| Year |
Citation |
Score |
| 2024 |
Morin A, Chu C, Pavlidis P. Identifying Reproducible Transcription Regulator Coexpression Patterns with Single Cell Transcriptomics. Biorxiv : the Preprint Server For Biology. PMID 38559016 DOI: 10.1101/2024.02.15.580581 |
0.741 |
|
| 2023 |
Morin A, Chu EC, Sharma A, Adrian-Hamazaki A, Pavlidis P. Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets. Genome Research. 33: 763-778. PMID 37308292 DOI: 10.1101/gr.277273.122 |
0.793 |
|
| 2023 |
Novakovsky G, Sasaki S, Fornes O, Omur ME, Huang H, Bayly CL, Zhang D, Lim N, Cherkasov A, Pavlidis P, Mostafavi S, Lynn FC, Wasserman WW. In silico discovery of small molecules for efficient stem cell differentiation into definitive endoderm. Stem Cell Reports. PMID 36801003 DOI: 10.1016/j.stemcr.2023.01.008 |
0.729 |
|
| 2021 |
Chu EC, Morin A, Chang THC, Nguyen T, Tsai YC, Sharma A, Liu CC, Pavlidis P. Experiment level curation of transcriptional regulatory interactions in neurodevelopment. Plos Computational Biology. 17: e1009484. PMID 34665801 DOI: 10.1371/journal.pcbi.1009484 |
0.787 |
|
| 2021 |
Lim N, Pavlidis P. Evaluation of connectivity map shows limited reproducibility in drug repositioning. Scientific Reports. 11: 17624. PMID 34475469 DOI: 10.1038/s41598-021-97005-z |
0.747 |
|
| 2021 |
Sicherman J, Newton DF, Pavlidis P, Sibille E, Tripathy SJ. Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data. Frontiers in Molecular Neuroscience. 14: 637143. PMID 33746712 DOI: 10.3389/fnmol.2021.637143 |
0.677 |
|
| 2021 |
Lim N, Tesar S, Belmadani M, Poirier-Morency G, Mancarci BO, Sicherman J, Jacobson M, Leong J, Tan P, Pavlidis P. Curation of over 10 000 transcriptomic studies to enable data reuse. Database : the Journal of Biological Databases and Curation. PMID 33599246 DOI: 10.1093/database/baab006 |
0.782 |
|
| 2020 |
Farahbod M, Pavlidis P. Untangling the effects of cellular composition on coexpression analysis. Genome Research. PMID 32580998 DOI: 10.1101/Gr.256735.119 |
0.795 |
|
| 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 |
0.302 |
|
| 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 |
0.709 |
|
| 2020 |
Boycott KM, Campeau PM, Howley HE, Pavlidis P, Rogic S, Oriel C, Berman JN, Hamilton RM, Hicks GG, Lipshitz HD, Masson JY, Shoubridge EA, Junker A, Leroux MR, McMaster CR, et al. The Canadian Rare Diseases Models and Mechanisms (RDMM) Network: Connecting Understudied Genes to Model Organisms. American Journal of Human Genetics. 106: 143-152. PMID 32032513 DOI: 10.1016/J.Ajhg.2020.01.009 |
0.341 |
|
| 2020 |
Nagy C, Maitra M, Tanti A, Suderman M, Théroux J, Tripathy S, Pavlidis P, Mechawar N, Turecki G. Single-Cell Genomic Strategies to Understand Psychopathological Processes in Depression and Suicide Biological Psychiatry. 87: S43. DOI: 10.1016/J.Biopsych.2020.02.134 |
0.631 |
|
| 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 |
0.787 |
|
| 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 |
0.373 |
|
| 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 |
0.339 |
|
| 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 |
0.727 |
|
| 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 |
0.315 |
|
| 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 |
0.791 |
|
| 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 |
0.787 |
|
| 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 |
0.76 |
|
| 2018 |
Bhuiyan SA, Ly S, Phan M, Huntington B, Hogan E, Liu CC, Liu J, Pavlidis P. Systematic evaluation of isoform function in literature reports of alternative splicing. Bmc Genomics. 19: 637. PMID 30153812 DOI: 10.1186/S12864-018-5013-2 |
0.787 |
|
| 2018 |
Jacobson M, Sedeño-Cortés AE, Pavlidis P. Monitoring changes in the Gene Ontology and their impact on genomic data analysis. Gigascience. PMID 30107399 DOI: 10.1093/gigascience/giy103 |
0.394 |
|
| 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 |
0.781 |
|
| 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 |
0.664 |
|
| 2018 |
Lussier AA, Morin AM, MacIsaac JL, Salmon J, Weinberg J, Reynolds JN, Pavlidis P, Chudley AE, Kobor MS. DNA methylation as a predictor of fetal alcohol spectrum disorder. Clinical Epigenetics. 10: 5. PMID 29344313 DOI: 10.1186/S13148-018-0439-6 |
0.684 |
|
| 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 |
0.659 |
|
| 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 |
0.789 |
|
| 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 |
0.793 |
|
| 2017 |
Bainer RO, Trendowski MR, Cheng C, Pei D, Yang W, Paugh SW, Goss KH, Skol AD, Pavlidis P, Pui CH, Gilliam TC, Evans WE, Onel K. A p53-regulated apoptotic gene signature predicts treatment response and outcome in pediatric acute lymphoblastic leukemia. Cancer Management and Research. 9: 397-410. PMID 28979163 DOI: 10.2147/Cmar.S139864 |
0.362 |
|
| 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 |
0.671 |
|
| 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 |
0.695 |
|
| 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 |
0.411 |
|
| 2017 |
Toker L, Mancarci O, Pavlidis P. 11. Changes in Cellular Abundance Underlying Transcriptional Alterations in Psychiatric Patients Biological Psychiatry. 81: S5. DOI: 10.1016/j.biopsych.2017.02.022 |
0.711 |
|
| 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 |
0.353 |
|
| 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.9471.2 |
0.733 |
|
| 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 |
0.346 |
|
| 2016 |
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. Alcoholism, Clinical and Experimental Research. PMID 26996386 DOI: 10.1111/acer.13007 |
0.441 |
|
| 2016 |
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 : the Journal of Biological Databases and Curation. 2016. PMID 26989148 DOI: 10.1093/Database/Baw015 |
0.396 |
|
| 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 |
0.711 |
|
| 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 |
0.373 |
|
| 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 |
0.716 |
|
| 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 |
0.66 |
|
| 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 |
0.694 |
|
| 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 |
0.415 |
|
| 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 |
0.352 |
|
| 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 |
0.712 |
|
| 2015 |
Mancarcı O, Toker L, Tripathy S, Pavlidis P. A comprehensive database of cell-type specific marker genes for the mammalian brain F1000research. 4. DOI: 10.7490/F1000Research.1110181.1 |
0.712 |
|
| 2015 |
Tebaykin D, Tripathy S, Li B, Abdollahzadeh D, Anderson K, Pavlidis P. Application of large-scale text-mining and curation for extracting neuronal electrophysiology data F1000research. 4. DOI: 10.7490/F1000Research.1110179.1 |
0.642 |
|
| 2015 |
Tripathy SJ, Tebaykin D, Li B, Marcarci O, Toker L, Pavlidis P. Large-scale analysis of brain-wide electrophysiological diversity reveals novel characterization of mammalian neuron types Bmc Neuroscience. 16. DOI: 10.1186/1471-2202-16-S1-O4 |
0.796 |
|
| 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 |
0.323 |
|
| 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 |
0.378 |
|
| 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 |
0.702 |
|
| 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 |
0.616 |
|
| 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 |
0.343 |
|
| 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 |
0.327 |
|
| 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 |
0.38 |
|
| 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 |
0.366 |
|
| 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 |
0.648 |
|
| 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 |
0.355 |
|
| 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 |
0.412 |
|
| 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 |
0.701 |
|
| 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 |
0.413 |
|
| 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 |
0.486 |
|
| 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 |
0.699 |
|
| 2013 |
Portales-Casamar E, Tseng L, Ch’ng C, Lui F, St-Georges N, Zoubarev A, Pavlidis P. Neurocarta: aggregating and sharing disease-gene relations for the interpretation of genomics studies F1000research. 4. DOI: 10.7490/F1000Research.1094297.1 |
0.327 |
|
| 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 |
0.38 |
|
| 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 |
0.659 |
|
| 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 |
0.36 |
|
| 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 |
0.384 |
|
| 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 |
0.33 |
|
| 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 |
0.31 |
|
| 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 |
0.498 |
|
| 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 |
0.666 |
|
| 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 |
0.33 |
|
| 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 |
0.729 |
|
| 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 |
0.353 |
|
| 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 |
0.3 |
|
| 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 |
0.405 |
|
| 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: 10.7490/F1000Research.1007.1 |
0.714 |
|
| 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 |
0.412 |
|
| 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 |
0.677 |
|
| 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 |
0.398 |
|
| 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 |
0.672 |
|
| 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 |
0.427 |
|
| 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 |
0.441 |
|
| 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 DOI: 10.4137/Cin.S1046 |
0.319 |
|
| 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 |
0.398 |
|
| 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 |
0.398 |
|
| 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 |
0.662 |
|
| 2009 |
Aid-Pavlidis T, Pavlidis P, Timmusk T. Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation. Bmc Genomics. 10: 420. PMID 19737418 DOI: 10.1186/1471-2164-10-420 |
0.316 |
|
| 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 |
0.371 |
|
| 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 |
0.421 |
|
| 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 |
0.691 |
|
| 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 |
0.309 |
|
| 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 |
0.377 |
|
| 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 |
0.635 |
|
| 2007 |
French L, Pavlidis P. Informatics in neuroscience. Briefings in Bioinformatics. 8: 446-56. PMID 17932081 DOI: 10.1093/Bib/Bbm047 |
0.642 |
|
| 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 |
0.379 |
|
| 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 |
0.383 |
|
| 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 |
0.318 |
|
| 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 |
0.385 |
|
| 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 |
0.364 |
|
| 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 |
0.421 |
|
| 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 |
0.439 |
|
| 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 |
0.32 |
|
| 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 |
0.357 |
|
| 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 |
0.349 |
|
| 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 |
0.328 |
|
| 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 |
0.428 |
|
| 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 |
0.412 |
|
| 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 |
0.4 |
|
| 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 |
0.435 |
|
| 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 |
0.347 |
|
| 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 |
0.368 |
|
| 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 |
0.398 |
|
| 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 |
0.324 |
|
| 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 |
0.423 |
|
| 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 |
0.454 |
|
| 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 |
0.364 |
|
| 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 |
0.393 |
|
| 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 |
0.376 |
|
| 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 DOI: 10.4049/Jimmunol.168.3.996 |
0.353 |
|
| 2001 |
Pavlidis P, Noble WS. Analysis of strain and regional variation in gene expression in mouse brain. Genome Biology. 2: RESEARCH0042. PMID 11597334 DOI: 10.1186/Gb-2001-2-10-Research0042 |
0.411 |
|
| 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 |
0.331 |
|
| 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 |
0.685 |
|
| 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 DOI: 10.1523/Jneurosci.20-14-05264.2000 |
0.375 |
|
| 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 DOI: 10.1523/Jneurosci.20-12-04497.2000 |
0.688 |
|
| 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 DOI: 10.1152/Jn.1999.81.6.2787 |
0.61 |
|
| 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 DOI: 10.1101/Lm.3.4.289 |
0.669 |
|
| 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 DOI: 10.1523/Jneurosci.15-08-05810.1995 |
0.623 |
|
| 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 |
0.73 |
|
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