Research Topics
| P PavlidisSummaryAffiliation: Columbia University Country: USA Publications
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Detail Information
Publications
Sex genes for genomic analysis in human brain: internal controls for comparison of probe level data extractionHanga 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...
Support vector machine classification on the webPaul 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...- Using ANOVA for gene selection from microarray studies of the nervous systemPaul 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/... - The effect of replication on gene expression microarray experimentsPaul Pavlidis
Columbia Genome Center, Columbia University, 1150 St Nicholas Avenue, New York, NY 10032, USA
Bioinformatics 19:1620-7. 2003..Our methods will be of use in evaluating existing data sets and in helping to design new studies... - Using the gene ontology for microarray data mining: a comparison of methods and application to age effects in human prefrontal cortexPaul Pavlidis
Department of Biomedical Informatics and Columbia Genome Center, Columbia University, New York, New York 10032, USA
Neurochem Res 29:1213-22. 2004..quot;.. - Matrix2png: a utility for visualizing matrix dataPaul Pavlidis
Columbia Genome Center, Columbia University, New York, USA
Bioinformatics 19:295-6. 2003..AVAILABILITY: A simple web interface is available, and Unix binaries are available from http://microarray.cpmc.columbia.edu/matrix2png. Source code is available on request... - Analysis of strain and regional variation in gene expression in mouse brainP Pavlidis
Columbia Genome Center, Columbia University, 1150 St Nicholas Avenue, New York, NY 10032, USA
Genome Biol 2:RESEARCH0042. 2001.... - Molecular aging in human prefrontal cortex is selective and continuous throughout adult lifeLoubna Erraji-Benchekroun
Department of Psychiatry, Columbia University, New York, New York, USA
Biol Psychiatry 57:549-58. 2005.... - Transcriptomes in healthy and diseased gingival tissuesRyan 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... - Learning gene functional classifications from multiple data typesPaul 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... - A high-throughput study of gene expression in preterm labor with a subtractive microarray approachR 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... - Differential amplification of gene expression in lens cell lines conditioned to survive peroxide stressAbraham 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... - Microarray analysis of gene expression following the formalin test in the infant ratGordon 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... - Gene expression signatures in chronic and aggressive periodontitis: a pilot studyPanos 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... - ErmineJ: tool for functional analysis of gene expression data setsHomin 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... - Transcriptional and behavioral interaction between 22q11.2 orthologs modulates schizophrenia-related phenotypes in miceMarta 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... - Gene expression profiling of depression and suicide in human prefrontal cortexEtienne Sibille
Department of Psychiatry, Columbia University, New York, NY, USA
Neuropsychopharmacology 29:351-61. 2004.... - Subgingival bacterial colonization profiles correlate with gingival tissue gene expressionPanos 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... - beta-catenin/TCF/Lef controls a differentiation-associated transcriptional program in renal epithelial progenitorsKai 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... - Periodontal therapy alters gene expression of peripheral blood monocytesPanos 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... - Classification and subtype prediction of adult soft tissue sarcoma by functional genomicsNeil 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... - Molecular and functional heterogeneity of hyperpolarization-activated pacemaker channels in the mouse CNSB 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... - Classification of clear-cell sarcoma as a subtype of melanoma by genomic profilingNeil 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... - Coexpression analysis of human genes across many microarray data setsHomin 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... - Altered hippocampal transcript profile accompanies an age-related spatial memory deficit in miceMiguel 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... 
Bioinformatics techniques in microarray research: applied microarray data analysis using R and SAS softwareRyan 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...- Bioinformatic analysis of autism positional candidate genes using biological databases and computational gene network predictionA 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... - Cutting edge: STAT6 serves as a positive and negative regulator of gene expression in IL-4-stimulated B lymphocytesAndreas 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... - Akt1 deficiency affects neuronal morphology and predisposes to abnormalities in prefrontal cortex functioningWen 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.... - Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse modelKimberly 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... - Activation of MAPK pathways links LMNA mutations to cardiomyopathy in Emery-Dreifuss muscular dystrophyAntoine 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... - A Mendelian locus on chromosome 16 determines susceptibility to doxorubicin nephropathy in the mouseZongyu 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... - Inducible enhancement of memory storage and synaptic plasticity in transgenic mice expressing an inhibitor of ATF4 (CREB-2) and C/EBP proteinsAmy 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... - Activation of MAPK in hearts of EMD null mice: similarities between mouse models of X-linked and autosomal dominant Emery Dreifuss muscular dystrophyAntoine 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... - Hierarchical model of gene regulation by transforming growth factor betaYaw-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.... - Sharing and reusing gene expression profiling data in neuroscienceXiang 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... - Gene Ontology term overlap as a measure of gene functional similarityMeeta 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)... - Cluster analysis of genes with significant change in expression in cells conditioned to survive TBOOHDayu 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... - Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platformsMichael 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... - Zac1 regulates an imprinted gene network critically involved in the control of embryonic growthAnnie 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... - Informatics in neuroscienceLeon 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...