RAD (RNA Abundance Database)

A curated resource for gene expression studies

Last Modified: 2006/2/11
 
 2004
Marciano P.G., Brettschneider J., Manduchi E., Davies J.E., Eastman S., Raghupathi R., Saatman K.E., Speed T.P., Stoeckert C.J. Jr., Eberwine J.H., McIntosh T.K. (2004) Neuron-specific mRNA complexity responses during hippocampal apoptosis following traumatic brain injury, The Journal of Neuroscience, 24(12): 2866-2876.

Manduchi E., Grant G.R., He H., Liu J., Mailman M.D., Pizarro A.D., Whetzel P.L., Stoeckert C.J. Jr. (2004) RAD and the RAD Study-Annotator: an approach to collection, organization and exchange of all relevant information for high-throughput gene expression studies, Bioinformatics, 20(4): 452-459.

Passerini A.G., Polacek D.C., Shi C., Francesco N.M., Manduchi E., Grant G.R., Pritchard W.F., Powell S., Chang G.Y., Stoeckert C.J. Jr., Davies P. (2004) Coexisting pro-inflammatory and anti-oxidative endothelial transcription profiles in a disturbed flow region of the adult porcine aorta, PNAS, 101(8): 2482-2487.
 2003
Grant G.R., Manduchi E., Pizarro A., Stoeckert C.J. Jr. (2003) Maintaining data integrity in microarray data management, Biotechnology and Bioengineering, 84(7): 795-800.

Polacek, D.C., Passerini, A.G., Shi, C., Francesco, N.M., Manduchi, E., Grant, G.R., Powell, S., Bischof, H., Winkler, H., Stoeckert, C.J. Jr., Davies, P.F. (2003) Fidelity and enhanced sensitivity of differential transcription profiles following linear amplification of nanogram amounts of endothelial mRNA Physiological Genomics, 13: 147-156

Christian J. Stoeckert Jr, Helen Parkinson (2003) The MGED ontology: A Framework for Describing Functional Genomics Experiments Comparative and Functional Genomics Volume 4, Issue 1, 2003. Pages: 127-132
 2002

Manduchi, E., Scearce, L.M., Brestelli, J.E., Grant, G.R., Kaestner, K.H., Stoeckert, C.J. Jr. (2002) Comparison of different labeling methods for two-channel high-density microarray experiments. Physiol Genomics. 2002 Sep 3;10(3):169-179.

Spellman, Paul T., Miller, Michael, Stewart, Jason, Troup, Charles, Sarkans, Ugis, Chervitz, Steve, Bernhart, Derek, Sherlock, Gavin, Ball, Catherine, Lepage, Marc, Swiatek, Marcin, Marks, WL, Goncalves, Jason, Markel, Scott, Iordan, Daniel, Shojatalab, Mohammadreza, Pizarro, Angel, White, Joe, Hubley, Robert, Deutsch, Eric, Senger, Martin, Aronow, Bruce J., Robinson, Alan, Bassett, Doug, Stoeckert, Christian J., Brazma, Alvis (2002) Design and implementation of microarray gene expression markup language (MAGE-ML) Genome Biology 3: 9, 2002.

Scearce, L. Marie, Brestelli, John E., McWeeney, Shannon K., Lee, Catherine S., Mazzarelli, Joan, Pinney, Deborah F., Pizarro, Angel, Stoeckert, C. J. Jr., Clifton, Sandra, Permutt, M. Alan, Brown, Juliana, Melton, Douglas A., Kaestner, Klaus H. (2002) Functional Genomics of the Endocrine Pancreas: The Pancreas Clone Set and PancChip, New Resources for Diabetes Research Diabetes 51: 1997-2004, 2002.

Bahl, A., Brunk, B., Coppel, R.L., Crabtree, J., Diskin, S.J., Fraunholz, M.J., Grant, G.R., Gupta, D., Huestis, R.L., Kissinger, J.C., Labo, P., Li, L., McWeeney, S.K., Milgram, A.J., Roos, D.S., Schug, J., Stoeckert, C.J. (2002) PlasmoDB: The Plasmodium Genome Resource. An integrated database providing tools for accessing and analyzing mapping, expression and sequence data (both finished and unfinished). Nucleic Acids Res. 2002 30: 87-90

Grant, G., Manduchi, E., Stoeckert, C. (2002) Using Non-Parametric Methods in the Context of Multiple Testing to Identify Differentially Expressed Genes. Methods of microarray data analysis, editors S.M. Lin and K.F. Johnson, Kluwer Academic Publishers (Boston, 2002): 37-55. (Winner of the best presentation award CAMDA'00)
 
 2001

Brazma, A., Hingamp, P., Quackenbush, J., Sherlock, G., Spellman, P., Stoeckert, C., Aach, J., Ansorge, W., Ball, C.A., Causton, H.C., Gaasterland, T., Glenisson, P., Holstege, F.C.P., Kim, I.F., Markowitz, V., Matese, J.C., Parkinson, H., Robinson, A., Sarkans, U., Schulze-Kremer, S., Stewart, J., Taylor, R., Vilo, J., Vingron, M. (2001) Minimum Information About a Microarray Experiment (MIAME): Toward Standards for Microarray Data. Nature Genetics 29:365-371, 2001.

Manduchi, E., Pizarro, A., Stoeckert, C. (2001) RAD (RNA Abundance Database): an infrastructure for array data analysis. Proc. SPIE, vol 4266, pp. 68-78.

Stoeckert, C., Pizarro, A., Manduchi, E., Gibson, M., Brunk, B., Crabtree, J., Schug, S., Shen-Orr, S., Overton, G.C. (2001) A relational schema for both array-based and SAGE gene expression experiments. Bioinformatics 17(4), 300-308 (2001).

 
 2000
Manduchi, E., Grant, G.R., McKenzie, S.E., Overton, G.C., Surrey, S., Stoeckert, C.J. Jr. (2000) Generation of patterns from gene expression data by assigning confidence to differentially expressed genes. Bioinformatics 16(8), 685-698 (2000).
 
To contact:  RAD @ pcbi.upenn.edu