, L. Hummerich, G. Toedt, P. Lichter. 2005. FACT--a framework for the functional interpretation of high-throughput experiments. BMC Bioinformatics. 6: 161.

  • Barriot, R., J. Poix, A. Groppi, A. Barr, N. Goffard, D. Sherman, I. Dutour, A. de Daruvar. 2004. New strategy for the representation and the integration of biomolecular knowledge at a cellular scale. Nucleic Acids Research. 32: 12.

  • Cavalieri D. and C. De Filippo. 2005. Bioinformatic methods for integrating whole-genome expression results into cellular networks. Drug Discovery Today. 10: 727-734.

  • Marchevsky, A.M. and M.R. Wick. 2004. Evidence-based medicine, medical decision analysis, and pathology. Human Pathology. 35: 1179-1188.

  • Barriot R, J. Poix, A. Groppi, et al. 2004. New strategy for the representation and the integration of biomolecular knowledge at a cellular scale. Nucleic Acids Research. 32: 3581-3589.

  • Comparative and Functional Genomics. 2003. Volume 4, Issue 6, pp. 681-688. John Wiley & Sons, Ltd.

  • Greener, M. Exploring Data Mines Without Cave-Ins. 2003. Genomics & Proteomics Magazine. November/December Issue.


Visits to GeneMerge Server Each Month Since Publication

No. of visits per month since publication

GeneMerge - Post-genomic analysis, data mining, and hypothesis testing

Cristian I. Castillo-Davis
Department of Biology
University of Maryland
castill0@umd.edu