| Year |
Citation |
Score |
| 2024 |
Wen C, Margolis M, Dai R, Zhang P, Przytycki PF, Vo DD, Bhattacharya A, Matoba N, Tang M, Jiao C, Kim M, Tsai E, Hoh C, Aygün N, Walker RL, ... ... Jaffe AE, et al. Cross-ancestry atlas of gene, isoform, and splicing regulation in the developing human brain. Science (New York, N.Y.). 384: eadh0829. PMID 38781368 DOI: 10.1126/science.adh0829 |
0.317 |
|
| 2024 |
Rodriguez LA, Tran MN, Garcia-Flores R, Oh S, Phillips RA, Pattie EA, Divecha HR, Kim SH, Shin JH, Lee YK, Montoya C, Jaffe AE, Collado-Torres L, Page SC, Martinowich K. TrkB-dependent regulation of molecular signaling across septal cell types. Translational Psychiatry. 14: 52. PMID 38263132 DOI: 10.1038/s41398-024-02758-6 |
0.306 |
|
| 2023 |
Rodriguez LA, Tran MN, Garcia-Flores R, Pattie EA, Divecha HR, Kim SH, Shin JH, Lee YK, Montoya C, Jaffe AE, Collado-Torres L, Page SC, Martinowich K. TrkB-dependent regulation of molecular signaling across septal cell types. Biorxiv : the Preprint Server For Biology. PMID 37425939 DOI: 10.1101/2023.06.29.547069 |
0.306 |
|
| 2022 |
Shu C, Jaffe AE, Sabunciyan S, Ji H, Astemborski J, Sun J, Bakulski KM, Sosnowski DW, Mehta SH, Kirk GD, Maher BS. Epigenome-wide association analyses of active injection drug use. Drug and Alcohol Dependence. 235: 109431. PMID 35395503 DOI: 10.1016/j.drugalcdep.2022.109431 |
0.52 |
|
| 2022 |
Zandi PP, Jaffe AE, Goes FS, Burke EE, Collado-Torres L, Huuki-Myers L, Seyedian A, Lin Y, Seifuddin F, Pirooznia M, Ross CA, Kleinman JE, Weinberger DR, Hyde TM. Amygdala and anterior cingulate transcriptomes from individuals with bipolar disorder reveal downregulated neuroimmune and synaptic pathways. Nature Neuroscience. 25: 381-389. PMID 35260864 DOI: 10.1038/s41593-022-01024-6 |
0.307 |
|
| 2022 |
Perzel Mandell KA, Eagles NJ, Deep-Soboslay A, Tao R, Han S, Wilton R, Szalay AS, Hyde TM, Kleinman JE, Jaffe AE, Weinberger DR. Molecular phenotypes associated with antipsychotic drugs in the human caudate nucleus. Molecular Psychiatry. PMID 35236959 DOI: 10.1038/s41380-022-01453-6 |
0.304 |
|
| 2022 |
Ramnauth AD, Maynard KR, Kardian AS, Phan BN, Tippani M, Rajpurohit S, Hobbs JW, Page SC, Jaffe AE, Martinowich K. Induction of Bdnf from promoter I following electroconvulsive seizures contributes to structural plasticity in neurons of the piriform cortex. Brain Stimulation. PMID 35183789 DOI: 10.1016/j.brs.2022.02.003 |
0.7 |
|
| 2021 |
Perzel Mandell KA, Eagles NJ, Wilton R, Price AJ, Semick SA, Collado-Torres L, Ulrich WS, Tao R, Han S, Szalay AS, Hyde TM, Kleinman JE, Weinberger DR, Jaffe AE. Genome-wide sequencing-based identification of methylation quantitative trait loci and their role in schizophrenia risk. Nature Communications. 12: 5251. PMID 34475392 DOI: 10.1038/s41467-021-25517-3 |
0.305 |
|
| 2021 |
Eagles NJ, Burke EE, Leonard J, Barry BK, Stolz JM, Huuki L, Phan BN, Serrato VL, Gutiérrez-Millán E, Aguilar-Ordoñez I, Jaffe AE, Collado-Torres L. Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses. Bmc Bioinformatics. 22: 381. PMID 34294043 DOI: 10.1186/s12859-021-04283-5 |
0.679 |
|
| 2021 |
Eagles NJ, Burke EE, Leonard J, Barry BK, Stolz JM, Huuki L, Phan BN, Serrato VL, Gutiérrez-Millán E, Aguilar-Ordoñez I, Jaffe AE, Collado-Torres L. SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses. Bmc Bioinformatics. 22: 224. PMID 33932985 DOI: 10.1186/s12859-021-04142-3 |
0.702 |
|
| 2021 |
Takahashi Y, Maynard KR, Tippani M, Jaffe AE, Martinowich K, Kleinman JE, Weinberger DR, Hyde TM. Single molecule in situ hybridization reveals distinct localizations of schizophrenia risk-related transcripts SNX19 and AS3MT in human brain. Molecular Psychiatry. PMID 33649454 DOI: 10.1038/s41380-021-01046-9 |
0.328 |
|
| 2021 |
Maynard KR, Collado-Torres L, Weber LM, Uytingco C, Barry BK, Williams SR, Catallini JL, Tran MN, Besich Z, Tippani M, Chew J, Yin Y, Kleinman JE, Hyde TM, Rao N, ... ... Jaffe AE, et al. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. Nature Neuroscience. PMID 33558695 DOI: 10.7490/F1000Research.1118079.1 |
0.388 |
|
| 2020 |
Shu C, Jaffe AE, Sabunciyan S, Ji H, Astemborski J, Sun J, Bakulski KM, Mehta SH, Kirk GD, Maher BS. Epigenome-wide association scan identifies methylation sites associated with HIV infection. Epigenomics. PMID 33232214 DOI: 10.2217/epi-2020-0123 |
0.523 |
|
| 2020 |
Zhang D, Guelfi S, Garcia-Ruiz S, Costa B, Reynolds RH, D'Sa K, Liu W, Courtin T, Peterson A, Jaffe AE, Hardy J, Botía JA, Collado-Torres L, Ryten M. Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders. Science Advances. 6. PMID 32917675 DOI: 10.1126/Sciadv.Aay8299 |
0.401 |
|
| 2020 |
Haghani A, Johnson RG, Woodward NC, Feinberg JI, Lewis K, Ladd-Acosta C, Safi N, Jaffe AE, Sioutas C, Allayee H, Campbell DB, Volk HE, Finch CE, Morgan TE. Adult mouse hippocampal transcriptome changes associated with long-term behavioral and metabolic effects of gestational air pollution toxicity. Translational Psychiatry. 10: 218. PMID 32636363 DOI: 10.1038/S41398-020-00907-1 |
0.329 |
|
| 2020 |
Lin CW, Chang LC, Ma T, Oh H, French B, Puralewski R, Mathews F, Fang Y, Lewis DA, Kennedy JL, Mueller D, Marshe VS, Jaffe A, Chen Q, Ursini G, et al. Older molecular brain age in severe mental illness. Molecular Psychiatry. PMID 32632206 DOI: 10.1038/S41380-020-0834-1 |
0.363 |
|
| 2020 |
Perzel Mandell KA, Price AJ, Wilton R, Collado-Torres L, Tao R, Eagles NJ, Szalay AS, Hyde TM, Weinberger DR, Kleinman JE, Jaffe AE. Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex. Epigenetics. PMID 32602773 DOI: 10.1080/15592294.2020.1786304 |
0.417 |
|
| 2020 |
Tao R, Li C, Jaffe AE, Shin JH, Deep-Soboslay A, Yamin R, Weinberger DR, Hyde TM, Kleinman JE. Cannabinoid receptor CNR1 expression and DNA methylation in human prefrontal cortex, hippocampus and caudate in brain development and schizophrenia. Translational Psychiatry. 10: 158. PMID 32433545 DOI: 10.1038/S41398-020-0832-8 |
0.418 |
|
| 2020 |
Price AJ, Jaffe AE, Weinberger DR. Cortical cellular diversity and development in schizophrenia. Molecular Psychiatry. PMID 32404946 DOI: 10.1038/S41380-020-0775-8 |
0.372 |
|
| 2020 |
Maynard KR, Tippani M, Takahashi Y, Phan BN, Hyde TM, Jaffe AE, Martinowich K. dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues. Nucleic Acids Research. PMID 32383753 DOI: 10.1093/Nar/Gkaa312 |
0.727 |
|
| 2020 |
Jaffe AE, Hoeppner DJ, Saito T, Blanpain L, Ukaigwe J, Burke EE, Collado-Torres L, Tao R, Tajinda K, Maynard KR, Tran MN, Martinowich K, Deep-Soboslay A, Shin JH, Kleinman JE, et al. Profiling gene expression in the human dentate gyrus granule cell layer reveals insights into schizophrenia and its genetic risk. Nature Neuroscience. PMID 32203495 DOI: 10.1038/S41593-020-0604-Z |
0.395 |
|
| 2020 |
Imada EL, Sanchez DF, Collado-Torres L, Wilks C, Matam T, Dinalankara W, Stupnikov A, Pereira Lobo FP, Yip CW, Yasuzawa K, Kondo N, Itoh M, Suzuki H, Kasukawa T, Hon CC, ... ... Jaffe AE, et al. Recounting the FANTOM CAGEAssociated Transcriptome. Genome Research. PMID 32079618 DOI: 10.1101/Gr.254656.119 |
0.382 |
|
| 2020 |
Phan BN, Bohlen JF, Davis BA, Ye Z, Chen HY, Mayfield B, Sripathy SR, Cerceo Page S, Campbell MN, Smith HL, Gallop D, Kim H, Thaxton CL, Simon JM, Burke EE, ... ... Jaffe AE, et al. A myelin-related transcriptomic profile is shared by Pitt-Hopkins syndrome models and human autism spectrum disorder. Nature Neuroscience. PMID 32015540 DOI: 10.1038/S41593-019-0578-X |
0.725 |
|
| 2020 |
Burke EE, Chenoweth JG, Shin JH, Collado-Torres L, Kim SK, Micali N, Wang Y, Colantuoni C, Straub RE, Hoeppner DJ, Chen HY, Sellers A, Shibbani K, Hamersky GR, Diaz Bustamante M, ... ... Jaffe AE, et al. Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs. Nature Communications. 11: 462. PMID 31974374 DOI: 10.1038/S41467-019-14266-Z |
0.724 |
|
| 2019 |
Price AJ, Hwang T, Burke EE, Rajpurohit A, Shin JH, Hyde TM, Kleinman JE, Jaffe AE, Weinberger DR. Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation. Genome Research. PMID 31852722 DOI: 10.1101/Gr.250217.119 |
0.404 |
|
| 2019 |
Ren M, Hu Z, Chen Q, Jaffe A, Li Y, Sadashivaiah V, Zhu S, Rajpurohit N, Heon Shin J, Xia W, Jia Y, Wu J, Lang Qin S, Li X, Zhu J, et al. KCNH2-3.1 mediates aberrant complement activation and impaired hippocampal-medial prefrontal circuitry associated with working memory deficits. Molecular Psychiatry. PMID 31570775 DOI: 10.1038/S41380-019-0530-1 |
0.373 |
|
| 2019 |
Price AJ, Collado-Torres L, Ivanov NA, Xia W, Burke EE, Shin JH, Tao R, Ma L, Jia Y, Hyde TM, Kleinman JE, Weinberger DR, Jaffe AE. Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation. Genome Biology. 20: 196. PMID 31554518 DOI: 10.1186/S13059-019-1805-1 |
0.378 |
|
| 2019 |
Gådin JR, Buil A, Colantuoni C, Jaffe AE, Nielsen J, Shin JH, Hyde TM, Kleinman JE, Plath N, Eriksson P, Brunak S, Didriksen M, Weinberger DR, Folkersen L. Comparison of quantitative trait loci methods: Total expression and allelic imbalance method in brain RNA-seq. Plos One. 14: e0217765. PMID 31206532 DOI: 10.1371/Journal.Pone.0217765 |
0.396 |
|
| 2019 |
Collado-Torres L, Burke EE, Peterson A, Shin J, Straub RE, Rajpurohit A, Semick SA, Ulrich WS, Price AJ, Valencia C, Tao R, Deep-Soboslay A, Hyde TM, Kleinman JE, ... ... Jaffe AE, et al. Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia. Neuron. PMID 31174959 DOI: 10.1016/J.Neuron.2019.05.013 |
0.377 |
|
| 2019 |
Pergola G, Di Carlo P, Jaffe AE, Papalino M, Chen Q, Hyde TM, Kleinman JE, Shin JH, Rampino A, Blasi G, Weinberger DR, Bertolino A. Prefrontal Coexpression of Schizophrenia Risk Genes Is Associated With Treatment Response in Patients. Biological Psychiatry. PMID 31126695 DOI: 10.1016/J.Biopsych.2019.03.981 |
0.334 |
|
| 2019 |
Parsana P, Ruberman C, Jaffe AE, Schatz MC, Battle A, Leek JT. Addressing confounding artifacts in reconstruction of gene co-expression networks. Genome Biology. 20: 94. PMID 31097038 DOI: 10.1186/S13059-019-1700-9 |
0.324 |
|
| 2019 |
Semick SA, Bharadwaj RA, Collado-Torres L, Tao R, Shin JH, Deep-Soboslay A, Weiss JR, Weinberger DR, Hyde TM, Kleinman JE, Jaffe AE, Mattay VS. Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer's disease. Acta Neuropathologica. PMID 30712078 DOI: 10.1007/S00401-019-01966-5 |
0.389 |
|
| 2019 |
Ma L, Semick SA, Chen Q, Li C, Tao R, Price AJ, Shin JH, Jia Y, Brandon NJ, Cross AJ, Hyde TM, Kleinman JE, Jaffe AE, Weinberger DR, et al. Schizophrenia risk variants influence multiple classes of transcripts of sorting nexin 19 (SNX19). Molecular Psychiatry. PMID 30635639 DOI: 10.1038/S41380-018-0293-0 |
0.42 |
|
| 2019 |
Carlo PD, Pergola G, Jaffe AE, Papalino M, Chen Q, Hyde TM, Kleinman JE, Shin JH, Rampino A, Blasi G, Weinberger DR, Bertolino A. F104. GENE CO-EXPRESSION NETWORKS REVEAL PATHWAYS OF CONVERGENCE OF SCHIZOPHRENIA RISK GENES AND OF RESPONSE TO TREATMENT Schizophrenia Bulletin. 45: S293-S293. DOI: 10.1093/Schbul/Sbz018.516 |
0.323 |
|
| 2019 |
Di Carlo P, Deyssenroth M, Jaffe AE, Chen Q, Punzi G, Bertolino A, Marsit CJ, Chen J, Hao K, Weinberger DR, Ursini G. Genomic risk for schizophrenia converges into isoform-level coexpression network of the placental transcriptome Placenta. 83: e11-e12. DOI: 10.1016/J.Placenta.2019.06.043 |
0.309 |
|
| 2019 |
Shu C, Bakulski K, Benke K, Jaffe A, Wang S, Sabunciyan S, Mehta S, Kirk G, Maher B. DNA METHYLATION MARKERS ASSOCIATED WITH INJECTION DRUG USE STATUS AND HIV INFECTION AMONG CHRONIC INJECTION DRUG USERS IN THE ALIVE STUDY European Neuropsychopharmacology. 29: S1014-S1015. DOI: 10.1016/J.Euroneuro.2017.08.416 |
0.699 |
|
| 2019 |
Pergola G, Carlo PD, Jaffe A, Papalino M, Blasi G, Weinberger D, Bertolino A. Gene Co-Expression Reveals Pathways Of Convergence Of Schizophrenia Risk Genes European Neuropsychopharmacology. 29. DOI: 10.1016/J.Euroneuro.2017.08.413 |
0.41 |
|
| 2019 |
Radulescu E, Straub RE, Jaffe AE, Heon Shin J, Chen Q, Weinberger DR. DIFFERENTIAL DISTRIBUTION OF SCHIZOPHRENIA RISK GENES WITHIN GENE CO-EXPRESSION NETWORKS CONSTRUCTED FROM RNA-SEQ DATA (POSTMORTEM DLPFC) OF AFFECTED AND UNAFFECTED INDIVIDUALS European Neuropsychopharmacology. 29: S946-S947. DOI: 10.1016/J.Euroneuro.2017.08.295 |
0.404 |
|
| 2019 |
Ma L, Semick S, Chen Q, Tao R, Price A, Shin JH, Hyde T, Kleinman J, Brandon N, Cross A, Jaffe A, Weinberger D, Straub R. Overexpression Of Multiple Transcripts Of Snx19 (Sorting Nexin 19) In Multiple Brain Regions May Contribute To Schizophrenia Risk European Neuropsychopharmacology. 29. DOI: 10.1016/J.Euroneuro.2017.08.036 |
0.409 |
|
| 2019 |
Morris D, Mill J, Jaffe A. Functional Genomic Regulation In The Brain: (Epi)Genetic Variation, Neurodevelopment and Psychiatric Disease European Neuropsychopharmacology. 29. DOI: 10.1016/J.Euroneuro.2017.06.135 |
0.451 |
|
| 2019 |
Bierut L, Hancock D, Jaffe A, Johnson E. Putting Genes In Context: Applying Integrative 'Omics To Alcohol Use Disorder European Neuropsychopharmacology. 29. DOI: 10.1016/J.Euroneuro.2017.06.076 |
0.33 |
|
| 2019 |
Jaffe A. Developmental and Genetic Regulation of The Human Cortex Transcriptome In Schizophrenia European Neuropsychopharmacology. 29. DOI: 10.1016/J.Euroneuro.2017.06.075 |
0.422 |
|
| 2019 |
Wright C, Shin JH, Rajpurohit A, Williams C, Jaffe A, Brandon N, Hyde T, Kleinman J, Cross A, Weinberger D. Characterization of miRNA Isoform Expression In Schizophrenia Using Postmortem Human Brain Tissue European Neuropsychopharmacology. 29. DOI: 10.1016/J.Euroneuro.2017.06.034 |
0.3 |
|
| 2018 |
Punzi G, Ursini G, Viscanti G, Radulescu E, Shin JH, Quarto T, Catanesi R, Blasi G, Jaffe AE, Deep-Soboslay A, Hyde TM, Kleinman JE, Bertolino A, Weinberger DR. Association of a Noncoding RNA Postmortem With Suicide by Violent Means and In Vivo With Aggressive Phenotypes. Biological Psychiatry. PMID 30600091 DOI: 10.1016/J.Biopsych.2018.11.002 |
0.325 |
|
| 2018 |
Wang D, Liu S, Warrell J, Won H, Shi X, Navarro FCP, Clarke D, Gu M, Emani P, Yang YT, Xu M, Gandal MJ, Lou S, Zhang J, Park JJ, ... ... Jaffe AE, et al. Comprehensive functional genomic resource and integrative model for the human brain. Science (New York, N.Y.). 362. PMID 30545857 DOI: 10.1126/Science.Aat8464 |
0.412 |
|
| 2018 |
Gandal MJ, Zhang P, Hadjimichael E, Walker RL, Chen C, Liu S, Won H, van Bakel H, Varghese M, Wang Y, Shieh AW, Haney J, Parhami S, Belmont J, Kim M, ... ... Jaffe AE, et al. Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder. Science (New York, N.Y.). 362. PMID 30545856 DOI: 10.1126/Science.Aat8127 |
0.416 |
|
| 2018 |
Kuri-Magaña H, Collado-Torres L, Jaffe AE, Valdovinos-Torres H, Ovilla-Muñoz M, Téllez-Sosa J, Bonifaz LC, Martínez-Barnetche J. Non-coding Class Switch Recombination-Related Transcription in Human Normal and Pathological Immune Responses. Frontiers in Immunology. 9: 2679. PMID 30519242 DOI: 10.3389/Fimmu.2018.02679 |
0.356 |
|
| 2018 |
Radulescu E, Jaffe AE, Straub RE, Chen Q, Shin JH, Hyde TM, Kleinman JE, Weinberger DR. Identification and prioritization of gene sets associated with schizophrenia risk by co-expression network analysis in human brain. Molecular Psychiatry. PMID 30478419 DOI: 10.1038/S41380-018-0304-1 |
0.41 |
|
| 2018 |
Maynard KR, Hobbs JW, Phan BN, Gupta A, Rajpurohit S, Williams C, Rajpurohit N, Shin JH, Jaffe AE, Martinowich K. BDNF-TrkB signaling in oxytocin neurons contributes to maternal behavior. Elife. 7. PMID 30192229 DOI: 10.7554/Elife.33676 |
0.725 |
|
| 2018 |
Semick SA, Collado-Torres L, Markunas CA, Shin JH, Deep-Soboslay A, Tao R, Huestis MA, Bierut LJ, Maher BS, Johnson EO, Hyde TM, Weinberger DR, Hancock DB, Kleinman JE, Jaffe AE. Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome. Molecular Psychiatry. PMID 30131587 DOI: 10.1038/S41380-018-0223-1 |
0.338 |
|
| 2018 |
Boks MP, Houtepen LC, Xu Z, He Y, Ursini G, Maihofer AX, Rajarajan P, Yu Q, Xu H, Wu Y, Wang S, Shi JP, Hulshoff Pol HE, Strengman E, Rutten BPF, ... Jaffe AE, et al. Genetic vulnerability to DUSP22 promoter hypermethylation is involved in the relation between in utero famine exposure and schizophrenia. Npj Schizophrenia. 4: 16. PMID 30131491 DOI: 10.1038/S41537-018-0058-4 |
0.384 |
|
| 2018 |
Jaffe AE, Straub RE, Shin JH, Tao R, Gao Y, Collado-Torres L, Kam-Thong T, Xi HS, Quan J, Chen Q, Colantuoni C, Ulrich WS, Maher BJ, Deep-Soboslay A, et al. Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis. Nature Neuroscience. 21: 1117-1125. PMID 30050107 DOI: 10.1038/S41593-018-0197-Y |
0.434 |
|
| 2018 |
Ursini G, Punzi G, Chen Q, Marenco S, Robinson JF, Porcelli A, Hamilton EG, Mitjans M, Maddalena G, Begemann M, Seidel J, Yanamori H, Jaffe AE, Berman KF, Egan MF, et al. Convergence of placenta biology and genetic risk for schizophrenia. Nature Medicine. PMID 29808008 DOI: 10.1038/S41591-018-0021-Y |
0.39 |
|
| 2018 |
Giambartolomei C, Zhenli Liu J, Zhang W, Hauberg M, Shi H, Boocock J, Pickrell J, Jaffe AE, Pasaniuc B, Roussos P. A Bayesian Framework for Multiple Trait Colo-calization from Summary Association Statistics. Bioinformatics (Oxford, England). PMID 29579179 DOI: 10.1093/Bioinformatics/Bty147 |
0.389 |
|
| 2018 |
Ellis SE, Collado-Torres L, Jaffe A, Leek JT. Improving the value of public RNA-seq expression data by phenotype prediction. Nucleic Acids Research. PMID 29514223 DOI: 10.1093/Nar/Gky102 |
0.349 |
|
| 2018 |
Maynard KR, Hobbs JW, Phan BN, Gupta A, Rajpurohit S, Williams C, Rajpurohit A, Shin JH, Jaffe AE, Martinowich K. Author response: BDNF-TrkB signaling in oxytocin neurons contributes to maternal behavior Elife. DOI: 10.7554/Elife.33676.023 |
0.698 |
|
| 2018 |
Luidy-Imada E, Matam T, Collado-Torres L, Dinalankara W, Stupnikov A, Wilks C, Jaffe AE, Langmead B, Leek JT, Favorov A, Marchionni L. Abstract 2297: Differential analysis of gene expression across the human genome using recount2 and FANTOM-CAT Cancer Research. 78: 2297-2297. DOI: 10.1158/1538-7445.Am2018-2297 |
0.391 |
|
| 2018 |
Ursini G, Punzi G, Chen Q, Marenco S, Robinson JF, Porcelli A, Hamilton E, Mitjans M, Maddalena G, Begemann M, Seidel J, Yanamori H, Jaffe AE, Berman KF, Egan MF, et al. O4.7. PLACENTAL GENE EXPRESSION, OBSTETRICAL HISTORY AND POLYGENIC RISK FOR SCHIZOPHRENIA Schizophrenia Bulletin. 44: S85-S86. DOI: 10.1093/Schbul/Sby015.213 |
0.326 |
|
| 2018 |
Boks M, Houtepen L, Xu Z, He Y, Ursini G, Maihofer A, Rajarajan P, Hulshoff Pol H, Rutten B, Jaffe AE, Kleinmann JE, Baker D, Hol E, Akbarian S, Nievergelt C, et al. O4.1. GENETIC VULNERABILITY TO DUSP22 PROMOTOR HYPERMETHYLATION IS INVOLVED IN THE RELATION BETWEEN IN UTERO FAMINE EXPOSURE AND SCHIZOPHRENIA Schizophrenia Bulletin. 44: S82-S82. DOI: 10.1093/Schbul/Sby015.207 |
0.405 |
|
| 2018 |
Hoeppner D, Jaffe A, Ukaigwe J, Blanpain L, Tao R, McKay R, Matsumoto M, Kleinman J, Weinberger D, Hyde T. 262. Human Dg-Seq Reveals Cell-Type-Specific Effectors of Schizophrenia Risk Biological Psychiatry. 83. DOI: 10.1016/J.Biopsych.2018.02.281 |
0.303 |
|
| 2017 |
Collado-Torres L, Nellore A, Jaffe AE. recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor. F1000research. 6: 1558. PMID 29043067 DOI: 10.12688/F1000Research.12223.1 |
0.347 |
|
| 2017 |
Jaffe AE, Tao R, Norris AL, Kealhofer M, Nellore A, Shin JH, Kim D, Jia Y, Hyde TM, Kleinman JE, Straub RE, Leek JT, Weinberger DR. qSVA framework for RNA quality correction in differential expression analysis. Proceedings of the National Academy of Sciences of the United States of America. PMID 28634288 DOI: 10.1073/Pnas.1617384114 |
0.346 |
|
| 2017 |
Rutten BPF, Vermetten E, Vinkers CH, Ursini G, Daskalakis NP, Pishva E, de Nijs L, Houtepen LC, Eijssen L, Jaffe AE, Kenis G, Viechtbauer W, van den Hove D, Schraut KG, Lesch KP, et al. Longitudinal analyses of the DNA methylome in deployed military servicemen identify susceptibility loci for post-traumatic stress disorder. Molecular Psychiatry. PMID 28630453 DOI: 10.1038/Mp.2017.120 |
0.326 |
|
| 2017 |
Kozlenkov A, Jaffe AE, Timashpolsky A, Apontes P, Rudchenko S, Barbu M, Byne W, Hurd YL, Horvath S, Dracheva S. DNA Methylation Profiling of Human Prefrontal Cortex Neurons in Heroin Users Shows Significant Difference between Genomic Contexts of Hyper- and Hypomethylation and a Younger Epigenetic Age. Genes. 8. PMID 28556790 DOI: 10.3390/Genes8060152 |
0.399 |
|
| 2017 |
Wright C, Shin JH, Rajpurohit A, Deep-Soboslay A, Collado-Torres L, Brandon NJ, Hyde TM, Kleinman JE, Jaffe AE, Cross AJ, Weinberger DR. Altered expression of histamine signaling genes in autism spectrum disorder. Translational Psychiatry. 7: e1126. PMID 28485729 DOI: 10.1038/Tp.2017.87 |
0.41 |
|
| 2017 |
Birnbaum R, Jaffe AE, Chen Q, Shin JH, Kleinman JE, Hyde TM, Weinberger DR. Investigating the neuroimmunogenic architecture of schizophrenia. Molecular Psychiatry. PMID 28485405 DOI: 10.1038/Mp.2017.89 |
0.383 |
|
| 2017 |
Tao R, Davis KN, Li C, Shin JH, Gao Y, Jaffe AE, Gondré-Lewis MC, Weinberger DR, Kleinman JE, Hyde TM. GAD1 alternative transcripts and DNA methylation in human prefrontal cortex and hippocampus in brain development, schizophrenia. Molecular Psychiatry. PMID 28485403 DOI: 10.1038/Mp.2017.105 |
0.399 |
|
| 2017 |
McConnell MJ, Moran JV, Abyzov A, Akbarian S, Bae T, Cortes-Ciriano I, Erwin JA, Fasching L, Flasch DA, Freed D, Ganz J, Jaffe AE, Kwan KY, Kwon M, Lodato MA, et al. Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network. Science (New York, N.Y.). 356. PMID 28450582 DOI: 10.1126/Science.Aal1641 |
0.377 |
|
| 2017 |
Page SC, Hamersky GR, Gallo RA, Rannals MD, Calcaterra NE, Campbell MN, Mayfield B, Briley A, Phan BN, Jaffe AE, Maher BJ. The schizophrenia- and autism-associated gene, transcription factor 4 regulates the columnar distribution of layer 2/3 prefrontal pyramidal neurons in an activity-dependent manner. Molecular Psychiatry. PMID 28289282 DOI: 10.1038/Mp.2017.37 |
0.744 |
|
| 2017 |
Ursini G, Punzi G, Chen Q, Marenco S, Jaffe A, Straub R, Berman K, Hashimoto R, Colantuoni C, Blasi G, Annamaria P, Giancarlo M, Joshua R, Emily H, Allessandro B, et al. 115.1 Placental Gene Expression Mediates the Interaction Between Obstetrical History and Genetic Risk for Schizophrenia Schizophrenia Bulletin. 43: S60-S60. DOI: 10.1093/Schbul/Sbx021.158 |
0.392 |
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| 2017 |
Hibar D, Jaffe A, Shin JH, Hyde T, Kleinman J, Weinberger D, Drevets W, Saad Z, Furey M, Kolb H. 555. Gene Expression Differences Associated with Major Psychiatric Disorders in the Human Prefrontal Cortex and Hippocampus Biological Psychiatry. 81. DOI: 10.1016/J.Biopsych.2017.02.1163 |
0.354 |
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| 2016 |
Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips Iii RA, Karbhari N, Hansen KD, Langmead B, Leek JT. Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive. Genome Biology. 17: 266. PMID 28038678 DOI: 10.1186/S13059-016-1118-6 |
0.305 |
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| 2016 |
Bharadwaj RA, Jaffe AE, Chen Q, Deep-Soboslay A, Goldman AL, Mighdoll MI, Cotoia JA, Brandtjen AC, Shin J, Hyde TM, Mattay VS, Weinberger DR, Kleinman JE. Genetic risk mechanisms of posttraumatic stress disorder in the human brain. Journal of Neuroscience Research. PMID 27775175 DOI: 10.1002/Jnr.23957 |
0.397 |
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| 2016 |
Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE. Flexible expressed region analysis for RNA-seq with derfinder. Nucleic Acids Research. PMID 27694310 DOI: 10.1093/Nar/Gkw852 |
0.385 |
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| 2016 |
Jaffe AE, Kleinman JE. Genetic and epigenetic analysis of schizophrenia in blood-a no-brainer? Genome Medicine. 8: 96. PMID 27655387 DOI: 10.1186/S13073-016-0354-4 |
0.318 |
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| 2016 |
McFadden WC, Jaffe AE, Ye T, Paltán-Ortiz JD, Hyde TM, Kleinman JE. Assessment of genetic risk for distribution of total interstitial white matter neurons in dorsolateral prefrontal cortex: role in schizophrenia. Schizophrenia Research. PMID 27237599 DOI: 10.1016/J.Schres.2016.04.007 |
0.308 |
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| 2016 |
Li M, Jaffe AE, Straub RE, Tao R, Shin JH, Wang Y, Chen Q, Li C, Jia Y, Ohi K, Maher BJ, Brandon NJ, Cross A, Chenoweth JG, Hoeppner DJ, et al. A human-specific AS3MT isoform and BORCS7 are molecular risk factors in the 10q24.32 schizophrenia-associated locus. Nature Medicine. PMID 27158905 DOI: 10.1038/Nm.4096 |
0.43 |
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| 2016 |
Montano C, Taub MA, Jaffe A, Briem E, Feinberg JI, Trygvadottir R, Idrizi A, Runarsson A, Berndsen B, Gur RC, Moore TM, Perry RT, Fugman D, Sabunciyan S, Yolken RH, et al. Association of DNA Methylation Differences With Schizophrenia in an Epigenome-Wide Association Study. Jama Psychiatry. PMID 27074206 DOI: 10.1001/Jamapsychiatry.2016.0144 |
0.558 |
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| 2016 |
Rannals MD, Hamersky GR, Page SC, Campbell MN, Briley A, Gallo RA, Phan BN, Hyde TM, Kleinman JE, Shin JH, Jaffe AE, Weinberger DR, Maher BJ. Psychiatric Risk Gene Transcription Factor 4 Regulates Intrinsic Excitability of Prefrontal Neurons via Repression of SCN10a and KCNQ1. Neuron. PMID 26971948 DOI: 10.1016/j.neuron.2016.02.021 |
0.725 |
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| 2016 |
Ivanov NA, Tao R, Chenoweth JG, Brandtjen A, Mighdoll MI, Genova JD, McKay RD, Jia Y, Weinberger DR, Kleinman JE, Hyde TM, Jaffe AE. Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age. Plos Genetics. 12: e1005819. PMID 26913521 DOI: 10.1371/Journal.Pgen.1005819 |
0.336 |
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| 2016 |
Calcaterra NE, Hoeppner DJ, Wei H, Jaffe AE, Maher BJ, Barrow JC. Schizophrenia-Associated hERG channel Kv11.1-3.1 Exhibits a Unique Trafficking Deficit that is Rescued Through Proteasome Inhibition for High Throughput Screening. Scientific Reports. 6: 19976. PMID 26879421 DOI: 10.1038/Srep19976 |
0.31 |
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| 2016 |
Jaffe AE. Postmortem human brain genomics in neuropsychiatric disorders-how far can we go? Current Opinion in Neurobiology. 36: 107-11. PMID 26685806 DOI: 10.1016/J.Conb.2015.11.002 |
0.361 |
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| 2015 |
Collado-Torres L, Jaffe AE, Leek JT. regionReport: Interactive reports for region-level and feature-level genomic analyses. F1000research. 4: 105. PMID 27429738 DOI: 10.12688/F1000Research.6379.2 |
0.306 |
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| 2015 |
Jaffe AE, Gao Y, Deep-Soboslay A, Tao R, Hyde TM, Weinberger DR, Kleinman JE. Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex. Nature Neuroscience. PMID 26619358 DOI: 10.1038/Nn.4181 |
0.383 |
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| 2015 |
Akbarian S, Liu C, Knowles JA, Vaccarino FM, Farnham PJ, Crawford GE, Jaffe AE, Pinto D, Dracheva S, Geschwind DH, Mill J, Nairn AC, Abyzov A, Pochareddy S, Prabhakar S, et al. The PsychENCODE project. Nature Neuroscience. 18: 1707-1712. PMID 26605881 DOI: 10.1038/Nn.4156 |
0.389 |
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| 2015 |
Jaffe AE, Hyde T, Kleinman J, Weinbergern DR, Chenoweth JG, McKay RD, Leek JT, Colantuoni C. Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis. Bmc Bioinformatics. 16: 372. PMID 26545828 DOI: 10.1186/S12859-015-0808-5 |
0.358 |
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| 2015 |
Oliver V, Jaffe AE, Song J, Wang G, Zhang P, Branham KE, Swaroop A, Eberhart CG, Zack DJ, Qian J, Merbs SL. Differential DNA Methylation Identified in the Blood and Retina of AMD Patients. Epigenetics : Official Journal of the Dna Methylation Society. 0. PMID 26067391 DOI: 10.1080/15592294.2015.1060388 |
0.39 |
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| 2015 |
Frazee AC, Jaffe AE, Langmead B, Leek JT. Polyester: simulating RNA-seq datasets with differential transcript expression. Bioinformatics (Oxford, England). PMID 25926345 DOI: 10.1093/Bioinformatics/Btv272 |
0.329 |
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| 2015 |
Bakulski KM, Lee H, Feinberg JI, Wells EM, Brown S, Herbstman JB, Witter FR, Halden RU, Caldwell K, Mortensen ME, Jaffe AE, Moye J, Caulfield LE, Pan Y, Goldman LR, et al. Prenatal mercury concentration is associated with changes in DNA methylation at TCEANC2 in newborns. International Journal of Epidemiology. PMID 25906783 DOI: 10.1093/Ije/Dyv032 |
0.676 |
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| 2015 |
Feinberg JI, Bakulski KM, Jaffe AE, Tryggvadottir R, Brown SC, Goldman LR, Croen LA, Hertz-Picciotto I, Newschaffer CJ, Daniele Fallin M, Feinberg AP. Paternal sperm DNA methylation associated with early signs of autism risk in an autism-enriched cohort. International Journal of Epidemiology. 44: 1199-210. PMID 25878217 DOI: 10.1093/Ije/Dyv028 |
0.602 |
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| 2015 |
Marioni RE, Shah S, McRae AF, Chen BH, Colicino E, Harris SE, Gibson J, Henders AK, Redmond P, Cox SR, Pattie A, Corley J, Murphy L, Martin NG, Montgomery GW, ... ... Jaffe AE, et al. DNA methylation age of blood predicts all-cause mortality in later life. Genome Biology. 16: 25. PMID 25633388 DOI: 10.1186/S13059-015-0584-6 |
0.519 |
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| 2015 |
Birnbaum R, Jaffe AE, Chen Q, Hyde TM, Kleinman JE, Weinberger DR. Investigation of the prenatal expression patterns of 108 schizophrenia-associated genetic loci. Biological Psychiatry. 77: e43-51. PMID 25592863 DOI: 10.1016/J.Biopsych.2014.10.008 |
0.327 |
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| 2015 |
Multhaup ML, Seldin MM, Jaffe AE, Lei X, Kirchner H, Mondal P, Li Y, Rodriguez V, Drong A, Hussain M, Lindgren C, McCarthy M, Näslund E, Zierath JR, Wong GW, et al. Mouse-human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes. Cell Metabolism. 21: 138-49. PMID 25565211 DOI: 10.1016/J.Cmet.2014.12.014 |
0.355 |
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| 2015 |
Jaffe AE, Shin J, Collado-Torres L, Leek JT, Tao R, Li C, Gao Y, Jia Y, Maher BJ, Hyde TM, Kleinman JE, Weinberger DR. Developmental regulation of human cortex transcription and its clinical relevance at single base resolution. Nature Neuroscience. 18: 154-61. PMID 25501035 DOI: 10.1038/Nn.3898 |
0.419 |
|
| 2015 |
Collado-Torres L, Jaffe AE, Leek JT. regionReport: Interactive reports for region-based analyses F1000research. 4: 105. DOI: 10.12688/F1000Research.6379.1 |
0.308 |
|
| 2015 |
Schubert CR, O'Donnell P, Quan J, Wendland JR, Xi HS, Winslow AR, Domenici E, Essioux L, Kam-Thong T, Airey DC, Calley JN, Collier DA, Wang H, Eastwood B, Ebert P, ... ... Jaffe AE, et al. BrainSeq: Neurogenomics to Drive Novel Target Discovery for Neuropsychiatric Disorders Neuron. 88: 1078-1083. DOI: 10.1016/J.Neuron.2015.10.047 |
0.363 |
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| 2014 |
Jaffe AE, Deep-Soboslay A, Tao R, Hauptman DT, Kaye WH, Arango V, Weinberger DR, Hyde TM, Kleinman JE. Genetic neuropathology of obsessive psychiatric syndromes. Translational Psychiatry. 4: e432. PMID 25180571 DOI: 10.1038/Tp.2014.68 |
0.397 |
|
| 2014 |
Tao R, Cousijn H, Jaffe AE, Burnet PW, Edwards F, Eastwood SL, Shin JH, Lane TA, Walker MA, Maher BJ, Weinberger DR, Harrison PJ, Hyde TM, Kleinman JE. Expression of ZNF804A in human brain and alterations in schizophrenia, bipolar disorder, and major depressive disorder: a novel transcript fetally regulated by the psychosis risk variant rs1344706. Jama Psychiatry. 71: 1112-20. PMID 25162540 DOI: 10.1001/Jamapsychiatry.2014.1079 |
0.359 |
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| 2014 |
Birnbaum R, Jaffe AE, Hyde TM, Kleinman JE, Weinberger DR. Prenatal expression patterns of genes associated with neuropsychiatric disorders. The American Journal of Psychiatry. 171: 758-67. PMID 24874100 DOI: 10.1176/Appi.Ajp.2014.13111452 |
0.366 |
|
| 2014 |
Michailidi C, Soudry E, Brait M, Maldonado L, Jaffe A, Ili-Gangas C, Brebi-Mieville P, Perez J, Kim MS, Zhong X, Yang Q, Valle B, Meltzer SJ, Torbenson M, Esteller M, et al. Genome-wide and gene-specific epigenomic platforms for hepatocellular carcinoma biomarker development trials. Gastroenterology Research and Practice. 2014: 597164. PMID 24829571 DOI: 10.1155/2014/597164 |
0.311 |
|
| 2014 |
Jaffe AE, Irizarry RA. Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biology. 15: R31. PMID 24495553 DOI: 10.1186/Gb-2014-15-2-R31 |
0.347 |
|
| 2014 |
Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, Irizarry RA. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics (Oxford, England). 30: 1363-9. PMID 24478339 DOI: 10.1093/Bioinformatics/Btu049 |
0.316 |
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| 2014 |
Fertig EJ, Stein-O'Brien G, Jaffe A, Colantuoni C. Pattern identification in time-course gene expression data with the CoGAPS matrix factorization. Methods in Molecular Biology (Clifton, N.J.). 1101: 87-112. PMID 24233779 DOI: 10.1007/978-1-62703-721-1_6 |
0.319 |
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| 2014 |
Jaffe AE, Eaton WW, Straub RE, Marenco S, Weinberger DR. Paternal age, de novo mutations and schizophrenia. Molecular Psychiatry. 19: 274-5. PMID 23752248 DOI: 10.1038/Mp.2013.76 |
0.306 |
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| 2013 |
Oliver VF, Franchina M, Jaffe AE, Branham KE, Othman M, Heckenlively JR, Swaroop A, Campochiaro B, Vote BJ, Craig JE, Saffery R, Mackey DA, Qian J, Zack DJ, Hewitt AW, et al. Hypomethylation of the IL17RC promoter in peripheral blood leukocytes is not a hallmark of age-related macular degeneration. Cell Reports. 5: 1527-35. PMID 24373284 DOI: 10.1016/J.Celrep.2013.11.042 |
0.347 |
|
| 2013 |
Jaffe AE, Storey JD, Ji H, Leek JT. Gene set bagging for estimating the probability a statistically significant result will replicate. Bmc Bioinformatics. 14: 360. PMID 24330332 DOI: 10.1186/1471-2105-14-360 |
0.35 |
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| 2013 |
Gnanakkan VP, Jaffe AE, Dai L, Fu J, Wheelan SJ, Levitsky HI, Boeke JD, Burns KH. TE-array--a high throughput tool to study transposon transcription. Bmc Genomics. 14: 869. PMID 24325565 DOI: 10.1186/1471-2164-14-869 |
0.392 |
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| 2013 |
Horiuchi Y, Kano S, Ishizuka K, Cascella NG, Ishii S, Talbot CC, Jaffe AE, Okano H, Pevsner J, Colantuoni C, Sawa A. Olfactory cells via nasal biopsy reflect the developing brain in gene expression profiles: utility and limitation of the surrogate tissues in research for brain disorders. Neuroscience Research. 77: 247-50. PMID 24120685 DOI: 10.1016/J.Neures.2013.09.010 |
0.318 |
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| 2012 |
Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, Irizarry RA. Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies. International Journal of Epidemiology. 41: 200-9. PMID 22422453 DOI: 10.1093/Ije/Dyr238 |
0.547 |
|
| 2012 |
Lee H, Jaffe AE, Feinberg JI, Tryggvadottir R, Brown S, Montano C, Aryee MJ, Irizarry RA, Herbstman J, Witter FR, Goldman LR, Feinberg AP, Fallin MD. DNA methylation shows genome-wide association of NFIX, RAPGEF2 and MSRB3 with gestational age at birth. International Journal of Epidemiology. 41: 188-99. PMID 22422452 DOI: 10.1093/Ije/Dyr237 |
0.589 |
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| 2012 |
Jaffe AE, Feinberg AP, Irizarry RA, Leek JT. Significance analysis and statistical dissection of variably methylated regions. Biostatistics (Oxford, England). 13: 166-78. PMID 21685414 DOI: 10.1093/Biostatistics/Kxr013 |
0.367 |
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| 2011 |
Vincent A, Omura N, Hong SM, Jaffe A, Eshleman J, Goggins M. Genome-wide analysis of promoter methylation associated with gene expression profile in pancreatic adenocarcinoma. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. 17: 4341-54. PMID 21610144 DOI: 10.1158/1078-0432.Ccr-10-3431 |
0.391 |
|
| 2011 |
Guerrero-Preston R, Soudry E, Acero J, Orera M, Moreno-López L, Macía-Colón G, Jaffe A, Berdasco M, Ili-Gangas C, Brebi-Mieville P, Fu Y, Engstrom C, Irizarry RA, Esteller M, Westra W, et al. NID2 and HOXA9 promoter hypermethylation as biomarkers for prevention and early detection in oral cavity squamous cell carcinoma tissues and saliva Cancer Prevention Research. 4: 1061-1072. PMID 21558411 DOI: 10.1158/1940-6207.Capr-11-0006 |
0.326 |
|
| 2011 |
Guerrero-Preston R, Soudry E, Jaffe A, Ili-Gangas C, Brebi-Mieville P, Pérez J, Zhong X, Yang Q, Meltzer SJ, Esteller M, Sidransky D. Abstract 3172: Methylation portraits discriminate between hepatocellular carcinoma cases and controls Cancer Research. 71: 3172-3172. DOI: 10.1158/1538-7445.Am2011-3172 |
0.352 |
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| 2010 |
Guerrero-Preston RE, Soudry E, Ili-Gangas C, Brebi-Mieville P, Jaffe A, Barr C, Irizarry R, Berdasco M, Fu Y, Orera M, Acero J, Blanco A, Yang Q, Baez A, Esteller M, et al. Abstract 2924: Genome-wide microarray platforms uncover novel hypermethylated genes in an oral squamous cell carcinoma case-control study: A phase I preclinical biomarker development study Cancer Research. 70: 2924-2924. DOI: 10.1158/1538-7445.Am10-2924 |
0.382 |
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| 2009 |
Ganesh SK, Zakai NA, van Rooij FJ, Soranzo N, Smith AV, Nalls MA, Chen MH, Kottgen A, Glazer NL, Dehghan A, Kuhnel B, Aspelund T, Yang Q, Tanaka T, Jaffe A, et al. Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. Nature Genetics. 41: 1191-8. PMID 19862010 DOI: 10.1038/Ng.466 |
0.307 |
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