Selected Publications:


Zhang X, Sebastiani P, Liu G, Schembri F, Zhang X, Dumas Y, Langer E, Alekseyev Y, O’Connor G, Brooks D, Lenburg M, Spira A. Similarities and differences between smoking-related gene expression in nasal and bronchial epithelium. Physiol Genomics. 2009 Dec 1. ( Read here )


Steiling K, Lenberg ME, Spira A. Airway Gene Expression in Chronic Obstructive Pulmonary Disease.  Proc Am Thorac Soc.  2009;6:697-700.


Steiling K, Kadar AY, Bergerate A, Flanigon J, Sridhar S, Shah V, Ahmad QR, Brody JS, Lenburg ME, Steffen M, Spira A. Comparison of proteomic and transcriptomic profiles in the bronchial airway epithelium of current and never smokers. PLoS ONE. 2009;4(4):e5043.

Schembri F, Sridhar S, Perdomo C, Gustafson AM, Zhang X, Ergun A, Lu J, Liu G, Zhang X, Bowers J, Vaziri C, Ott K, Sensinger K, Collins JJ, Brody JS, Getts R, Lenburg ME, Spira A. MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium. PNAS. 2009 Feb 17;106(7):2319-24. Epub 2009 Jan 23. ( Read here )


Steiling K, Ryan J, Brody JS*, Spira A*. The field of tissue injury in the lung and airway. Cancer Prevention Research, 2008; 1(6):396-403. *contributed equally as senior author


Sridhar S, Schembri F, Zeskind J, Shah V, Gustafson A, Steiling K, Liu G, Dumas YM, Zhang X, Brody JS, Lenburg ME, Spira A. Smoking-induced gene expression changes in the bronchial airway are reflected in nasal and buccal epithelium. BMC Genomics 2008; 9:259.


Beane J, Sebastiani P, Whitfield TH, Steiling K, Dumas YM, Lenburg ME, Spira A. A prediction model for lung cancer diagnosis that integrates genomic and clinical features.  Cancer Preventation Research. 2008; 1:56-64.

Millien G, Beane J, Lenburg M, Tsao PN, Lu J, Spira A, Ramirez MI. Characterization of the mid-foregut transcriptome identifies genes regulated during lung bud induction. Gene Expr Patterns. 8(2):124-39. 2008.

Beane J, Sebastiani P, Liu G, Brody JS, Lenburg ME, Spira A. Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression. Genome Biol. 8(9):R201. 2007.

Spira A, Beane J, Shah V, Steiling K, Liu G, Schembri F, Gilman S, Dumas Y, Calner P, Sebastiani P, Sridhar S, Beamis J, Lamb C, Keane J, Lenburg M, Brody J. Airway Epithelial Gene Expression in the Diagnostic Evaluation of Smokers with Suspect Lung Cancer. Nature Medicine. 13:361-6. 2007.

Zhang X, Liu G, Lenburg M, Spira A. Comparison of smoking-induced gene expression on Affymetrix exon and 3' based expression arrays. Genome

Brody JS, Spira A. Inflammation, Lung Cancer and COPD. Proc Am Thorac Soc. 3:535-7. 2006.

Demeo D, Mariani T, Lange C, Srisuma S, Litonjua A, Celedon C, Lake S, Reilly J, Chapman H, Mecham B, Haley K, Sylvia J, Sparrow D, Spira A, Beane J, Pinto-Plata V, Speizer F, Shapiro S, Weiss S, Silverman E. The SERPINE2 gene is associated with Chronic Obstructive Pulmonary Disease. Am J Human Genetics. 78: 253-64, 2006.

Beane J, Kadar A, DeLisi C, Spira A. Diagnostic and Prognostic Impact of high-throughput genomic and proteomic technologies in the post-genomic era. In McPherson and Pincus M (ed): Henry's Clinical Diagnosis and Management by Laboratory Methods, 21st Edition. Saunders/Elsevier, Philadelphia. 2007.

Millien G, Spira A, Hinds A, Wang J, Williams M and Ramirez M. Alterations in gene expression in T1alpha null lung: a model of deficient alveolar sac development. BMC Developmental Biology. 6:35. 2006.

Vishal Shah, Sriram Sridhar, Jennifer Beane, Jerome S. Brody and Avrum Spira. SIEGE: Smoking Induced Epithelial Gene Expression Database. Nucleic Acids Research. 33(Database Issue):D573-D579. 2005. ( Read here )

Avrum Spira*, Jennifer Beane*, Victor Pinto-Plata*, Aran Kadar, Gang Liu, Vishal Shah, Bartolome Celli, and Jerome S. Brody. Gene Expression Profiling of Human Lung Tissue from Smokers with Severe Emphysema. Am J Respir Cell Mol Biol. 31:601-610. 2004. *contributed equally and should be considered co-first authors ( Read here )

Spira A, Beane J, Shah V, Liu G, Schembri F, Yang X, Palma J, Brody JS. Effects of cigarette smoke on the human airway epithelial cell transcriptome. PNAS 101(27):10143-8. 2004. ( Read here )

Spira, A, Beane J, Schembri F, Liu G, Gilman S, Yang X, Ding C, and Brody J. A noninvasive method for obtaining buccal mucosa RNA for measuring patterns of gene expression in epithelial cells from the mouth. Biotechniques. 36(3):484-7. 2004.

Hoffman A, Awad T, Spira A, Palma J, Webster T, Wright G, Buckley J, Davis R, Hubbell E, Jones W, Tibshirani R, Tompkins R, Triche T, Xiao W ,West M, Warrington J. Best Practices in expression profiling data generation and interpretation: A report from the oligonucleotide array Best Practices Workshops 2003. Nature Reviews Genetics. Volume 5:229-38. 2004. ( Read here )

Beane J. A look behind the scenes: bioterrorism, smallpox, and public health policy. The Journal of Biolaw and Business. 7(2):40-53. 2004.

Spira A, Carroll D, Aziz Z, Liu G, Shah V, Kornfeld H, Keane J. Apoptosis Genes in Human Alveolar Macrophages Infected with Virulent or Attenuated M. tuberculosis. Am J Respir Cell Mol Biol. 29(5):545-51. 2003.

Powell C*, Spira A*, Derti A, DeLisi C, Liu G, Borczuk A, Busche S, Sugarbaker D, Bueno R, Brody J. Gene Expression in lung adenocarcinomas of smokers and nonsmokers. Am J Respir Cell Mol Biol. 29:157-162. 2003. *contributed equally and should be considered co-first authors

Powell CA, Caracta C, Bueno R, Richards WG, Sugarbaker DJ, Brody JS. Patterns of allelic loss differ in lung adenocarcinomas of smokers and non-smokers. Lung Cancer 39(1): 23-9,2003.

Spira A, Yanai I, Chettier R, Wu J and DeLisi C. High-Throughput Functional Inference in the Post-Genomic Era. In Appasani K (ed): Perspectives in Gene Expression, Eaton Publishing, Westboro, MA. 2003: 345-357

Spira A. To tell or not to tell: Genetic testing and the physician's duty to disclose results to relatives. The Journal of Biolaw and Business. Special Bio-Ethix Supplement: 3-9, 2002.

Spira A, Brecher S, Karlinsky J. Pulmonary mucormycosis in the setting of COPD. Respiration. 69(6):560-3, 2002.

Powell CA, Klares S, O'Connor G, Brody JS. Loss of heterozygosity in epithelial cells obtained by bronchial brushing: clinical utility in lung cancer. Clinical Cancer Research 5: 2025-2034, 1999.

Brody JS. The Lung: Molecular Basis of Disease, p. 218. Philadelphia: W.B. Saunders, 1998.