P Pavlidis

Summary

Affiliation: Columbia University
Country: USA

Publications

  1. pmc Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction
    Hanga C Galfalvy
    Department of Neuroscience, New York State Psychiatric Institute, New York, NY 10032, USA
    BMC Bioinformatics 4:37. 2003
  2. ncbi request reprint Support vector machine classification on the web
    Paul Pavlidis
    Columbia Genome Center and Department of Biomedical Informatics, Columbia University, 1150 St Nicholas Avenue, New York, NY 10032, USA
    Bioinformatics 20:586-7. 2004
  3. ncbi request reprint Using ANOVA for gene selection from microarray studies of the nervous system
    Paul Pavlidis
    Department of Biomedical Informatics and Columbia Genome Center, Columbia University, Rm 121J, 1150 St Nicholas Avenue, New York, NY 10032, USA
    Methods 31:282-9. 2003
  4. ncbi request reprint The effect of replication on gene expression microarray experiments
    Paul Pavlidis
    Columbia Genome Center, Columbia University, 1150 St Nicholas Avenue, New York, NY 10032, USA
    Bioinformatics 19:1620-7. 2003
  5. ncbi request reprint Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex
    Paul Pavlidis
    Department of Biomedical Informatics and Columbia Genome Center, Columbia University, New York, New York 10032, USA
    Neurochem Res 29:1213-22. 2004
  6. ncbi request reprint Matrix2png: a utility for visualizing matrix data
    Paul Pavlidis
    Columbia Genome Center, Columbia University, New York, USA
    Bioinformatics 19:295-6. 2003
  7. pmc Analysis of strain and regional variation in gene expression in mouse brain
    P Pavlidis
    Columbia Genome Center, Columbia University, 1150 St Nicholas Avenue, New York, NY 10032, USA
    Genome Biol 2:RESEARCH0042. 2001
  8. ncbi request reprint Molecular aging in human prefrontal cortex is selective and continuous throughout adult life
    Loubna Erraji-Benchekroun
    Department of Psychiatry, Columbia University, New York, New York, USA
    Biol Psychiatry 57:549-58. 2005
  9. pmc Transcriptomes in healthy and diseased gingival tissues
    Ryan T Demmer
    Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
    J Periodontol 79:2112-24. 2008
  10. ncbi request reprint Learning gene functional classifications from multiple data types
    Paul Pavlidis
    Columbia Genome Center, Columbia University, New York, NY 10027, USA
    J Comput Biol 9:401-11. 2002

Collaborators

Detail Information

Publications41

  1. pmc Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extraction
    Hanga C Galfalvy
    Department of Neuroscience, New York State Psychiatric Institute, New York, NY 10032, USA
    BMC Bioinformatics 4:37. 2003
    ..We introduce the idea of using sex-chromosome genes as an alternative to spiked-in control genes or simulations for assessment of microarray data and analysis methods...
  2. ncbi request reprint Support vector machine classification on the web
    Paul Pavlidis
    Columbia Genome Center and Department of Biomedical Informatics, Columbia University, 1150 St Nicholas Avenue, New York, NY 10032, USA
    Bioinformatics 20:586-7. 2004
    ..More advanced users can download the software and source code for local installation. The availability of these tools will permit more widespread application of this powerful learning algorithm in bioinformatics...
  3. ncbi request reprint Using ANOVA for gene selection from microarray studies of the nervous system
    Paul Pavlidis
    Department of Biomedical Informatics and Columbia Genome Center, Columbia University, Rm 121J, 1150 St Nicholas Avenue, New York, NY 10032, USA
    Methods 31:282-9. 2003
    ..Instructions for running typical analyses are given in the R programming environment. R code and the sample data set used to generate the examples are available at http://microarray.cpmc.columbia.edu/pavlidis/pub/aovmethods/...
  4. ncbi request reprint The effect of replication on gene expression microarray experiments
    Paul Pavlidis
    Columbia Genome Center, Columbia University, 1150 St Nicholas Avenue, New York, NY 10032, USA
    Bioinformatics 19:1620-7. 2003
    ..We consider both the ability to find genes that meet particular statistical criteria as well as the stability of the results in the face of changing levels of replication...
  5. ncbi request reprint Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortex
    Paul Pavlidis
    Department of Biomedical Informatics and Columbia Genome Center, Columbia University, New York, New York 10032, USA
    Neurochem Res 29:1213-22. 2004
    ..quot;..
  6. ncbi request reprint Matrix2png: a utility for visualizing matrix data
    Paul Pavlidis
    Columbia Genome Center, Columbia University, New York, USA
    Bioinformatics 19:295-6. 2003
    ..In this note we describe some of matrix2png's features and describe some places it has been useful in the authors' work...
  7. pmc Analysis of strain and regional variation in gene expression in mouse brain
    P Pavlidis
    Columbia Genome Center, Columbia University, 1150 St Nicholas Avenue, New York, NY 10032, USA
    Genome Biol 2:RESEARCH0042. 2001
    ....
  8. ncbi request reprint Molecular aging in human prefrontal cortex is selective and continuous throughout adult life
    Loubna Erraji-Benchekroun
    Department of Psychiatry, Columbia University, New York, New York, USA
    Biol Psychiatry 57:549-58. 2005
    ..Aging leads to morphologic and functional changes in the brain and is associated with increased risk for psychiatric and neurological disorders...
  9. pmc Transcriptomes in healthy and diseased gingival tissues
    Ryan T Demmer
    Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
    J Periodontol 79:2112-24. 2008
    ..We hypothesized that a comparison of gene expression signatures between healthy and diseased gingival tissues would provide novel insights in the pathobiology of periodontitis and would inform the design of future studies...
  10. ncbi request reprint Learning gene functional classifications from multiple data types
    Paul Pavlidis
    Columbia Genome Center, Columbia University, New York, NY 10027, USA
    J Comput Biol 9:401-11. 2002
    ..In particular, we propose an SVM kernel function that is explicitly heterogeneous. In addition, we describe feature scaling methods for further exploiting prior knowledge of heterogeneity by giving each data type different weights...
  11. ncbi request reprint A high-throughput study of gene expression in preterm labor with a subtractive microarray approach
    R A Muhle
    Department of Obstetrics and Gynecology, Columbia University College of Physicians and Surgeons, New York, NY, USA
    Am J Obstet Gynecol 185:716-24. 2001
    ..CONCLUSION: This study demonstrates the potential of the subtractive DNA microarray technique to identify transcripts important specifically for bacterially induced preterm labor...
  12. ncbi request reprint Differential amplification of gene expression in lens cell lines conditioned to survive peroxide stress
    Abraham Spector
    Department of Ophthalmology, Columbia University, New York, New York 10032, USA
    Invest Ophthalmol Vis Sci 43:3251-64. 2002
    ..Therefore, mouse lens cell lines conditioned to survive different peroxide stresses have been analyzed to determine their global changes in gene expression...
  13. ncbi request reprint Microarray analysis of gene expression following the formalin test in the infant rat
    Gordon A Barr
    Department of Developmental Psychobiology, New York State Psychiatric Institute, New York, NY, USA
    Pain 117:6-18. 2005
    ..The increased expression of transcription factors and decreased expression of genes whose products are protective against cell death are hypothesized to underlie the long-term changes that are seen after injury in the neonate...
  14. ncbi request reprint Gene expression signatures in chronic and aggressive periodontitis: a pilot study
    Panos N Papapanou
    Division of Periodontics, Section of Oral and Diagnostic Sciences, School of Dental and Oral Surgery, Columbia University, New York, NY 10032, USA
    Eur J Oral Sci 112:216-23. 2004
    ..These early data point to the usefulness of gene expression profiling techniques in the identification of subclasses of periodontitis with common pathobiology...
  15. pmc ErmineJ: tool for functional analysis of gene expression data sets
    Homin K Lee
    Columbia Genome Center, Columbia University, New York, NY 10032, USA
    BMC Bioinformatics 6:269. 2005
    ..However, this method suffers from some limitations, and biologist-friendly tools that implement alternatives have not been reported...
  16. ncbi request reprint Transcriptional and behavioral interaction between 22q11.2 orthologs modulates schizophrenia-related phenotypes in mice
    Marta Paterlini
    Department of Physiology and Cellular Biophysics, Columbia University College of Physicians and Surgeons, 701 West 168th Street, New York, New York 10032, USA
    Nat Neurosci 8:1586-94. 2005
    ..This interaction modulates a number of schizophrenia-related phenotypes, providing a framework for understanding the high disease risk associated with this locus, the expression of the phenotype, or both...
  17. ncbi request reprint Gene expression profiling of depression and suicide in human prefrontal cortex
    Etienne Sibille
    Department of Psychiatry, Columbia University, New York, NY, USA
    Neuropsychopharmacology 29:351-61. 2004
    ....
  18. pmc Subgingival bacterial colonization profiles correlate with gingival tissue gene expression
    Panos N Papapanou
    Division of Periodontics, Section of Oral and Diagnostic Sciences, College of Dental Medicine, Columbia University, New York, NY, USA
    BMC Microbiol 9:221. 2009
    ..Random effects linear regression models considered bacterial levels as exposure and expression profiles as outcome variables. Gene Ontology analyses summarized the expression patterns into biologically relevant categories...
  19. ncbi request reprint beta-catenin/TCF/Lef controls a differentiation-associated transcriptional program in renal epithelial progenitors
    Kai M Schmidt-Ott
    Department of Medicine, Columbia University College of Physicians and Surgeons, 630 West 168th Street, New York, NY 10032, USA
    Development 134:3177-90. 2007
    ..Thus, beta-catenin/TCF/Lef-mediated transcriptional events control a subset of the differentiation-associated transcriptional program and thereby participate in maintenance, expansion and stage progression of the epithelial lineage...
  20. pmc Periodontal therapy alters gene expression of peripheral blood monocytes
    Panos N Papapanou
    Division of Periodontics, Section of Oral and Diagnostic Sciences, College of Dental Medicine, Columbia University, New York, NY 10032, USA
    J Clin Periodontol 34:736-47. 2007
    ..We investigated the effects of periodontal therapy on gene expression of peripheral blood monocytes...
  21. pmc Classification and subtype prediction of adult soft tissue sarcoma by functional genomics
    Neil H Segal
    Swim Across America Laboratory, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York and Columbia Genome Center, Columbia University, New York, New York 10021, USA
    Am J Pathol 163:691-700. 2003
    ..In conclusion, we showed gene expression profiling to be useful in classification and diagnosis, providing insights into pathogenesis and pointing to potential new therapeutic targets of soft tissue sarcoma...
  22. ncbi request reprint Molecular and functional heterogeneity of hyperpolarization-activated pacemaker channels in the mouse CNS
    B Santoro
    Center for Neurobiology and Behavior, Departments of Pharmacology and Anesthesiology, and Howard Hughes Medical Institute, Columbia University, New York, New York 10032, USA
    J Neurosci 20:5264-75. 2000
    ..Moreover, in some neurons, specific functional roles can be proposed for I(h) channels with defined subunit composition...
  23. ncbi request reprint Classification of clear-cell sarcoma as a subtype of melanoma by genomic profiling
    Neil H Segal
    Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY 10021, USA
    J Clin Oncol 21:1775-81. 2003
    ..CCS/MSP also has typical melanoma features, including immunoreactivity for S100 and HMB45, pigmentation, MITF-M expression, and a propensity for regional lymph node metastases...
  24. pmc Coexpression analysis of human genes across many microarray data sets
    Homin K Lee
    Columbia Genome Center, Columbia University, New York, New York 10032, USA
    Genome Res 14:1085-94. 2004
    ..Our findings demonstrate how the large body of accumulated microarray data can be exploited to increase the reliability of inferences about gene function...
  25. pmc Altered hippocampal transcript profile accompanies an age-related spatial memory deficit in mice
    Miguel Verbitsky
    Columbia Genome Center, College of Physicians and Surgeons, Columbia University, New York, New York 10032, USA
    Learn Mem 11:253-60. 2004
    ..Those changes could be involved in the memory deficits we observed in the 15-month-old mice. In agreement with previous reports, we also found altered expression in genes related to inflammation, protein processing, and oxidative stress...
  26. doi request reprint Bioinformatics techniques in microarray research: applied microarray data analysis using R and SAS software
    Ryan T Demmer
    Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
    Methods Mol Biol 666:395-417. 2010
    ..All analyses described in this chapter can be performed using relatively limited computational resources such as a lap top PC with at least 2.0 GB of memory and 2.0 GHz of processing speed...
  27. ncbi request reprint Bioinformatic analysis of autism positional candidate genes using biological databases and computational gene network prediction
    A L Yonan
    Columbia Genome Center, Columbia University, New York, NY 10032, USA
    Genes Brain Behav 2:303-20. 2003
    ..The studies are intended both to inform studies of autism, and to illustrate and explore the increasing potential of bioinformatic approaches as a compliment to linkage analysis...
  28. ncbi request reprint Cutting edge: STAT6 serves as a positive and negative regulator of gene expression in IL-4-stimulated B lymphocytes
    Andreas J Schroder
    Department of Medicine, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, NY 10032, USA
    J Immunol 168:996-1000. 2002
    ..Furthermore, IL-4 induces expression of the transcription factor Krox20, which is required for maximal IL-4-induced transcription...
  29. pmc Akt1 deficiency affects neuronal morphology and predisposes to abnormalities in prefrontal cortex functioning
    Wen Sung Lai
    Department of Physiology and Cellular Biophysics, Columbia University College of Physicians and Surgeons, 630 West 168th Street, New York, NY 10032, USA
    Proc Natl Acad Sci U S A 103:16906-11. 2006
    ....
  30. doi request reprint Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model
    Kimberly L Stark
    Department of Psychiatry, College of Physicians and Surgeons, Columbia University, 1051 Riverside Drive, New York, New York 10032, USA
    Nat Genet 40:751-60. 2008
    ..2 microdeletion...
  31. pmc Activation of MAPK pathways links LMNA mutations to cardiomyopathy in Emery-Dreifuss muscular dystrophy
    Antoine Muchir
    Department of Medicine, College of Physicians and Surgeons, Columbia University, 630 West 168th Street New York, NY 10032, USA
    J Clin Invest 117:1282-93. 2007
    ..Activation of MAPK signaling by mutant A-type lamins could be a cornerstone in the development of heart disease in autosomal dominant Emery-Dreifuss muscular dystrophy...
  32. pmc A Mendelian locus on chromosome 16 determines susceptibility to doxorubicin nephropathy in the mouse
    Zongyu Zheng
    Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
    Proc Natl Acad Sci U S A 102:2502-7. 2005
    ..Elucidation of DOX nephropathy may simultaneously provide insight into the pathogenesis of renal failure and mechanisms of cytotoxicity induced by chemotherapeutic agents...
  33. ncbi request reprint Inducible enhancement of memory storage and synaptic plasticity in transgenic mice expressing an inhibitor of ATF4 (CREB-2) and C/EBP proteins
    Amy Chen
    Center for Neurobiology and Behavior, Columbia University, College of Physicians and Surgeons, New York, NY 10032, USA
    Neuron 39:655-69. 2003
    ..Relief of this inhibition lowers the threshold for hippocampal-dependent long-term synaptic potentiation and memory storage in mice...
  34. ncbi request reprint Activation of MAPK in hearts of EMD null mice: similarities between mouse models of X-linked and autosomal dominant Emery Dreifuss muscular dystrophy
    Antoine Muchir
    Department of Medicine, College of Physicians and Surgeons, Columbia University, New York 10032, USA
    Hum Mol Genet 16:1884-95. 2007
    ..Activation of MAPK signaling appears to be a cornerstone in the development of heart disease in both X-linked and autosomal dominant EDMD...
  35. pmc Hierarchical model of gene regulation by transforming growth factor beta
    Yaw Ching Yang
    Departments of Medicine and Molecular Genetics, Albert Einstein College of Medicine, Bronx, NY 10461
    Proc Natl Acad Sci U S A 100:10269-74. 2003
    ....
  36. pmc Sharing and reusing gene expression profiling data in neuroscience
    Xiang Wan
    Department of Psychiatry, UBC Bioinformatics Centre, University of British Columbia, 177 Michael Smith Laboratories 2185 East Mall, Vancouver, BC V6T1Z4, Canada
    Neuroinformatics 5:161-75. 2007
    ..Techniques and tools for data reuse are also in need of improvement. Integration of expression profiling data with neuroscience-specific resources such as anatomical atlases will further increase the value of expression data...
  37. pmc Gene Ontology term overlap as a measure of gene functional similarity
    Meeta Mistry
    Department of Psychiatry and Centre for High Throughput Biology, University of British Columbia, British Columbia, Canada
    BMC Bioinformatics 9:327. 2008
    ..A number of groups have suggested that the semantic similarity of the GO annotations of genes can serve as a proxy for functional relatedness. Here we evaluate a simple measure of semantic similarity, term overlap (TO)...
  38. ncbi request reprint Cluster analysis of genes with significant change in expression in cells conditioned to survive TBOOH
    Dayu Li
    Exp Eye Res 78:301-8. 2004
    ..The analysis has revealed a small group of antioxidative defense genes that contribute to the survival of T and H cells when exposed to oxidative stress...
  39. pmc Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platforms
    Michael Barnes
    Cincinnati Children s Hospital Medical Center, Division of Rheumatology, Cincinnati, OH, USA
    Nucleic Acids Res 33:5914-23. 2005
    ..The set of probes we found to be most highly reproducible can be used by others to help increase confidence in analyses of other data sets using these platforms...
  40. ncbi request reprint Zac1 regulates an imprinted gene network critically involved in the control of embryonic growth
    Annie Varrault
    Institut de Genomique Fonctionnelle, CNRS UMR5203, INSERM U661, Universite Montpellier 1, Universite Montpellier 2, Montpellier, F 34094, France
    Dev Cell 11:711-22. 2006
    ..Accordingly, these data identify a network of imprinted genes, including Zac1, which controls embryonic growth and which may be the basis for the implementation of a common mechanism of gene regulation during mammalian evolution...
  41. ncbi request reprint Informatics in neuroscience
    Leon French
    UBC Bioinformatics Centre UBiC, 177, Michael Smith Laboratories, 2185 East Mall, University of British Columbia, Vancouver BC V6T1Z4, Canada
    Brief Bioinform 8:446-56. 2007
    ..The continuing development of standards for data exchange and interoperability, together with increasing awareness and acceptance of the importance of data sharing, are among the key efforts required to advance the field...