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Paul Pavlidis - Publications

University of British Columbia, Vancouver, Vancouver, BC, Canada 

136 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Farahbod M, Pavlidis P. Untangling the effects of cellular composition on coexpression analysis. Genome Research. PMID 32580998 DOI: 10.1101/gr.256735.119  1
2020 Post KL, Belmadani M, Ganguly P, Meili F, Dingwall R, McDiarmid TA, Meyers WM, Herrington C, Young BP, Callaghan DB, Rogic S, Edwards M, Niciforovic A, Cau A, Rankin CH, ... ... Pavlidis P, et al. Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction. Nature Communications. 11: 2073. PMID 32350270 DOI: 10.1038/s41467-020-15943-0  0.84
2020 Nagy C, Maitra M, Tanti A, Suderman M, Théroux JF, Davoli MA, Perlman K, Yerko V, Wang YC, Tripathy SJ, Pavlidis P, Mechawar N, Ragoussis J, Turecki G. Single-nucleus transcriptomics of the prefrontal cortex in major depressive disorder implicates oligodendrocyte precursor cells and excitatory neurons. Nature Neuroscience. PMID 32341540 DOI: 10.1038/s41593-020-0621-y  0.84
2019 Zhuang B, Mancarci BO, Toker L, Pavlidis P. Mega-Analysis of Gene Expression in Mouse Models of Alzheimer's Disease. Eneuro. 6. PMID 31767574 DOI: 10.1523/ENEURO.0226-19.2019  1
2019 McDiarmid TA, Belmadani M, Liang J, Meili F, Mathews EA, Mullen GP, Hendi A, Wong WR, Rand JB, Mizumoto K, Haas K, Pavlidis P, Rankin CH. Systematic phenomics analysis of autism-associated genes reveals parallel networks underlying reversible impairments in habituation. Proceedings of the National Academy of Sciences of the United States of America. PMID 31754030 DOI: 10.1073/pnas.1912049116  0.84
2019 Belmadani M, Jacobson M, Holmes N, Phan M, Nguyen T, Pavlidis P, Rogic S. VariCarta: A Comprehensive Database of Harmonized Genomic Variants Found in Autism Spectrum Disorder Sequencing Studies. Autism Research : Official Journal of the International Society For Autism Research. PMID 31705629 DOI: 10.1002/aur.2236  0.84
2019 Bomkamp C, Tripathy SJ, Bengtsson Gonzales C, Hjerling-Leffler J, Craig AM, Pavlidis P. Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes. Plos Computational Biology. 15: e1007113. PMID 31211786 DOI: 10.1371/journal.pcbi.1007113  0.84
2019 Callaghan DB, Rogic S, Tan PPC, Calli K, Qiao Y, Baldwin R, Jacobson M, Belmadani M, Holmes N, Yu C, Li Y, Li Y, Kurtzke FE, Kuzeljevic B, Yu A, ... ... Pavlidis P, et al. Whole genome sequencing and variant discovery in the ASPIRE autism spectrum disorder cohort. Clinical Genetics. PMID 31038196 DOI: 10.1111/cge.13556  0.84
2019 Crow M, Lim N, Ballouz S, Pavlidis P, Gillis J. Predictability of human differential gene expression. Proceedings of the National Academy of Sciences of the United States of America. PMID 30846554 DOI: 10.1073/pnas.1802973116  0.48
2018 Tripathy SJ, Toker L, Bomkamp C, Mancarci BO, Belmadani M, Pavlidis P. Assessing Transcriptome Quality in Patch-Seq Datasets. Frontiers in Molecular Neuroscience. 11: 363. PMID 30349457 DOI: 10.3389/fnmol.2018.00363  1
2018 Toker L, Mancarci BO, Tripathy S, Pavlidis P. Transcriptomic Evidence for Alterations in Astrocytes and Parvalbumin Interneurons in Subjects With Bipolar Disorder and Schizophrenia. Biological Psychiatry. PMID 30177255 DOI: 10.1016/j.biopsych.2018.07.010  1
2018 Farahbod M, Pavlidis P. Differential coexpression in human tissues and the confounding effect of mean expression levels. Bioinformatics (Oxford, England). PMID 29982380 DOI: 10.1093/bioinformatics/bty538  1
2018 Dufour A, Bellac CL, Eckhard U, Solis N, Klein T, Kappelhoff R, Fortelny N, Jobin P, Rozmus J, Mark J, Pavlidis P, Dive V, Barbour SJ, Overall CM. C-terminal truncation of IFN-γ inhibits proinflammatory macrophage responses and is deficient in autoimmune disease. Nature Communications. 9: 2416. PMID 29925830 DOI: 10.1038/s41467-018-04717-4  0.64
2017 Tebaykin D, Tripathy SJ, Binnion N, Li B, Gerkin RC, Pavlidis P. Modeling sources of inter-laboratory variability in electrophysiological properties of mammalian neurons. Journal of Neurophysiology. PMID 29357465 DOI: 10.1152/jn.00604.2017  0.84
2017 Mancarci BO, Toker L, Tripathy SJ, Li B, Rocco B, Sibille E, Pavlidis P. Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data. Eneuro. 4. PMID 29204516 DOI: 10.1523/ENEURO.0212-17.2017  1
2017 Tripathy SJ, Toker L, Li B, Crichlow CL, Tebaykin D, Mancarci BO, Pavlidis P. Transcriptomic correlates of neuron electrophysiological diversity. Plos Computational Biology. 13: e1005814. PMID 29069078 DOI: 10.1371/journal.pcbi.1005814  1
2017 Fortelny N, Overall CM, Pavlidis P, Freue GVC. Can we predict protein from mRNA levels? Nature. 547: E19-E20. PMID 28748932 DOI: 10.1038/nature22293  0.64
2017 Fortelny N, Butler GS, Overall CM, Pavlidis P. Protease-inhibitor interaction predictions: Lessons on the complexity of protein-protein interactions. Molecular & Cellular Proteomics : McP. PMID 28385878 DOI: 10.1074/mcp.M116.065706  0.64
2017 Ballouz S, Pavlidis P, Gillis J. Using predictive specificity to determine when gene set analysis is biologically meaningful. Nucleic Acids Research. 45: e20. PMID 28204549 DOI: 10.1093/nar/gkw957  0.48
2016 Ballouz S, Weber M, Pavlidis P, Gillis J. EGAD: ultra-fast functional analysis of gene networks. Bioinformatics (Oxford, England). PMID 27993773 DOI: 10.1093/bioinformatics/btw695  0.48
2016 Ballouz S, Pavlidis P, Gillis J. Using predictive specificity to determine when gene set analysis is biologically meaningful. Nucleic Acids Research. PMID 27924030 DOI: 10.1093/nar/gkw957  0.48
2016 Toker L, Feng M, Pavlidis P. Whose sample is it anyway? Widespread misannotation of samples in transcriptomics studies. F1000research. 5: 2103. PMID 27746907 DOI: 10.12688/f1000research.9471.1  1
2016 Tan PP, Rogic S, Zoubarev A, McDonald C, Lui F, Charathsandran G, Jacobson M, Belmadani M, Leong J, Van Rossum T, Portales-Casamar E, Qiao Y, Calli K, Liu X, Hudson M, ... ... Pavlidis P, et al. Interactive Exploration, Analysis and Visualization of Complex Phenome-Genome Datasets with ASPIREdb. Human Mutation. PMID 27158917 DOI: 10.1002/humu.23011  1
2016 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. 9: 6. PMID 26889207 DOI: 10.1186/s13072-016-0054-8  1
2015 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, et al. Secondary neurotransmitter deficiencies in epilepsy caused by voltage-gated sodium channelopathies: A potential treatment target? Molecular Genetics and Metabolism. PMID 26647175 DOI: 10.1016/j.ymgme.2015.11.008  1
2015 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. The American Journal of Psychiatry. appiajp201514101279. PMID 26238605 DOI: 10.1176/appi.ajp.2015.14101279  1
2015 Toker L, Pavlidis P. Metaanalysis of flawed expression profiling data leading to erroneous Parkinson's biomarker identification. Proceedings of the National Academy of Sciences of the United States of America. 112: E3637. PMID 26106167 DOI: 10.1073/pnas.1507563112  1
2015 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. Frontiers in Neuroinformatics. 9: 13. PMID 26052282 DOI: 10.3389/fninf.2015.00013  1
2015 Fortelny N, Pavlidis P, Overall CM. The path of no return-Truncated protein N-termini and current ignorance of their genesis. Proteomics. 15: 2547-52. PMID 26010509 DOI: 10.1002/pmic.201500043  1
2015 Ch'ng C, Kwok W, Rogic S, Pavlidis P. Meta-Analysis of Gene Expression in Autism Spectrum Disorder. Autism Research : Official Journal of the International Society For Autism Research. PMID 25720351 DOI: 10.1002/aur.1475  1
2015 Lussier AA, Stepien KA, Neumann SM, Pavlidis P, Kobor MS, Weinberg J. Prenatal alcohol exposure alters steady-state and activated gene expression in the adult rat brain. Alcoholism, Clinical and Experimental Research. 39: 251-61. PMID 25684047 DOI: 10.1111/acer.12622  1
2015 Salvarinova R, Ye CX, Rossi A, Biancheri R, Roland EH, Pavlidis P, Ross CJ, Tarailo-Graovac M, Wasserman WW, van Karnebeek CD. Expansion of the QARS deficiency phenotype with report of a family with isolated supratentorial brain abnormalities. Neurogenetics. 16: 145-9. PMID 25432320 DOI: 10.1007/s10048-014-0432-y  1
2015 Fortelny N, Yang S, Pavlidis P, Lange PF, Overall CM. Proteome TopFIND 3.0 with TopFINDer and PathFINDer: database and analysis tools for the association of protein termini to pre- and post-translational events. Nucleic Acids Research. 43: D290-7. PMID 25332401 DOI: 10.1093/nar/gku1012  1
2014 Edgar R, Tan PP, Portales-Casamar E, Pavlidis P. Meta-analysis of human methylomes reveals stably methylated sequences surrounding CpG islands associated with high gene expression. Epigenetics & Chromatin. 7: 28. PMID 25493099 DOI: 10.1186/1756-8935-7-28  0.56
2014 Sedeño-Cortés AE, Pavlidis P. Pitfalls in the application of gene-set analysis to genetics studies. Trends in Genetics : Tig. 30: 513-4. PMID 25459301 DOI: 10.1016/j.tig.2014.10.001  1
2014 Qiao Y, Mercier E, Dastan J, Hurlburt J, McGillivray B, Chudley AE, Farrell S, Bernier FP, Lewis MS, Pavlidis P, Rajcan-Separovic E. Copy number variants (CNVs) analysis in a deeply phenotyped cohort of individuals with intellectual disability (ID). Bmc Medical Genetics. 15: 82. PMID 25030379 DOI: 10.1186/1471-2350-15-82  1
2014 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 is a primate-specific and brain-enriched microRNA involved in major depression and antidepressant treatment. Nature Medicine. 20: 764-8. PMID 24908571 DOI: 10.1038/nm.3582  1
2014 Fortelny N, Cox JH, Kappelhoff R, Starr AE, Lange PF, Pavlidis P, Overall CM. Network analyses reveal pervasive functional regulation between proteases in the human protease web. Plos Biology. 12: e1001869. PMID 24865846 DOI: 10.1371/journal.pbio.1001869  1
2014 McCarthy SE, 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, et al. De novo mutations in schizophrenia implicate chromatin remodeling and support a genetic overlap with autism and intellectual disability. Molecular Psychiatry. 19: 652-8. PMID 24776741 DOI: 10.1038/mp.2014.29  1
2014 Kebschull M, Demmer RT, Grün B, Guarnieri P, Pavlidis P, Papapanou PN. Gingival tissue transcriptomes identify distinct periodontitis phenotypes. Journal of Dental Research. 93: 459-68. PMID 24646639 DOI: 10.1177/0022034514527288  1
2014 Jeffries KM, Hinch SG, Sierocinski T, Pavlidis P, Miller KM. Transcriptomic responses to high water temperature in two species of Pacific salmon. Evolutionary Applications. 7: 286-300. PMID 24567748 DOI: 10.1111/eva.12119  1
2014 Gillis J, Ballouz S, Pavlidis P. Bias tradeoffs in the creation and analysis of protein-protein interaction networks. Journal of Proteomics. 100: 44-54. PMID 24480284 DOI: 10.1016/j.jprot.2014.01.020  1
2013 Pavlidis P, Gillis J. Progress and challenges in the computational prediction of gene function using networks: 2012-2013 update. F1000research. 2: 230. PMID 24715959 DOI: 10.12688/f1000research.2-230.v1  1
2013 Kebschull M, Guarnieri P, Demmer RT, Boulesteix AL, Pavlidis P, Papapanou PN. Molecular differences between chronic and aggressive periodontitis. Journal of Dental Research. 92: 1081-8. PMID 24122488 DOI: 10.1177/0022034513506011  1
2013 Mistry M, Gillis J, Pavlidis P. Meta-analysis of gene coexpression networks in the post-mortem prefrontal cortex of patients with schizophrenia and unaffected controls. Bmc Neuroscience. 14: 105. PMID 24070017 DOI: 10.1186/1471-2202-14-105  1
2013 Qiao Y, Badduke C, Mercier E, Lewis SM, Pavlidis P, Rajcan-Separovic E. miRNA and miRNA target genes in copy number variations occurring in individuals with intellectual disability. Bmc Genomics. 14: 544. PMID 23937676 DOI: 10.1186/1471-2164-14-544  1
2013 Gillis J, Pavlidis P. 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. 14: S15. PMID 23630983 DOI: 10.1186/1471-2105-14-S3-S15  1
2013 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. Neurocarta: aggregating and sharing disease-gene relations for the neurosciences. Bmc Genomics. 14: 129. PMID 23442263 DOI: 10.1186/1471-2164-14-129  1
2013 Tan PP, French L, Pavlidis P. Neuron-Enriched Gene Expression Patterns are Regionally Anti-Correlated with Oligodendrocyte-Enriched Patterns in the Adult Mouse and Human Brain. Frontiers in Neuroscience. 7: 5. PMID 23440889 DOI: 10.3389/fnins.2013.00005  1
2013 Gillis J, Pavlidis P. Assessing identity, redundancy and confounds in Gene Ontology annotations over time. Bioinformatics (Oxford, England). 29: 476-82. PMID 23297035 DOI: 10.1093/bioinformatics/bts727  1
2013 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, ... ... Pavlidis P, et al. FTO, obesity and the adolescent brain. Human Molecular Genetics. 22: 1050-8. PMID 23201753 DOI: 10.1093/hmg/dds504  1
2013 Mistry M, Gillis J, Pavlidis P. Genome-wide expression profiling of schizophrenia using a large combined cohort. Molecular Psychiatry. 18: 215-25. PMID 22212594 DOI: 10.1038/mp.2011.172  1
2013 Pantazatos SP, Talati A, Pavlidis P, Hirsch J. Corrigendum to Cortical functional connectivity decodes subconscious, task-irrelevant threat related emotion processing [Neuroimage 61/4 (2012) 1355-1363] (DOI:10.1016/j.neuroimage.2012.03.051) Neuroimage. DOI: 10.1016/j.neuroimage.2013.01.019  1
2012 Pavlidis P, Gillis J. Progress and challenges in the computational prediction of gene function using networks. F1000research. 1: 14. PMID 23936626 DOI: 10.12688/f1000research.1-14.v1  1
2012 Jeffries KM, Hinch SG, Sierocinski T, Clark TD, Eliason EJ, Donaldson MR, Li S, Pavlidis P, Miller KM. Consequences of high temperatures and premature mortality on the transcriptome and blood physiology of wild adult sockeye salmon (Oncorhynchus nerka). Ecology and Evolution. 2: 1747-64. PMID 22957178 DOI: 10.1002/ece3.274  1
2012 French L, Lane S, Xu L, Siu C, Kwok C, Chen Y, Krebs C, Pavlidis P. Application and evaluation of automated methods to extract neuroanatomical connectivity statements from free text. Bioinformatics (Oxford, England). 28: 2963-70. PMID 22954628 DOI: 10.1093/bioinformatics/bts542  1
2012 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. Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. Bioinformatics (Oxford, England). 28: 2272-3. PMID 22782548 DOI: 10.1093/bioinformatics/bts430  1
2012 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. Diverse epigenetic strategies interact to control epidermal differentiation. Nature Cell Biology. 14: 753-63. PMID 22729083 DOI: 10.1038/ncb2520  1
2012 Pantazatos SP, Talati A, Pavlidis P, Hirsch J. Cortical functional connectivity decodes subconscious, task-irrelevant threat-related emotion processing. Neuroimage. 61: 1355-63. PMID 22484206 DOI: 10.1016/j.neuroimage.2012.03.051  1
2012 Gillis J, Pavlidis P. "Guilt by association" is the exception rather than the rule in gene networks. Plos Computational Biology. 8: e1002444. PMID 22479173 DOI: 10.1371/journal.pcbi.1002444  1
2012 Pantazatos SP, Talati A, Pavlidis P, Hirsch J. Decoding unattended fearful faces with whole-brain correlations: an approach to identify condition-dependent large-scale functional connectivity. Plos Computational Biology. 8: e1002441. PMID 22479172 DOI: 10.1371/journal.pcbi.1002441  1
2012 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, et al. KCTD8 gene and brain growth in adverse intrauterine environment: a genome-wide association study. Cerebral Cortex (New York, N.Y. : 1991). 22: 2634-42. PMID 22156575 DOI: 10.1093/cercor/bhr350  1
2012 French L, Pavlidis P. Using text mining to link journal articles to neuroanatomical databases. The Journal of Comparative Neurology. 520: 1772-83. PMID 22120205 DOI: 10.1002/cne.23012  1
2012 Hammill E, Curtis JMR, Patterson DA, Farrell AP, Sierocinski T, Pavlidis P, Hinch SG, Miller K. Comparison of techniques for correlating survival and gene expression data from wild salmon Ecology of Freshwater Fish. 21: 189-199. DOI: 10.1111/j.1600-0633.2011.00536.x  1
2011 French L, Tan PP, Pavlidis P. Large-Scale Analysis of Gene Expression and Connectivity in the Rodent Brain: Insights through Data Integration. Frontiers in Neuroinformatics. 5: 12. PMID 21863139 DOI: 10.3389/fninf.2011.00012  1
2011 Harvard C, Strong E, Mercier E, Colnaghi R, Alcantara D, Chow E, Martell S, Tyson C, Hrynchak M, McGillivray B, Hamilton S, Marles S, Mhanni A, Dawson AJ, Pavlidis P, et al. Understanding the impact of 1q21.1 copy number variant. Orphanet Journal of Rare Diseases. 6: 54. PMID 21824431 DOI: 10.1186/1750-1172-6-54  1
2011 Portales-Casamar E, Evans A, Wasserman W, Pavlidis P. The NeuroDevNet Neuroinformatics Core. Seminars in Pediatric Neurology. 18: 17-20. PMID 21575836 DOI: 10.1016/j.spen.2011.02.001  1
2011 Gillis J, Pavlidis P. The role of indirect connections in gene networks in predicting function. Bioinformatics (Oxford, England). 27: 1860-6. PMID 21551147 DOI: 10.1093/bioinformatics/btr288  1
2011 Gillis J, Pavlidis P. The impact of multifunctional genes on "guilt by association" analysis. Plos One. 6: e17258. PMID 21364756 DOI: 10.1371/journal.pone.0017258  1
2011 French L, Pavlidis P. Relationships between gene expression and brain wiring in the adult rodent brain. Plos Computational Biology. 7: e1001049. PMID 21253556 DOI: 10.1371/journal.pcbi.1001049  1
2011 Miller KM, Li S, Kaukinen KH, Ginther N, Hammill E, Curtis JM, Patterson DA, Sierocinski T, Donnison L, Pavlidis P, Hinch SG, Hruska KA, Cooke SJ, English KK, Farrell AP. Genomic signatures predict migration and spawning failure in wild Canadian salmon. Science (New York, N.Y.). 331: 214-7. PMID 21233388 DOI: 10.1126/science.1196901  1
2010 Demmer RT, Pavlidis P, Papapanou PN. Bioinformatics techniques in microarray research: applied microarray data analysis using R and SAS software. Methods in Molecular Biology (Clifton, N.J.). 666: 395-417. PMID 20717798 DOI: 10.1007/978-1-60761-820-1_25  1
2010 Gillis J, Mistry M, Pavlidis P. Gene function analysis in complex data sets using ErmineJ. Nature Protocols. 5: 1148-59. PMID 20539290 DOI: 10.1038/nprot.2010.78  1
2010 Qiao Y, Harvard C, Tyson C, Liu X, Fawcett C, Pavlidis P, Holden JJ, Lewis ME, Rajcan-Separovic E. Outcome of array CGH analysis for 255 subjects with intellectual disability and search for candidate genes using bioinformatics. Human Genetics. 128: 179-94. PMID 20512354 DOI: 10.1007/s00439-010-0837-0  1
2010 Mistry M, Pavlidis P. A cross-laboratory comparison of expression profiling data from normal human postmortem brain. Neuroscience. 167: 384-95. PMID 20138973 DOI: 10.1016/j.neuroscience.2010.01.016  1
2010 Becanovic K, Pouladi MA, Lim RS, Kuhn A, Pavlidis P, Luthi-Carter R, Hayden MR, Leavitt BR. Transcriptional changes in Huntington disease identified using genome-wide expression profiling and cross-platform analysis. Human Molecular Genetics. 19: 1438-52. PMID 20089533 DOI: 10.1093/hmg/ddq018  1
2009 Rogic S, Pavlidis P. Meta-analysis of kindling-induced gene expression changes in the rat hippocampus. Frontiers in Neuroscience. 3: 53. PMID 20582280 DOI: 10.3389/neuro.15.001.2009  1
2009 Pantazatos SP, Li J, Pavlidis P, Lussier YA. Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes. Cancer Informatics. 8: 75-94. PMID 20495688  1
2009 Papapanou PN, Behle JH, Kebschull M, Celenti R, Wolf DL, Handfield M, Pavlidis P, Demmer RT. Subgingival bacterial colonization profiles correlate with gingival tissue gene expression. Bmc Microbiology. 9: 221. PMID 19835625 DOI: 10.1186/1471-2180-9-221  1
2009 Gillis J, Pavlidis P. A methodology for the analysis of differential coexpression across the human lifespan. Bmc Bioinformatics. 10: 306. PMID 19772654 DOI: 10.1186/1471-2105-10-306  1
2009 French L, Lane S, Xu L, Pavlidis P. Automated recognition of brain region mentions in neuroscience literature. Frontiers in Neuroinformatics. 3: 29. PMID 19750194 DOI: 10.3389/neuro.11.029.2009  1
2009 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 NT, Gottlieb BS, Olson JC, et al. Subtype-specific peripheral blood gene expression profiles in recent-onset juvenile idiopathic arthritis. Arthritis and Rheumatism. 60: 2102-12. PMID 19565513 DOI: 10.1002/art.24601  1
2009 Griffin TA, Barnes MG, Ilowite NT, Olson JC, Sherry DD, Gottlieb BS, Aronow BJ, Pavlidis P, Hinze CH, 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 Rheumatism. 60: 2113-23. PMID 19565504 DOI: 10.1002/art.24534  1
2009 French L, Lane S, Law T, Xu L, Pavlidis P. Application and evaluation of automated semantic annotation of gene expression experiments. Bioinformatics (Oxford, England). 25: 1543-9. PMID 19376825 DOI: 10.1093/bioinformatics/btp259  1
2009 Ware CB, Wang L, Mecham BH, Shen L, Nelson AM, Bar M, Lamba DA, Dauphin DS, Buckingham B, Askari B, Lim R, Tewari M, Gartler SM, Issa JP, Pavlidis P, et al. Histone deacetylase inhibition elicits an evolutionarily conserved self-renewal program in embryonic stem cells. Cell Stem Cell. 4: 359-69. PMID 19341625 DOI: 10.1016/j.stem.2009.03.001  1
2009 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. Journal of Periodontal Research. 44: 465-71. PMID 18842116 DOI: 10.1111/j.1600-0765.2008.01134.x  1
2008 Demmer RT, Behle JH, Wolf DL, Handfield M, Kebschull M, Celenti R, Pavlidis P, Papapanou PN. Transcriptomes in healthy and diseased gingival tissues. Journal of Periodontology. 79: 2112-24. PMID 18980520 DOI: 10.1902/jop.2008.080139  1
2008 Mistry M, Pavlidis P. Gene Ontology term overlap as a measure of gene functional similarity. Bmc Bioinformatics. 9: 327. PMID 18680592 DOI: 10.1186/1471-2105-9-327  1
2008 Stark KL, Xu B, Bagchi A, Lai WS, Liu H, Hsu R, Wan X, Pavlidis P, Mills AA, Karayiorgou M, Gogos JA. Altered brain microRNA biogenesis contributes to phenotypic deficits in a 22q11-deletion mouse model. Nature Genetics. 40: 751-60. PMID 18469815 DOI: 10.1038/ng.138  1
2007 French L, Pavlidis P. Informatics in neuroscience. Briefings in Bioinformatics. 8: 446-56. PMID 17932081 DOI: 10.1093/bib/bbm047  1
2007 Wan X, Pavlidis P. Sharing and reusing gene expression profiling data in neuroscience. Neuroinformatics. 5: 161-75. PMID 17917127 DOI: 10.1007/s12021-007-0012-5  1
2007 Papapanou PN, Sedaghatfar MH, Demmer RT, Wolf DL, Yang J, Roth GA, Celenti R, Belusko PB, Lalla E, Pavlidis P. Periodontal therapy alters gene expression of peripheral blood monocytes. Journal of Clinical Periodontology. 34: 736-47. PMID 17716309 DOI: 10.1111/j.1600-051X.2007.01113.x  1
2007 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. beta-catenin/TCF/Lef controls a differentiation-associated transcriptional program in renal epithelial progenitors. Development (Cambridge, England). 134: 3177-90. PMID 17693601 DOI: 10.1242/dev.006544  1
2007 Muchir A, Pavlidis P, Bonne G, Hayashi YK, Worman HJ. 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. 16: 1884-95. PMID 17567779 DOI: 10.1093/hmg/ddm137  1
2007 Muchir A, Pavlidis P, Decostre V, Herron AJ, Arimura T, Bonne G, Worman HJ. Activation of MAPK pathways links LMNA mutations to cardiomyopathy in Emery-Dreifuss muscular dystrophy. The Journal of Clinical Investigation. 117: 1282-93. PMID 17446932 DOI: 10.1172/JCI29042  1
2006 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. Zac1 regulates an imprinted gene network critically involved in the control of embryonic growth. Developmental Cell. 11: 711-22. PMID 17084362 DOI: 10.1016/j.devcel.2006.09.003  1
2006 Lai WS, Xu B, Westphal KG, Paterlini M, Olivier B, Pavlidis P, Karayiorgou M, Gogos JA. 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. 103: 16906-11. PMID 17077150 DOI: 10.1073/pnas.0604994103  1
2006 Zheng Z, Pavlidis P, Chua S, D'Agati VD, Gharavi AG. An ancestral haplotype defines susceptibility to doxorubicin nephropathy in the laboratory mouse. Journal of the American Society of Nephrology : Jasn. 17: 1796-800. PMID 16775033 DOI: 10.1681/ASN.2005121373  1
2005 Lee HK, Braynen W, Keshav K, Pavlidis P. ErmineJ: tool for functional analysis of gene expression data sets. Bmc Bioinformatics. 6: 269. PMID 16280084 DOI: 10.1186/1471-2105-6-269  1
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 Research. 33: 5914-23. PMID 16237126 DOI: 10.1093/nar/gki890  1
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. Nature Neuroscience. 8: 1586-94. PMID 16234811 DOI: 10.1038/nn1562  1
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: 6-18. PMID 16043289 DOI: 10.1016/j.pain.2005.04.024  1
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. Biological Psychiatry. 57: 549-58. PMID 15737671 DOI: 10.1016/j.biopsych.2004.10.034  1
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. Proceedings of the National Academy of Sciences of the United States of America. 102: 2502-7. PMID 15699352 DOI: 10.1073/pnas.0409786102  1
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. Neurochemical Research. 29: 1213-22. PMID 15176478 DOI: 10.1023/B:NERE.0000023608.29741.45  1
2004 Lee HK, Hsu AK, Sajdak J, Qin J, Pavlidis P. Coexpression analysis of human genes across many microarray data sets. Genome Research. 14: 1085-94. PMID 15173114 DOI: 10.1101/gr.1910904  1
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. Learning & Memory (Cold Spring Harbor, N.Y.). 11: 253-60. PMID 15169854 DOI: 10.1101/lm.68204  1
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. European Journal of Oral Sciences. 112: 216-23. PMID 15154918 DOI: 10.1111/j.1600-0722.2004.00124.x  1
2004 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, England). 43: 973-9. PMID 15150433 DOI: 10.1093/rheumatology/keh224  1
2004 Pavlidis P, Wapinski I, Noble WS. Support vector machine classification on the web. Bioinformatics (Oxford, England). 20: 586-7. PMID 14990457 DOI: 10.1093/bioinformatics/btg461  1
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. Experimental Eye Research. 78: 301-8. PMID 14729362 DOI: 10.1016/j.exer.2003.10.016  1
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 : Official Publication of the American College of Neuropsychopharmacology. 29: 351-61. PMID 14603265 DOI: 10.1038/sj.npp.1300335  1
2003 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, and Behavior. 2: 303-20. PMID 14606695 DOI: 10.1034/j.1601-183X.2003.00041.x  1
2003 Pavlidis P. Using ANOVA for gene selection from microarray studies of the nervous system. Methods (San Diego, Calif.). 31: 282-9. PMID 14597312 DOI: 10.1016/S1046-2023(03)00157-9  1
2003 Pavlidis P, Li Q, Noble WS. The effect of replication on gene expression microarray experiments. Bioinformatics (Oxford, England). 19: 1620-7. PMID 12967957 DOI: 10.1093/bioinformatics/btg227  1
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. 4: 37. PMID 12962547 DOI: 10.1186/1471-2105-4-37  1
2003 Yang YC, Piek E, Zavadil J, Liang D, Xie D, Heyer J, Pavlidis P, Kucherlapati R, Roberts AB, Böttinger EP. Hierarchical model of gene regulation by transforming growth factor beta. Proceedings of the National Academy of Sciences of the United States of America. 100: 10269-74. PMID 12930890 DOI: 10.1073/pnas.1834070100  1
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: 655-69. PMID 12925279 DOI: 10.1016/S0896-6273(03)00501-4  1
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. The American Journal of Pathology. 163: 691-700. PMID 12875988 DOI: 10.1016/S0002-9440(10)63696-6  1
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. Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology. 21: 1775-81. PMID 12721254 DOI: 10.1200/JCO.2003.10.108  1
2003 Pavlidis P, Noble WS. Matrix2png: a utility for visualizing matrix data. Bioinformatics (Oxford, England). 19: 295-6. PMID 12538257 DOI: 10.1093/bioinformatics/19.2.295  1
2002 Spector A, Li D, Ma W, Sun F, Pavlidis P. Differential amplification of gene expression in lens cell lines conditioned to survive peroxide stress. Investigative Ophthalmology & Visual Science. 43: 3251-64. PMID 12356832  1
2002 Pavlidis P, Weston J, Cai J, Noble WS. Learning gene functional classifications from multiple data types. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 9: 401-11. PMID 12015889 DOI: 10.1089/10665270252935539  1
2002 Pavlidis P, Lewis DP, Noble WS. Exploring gene expression data with class scores. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 474-85. PMID 11928500  1
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. Journal of Immunology (Baltimore, Md. : 1950). 168: 996-1000. PMID 11801631  1
2001 Pavlidis P, Noble WS. Analysis of strain and regional variation in gene expression in mouse brain. Genome Biology. 2: RESEARCH0042. PMID 11597334  1
2001 Muhle RA, Pavlidis P, Grundy WN, Hirsch E. A high-throughput study of gene expression in preterm labor with a subtractive microarray approach. American Journal of Obstetrics and Gynecology. 185: 716-24. PMID 11568803 DOI: 10.1067/mob.2001.117183  1
2001 Montgomery JM, Pavlidis P, Madison DV. Pair recordings reveal all-silent synaptic connections and the postsynaptic expression of long-term potentiation. Neuron. 29: 691-701. PMID 11301028 DOI: 10.1016/S0896-6273(01)00244-6  1
2001 Pavlidis P, Furey TS, Liberto M, Haussler D, Grundy WN. Promoter region-based classification of genes. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 151-63. PMID 11262936  1
2001 Pavlidis P, Cai J, Weston J, Grundy WN. Gene functional classification from heterogeneous data Proceedings of the Annual International Conference On Computational Molecular Biology, Recomb. 249-255.  1
2000 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. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 20: 5264-75. PMID 10884310  1
2000 Pavlidis P, Montgomery J, Madison DV. Presynaptic protein kinase activity supports long-term potentiation at synapses between individual hippocampal neurons. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 20: 4497-505. PMID 10844019  1
1999 Pavlidis P, Madison DV. Synaptic transmission in pair recordings from CA3 pyramidal cells in organotypic culture. Journal of Neurophysiology. 81: 2787-97. PMID 10368397  1
1996 Haley JE, Schaible E, Pavlidis P, Murdock A, Madison DV. Basal and apical synapses of CA1 pyramidal cells employ different LTP induction mechanisms. Learning & Memory (Cold Spring Harbor, N.Y.). 3: 289-95. PMID 10456098  1
1995 Pavlidis P, Tanouye MA. Seizures and failures in the giant fiber pathway of Drosophila bang-sensitive paralytic mutants. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 15: 5810-9. PMID 7643221  1
1994 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: 23-33. PMID 7923374 DOI: 10.1016/0092-8674(94)90397-2  1
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