Publications

in PDF format
Programs in Genomic Applications,
National Heart, Lung, Blood Institute

Bioinformatics Papers

TM4: A Free, Open Source System for Microarray Data Management and Analysis
Saeed et al. BioTechniques February 2003.

John Quackenbush talks about the clinical promise of genetic microarrays.
Interviewed by Brian Vastag. JAMA. 2003 Jan 8;289(2):159-60, 163.

Microarray data normalization and transformation.
John Quackenbush Nat Genet. 2002 Dec;32 Suppl:496-501. Review.

Genesis: cluster analysis of microarray data.
Sturn A, Quackenbush J, Trajanoski Z. Bioinformatics. 2002, 18(1): 207-208.

Editorial: An Open Letter to the Scientific Journals.
Ball CA, Sherlock G, Parkinson H, Rocca-Sera P, Brooksbank C, Causton HC, Cavalieri D, Gaasterland T, Hingamp P, Holstege F, Ringwald M, Spellman P, Stoeckert CJ Jr, Stewart JE, Taylor R, Brazma A, Quackenbush J. Bioinformatics. 2002 Nov;18(11):1409.

Standards for Microarray Data.
Catherine A. Ball, Gavin Sherlock, Helen Parkinson, Philippe Rocca-Sera, Catherine Brooksbank, Helen C. Causton, Duccio Cavalieri, Terry Gaasterland, Pascal Hingamp, Frank Holstege, Martin Ringwald, Paul Spellman, Christian J. Stoeckert, Jr., Jason E. Stewart, Ronald Taylor, Alvis Brazma, and John Quackenbush. Science 2002 October 18; 298: 539 (in Letters).

Minimum information about a microarray experiment (MIAME) - toward standards for microarray data
Brazma et al. Nature Genetics vol 29 December 2001.

Computational Analysis of Microarray Data
Quackenbush Nature Reviews vol 2 June 2001.

RESOURCERER: a database for annotating and linking microarray resources within and across species
Tsai et al. Genome Biology vol 2 no 11 October 2001.

Human Papers

A robust method for the amplification of RNA in the sense orientation.
Marko NF, Frank B, Quackenbush J, Lee NH. BMC Genomics. 2005 Mar 1;6(1):27.

Within the fold: assessing differential expression measures and reproducibility in microarray assays.
Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed AI, White J, Li J, Lee NH, Yeatman TJ, Quackenbush J. Genome Biol. 2002 Oct 24;3(11):research0062.

Identification of Tumor Markers in Models of Human Colorectal Cancer Using a 19,200-Element Complementary DNA Microarray
Hegde et al. Cancer Research vol 61 November 2001.

Rat Microarray Publications

Iterative microarray and RNA interference-based interrogation of the SRC-induced invasive phenotype.
Irby, R., Malek, R.L., Letwin, N., Bloom, G.C., Yeatman, T.,Lee, N.H. (2005) Can Res 65:1814-21.

A robust method for the amplification of RNA in the sense orientation.
Marko NF, Frank B, Quackenbush J, Lee NH. BMC Genomics. 2005 Mar 1;6(1):27.

Standardizing global gene expression analysis between laboratories and across platforms.
Bammler, T. and Members of the Toxicogenomic Research Consortium. (2005) Nat Meth 2:351-356.

Autocrine activation of osteoponting-CD44-Ras/Rac pathway enhances invasion and transformation of H-RasV12.
Teramoto, H., Castellone, M.D., Malek, R.L., Letwin, N., Gutkind, J.S., and Lee, N.H. (2005) Oncogene 24: 489-501.

Growth hormone-mediated alteration of fuel metabolism in the aged rat as determined from transcript profiles.
Tollet-Egnell P, Parini P, Stahlberg N, Lonnstedt I, Lee NH, Rudling M, Flores-Morales A, Norstedt G. (2004) Physiol Genomics.15:261-7.

Identification of H-Ras, RhoA, Rac1 and Cdc42 responsive genes.
Teramoto H., Malek R.L., Behbahani B., Domenica Castellone M., Lee N.H., and Gutkind J.S. (2003) Oncogene 22:2689-97.

Assessing unmodified 70-mer oligonucleotide probe performance on glass slide microarrays.
Wang, H.Y., Malek, R.L., Kwitek, A.E., Green, A.S., Luu, T.V., Behbahani, B., Frank, B., Quackenbush, J. and Lee, N.H. (2003) Genome Biol. 4:R5 Epub.

Identification of a Src Transformation Fingerprint in Human Colon Cancer.
Malek, R.L., Irby, R.B., Guo, Q.M., Lee, K., Wong, S., Ruffy, M., Tsai, J., Liu, E.T., Quackenbush, J., Jove, R., Yeatman, T. and Lee, N.H. (2002) Oncogene 21:7256-7265.

Supplemental Material

Silencing of Wnt signaling and activation of multiple metabolic pathways in response to thyroid hormone-stimulated cell proliferation.
Miller, L.D., Park, K.S., Guo, Q.M., Alkharoufy, N.W., Malek, R.L., Lee, N.H., Liu, E.T., Cheng, S.-Y. (2001) Molec. Cell. Biol. 21:6626-39.

Microarray analysis of the in vivo effects of hypophysectomy and growth hormone treatment on gene expression in the rat.
Flores-Morales, A., Ståhlberg,, N., Tollet-Egnell, P., Lundeberg, P., Malek, R.L., Quackenbush, J., Lee, N.H. and Norstedt, G. (2001) Endocrinol. 142:3163-76.

Gene expression profile of the aging process in rat liver: normalizing effects of growth hormone replacement.
Tollet-Egnell, P., Flores-Morales, A., Ståhlberg, N., Malek, R.L., Lee, N.H. and Norstedt, G. (2001) Mol. Endocrinol. 15:308-318.

Identification of c-Myc responsive genes using rat cDNA microarray.
Guo, Q.M., Malek, R.L., Kim, S., Chiao, C., He, M., Ruffy, M., Sanka, K., Dang, C.V., Lee, N.H., and Liu, E.T. (2000) Cancer Res 60:5922-28.

Lung Disease Models Publications (David Schwartz, TREX PGA)

TNF- and IL-1 are not essential to the inflammatory response in LPS induced airway disease.
Moreland JG, Fuhrman RM, Wohlford-Lenane CL, Quinn TJ, Benda E, Pruessner JA, Schwartz DA. Am J Physiol: Lung Cell Mol Biol 2001; 280(1):L173-L180.

Endotoxin responsiveness and subchronic grain dust-induced airway disease.
George CLS, Jin H, Wohlford-Lenane CL, O'Neill ME, Phipps JC, O'Shaughnessy P, Kline JN, Thorne PS, Schwartz DA. Am J Physiol: Lung Cell Mol Biol 2001; 280(2):L203-L213.

Does inhalation of endotoxin cause asthma?
Schwartz DA. Am J Resp Crit Care Med 2001; 163(2): 305-306.

Inhibition of LPS induced airway hyperresponsiveness and airway inflammation by LPS antagonists.
Schwartz DA, Christ WJ, Wohlford-Lenane CL. Am J Physiol: Lung Cell Mol Physiol 2001; 280: L771-L778.

Molecular genetic analysis of an endotoxin non-responder mutant cell line: a point mutation in a conserved region of MD-2 abolishes endotoxin-induced signaling.
Schromm AB, Lien E, Henneke P, Chow JC, Yoshimura A, Heine H, Latz E, Monks BG, Schwartz DA, Miyake K, Golenbock DT. J Exp Med 2001; 194:79-88.

Airway inflammation and responsiveness in prostaglandin H synthase-deficient mice exposed to bacterial lipopolysaccharide.
Zeldin DC, Wohlford-Lenane C, Chulada P, Bradbury JA, Scarborough PE, Roggli V, Langenbach R, Schwartz DA. Am J Respir Cell Biol 2001; 25:457-465.

Genes, other than TLR4, are involved in the response to inhaled LPS.
Lorenz E, Jones M, Wohlford-Lenane C, Meyer N, Frees KL, Arbour NC, Schwartz DA. Am J Physiol: Lung Cell Mol Physiol 2001; 281:L1106-1114.

Association of TLR-4 mutations and the risk for acute GVHD after HLA-matched sibling hematopoietic stem cell transplantation.
Lorenz E, Schwartz DA, Martin PJ, Gooley T, Lin MT, Chien JW, Hansen JA, Clark JG. Biol Blood Marrow Transplant 2001; 7:384-387.

The genetics of innate immunity.
Schwartz, DA. Chest 2002; 121:62S-68S.

Relevance of mutations in the TLR4 receptor in patients with Gram negative septic shock.
Lorenz E, Mira JP, Frees KL, Schwartz DA. Arch Int Med 2002; 162:1028-1032.

Toll-like receptor 4 mutations and atherogenesis in humans.
Kiechl S, Lorenz E, Reindl M, Wiedermann CJ, Oberhollenzer F, Willeit J, Schwartz DA. N Engl J Med 2002; 347(3):185-192.

Association between alleles in the toll-like receptor 4 gene and premature births in the Finnish population.
Lorenz E, Hallman M, Marttila R, Haataja R, Schwartz DA. Pediatr Res 2002; 52:373-376.

A matrix for new ideas in pulmonary fibrosis.
Cook DN, Brass DM, Schwartz DA. Amer J Respir Cell Mol Biol 2002; 27:122-124.

Toll-like receptor 4 (TLR4)-deficient murine macrophage cell line as an in vitro assay system to show TLR4-independent signaling of Bacteroides fragilis lipoppolysaccharide.
Lorenz E, Patel DD, Hartung T, Schwartz DA. Infect Immun 2002; 70:4892-4896.

CD11b and ICAM-1 are essential to pulmonary neutrophil recruitment in LPS-induced airway disease.
Moreland JG, Fuhrman RM, Pruessner JA, Schwartz DA. Am J Respir Cell Mol Biol 2002; 27(4): 474-480.

Neutrophils play a critical role in the development of LPS-induced airway disease.
Savov JD, Gavett SH, Brass DM, Costa DL, Schwartz DA. Am J Physiol: Lung Cell Mol Physiol 2002; 27(5): L952-L962.

Susceptibility to asbestos-induced and TGF-1-induced fibroproliferative lung disease in two strains of mice.
Warshamana GS, Pociask DA, Sime P, Schwartz DA, Brody AR. Amer J Respir Cell Mol Biol 2002; 27:705-713.

Protocols

Use of RNA and genomic DNA references for inferred comparisons in DNA microarray analyses.
Kim H, Zhao B, Snesrud EC, Haas BJ, Town CD, Quackenbush J. Biotechniques. 2002 Oct;33(4):924-30.
BiotechniquesCookbook_II
Hegde et al. Biotechniques vol 29 no 3 September 2000.