Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays von Aryee, Martin J., Jaffe, Andrew E., Corrada-Bravo, Hector, Ladd-Acosta, Christine, Feinberg, Andrew P., Hansen, Kasper D., Irizarry, Rafael A.

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Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex von Jaffe, Andrew E, Gao, Yuan, Deep-Soboslay, Amy, Tao, Ran, Hyde, Thomas M, Weinberger, Daniel R, Kleinman, Joel E

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Accounting for cellular heterogeneity is critical in epigenome-wide association studies von Jaffe, Andrew E, Irizarry, Rafael A

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A Bayesian framework for multiple trait colocalization from summary association statistics von Giambartolomei, Claudia, Zhenli Liu, Jimmy, Zhang, Wen, Hauberg, Mads, Shi, Huwenbo, Boocock, James, Pickrell, Joe, Jaffe, Andrew E, Pasaniuc, Bogdan, Roussos, Panos

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The sva package for removing batch effects and other unwanted variation in high-throughput experiments von LEEK, Jeffrey T, EVAN JOHNSON, W, PARKER, Hilary S, JAFFE, Andrew E, STOREY, John D

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recount3: summaries and queries for large-scale RNA-seq expression and splicing von Wilks, Christopher, Zheng, Shijie C, Chen, Feng Yong, Charles, Rone, Solomon, Brad, Ling, Jonathan P, Imada, Eddie Luidy, Zhang, David, Joseph, Lance, Leek, Jeffrey T, Jaffe, Andrew E, Nellore, Abhinav, Collado-Torres, Leonardo, Hansen, Kasper D, Langmead, Ben

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Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis von Jaffe, Andrew E., Straub, Richard E., Shin, Joo Heon, Tao, Ran, Gao, Yuan, Collado-Torres, Leonardo, Kam-Thong, Tony, Xi, Hualin S., Quan, Jie, Chen, Qiang, Colantuoni, Carlo, Ulrich, William S., Maher, Brady J., Deep-Soboslay, Amy, Cross, Alan J., Brandon, Nicholas J., Leek, Jeffrey T., Hyde, Thomas M., Kleinman, Joel E., Weinberger, Daniel R.

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spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data von Pardo, Brenda, Spangler, Abby, Weber, Lukas M, Page, Stephanie C, Hicks, Stephanie C, Jaffe, Andrew E, Martinowich, Keri, Maynard, Kristen R, Collado-Torres, Leonardo

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Addressing confounding artifacts in reconstruction of gene co-expression networks von Parsana, Princy, Ruberman, Claire, Jaffe, Andrew E, Schatz, Michael C, Battle, Alexis, Leek, Jeffrey T

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Regional Heterogeneity in Gene Expression, Regulation, and Coherence in the Frontal Cortex and Hippocampus across Development and Schizophrenia von Collado-Torres, Leonardo, Burke, Emily E., Peterson, Amy, Shin, JooHeon, Straub, Richard E., Rajpurohit, Anandita, Semick, Stephen A., Ulrich, William S., Price, Amanda J., Valencia, Cristian, Tao, Ran, Deep-Soboslay, Amy, Hyde, Thomas M., Kleinman, Joel E., Weinberger, Daniel R., Jaffe, Andrew E.

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Convergence of placenta biology and genetic risk for schizophrenia von Ursini, Gianluca, Punzi, Giovanna, Chen, Qiang, Marenco, Stefano, Robinson, Joshua F., Porcelli, Annamaria, Hamilton, Emily G., Mitjans, Marina, Maddalena, Giancarlo, Begemann, Martin, Seidel, Jan, Yanamori, Hidenaga, Jaffe, Andrew E., Berman, Karen F., Egan, Michael F., Straub, Richard E., Colantuoni, Carlo, Blasi, Giuseppe, Hashimoto, Ryota, Rujescu, Dan, Ehrenreich, Hannelore, Bertolino, Alessandro, Weinberger, Daniel R.

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Psychiatric Risk Gene Transcription Factor 4 Regulates Intrinsic Excitability of Prefrontal Neurons via Repression of SCN10a and KCNQ1 von Rannals, Matthew D., Hamersky, Gregory R., Page, Stephanie Cerceo, Campbell, Morganne N., Briley, Aaron, Gallo, Ryan A., Phan, BaDoi N., Hyde, Thomas M., Kleinman, Joel E., Shin, Joo Heon, Jaffe, Andrew E., Weinberger, Daniel R., Maher, Brady J.

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BiocMAP: a Bioconductor-friendly, GPU-accelerated pipeline for bisulfite-sequencing data von Eagles, Nicholas J, Wilton, Richard, Jaffe, Andrew E, Collado-Torres, Leonardo

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Mouse-Human Experimental Epigenetic Analysis Unmasks Dietary Targets and Genetic Liability for Diabetic Phenotypes von Multhaup, Michael L., Seldin, Marcus M., Jaffe, Andrew E., Lei, Xia, Kirchner, Henriette, Mondal, Prosenjit, Li, Yuanyuan, Rodriguez, Varenka, Drong, Alexander, Hussain, Mehboob, Lindgren, Cecilia, McCarthy, Mark, Näslund, Erik, Zierath, Juleen R., Wong, G. William, Feinberg, Andrew P.

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A myelin-related transcriptomic profile is shared by Pitt–Hopkins syndrome models and human autism spectrum disorder von Phan, BaDoi N., Bohlen, Joseph F., Davis, Brittany A., Ye, Zengyou, Chen, Huei-Ying, Mayfield, Brent, Sripathy, Srinidhi Rao, Cerceo Page, Stephanie, Campbell, Morganne N., Smith, Hannah L., Gallop, Danisha, Kim, Hyojin, Thaxton, Courtney L., Simon, Jeremy M., Burke, Emily E., Shin, Joo Heon, Kennedy, Andrew J., Sweatt, J. David, Philpot, Benjamin D., Jaffe, Andrew E., Maher, Brady J.

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Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods von Wright, Carrie, Rajpurohit, Anandita, Burke, Emily E, Williams, Courtney, Collado-Torres, Leonardo, Kimos, Martha, Brandon, Nicholas J, Cross, Alan J, Jaffe, Andrew E, Weinberger, Daniel R, Shin, Joo Heon

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Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer’s disease von Semick, Stephen A., Bharadwaj, Rahul A., Collado-Torres, Leonardo, Tao, Ran, Shin, Joo Heon, Deep-Soboslay, Amy, Weiss, James R., Weinberger, Daniel R., Hyde, Thomas M., Kleinman, Joel E., Jaffe, Andrew E., Mattay, Venkata S.

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dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues von Maynard, Kristen R, Tippani, Madhavi, Takahashi, Yoichiro, Phan, BaDoi N, Hyde, Thomas M, Jaffe, Andrew E, Martinowich, Keri

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A human-specific AS3MT isoform and BORCS7 are molecular risk factors in the 10q24.32 schizophrenia-associated locus von Li, Ming, Jaffe, Andrew E, Straub, Richard E, Tao, Ran, Shin, Joo Heon, Wang, Yanhong, Chen, Qiang, Li, Chao, Jia, Yankai, Ohi, Kazutaka, Maher, Brady J, Brandon, Nicholas J, Cross, Alan, Chenoweth, Joshua G, Hoeppner, Daniel J, Wei, Huijun, Hyde, Thomas M, McKay, Ronald, Kleinman, Joel E, Weinberger, Daniel R

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Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation von Price, Amanda J, Collado-Torres, Leonardo, Ivanov, Nikolay A, Xia, Wei, Burke, Emily E, Shin, Joo Heon, Tao, Ran, Ma, Liang, Jia, Yankai, Hyde, Thomas M, Kleinman, Joel E, Weinberger, Daniel R, Jaffe, Andrew E

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