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Paul Pavlidis

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Gene Expression Profiling

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Oligonucleotide Array Sequence Analysis

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TOP 3
Jesse Gillis; Paul Pavlidis
Assessing identity, redundancy and confounds in Gene Ontology annotations over time.
Elodie Portales-Casamar; Nicolas St-Georges; Luchia Tseng; Anton Zoubarev; Carolyn Ch'ng; Cathy Kwok; Willie Kwok; Artemis Y Lai; Mark Lee; Frances Lui; Paul Pavlidis
Neurocarta: aggregating and sharing disease-gene relations for the neurosciences.
Powell Patrick Cheng Tan; Leon French; Paul Pavlidis
Neuron-Enriched Gene Expression Patterns are Regionally Anti-Correlated with Oligodendrocyte-Enriched Patterns in the Adult Mouse and Human Brain.

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All Publications

2013: Jesse Gillis; Paul Pavlidis
Assessing identity, redundancy and confounds in Gene Ontology annotations over time.
Bioinformatics (Oxford, England) 2013;29(4):476-82.
2013: Elodie Portales-Casamar; Nicolas St-Georges; Luchia Tseng; Anton Zoubarev; Carolyn Ch'ng; Cathy Kwok; Willie Kwok; Artemis Y Lai; Mark Lee; Frances Lui; Paul Pavlidis
Neurocarta: aggregating and sharing disease-gene relations for the neurosciences.
BMC genomics 2013;14():129.
2013: Powell Patrick Cheng Tan; Leon French; Paul Pavlidis
Neuron-Enriched Gene Expression Patterns are Regionally Anti-Correlated with Oligodendrocyte-Enriched Patterns in the Adult Mouse and Human Brain.
Frontiers in neuroscience 2013;7():5.
2012: Leon French; Claudia Krebs; Cathy Kwok; Suzanne Lane; Celia Siu; Lydia Xu; Yiqi Chen; Paul Pavlidis
Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text.
Bioinformatics (Oxford, England) 2012;28(22):2963-70.
2012: Anton Zoubarev; Joseph Roy C Santos; Thea Van Rossum; Xiang Wan; Jesse Gillis; Adam Hall; Kelsey M Hamer; Kiran D Keshav; Raymond Lim; E Luke McCarthy; Cameron McDonald; Paul Pavlidis
Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data.
Bioinformatics (Oxford, England) 2012;28(17):2272-3.
2012: Spiro P Pantazatos; Paul Pavlidis; Ardesheer Talati; Joy Hirsch
Cortical functional connectivity decodes subconscious, task-irrelevant threat-related emotion processing.
NeuroImage 2012;61(4):1355-63.
2012: Leon French; Paul Pavlidis
Using text mining to link journal articles to neuroanatomical databases.
The Journal of comparative neurology 2012;520(8):1772-83.
2012: Jesse Gillis; Paul Pavlidis
"Guilt by association" is the exception rather than the rule in gene networks.
PLoS computational biology 2012;8(3):e1002444.
2012: Spiro P Pantazatos; Paul Pavlidis; Ardesheer Talati; Joy Hirsch
Decoding unattended fearful faces with whole-brain correlations: an approach to identify condition-dependent large-scale functional connectivity.
PLoS computational biology 2012;8(3):e1002441.
2011: Jesse Gillis; Paul Pavlidis
The role of indirect connections in gene networks in predicting function.
Bioinformatics (Oxford, England) 2011;27(13):1860-6.
2011: Elodie Portales-Casamar; Alan Evans; Wyeth W Wasserman; Paul Pavlidis
The NeuroDevNet Neuroinformatics Core.
Seminars in pediatric neurology 2011;18(1):17-20.
2011: Leon French; Powell Patrick Cheng Tan; Paul Pavlidis
Large-Scale Analysis of Gene Expression and Connectivity in the Rodent Brain: Insights through Data Integration.
Frontiers in neuroinformatics 2011;5():12.
2011: Leon French; Paul Pavlidis
Relationships between gene expression and brain wiring in the adult rodent brain.
PLoS computational biology 2011;7(1):e1001049.
2010: Jesse Gillis; Meeta Mistry; Paul Pavlidis
Gene function analysis in complex data sets using ErmineJ.
Nature protocols 2010;5(6):1148-59.
2010: Ryan T Demmer; Paul Pavlidis; Panos N Papapanou
Bioinformatics techniques in microarray research: applied microarray data analysis using R and SAS software.
Methods in molecular biology (Clifton, N.J.) 2010;666():395-417.
2009: Moritz Kebschull; R Demmer; J H Behle; A Pollreisz; J Heidemann; P B Belusko; Romanita Celenti; Paul Pavlidis; Panos N Papapanou
Granulocyte chemotactic protein 2 (gcp-2/cxcl6) complements interleukin-8 in periodontal disease.
Journal of periodontal research 2009;44(4):465-71.
2009: Leon French; Suzanne Lane; Tamryn Law; Lydia Xu; Paul Pavlidis
Application and evaluation of automated semantic annotation of gene expression experiments.
Bioinformatics (Oxford, England) 2009;25(12):1543-9.
2009: Sanja Rogic; Paul Pavlidis
Meta-analysis of kindling-induced gene expression changes in the rat hippocampus.
Frontiers in neuroscience 2009;3():53.
2009: Panos N Papapanou; Jan H Behle; Moritz Kebschull; Romanita Celenti; Dana L Wolf; Martin Handfield; Paul Pavlidis; Ryan T Demmer
Subgingival bacterial colonization profiles correlate with gingival tissue gene expression.
BMC microbiology 2009;9():221.
2009: Jesse Gillis; Paul Pavlidis
A methodology for the analysis of differential coexpression across the human lifespan.
BMC bioinformatics 2009;10():306.
2009: Leon French; Suzanne Lane; Lydia Xu; Paul Pavlidis
Automated recognition of brain region mentions in neuroscience literature.
Frontiers in neuroinformatics 2009;3():29.
2008: Ryan T Demmer; Jan H Behle; Dana L Wolf; Martin Handfield; Moritz Kebschull; Romanita Celenti; Paul Pavlidis; Panos N Papapanou
Transcriptomes in healthy and diseased gingival tissues.
Journal of periodontology 2008;79(11):2112-24.
2008: KL Stark; Bin Xu; Anindya Bagchi; Wen-Sung Lai; Hui Liu; Ruby Hsu; Xiang Wan; Paul Pavlidis; Alea A Mills; Maria Karayiorgou; Joseph A Gogos
Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model.
Nature genetics 2008;40(6):751-60.
2008: Meeta Mistry; Paul Pavlidis
Gene Ontology term overlap as a measure of gene functional similarity.
BMC bioinformatics 2008;9():327.
2007: Leon French; Paul Pavlidis
Informatics in neuroscience.
Briefings in bioinformatics 2007;8(6):446-56.
2007: Panos N Papapanou; Michael H Sedaghatfar; Ryan T Demmer; Dana L Wolf; Jun Yang; Georg A Roth; Romanita Celenti; Paul B Belusko; Evanthia Lalla; Paul Pavlidis
Periodontal therapy alters gene expression of peripheral blood monocytes.
Journal of clinical periodontology 2007;34(9):736-47.
2007: Kai M Schmidt-Ott; T Nestor H Masckauchan; Xia Chen; Benjamin J Hirsh; Abby Sarkar; Jun Yang; Neal Paragas; Valerie A Wallace; Daniel Dufort; Paul Pavlidis; Bernd Jagla; Jan Kitajewski; Jonathan Barasch
beta-catenin/TCF/Lef controls a differentiation-associated transcriptional program in renal epithelial progenitors.
Development (Cambridge, England) 2007;134(17):3177-90.
2007: Antoine Muchir; Paul Pavlidis; Gisèle Bonne; Yukiko K Hayashi; Howard J Worman
Activation of MAPK in hearts of EMD null mice: similarities between mouse models of X-linked and autosomal dominant Emery Dreifuss muscular dystrophy.
Human molecular genetics 2007;16(15):1884-95.
2007: Antoine Muchir; Paul Pavlidis; Valérie Decostre; Alan J Herron; Takuro Arimura; Gisèle Bonne; Howard J Worman
Activation of MAPK pathways links LMNA mutations to cardiomyopathy in Emery-Dreifuss muscular dystrophy.
The Journal of clinical investigation 2007;117(5):1282-93.
2007: Xiang Wan; Paul Pavlidis
Sharing and reusing gene expression profiling data in neuroscience.
Neuroinformatics 2007;5(3):161-75.
2006: Wen-Sung Lai; Bin Xu; Koen G C Westphal; Marta Paterlini; Berend Olivier; Paul Pavlidis; Maria Karayiorgou; Joseph A Gogos
Akt1 deficiency affects neuronal morphology and predisposes to abnormalities in prefrontal cortex functioning.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(45):16906-11.
2006: Zongyu Zheng; Paul Pavlidis; Streamson Chua Jr.; Vivette D D'Agati; Ali G Gharavi
An ancestral haplotype defines susceptibility to doxorubicin nephropathy in the laboratory mouse.
Journal of the American Society of Nephrology : JASN 2006;17(7):1796-800.
2005: Marta Paterlini; Stanislav S Zakharenko; Wen-Sung Lai; Jie Qin; Hui Zhang; Jun Mukai; Koen G C Westphal; Berend Olivier; David Sulzer; Paul Pavlidis; Steven A Siegelbaum; Maria Karayiorgou; Joseph A Gogos
Transcriptional and behavioral interaction between 22q11.2 orthologs modulates schizophrenia-related phenotypes in mice.
Nature neuroscience 2005;8(11):1586-94.
2005: Loubna Erraji-Benchekroun; Mark D Underwood; Victoria Arango; Hanga C Galfalvy; Paul Pavlidis; Peggy Smyrniotopoulos; J John Mann; Etienne Sibille
Molecular aging in human prefrontal cortex is selective and continuous throughout adult life.
Biological psychiatry 2005;57(5):549-58.
2005: Zongyu Zheng; Kai M Schmidt-Ott; Streamson Chua Jr.; Kirk A Foster; Rachelle Z Frankel; Paul Pavlidis; Jonathan Barasch; Vivette D D'Agati; Ali G Gharavi
A Mendelian locus on chromosome 16 determines susceptibility to doxorubicin nephropathy in the mouse.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(7):2502-7.
2005: Homin K Lee; William Braynen; Kiran Keshav; Paul Pavlidis
ErmineJ: tool for functional analysis of gene expression data sets.
BMC bioinformatics 2005;6():269.
2004: Paul Pavlidis; Jie Qin; Victoria Arango; J John Mann; Etienne Sibille
Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex.
Neurochemical research 2004;29(6):1213-22.
2004: Homin K Lee; Amy K Hsu; Jon Sajdak; Jie Qin; Paul Pavlidis
Coexpression analysis of human genes across many microarray data sets.
Genome research 2004;14(6):1085-94.
2004: Panos N Papapanou; Armin Abron; Miguel Verbitsky; Doros Picolos; Jun Yang; Jie Qin; James B Fine; Paul Pavlidis
Gene expression signatures in chronic and aggressive periodontitis: a pilot study.
European journal of oral sciences 2004;112(3):216-23.
2004: Miguel Verbitsky; Amanda L Yonan; Gaël Malleret; Eric R Kandel; T Conrad Gilliam; Paul Pavlidis
Altered hippocampal transcript profile accompanies an age-related spatial memory deficit in mice.
Learning & memory (Cold Spring Harbor, N.Y.) 2004;11(3):253-60.
2004: Paul Pavlidis; Ilan Wapinski; William Stafford Noble
Support vector machine classification on the web.
Bioinformatics (Oxford, England) 2004;20(4):586-7.
2004: Dayu Li; Wanchao Ma; Fang Sun; Paul Pavlidis; Abraham Spector
Cluster analysis of genes with significant change in expression in cells conditioned to survive TBOOH.
Experimental eye research 2004;78(2):301-8.
2004: Etienne Sibille; Victoria Arango; Hanga C Galfalvy; Paul Pavlidis; Loubna Erraji-Benchekroun; Steven P Ellis; J John Mann
Gene expression profiling of depression and suicide in human prefrontal cortex.
Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology 2004;29(2):351-61.
2003: Paul Pavlidis
Using ANOVA for gene selection from microarray studies of the nervous system.
Methods (San Diego, Calif.) 2003;31(4):282-9.
2003: Amanda L Yonan; Abraham A Palmer; K C Smith; I Feldman; H K Lee; J M Yonan; SG Fischer; Paul Pavlidis; T Conrad Gilliam
Bioinformatic analysis of autism positional candidate genes using biological databases and computational gene network prediction.
Genes, brain, and behavior 2003;2(5):303-20.
2003: Hanga C Galfalvy; Loubna Erraji-Benchekroun; Peggy Smyrniotopoulos; Paul Pavlidis; Steven P Ellis; J John Mann; Etienne Sibille; Victoria Arango
Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction.
BMC bioinformatics 2003;4():37.
2003: Paul Pavlidis; Qinghong Li; William Stafford Noble
The effect of replication on gene expression microarray experiments.
Bioinformatics (Oxford, England) 2003;19(13):1620-7.
2003: Amy Chen; Isabel A Muzzio; Gaël Malleret; Dusan Bartsch; Miguel Verbitsky; Paul Pavlidis; Amanda L Yonan; Svetlana Vronskaya; Michael B Grody; Ivan Cepeda; T Conrad Gilliam; Eric R Kandel
Inducible enhancement of memory storage and synaptic plasticity in transgenic mice expressing an inhibitor of ATF4 (CREB-2) and C/EBP proteins.
Neuron 2003;39(4):655-69.
2003: Neil H Segal; Paul Pavlidis; Cristina R Antonescu; ROBERT G MAKI; William Stafford Noble; Diann DeSantis; James M Woodruff; Jonathan J Lewis; Murray F Brennan; Alan N Houghton; Carlos Cordon-Cardo
Classification and subtype prediction of adult soft tissue sarcoma by functional genomics.
The American journal of pathology 2003;163(2):691-700.
2003: Neil H Segal; Paul Pavlidis; William Stafford Noble; Cristina R Antonescu; Agnes Viale; Umadevi V Wesley; Klaus J Busam; Humilidad F Gallardo; Diann DeSantis; Murray F Brennan; Carlos Cordon-Cardo; Jedd D Wolchok; Alan N Houghton
Classification of clear-cell sarcoma as a subtype of melanoma by genomic profiling.
Journal of clinical oncology : official journal of the American Society of Clinical Oncology 2003;21(9):1775-81.
2003: Paul Pavlidis; William Stafford Noble
Matrix2png: a utility for visualizing matrix data.
Bioinformatics (Oxford, England) 2003;19(2):295-6.
2002: Abraham Spector; Dayu Li; Wanchao Ma; Fang Sun; Paul Pavlidis
Differential amplification of gene expression in lens cell lines conditioned to survive peroxide stress.
Investigative ophthalmology & visual science 2002;43(10):3251-64.
2002: Andreas J Schroder; Paul Pavlidis; Akinori Arimura; Danielle Capece; Paul B Rothman
Cutting edge: STAT6 serves as a positive and negative regulator of gene expression in IL-4-stimulated B lymphocytes.
Journal of immunology (Baltimore, Md. : 1950) 2002;168(3):996-1000.
2002: Paul Pavlidis; Jason Weston; Jinsong Cai; William Stafford Noble
Learning gene functional classifications from multiple data types.
Journal of computational biology : a journal of computational molecular cell biology 2002;9(2):401-11.
2002: Paul Pavlidis; Darrin P Lewis; William Stafford Noble
Exploring gene expression data with class scores.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2002;():474-85.
2001: R A Muhle; Paul Pavlidis; WN Grundy; Emmet Hirsch
A high-throughput study of gene expression in preterm labor with a subtractive microarray approach.
American journal of obstetrics and gynecology 2001;185(3):716-24.
2001: Paul Pavlidis; William Stafford Noble
Analysis of strain and regional variation in gene expression in mouse brain.
Genome biology 2001;2(10):RESEARCH0042.
2001: Paul Pavlidis; Terrence S Furey; M Liberto; David Haussler; WN Grundy
Promoter region-based classification of genes.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001;():151-63.
2000: Bina Santoro; S Chen; A Luthi; Paul Pavlidis; Gleb P Shumyatsky; Gareth R Tibbs; Steven A Siegelbaum
Molecular and functional heterogeneity of hyperpolarization-activated pacemaker channels in the mouse CNS.
The Journal of neuroscience : the official journal of the Society for Neuroscience 2000;20(14):5264-75.