Pavlidis lab publications | CHIBI

Pavlidis lab publications

2009 Publications

French L., Lane S., Xu L., Loo T and Pavlidis P (2009), Application and Evaluation of automated semantic annotation of gene expression experiments. Bioinformatics, Jun 15;25(12):1543-9.

Ware CB, Wang L, Mecham BH, Shen L, Nelson AM, Merav Bar MD, Lambda DA, Dauphin DS, Buckingham BS, Askari B, Lim R, Tewari M, Gartler S, Issa J-P, Pavlidis P, Duan Z, Blau CA. (2009) Histone deacetylase inhibition elicits an evolutionarily conserved self-renewal program in embryonic stem cells. Cell Stem Cell, Apr 3;4(4):359-69.

Barnes MG, Grom AA, Thompson SD, Griffin TA, Pavlidis P, Itert L, Fall N, Sowders DP, Hinze CH, Aronow BJ, Luyrink LK, Srivastava S, Ilowite N, Gottlieb B, Olson J, Sherry D, Glass DN, Colbert RA. (2009) Subtype-specific peripheral blood gene expression profiles in recent onset juvenile idiopathic arthritis. Arthritis and Rheumatology, In press.

Griffin TA, Barnes MG, Illowite NT Olson JC, Sherry DD, Gottlieb BS, Aronow BJ, Pavlidis P, Hinze C, Thornton S, Thompson SD, Grom AA, Colbert RA, Glass DN. Gene Expression Signatures in Polyarticular Juvenile Idiopathic Arthritis Demonstrate Disease Heterogeneity and Offer a Molecular Classification of Disease Subsets. Arthritis and Rhematology, In press.

2008 Publications

Kebschull M, Demmer R, Behle JH, Pollreisz A, Heidemann J, Belusko PB, Celenti R, Pavlidis P, Papapanou PN. Granulocyte chemotactic protein 2 (gcp-2/cxcl6) complements interleukin-8 in periodontal disease. J Periodontal Res. 2008.

Demmer RT, Behle JH, Wolf DL, Handfield M, Kebschull M, Celenti R, Pavlidis P, Papapanou PN. (2008) Transcriptomes in healthy and diseased gingival tissues. J Periodontol. Nov;79(11):2112-24.

Mistry M, Pavlidis P. Gene Ontology term overlap as a measure of gene functional similarity (2008). BMC Bioinformatics, 9:327.

Stark KL, Xu B, Bagchi A, Lai WS, Liu H, Hsu R, Wan X, Pavlidis P, Mills AA, Karayiorgou M, Gogos JA.(2008) Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model. Nature Genetics, Jun;40(6):751-60.

2007 Publications

French L, Pavlidis P (2007) Informatics in Neuroscience. Briefings in Bioinformatics doi:10.1093/bib/bbm047 [Review]

Wan X, Pavlidis P. (2007) Sharing and reusing gene expression profiling data in neuroscience. Neuroinformatics. 2007 Fall;5(3):161-75. [Review]

Papapanou PN, Sedaghatfar MH, Demmer RT, Wolf DL, Yang J, Roth GA, Celenti R, Belusko PB, Lalla E, Pavlidis P. (2007) Periodontal therapy alters gene expression of peripheral blood monocytes. J Clin Periodontol. 2007 Sep;34(9):736-47.

Schmidt-Ott KM, Masckauchan TN, Chen X, Hirsh BJ, Sarkar A, Yang J, Paragas N, Wallace VA, Dufort D, Pavlidis P, Jagla B, Kitajewski J, Barasch J. (2007) β-catenin/TCF/Lef controls a differentiation-associated transcriptional program in renal epithelial progenitors. Development. 2007 Sep;134(17):3177-90.

Muchir A, Pavlidis P, Bonne G, Hayashi YK, Worman HJ. (2007) Activation of MAPK in hearts of Emd null mice: similarities between mouse models of X-linked and autosomal dominant Emery-Dreifuss muscular dystrophy. Hum. Mol. Genetics Jun 13.

Muchir A, Pavlidis P, Decostre V, Herron AJ, Arimura T, Bonne G, Worman HJ. (2007) Activation of MAPK pathways links LMNA mutations to cardiomyopathy in Emery-Dreifuss muscular dystrophy. J Clin Invest. 5, 1282-93.

2006 Publications

Varrault A, Gueydan C, Delalbre A, Bellmann A, Houssami S, Aknin C, Severac D, Chotard L, Kahli M, Le Digarcher A, Pavlidis P, Journot L. (2006) Zac1 regulates an imprinted gene network critically involved in the control of embryonic growth. Developmental Cell 11(5), 711 - 722.

Lai W, Xu B, Westphal K, Paterlini M, Olivier B, Pavlidis P, Karayiorgou M, and Gogos J. Akt1 deficiency affects neuronal morphology and predisposes to abnormalities in prefrontal cortex functioning. PNAS. 2006 Nov 7;103(45):16906 - 16911.

Zheng Z, Pavlidis P, Chua S, D'Agati VD, Gharavi AG. An ancestral haplotype defines susceptibility to doxorubicin nephropathy in the laboratory mouse. J Am Soc Nephrol. 2006 Jul;17(7):1796-800. (2006)

2005 Publications

Lee HK, Braynen W, Keshav K, Pavlidis P. ErmineJ: Tool for functional analysis of gene expression data sets. BMC Bioinformatics 6(1):269. (2005).

Paterlini M, Zakharenko SS, Lai WS, Qin J, Zhang H, Mukai J, Westphal KG, Olivier B, Sulzer D, Pavlidis P, Siegelbaum SA, Karayiorgou M, Gogos JA. Transcriptional and behavioral interaction between 22q11.2 orthologs modulates schizophrenia-related phenotypes in mice. Nat Neurosci 8(11):1586-94. (2005).

Barnes M, Freudenberg J, Thompson S, Aronow B, Pavlidis P. Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms. Nucleic Acids Res 33(18):5914-23. (2005).

Barr GA, Gao P, Wang S, Cheng J, Qin J, Sibille EL, Pavlidis P. Microarray analysis of gene expression following the formalin test in the infant rat. Pain 117(1):6-18. (2005).

Erraji-Benchekroun L, Underwood MD, Arango V, Galfalvy H, Pavlidis P, Smyrniotopoulos P, Mann JJ, Sibille E. Molecular aging in human prefrontal cortex is selective and continuous throughout adult life. Biol Psychiatry 57(5):549-58. (2005).

Zheng Z, Schmidt-Ott KM, Chua S, Foster KA, Frankel RZ, Pavlidis P, Barasch J, D'Agati VD, Gharavi AG. A Mendelian locus on chromosome 16 determines susceptibility to doxorubicin nephropathy in the mouse. Proc Natl Acad Sci 102(7):2502-7. (2005).

2004 Publications

Barnes MG, Aronow BJ, Luyrink LK, Moroldo MB, Pavlidis P, Passo MH, Grom AA, Hirsch R, Giannini EH, Colbert RA, Glass DN, Thompson SD. Gene expression in juvenile arthritis and spondyloarthropathy: pro-angiogenic ELR+ chemokine genes relate to course of arthritis. Rheumatology (Oxford) 43(8):973-9. (2004).

Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Res 14(6):1085-94. (2004).

Papapanou PN, Abron A, Verbitsky M, Picolos D, Yang J, Qin J, Fine JB, Pavlidis P. Gene expression signatures in chronic and aggressive periodontitis: a pilot study. Eur J Oral Sci 112(3):216-23. (2004).

Pavlidis P, Qin J, Arango V, Mann JJ, Sibille E. Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex. Neurochem Res 29(6):1213-22. (2004).

Verbitsky M, Yonan AL, Malleret G, Kandel ER, Gilliam TC, Pavlidis P. Altered hippocampal transcript profile accompanies an age-related spatial memory deficit in mice. Learn Mem 11(3):253-60. (2004).

Pavlidis P, Wapinski I, Noble WS. Support vector machine classification on the web. Bioinformatics 20(4):586-7. (2004).

Sibille E, Arango V, Galfalvy HC, Pavlidis P, Erraji-Benchekroun L, Ellis SP, John Mann J. Gene expression profiling of depression and suicide in human prefrontal cortex. Neuropsychopharmacology 29(2):351-61. (2004).

Li D, Ma W, Sun F, Pavlidis P, Spector A. Cluster analysis of genes with significant change in expression in cells conditioned to survive TBOOH. Exp Eye Res 78(2):301-8. (2004).

2003 Publications

Pavlidis P. Using ANOVA for gene selection from microarray studies of the nervous system. Methods 31(4):282-9. (2003).

Yonan, A.L., Palmer A.A., Gilliam T.C., Smith, K.C., Pavlidis, P., Lee, H.K., Feldman I., Fischer, S., Yonan, J.M. and Geschwind, D.H. (2003) A search for candidate genes in regions defined by a genome-wide scan of 345 autism families. Genes, Brain and Behavior, 2:303-320.

Yonan AL, Palmer AA, Smith KC, Feldman I, Lee HK, Yonan JM, Fischer SG, Pavlidis P, Gilliam TC. Bioinformatic analysis of autism positional candidate genes using biological databases and computational gene network prediction. Genes Brain Behav 2(5):303-20. (2003).

Galfalvy HC, Erraji-Benchekroun L, Smyrniotopoulos P, Pavlidis P, Ellis SP, Mann JJ, Sibille E, Arango V. Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction. BMC Bioinformatics 437. (2003).

Yang YC, Piek E, Zavadil J, Liang D, Xie D, Heyer J, Pavlidis P, Kucherlapati R, Roberts AB, Bottinger EP. Hierarchical model of gene regulation by transforming growth factor beta. Proc Natl Acad Sci U S A 100(18):10269-74. (2003).

Pavlidis P, Li Q, Noble WS. The effect of replication on gene expression microarray experiments. Bioinformatics 19(13):1620-7. (2003).

Chen A, Muzzio IA, Malleret G, Bartsch D, Verbitsky M, Pavlidis P, Yonan AL, Vronskaya S, Grody MB, Cepeda I, Gilliam TC, Kandel ER. Inducible enhancement of memory storage and synaptic plasticity in transgenic mice expressing an inhibitor of ATF4 (CREB-2) and C/EBP proteins. Neuron 39(4):655-69. (2003).

Segal NH, Pavlidis P, Antonescu CR, Maki RG, Noble WS, DeSantis D, Woodruff JM, Lewis JJ, Brennan MF, Houghton AN, Cordon-Cardo C. Classification and subtype prediction of adult soft tissue sarcoma by functional genomics. Am J Pathol 163(2):691-700. (2003).

Segal NH, Pavlidis P, Noble WS, Antonescu CR, Viale A, Wesley UV, Busam K, Gallardo H, DeSantis D, Brennan MF, Cordon-Cardo C, Wolchok JD, Houghton AN. Classification of clear-cell sarcoma as a subtype of melanoma by genomic profiling. J Clin Oncol. 2003 May 1;21(9):1775-81. (2003)

Pavlidis P, Noble WS. Matrix2png: a utility for visualizing matrix data. Bioinformatics 19(2):295-6. (2003).

2002 Publications

Spector A, Li D, Ma W, Sun F, Pavlidis P. Differential amplification of gene expression in lens cell lines conditioned to survive peroxide stress. Invest Ophthalmol Vis Sci 43(10):3251-64. (2002).

Schroder AJ, Pavlidis P, Arimura A, Capece D, Rothman PB. Cutting edge: STAT6 serves as a positive and negative regulator of gene expression in IL-4-stimulated B lymphocytes. J Immunol 168(3):996-1000. (2002).

Pavlidis P, Lewis DP, Noble WS. Exploring gene expression data with class scores. Pac Symp Biocomput 474-85. (2002).

Pavlidis P, Weston J, Cai J, Noble WS. Learning gene functional classifications from multiple data types. J Comput Biol 9(2):401-11. (2002).

2001 Publications

Pavlidis P, Noble WS. Analysis of strain and regional variation in gene expression in mouse brain. Genome Biol 2(10):RESEARCH0042. (2001).

Muhle RA, Pavlidis P, Grundy WN, Hirsch E. A high-throughput study of gene expression in preterm labor with a subtractive microarray approach. Am J Obstet Gynecol 185(3):716-24. (2001).

Pavlidis, P., Tang, C. and Grundy, W.N. (2001) Classification of genes using probabilistic models of microarray expression profiles. Workshop on Data Mining in Bioinformatics, held in conjunction with SIGKDD01.

Pavlidis, P., Weston, J., Cai, J., and Grundy, W.N. (2001) Gene functional classification from heterogeneous data Proceedings of the Fifth Annual International Conference on Computational Biology (RECOMB), 249-255.

Montgomery JM, Pavlidis P, Madison DV. Pair recordings reveal all-silent synaptic connections and the postsynaptic expression of long-term potentiation. Neuron 29(3):691-701. (2001).

Pavlidis P, Furey TS, Liberto M, Haussler D, Grundy WN. Promoter region-based classification of genes. Pac Symp Biocomput 151-63. (2001).

2000 Publications

Santoro B, Chen S, Luthi A, Pavlidis P, Shumyatsky GP, Tibbs GR, Siegelbaum SA. Molecular and functional heterogeneity of hyperpolarization-activated pacemaker channels in the mouse CNS. J Neurosci 20(14):5264-75. (2000).

Pavlidis P, Montgomery J, Madison DV. Presynaptic protein kinase activity supports long-term potentiation at synapses between individual hippocampal neurons. J Neurosci 20(12):4497-505. (2000).

1999 Publications

Pavlidis P, Madison DV. Synaptic transmission in pair recordings from CA3 pyramidal cells in organotypic culture. J Neurophysiol 81(6):2787-97. (1999).

1996 Publications

Haley JE, Schaible E, Pavlidis P, Murdock A, Madison DV. Basal and apical synapses of CA1 pyramidal cells employ different LTP induction mechanisms. Learn Mem 3(4):289-95. (1996).

1995 Publications

Pavlidis P, Tanouye MA. Seizures and failures in the giant fiber pathway of Drosophila bang-sensitive paralytic mutants. J Neurosci 15(8):5810-9. (1995).
Pavlidis, P. (1995) Bang-sensitive Drosophila phenotype shows parallels to human seizure disorders. Journal of NIH Research 7, 43-44. (Perspectives article)

1994 Publications

Pavlidis P, Ramaswami M, Tanouye MA. The Drosophila easily shocked gene: a mutation in a phospholipid synthetic pathway causes seizure, neuronal failure, and paralysis. Cell 79(1):23-33. (1994).

1993 Publications

Pavlidis, P., Reynolds, E.R., and Tanouye, M.A. (1993) Drosophila mutations affecting electrical excitability. Proceedings of the 21st Gottingen Neurobiology Conference. Elsner, N. and Heisenberg, M., eds. (Verlag: New York) pp. 123-128.