We try to keep this page up to date, but you might want to check my Google scholar profile or my ORCiD records.

Links by Date

2017 Publications

Fortelny N, Overall CM, Pavlidis P, Freue GVC. Can we predict proteins from mRNA levels? Nature. 2017 Jul 26;547(7664):E19-E20. pubmed

Fortelny N, Butler GS, Overall CM, Pavlidis P. Protease-Inhibitor Interaction Predictions: Lessons on the complxity of Protein-Protein Interactions. Mol Cell Proteomics. 2017 Jun;16(6):1038-1051. pubmed

Ballouz S, Pavlidis P, Gillis J. Using predictive specificity to determine when gene set analysis is biologically meaningful. Nucleic Acids Res. 2017 Feb 28;45(4):e20. pubmed

Ballouz S, Weber M, Pavlidis P, Gillis J. EGAD: ultra-fast functional analysis of gene networks. Bioinformatics. 2017 Feb 15;33(4):612-614. pubmed

2016 Publications

Toker L, Feng M, Pavlidis P. “Whose sample is it anyways? Widespread misannotation of samples in transcriptomics studies.” F1000Res. 2016 Aug 30. pubmed

Jiang Y … Gillis J, Sedeño-Cortés AE, Pavlidis P … Friedberg I, Radivojac P. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biol. 2016 Sep 7;17(1):184. pubmed

Portales-Casamar E, Lussier AA, Jones MJ, MacIsaac JL, Edgar RD, Mah SM, Barhdadi A, Provost S, Lemieux-Perreault LP, Cynader MS, Chudley AE, Dube MP, Reynolds JN, Pavlidis P, Kobor M.S. “DNA methylation signature of human fetal alcohol spectrum disorder.” Epigenetics & Chromatin. 2016 June 9:25. pubmed

Rogic S, Wong A, Pavlidis P. “Meta-analysis of Gene Expression Patterns in Animal Models of Prenatal Alcohol Exposure Suggests Role for Protein Synthesis Inhibition and Chromatin Remodeling.” Alcohol Clin Exp Res. 2016 Apr;40(4):717-27. pubmed

Tan PP, Rogic S, Zoubarev A, McDonald C, Lui F, Charathsandrea G, Jacobson M, Belmadani M, Leong J, Van Rossum T, Portales-Casamar E, Qiao Y, Calli K, Liu X, Hudson M, Rajcan-Separovic E, Lewis MS, Pavlidis P. “Interactive Exploration, Analysis and Visualization of Complex Phenome-Genome Datasets with ASPIREdb.” Hum Mutat. 2016 Aug;37(8):719-26. pubmed

Burgstaller-Muehlbacher S, Waagmeester A, Mitraka E, Turner J, Putman T, Leong J, Naik C, Pavlidis P, Schriml L, Good BM, Su AI. Wikidata as a semantic framework for the Gene Wiki initiative. Database (Oxford). 2016 Mar 17;2016. pubmed

Price EM, Peñaherrera MS, Portales-Casamar E, Pavlidis P, Van Allen MI, McFadden DE, Robinson WP. “Profiling Placental and Fetal DNA Methylation in Human Neural Tube Defects.”. Epigenetics & Chromatin. 2016 Feb 16;9:6. pubmed

Horvath GA, Demos M, Shyr C, Matthews A, Zhang L, Race S, Stockler-Ipsiroglu S, Van Allen MI, Mancarci O, Toker L, Pavlidis P, Ross CJ, Wasserman WW, Trump N, Heales S, Pope S, Cross JH, van Karnebeek CD. Secondary neurotransmitter deficiencies in epilepsy caused by voltage-gated sodium channelopathies: A potential treatment target? Mol Genet Metab. 2016 Jan;117(1):42-8. pubmed

2015 Publications

Cruceanu C, Tan PP, Rogic S, Lopez JP, Torres-Platas SG, Gigek CO, Alda M, Rouleau GA, Pavlidis P, Turecki G. “Transcriptome Sequencing of the Anterior Cingulate in Bipolar Disorder: Dysregulation of G Protein-Coupled Receptors”. Am J Psychiatry. 2015 Nov 1;172(11):1131-40. pubmed

French L, Liu P, Marais O, Koreman T, Tseng L, Lai A, Pavlidis P. Text mining for neuroanatomy using WhiteText with an updated corpus and a new web application. Front. Neuroinform. 2015 May 21;9:13. pubmed

Ch’ng C, Kowk W, Rogic S, Pavlidis P. Meta-analysis of gene expression profiles in the blood and brain tissues of individuals with autism spectrum disorder. Autism Res. 2015 Oct;8(5):593-608. pubmed

Lussier, A, Stepien KA, Neumann SM, Pavlidis P, Kobor MS and Weinberg J. Prenatal Alcohol Exposure Alters Steady-state and activated gene expression in adult rat brain. Alcoholism: Clinical and Experimental Research 2015 39(2):251-26. pubmed

2014 Publications

Edgar R, Tan PP, Portales-Casamar E and Pavlidis P. “Meta-analysis of human methylomes reveals stably methylated sequences surrounding CpG islands associated with high gene expression”. Epigenetics & Chromatin 2014, 7:28. pubmed

Qiao Y, Mercier E, Dastan J, Hurlburt J, McGillivray B, Chudley AE, Farrell S, Bernier FP, Lewis SME, Pavlidis P and Rajcan-Separovic E. (2014) “Copy Number Variants (CNVs) Analysis in a Deeply Phenotyped Cohort of Individuals with Intellectual Disability (ID)”. BMC Medical Genetics 2014 Jul 16;15:82.pubmed

Fortelny N, Cox J, Lange P, Kappelhoff, Pavlidis P, Overall CM. “Network modeling of proteolytic systems reveals a pervasive protease web in multiple human tissues”. PLoS Biol. 2014 May 27;12(5):e1001869.

Lopez JP, Lim R , Cruceanu C, Crapper L, Fasano C, Labonte B, Maussion G, Yang JP, Yerko V, Vigneault E, El Mestikawy S, Mechawar N, Pavlidis P, Turecki G. “miR-1202: A Primate Specific and Brain Enriched miRNA Involved in Major Depression and Antidepressant Treatment”. Nat Med. 2014 Jul;20(7):764-8.pubmed

McCarthy J, Gillis J, Kramer M, Lihm J, Yoon S, Berstein Y, Mistry M, Pavlidis P, Solomon R, Ghiban E, Antoniou E, Kelleher E, O’Brien C, Donohoe G, Gill M, Morris D, McCombie R, and Corvin A. “De novo Mutations in Schizophrenia Implicate Chromatin Remodeling and Support a Genetic Overlap with Autism and Intellectual Disability”. Mol Psychiatry. 2014 Jun;19(6):652-8. pubmed

Kebschull M, Demmer RT, Grün B, Guarnieri P, Pavlidis P, Papapanou PN. “Gingival tissue transcriptomes identify distinct periodontitis phenotypes”. J Dent Res. 2014 May;93(5):459-68. pubmed

Gillis J, Ballouz S, Pavlidis P. “Bias tradeoffs in the creation and analysis of protein–protein interaction networks”. J Proteomics 2014. Published online before print on Jan 27, 2014. pubmed

Jeffries KM, Hinch SG, Sierocinski T, Pavlidis P, Miller KM.  “Transcriptomic responses to high water temperature in two species of Pacific salmon”. Evol Appl 2014, 7(2): 286-300. pubmed

2013 Publications

Kebschull M, Guarnier P, Demmer RT, Boulesteix AL, Pavlidis P, Papapanou PN. (2013) “Molecular Differences Between Chronic and Aggressive Periodontitis”. J Dent Res. Published online before print. Oct 11, 2013. Recipient of the 2015 AADR William J. Gies Awards in the Clinical Category pubmed reprint

Mistry M, Gillis J and Pavlidis P. (2013) “Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls”. BMC Neuroscience 2013, 14:105. pubmed reprint

Qiao Y, Badduke C, Mercier E, Lewis SME, Pavlidis P, Rajcan-Separovic E. (2013) “miRNA and miRNA target genes in copy number variations occurring in individuals with intellectual disability”. BMC Genomics 2013, 14:544. pubmed reprint

Gillis J and Pavlidis P. (2013) “Characterizing the state of the art in the computational assignment of gene function: lessons from the first critical assessment of functional annotation (CAFA).” BMC Bioinformatics 2013, 14(Suppl 3):S15. pubmed reprint

Portales-Casamar E, Ch Ng C, Lui F, St-Georges N, Zoubarev A, Lai AY, Lee M, Kwok C, Kwok W, Tseng L, Pavlidis P. (2013) “Neurocarta: aggregating and sharing disease-gene relations for the neurosciences.” BMC Genomics. 2013 Feb 26;14(1):129. pubmed reprint

Gillis J, Pavlidis P. (2013) “Assessing identity, redundancy and confounds in Gene Ontology annotations over time.” Bioinformatics. 2013 Feb 15;29(4):476-82. pubmed reprint supplement

Tan PPC, French L, Pavlidis P. (2013) “Neuron-enriched gene expression patterns are regionally anti-correlated with oligodendrocyte-enriched patterns in the adult mouse and human brain.” Front Neurosci. 2013;7:5. pubmed reprint supplement


2012 Publications

Pavlidis P, Gillis J. (2012) “Progress and challenges in the computational prediction of gene function using networks.” F1000Research 2012, 1:14. f1000 reprint

Melka MG, Gillis J, Bernard M, Abrahamowicz M, Chakravarty MM, Leonard GT, Perron M, Richer L, Veillette S, Banaschewski T, Barker GJ, Büchel C, Conrod P, Flor H, Heinz A, Garavan H, Brühl R, Mann K, Artiges E, Lourdusamy A, Lathrop M, Loth E, Schwartz Y, Frouin V, Rietschel M, Smolka MN, Ströhle A, Gallinat J, Struve M, Lattka E, Waldenberger M, Schumann G, Pavlidis P, Gaudet D, Paus T, Pausova Z. (2012) “FTO, obesity and the adolescent brain.” Hum Mol Genet. 2013 Mar 1;22(5):1050-8. pubmed reprint supplement

Jeffries KM, Hinch SG, Sierocinski T, Clark TD, Eliason EJ, Donaldson MR, Li S, Pavlidis P, Miller KM. (2012) “Consequences of high temperatures and premature mortality on the transcriptome and blood physiology of wild adult sockeye salmon (Oncorhynchus nerka).” Ecol Evol. 2012 Jul;2(7):1747-64. pubmed reprint

French L, Lane S, Xu L, Siu C, Kwok C, Chen Y, Krebs C, Pavlidis P. (2012) “Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text.” Bioinformatics. 2012 Nov 15;28(22):2963-70. pubmed reprint supplement

Zoubarev A, Hamer KM, Keshav KD, McCarthy EL, Santos JR, Van Rossum T, McDonald C, Hall A, Wan X, Lim R, Gillis J, Pavlidis P. (2012) “Gemma: A resource for the re-use, sharing and meta-analysis of expression profiling data.” Bioinformatics. 2012 Sep 1;28(17):2272-3. pubmed reprint

Pantazatos SP, Talati A, Pavlidis P, Hirsch J. (2012) “Cortical functional connectivity decodes subconscious, task-irrelevant threat-related emotion processing.” Neuroimage. 2012 Jul 16;61(4):1355-63. pubmed reprint

Gillis J, Pavlidis P (2012) “’Guilt by Association’ Is the Exception Rather Than the Rule in Gene Networks.” PLoS Comput Biol 8(3): e1002444.pubmed reprint supplement
Recommended by Faculty of 1000: f1000

Pantazatos SP, Talati A, Pavlidis P, Hirsch J (2012) “Decoding Unattended Fearful Faces with Whole-Brain Correlations: An Approach to Identify Condition-Dependent Large-Scale Functional Connectivity.” PLoS Comput Biol 8(3): e1002441.  pubmed reprint

Mistry M., Gillis J., Pavlidis P. (2012) “Genome-wide expression profiling of schizophrenia using a large combined cohort.” Mol Psychiatry. 2013 Feb;18(2):215-25. pubmed reprint supplement

Mulder KW, Wang X, Escriu C, Ito Y, Schwarz RF, Gillis J, Sirokmány G, Donati G, Uribe-Lewis S, Pavlidis P, Murrell A, Markowetz F, Watt FM (2012) “Diverse epigenetic strategies interact to control epidermal differentiation.” Jun 24;14(7):753-63. pubmed reprint

French L, Pavlidis P. (2011) “Using text mining to link journal articles to neuroanatomical databases.” J Comp Neurol. 2012 Jun 1;520(8):1772-83. pubmed reprint supplement


2011 Publications

Paus T, Bernard M, Chakravarty MM, Davey Smith G, Gillis J, Lourdusamy A, Melka MG, Leonard G, Pavlidis P, Perron M, Pike GB, Richer L, Schumann G, Timpson N, Toro R, Veillette S, Pausova Z (2011) “KCTD8 Gene and Brain Growth in Adverse Intrauterine Environment: A Genome-wide Association Study.” Cereb Cortex. 2012 Nov;22(11):2634-42.  pubmed reprint supplement

Harvard C, Strong E, Mercier E, Colnaghi R, Alcantra D, Chow E, Martell S, Tyson C, Hrynchak M, McGillivray B, Hamilton S, Marles S, Mhanni A, Dawson A, Pavlidis P, Qiao Y, Holden JJ, Lewis SM, O’Driscoll M, Rajcan-Separovic E.. (2011) “Understanding the impact of 1q21.1 Copy Number Variant.” Orphanet J Rare Dis. 2011 Aug 8;6(1):54. pubmed reprint

French L, Tan PP, Pavlidis P. (2011) “Large-Scale Analysis of Gene Expression and Connectivity in the Rodent Brain: Insights through Data Integration.” Front Neuroinform.;5:12. pubmed reprint supplement

Gillis J., Pavlidis P. (2011) “The role of indirect connections in gene networks in predicting function.” Bioinformatics 27(13):1860-6 pubmed reprint supplement

Portales-Casamar E, Evans A, Wasserman W, Pavlidis P. (2011) “The NeuroDevNet Neuroinformatics Core.” Semin Pediatr Neurol. 2011 Mar;18(1):17-20. pubmed reprint

Gillis J., Pavlidis P. (2011) “The impact of multifunctional genes on “guilt by association” analysis.” PLoS ONE. 6(2):e17258. pubmed reprint supplement
Rated “Must read” by Faculty of 1000: f1000
Rated Among the top 10% most cited PLOS ONE articles as of June 2017

Miller KM, Li S, Kaukinen K, Ginther N, Hammill E, Curtis JMR, Patterson D, Siercinski T, Donnison L, Pavlidis P, Hinch SG, Hruska KA, Cooke SJ, English KK, and Farrell AP (2011) “Genomic signatures predict migration and spawning failure in wild salmon.” Science. 331 (6014):214-7. pubmed reprint

French L, Pavlidis P. (2011) “Relationships between gene expression and brain wiring in the adult rodent brain.” PLoS Computational Biology. 7(1):e1001049. pubmed reprint supplement


2010 Publications

Gillis J, Mistry M, Pavlidis P. (2010) “Gene function analysis in complex data sets using ErmineJ.” Nat Protoc. 2010 Jun;5(6):1148-59. pubmed reprint

Qiao Y, Harvard C, Tyson C, Liu X, Fawcett C, Pavlidis P., Holden JAA, Lewis MES, Rajcan-Separovic E (2010) “Outcome of array CGH analysis for 255 subjects with intellectual disability and search for candidate genes using bioinformatics.” Human Genetics, 2010 Aug;128(2):179-94. pubmed reprint

Becanovic, K., Pouladi, M., Lim, R. S, Kuhn, A.3, Pavlidis, P, Luthi-Carter, R., Hayden, M.R., and B.R. Leavitt (2010) “Transcriptional changes in Huntington Disease identified using genome-wide expression profiling and cross-platform analysis.” Human Molecular Genetics, Apr 15;19(8):1438-52. pubmed reprint

Mistry, M., Pavlidis P. (2010) “A cross-laboratory comparison of expression profiling data from normal human postmortem brain.” Neuroscience May 5;167(2):384-95. pubmed reprint supplement


2009 Publications

Gillis J, Pavlidis P. (2009) “A methodology for the analysis of differential coexpression across the human lifespan.” BMC Bioinformatics 10:306.pubmed reprint supplement

Rogic S., Pavlidis P. (2009) “Meta-analysis of kindling-induced gene expression changes in the rat hippocampus.” Front Neurosci. 2009 Sep 15;3:53.  pubmed reprint supplement

French L, Lane S, Xu L., Pavlidis P. (2009) “Automated recognition of brain region mentions in neuroscience literature.” Front Neuroinform. 2009;3:29.  pubmed reprint supplement

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, 2009 Jul;60(7):2102-12. pubmed reprint

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. (2009) “Gene Expression Signatures in Polyarticular Juvenile Idiopathic Arthritis Demonstrate Disease Heterogeneity and Offer a Molecular Classification of Disease Subsets.” Arthritis and Rhematology, 2009 Jul;60(7):2113-23. pubmed reprint

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.  reprint supplement

Pantazatos SP, Li J, Pavlidis P, Lussier YA. (2012) “Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes.” Cancer Inform. Jun 8;8:75-94.  reprint
See also Summit on Translat Bioinforma. 2009 Mar 1;2009:85-9.  reprint

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. reprint

Papapanou PN, Behle JH, Kebschull M, Celenti R, Wolf DL, Handfield M, Pavlidis P, Demmer RT. (2009) “Subgingival bacterial colonization profiles correlate with gingival tissue gene expression.” BMC Microbiol. 2009 Oct 18;9:221. reprint


2008 Publications

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

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.  reprint

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

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.  reprint


2007 Publications

French L, Pavlidis P. (2007) “Informatics in Neuroscience.” Briefings in Bioinformatics. 2007 Nov;8(6):446-56. [Review] reprint

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

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.pubmed reprint

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. pubmed reprint

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. pubmed reprint

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. pubmed reprint


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. pubmed reprint

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

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


2005 Publications

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

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. (2005) “Transcriptional and behavioral interaction between 22q11.2 orthologs modulates schizophrenia-related phenotypes in mice.” Nat Neurosci 8(11):1586-94. pubmed reprint

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

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

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

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


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. (2004) “Gene expression in juvenile arthritis and spondyloarthropathy: pro-angiogenic ELR+ chemokine genes relate to course of arthritis.” Rheumatology (Oxford) 43(8):973-9. pubmed reprint

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

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

Pavlidis P, Qin J, Arango V, Mann JJ, Sibille E. (2004) “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. pubmed reprint

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

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

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

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


2003 Publications

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

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

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

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

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

Chen A, Muzzio IA, Malleret G, Bartsch D, Verbitsky M, Pavlidis P, Yonan AL, Vronskaya S, Grody MB, Cepeda I, Gilliam TC, Kandel ER. (2003) “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. pubmed reprint

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

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. (2003) “Classification of clear-cell sarcoma as a subtype of melanoma by genomic profiling.” J Clin Oncol. 2003 May 1;21(9):1775-81. pubmed reprint

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


2002 Publications

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

Schroder AJ, Pavlidis P, Arimura A, Capece D, Rothman PB. (2002) “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. pubmed reprint

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

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


2001 Publications

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

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

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. reprint

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. reprint

2000 Publications

Pavlidis, P., Montgomery, J., and Madison, D.V. (2000) “Presynaptic Protein Kinase Activity Supports Long-Term Potentiation at Synapses Between Individual Hippocampal Neurons.” Journal of Neuroscience 20, 4497-4505. pubmed reprint

Santoro, B., Chen S., Luthi, A., Pavlidis, P., Shumyatsky, G.P., Tibbs, G.R. and Siegelbaum, S.A. (2000) “Molecular and functional heterogeneity of hyperpolarization-activated pacemaker channels in the mouse CNS.” Journal of Neuroscience 20, 5264-5275. pubmed reprint


1999 & Earlier Publications

Pavlidis, P. and Madison, D.V. (1999) “Synaptic transmission in pair recordings from CA3 pyramidal cells in organotypic culture.” Journal of Neurophysiology 81, 2787-2797. pubmed reprint

Haley, J.E., Schaible, E., Pavlidis, P., Murdock, A., and Madison, D.V. (1996) “Basal and apical synapses of CA1 pyramidal cells employ different LTP induction mechanisms.” Learning and Memory 3, 289-295. pubmed reprint

Pavlidis, P. and Tanouye, M.A. (1995) “Seizures and failures in the giant fiber pathway of Drosophila bang-sensitive paralytic mutants.” Journal of Neuroscience 15, 5810-5819. pubmed reprint

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