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• Roberson ED, Pevsner J. Visualization of shared genomic regions and meiotic recombination in high-density SNP data. PLoS One . 2009 Aug 21;4(8):e6711. PMID: 19696932 (Link to PubMed)
• Scharpf RB, Parmigiani G, Pevsner J, Ruczinski I. Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays. Ann Appl Stat . 2008 Jun 1;2(2):687-713. PMID: 19609370 (Link to PubMed)
• Pevsner J. Analysis of genomic DNA with the UCSC genome browser. Methods Mol Biol . 2009;537:277-301. PMID: 19378150 (Link to PubMed)
• Miller ND, Nance MA, Wohler ES, Hoover-Fong JE, Lisi E, Thomas GH, Pevsner J. Molecular (SNP) analyses of overlapping hemizygous deletions of 10q25.3 to 10qter in four patients: evidence for HMX2 and HMX3 as candidate genes in hearing and vestibular function. Am J Med Genet A . 2009 Feb 15;149A(4):669-80. PMID: 19253379 (Link to PubMed)
• Wang W, Carvalho B, Miller ND, Pevsner J, Chakravarti A, Irizarry RA. Estimating genome-wide copy number using allele-specific mixture models. J Comput Biol . 2008 Sep;15(7):857-66. PMID: 18707534 (Link to PubMed)
• Ting JC, Roberson ED, Miller ND, Lysholm-Bernacchi A, Stephan DA, Capone GT, Ruczinski I, Thomas GH, Pevsner J. Visualization of uniparental inheritance, Mendelian inconsistencies, deletions, and parent of origin effects in single nucleotide polymorphism trio data with SNPtrio. Hum Mutat . 2007 Dec;28(12):1225-35. PMID: 17661425
• Scharpf RB, Ting JC, Pevsner J, Ruczinski I. SNPchip: R classes and methods for SNP array data. Bioinformatics 2007 Mar 1;23(5):627-8. PMID: 17204461 (Link to PubMed)
• Ting JC, Ye Y, Thomas GH, Ruczinski I, Pevsner J. Analysis and visualization of chromosomal abnormalities in SNP data with SNPscan. BMC Bioinformatics, 2006, 7:25.
• Mao R, Pevsner J. The use of genomic microarrays to study chromosomal abnormalities in mental retardation. Ment Retard Dev Disabil Res Rev. 2005;11(4):279-85.
• Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, Surendranath V, Niranjan V, Muthusamy B, Gandhi TK, Gronborg M, Ibarrola N, Deshpande N, Shanker K, Shivashankar HN, Rashmi BP, Ramya MA, Zhao Z, Chandrika KN, Padma N, Harsha HC, Yatish AJ, Kavitha MP, Menezes M, Choudhury DR, Suresh S, Ghosh N, Saravana R, Chandran S, Krishna S, Joy M, Anand SK, Madavan V, Joseph A, Wong GW, Schiemann WP, Constantinescu SN, Huang L, Khosravi-Far R, Steen H, Tewari M, Ghaffari S, Blobe GC, Dang CV, Garcia JG, Pevsner J, Jensen ON, Roepstorff P, Deshpande KS, Chinnaiyan AM, Hamosh A, Chakravarti A, Pandey A. Development of human protein reference database as an initial platform for approaching systems biology in humans. Genome Res. 2003 Oct;13(10):2363-71.
• Colantuoni C, Henry G, Zeger S, Pevsner J. SNOMAD (Standardization and NOrmalization of MicroArray Data): web accessible gene expression data analysis. Bioinformatics, 2002 Nov;18(11):1540-1.
• Colantuoni C, Henry G, Zeger S, Pevsner J. Local mean normalization of microarray element signal intensities across an array surface: quality control and correction of spatically systematic hybridization artifacts. Biotechniques, 2002; 32(6):1316-20.
• Bouton CM, Pevsner J. DRAGON View: Information Visualization for Annotated Microarray Data. Bioinformatics, 2002 Feb;18(2):323-4.
• Bouton CM, and Pevsner J. DRAGON: Database Referencing of Array Genes Online. Bioinformatics, 2000 Nov;16(11):1038-9.

• Miller RA, Christoforou N, Pevsner J, McCallion AS, Gearhart JD. Efficient array-based identification of novel cardiac genes through differentiation of mouse ESCs. PLoS One . 2008 May 14;3(5):e2176. PMID: 18478100
• Mao R, Wang X, Spitznagel EL, Frelin LP, Ting JC, Ding H, Kim J, Ruczinski I, Downey TJ, Pevsner J. Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart. Genome Biology. 2005;
• Masayesva BG, Ha P, Garrett-Mayer E, Pilkington T, Mao R, Pevsner J, Speed T, Benoit N, Moon CS, Sidransky D, Westra WH, Califano J. Gene expression alterations over large chromosomal regions in cancers include multiple genes unrelated to malignant progression Proc Natl Acad Sci U S A. 2004 Jun 8;101(23):8715-20.
• Mirnics K, Pevsner J. Progress in the use of microarray technology to study the neurobiology of disease. Nat Neurosci. 2004 May;7(5):434-9.
• Polster BM, Pevsner J, Hardwick JM. Viral Bcl-2 homologs and their role in virus replication and associated diseases. Biochim Biophys Acta. 2004 Mar 1;1644(2-3):211-27.
• Petrova PS, Raibekas A, Pevsner J, Vigo N, Anafi M, Moore MK, Peaire A, Shridhar V, Smith DI, Kelly J, Durocher Y, Commissiong JW. Discovering novel phenotype-selective neurotrophic factors to treat neurodegenerative diseases. Prog Brain Res. 2004;146:168-83.
• Mao R, Zielke CL, Zielke HR, Pevsner J. Global up-regulation of chromosome 21 gene expression in the developing down syndrome brain. Genomics. 2003 May;81(5):457-67.
• Comi AM, Hunt P, Vawter MP, Pardo CA, Becker KG, Pevsner J. Increased Fibronectin Expression in Sturge-Weber Syndrome Fibroblasts and Brain Tissue Pediatric Res 2003 Mar 5.
• Poole LJ, Yu Y, Kim PS, Zheng QZ, Pevsner J, Hayward GS. Altered Patterns of Cellular Gene Expression in Dermal Microvascular Endothelial Cells Infected with Kaposi's Sarcoma-Associated Herpesvirus. J Virol 2002 Apr;76(7):3395-420.
• Johnston-Wilson NL, Bouton CM, Pevsner J, Breen JJ, Torrey EF, Yolken RH. Emerging technologies for large-scale screening of human tissues and fluids in the study of severe psychiatric disease. Int J Neuropsychopharmacol. 2001 Mar;4(1):83-92. Review.
• Colantuoni C, Purcell AE, Bouton CM, Pevsner J. High throughput analysis of gene expression in the human brain. J Neurosci Res. 2000 Jan 1;59(1):1-10. Review.
• Kadkol SS, Brody JR, Pevsner J, Bai J, Pasternack GR. Modulation of oncogenic potential by alternative gene use in human prostate cancer. Nat Med. 1999 Mar;5(3):275-9. Correction published here: Nat Med. 1999 Sep;5(9):1087.
• Smith KD, Kemp S, Braiterman LT, Lu JF, Wei HM, Geraghty M, Stetten G, Bergin JS, Pevsner J, Watkins PA. X-linked adrenoleukodystrophy: genes, mutations, and phenotypes. Neurochem Res. 1999 Apr;24(4):521-35. Review.

Autism and Rett Syndrome

• Deng V, Matagne V, Banine F, Frerking M, Ohliger P, Budden S, Pevsner J, Dissen GA, Sherman LS, Ojeda SR. FXYD1 is an MeCP2 target gene overexpressed in the brains of Rett syndrome patients and Mecp2-null mice. Hum Mol Genet . 2007 Mar 15;16(6):640-50. PMID: 17309881
• Naidu S, Bibat G, Kratz L, Kelley RI, Pevsner J, Hoffman E, Cuffari C, Rohde C, Blue ME, Johnston MV. Clinical variability in Rett syndrome. J Child Neurol. 2003 Oct;18(10):662-8.
• Cohen DR, Matarazzo V, Palmer AM, Tu Y, Jeon OH, Pevsner J, Ronnett GV. Expression of MeCP2 in olfactory receptor neurons is developmentally regulated and occurs before synaptogenesis. Mol Cell Neurosci. 2003 Apr;22(4):417-29.
• Johnston MV, Jeon OH, Pevsner J, Blue ME, Naidu S. Neurobiology of Rett syndrome: a genetic disorder of synapse development. Brain Dev. 2001 Dec;23 Suppl 1:S206-S213.
• Colantuoni C, Jeon OH, Hyder K, Chenchik A, Khimani AH, Narayanan V, Hoffman EP, Kaufmann WE, Naidu S, Pevsner J. Gene expression profiling in postmortem Rett Syndrome brain: differential gene expression and patient classification. Neurobiol. Dis. 2001; 8:847-865.
• Purcell AE, Jeon OH, Pevsner J. The abnormal regulation of gene expression in autistic brain tissue. J Autism Dev Disord. 2001 Dec;31(6):545-9.
• Purcell AE, Jeon OH, Zimmerman AW, Blue ME, Pevsner J. Postmortem brain abnormalities of the glutamate neurotransmitter system in autism. Neurology. 2001 Nov 13;57(9):1618-1628.
• Purcell AE, Rocco MM, Lenhart JA, Hyder K, Zimmerman AW, Pevsner J. Assessment of neural cell adhesion molecule (NCAM) in autistic serum and postmortem brain. J Autism Dev Disord. 2001 Apr;31(2):183-94.

• Fannjiang Y, Cheng WC, Lee SJ, Qi B, Pevsner J, McCaffery JM, Hill RB, Basanez G, Hardwick JM. Mitochondrial fission proteins regulate programmed cell death in yeast. Genes Dev. 2004 Nov 15;18(22):2785-97.
• Ha PK, Benoit NE, Yochem R, Sciubba J, Zahurak M, Sidransky D, Pevsner J, Westra WH, Califano J. A transcriptional progression model for head and neck cancer. Clin Cancer Res. 2003 Aug 1;9(8):3058-64.
• Petrova P, Raibekas A, Pevsner J, Vigo N, Anafi M, Moore MK, Peaire AE, Shridhar V, Smith DI, Kelly J, Durocher Y, Commissiong JW. MANF: a new mesencephalic, astrocyte-derived neurotrophic factor with selectivity for dopaminergic neurons. J Mol Neurosci. 2003 Apr;20(2):173-88
• Sung YK, Moon C, Yoo JY, Moon C, Pearse D, Pevsner J, Ronnett GV. Plunc, a member of the secretory gland protein family, is up-regulated in nasal respiratory epithelium after olfactory bulbectomy. J Biol Chem. 2002 Jan 30
• Wang H, Wolosker H, Morris JF, Pevsner J, Snyder SH, Selkoe DJ. Naturally occurring free D-aspartate is a nuclear component of cells in the mammalian hypothalamo-neurohypophyseal system. Neuroscience. 2002 Jan 18;109(1):1-4.
• Dang DT, Pevsner J, Yang VW. The biology of the mammalian Kruppel-like family of transcription factors. Int J Biochem Cell Biol. 2000 Nov-Dec;32(11-12):1103-21. Review.
• Wang H, Wolosker H, Pevsner J, Snyder SH, Selkoe DJ. Regulation of rat magnocellular neurosecretory system by D-aspartate: evidence for biological role(s) of a naturally occurring free D-amino acid in mammals. J Endocrinol. 2000 Nov;167(2):247-52.
• Wang H, Pevsner J. Detection of endogenous biotin in various tissues: novel functions in the hippocampus and implications for its use in avidin-biotin technology. Cell Tissue Res. 1999 Jun;296(3):511-6.
• Lo NW, Shaper JH, Pevsner J, Shaper NL. The expanding beta 4-galactosyltransferase gene family: messages from the databanks. Glycobiology. 1998 May;8(5):517-26.