Jaffe, Andrew E.

The <tt>sva</tt> package for removing batch effects and other unwanted variation in high-throughput experiments

Leek, J. T., Johnson, W. E., Parker, H. S., Jaffe, A. E., & Storey, J. D. (2012) · Bioinformatics

Gene expression and cancer classificationSingle-cell and spatial transcriptomics

Cited by 6,231

Mapping genomic loci implicates genes and synaptic biology in schizophrenia

Trubetskoy, V., Pardiñas, A. F., Qi, T., Panagiotaropoulou, G., Awasthi, S., Bigdeli, T. B., Bryois, J., Chen, C.-Y., Dennison, C. A., Hall, L. S., et al. (2022) · Nature

Schizophrenia research and treatmentGenetic Associations and Epidemiology

Cited by 2,964

DNA methylation age of blood predicts all-cause mortality in later life

Marioni, R. E., Shah, S., McRae, A. F., Chen, B. H., Colicino, E., Harris, S. E., Gibson, J., Henders, A. K., Redmond, P., Cox, S. R., et al. (2015) · Genome Biology

Epigenetics and DNA MethylationGenetics, Aging, and Longevity in Model Organisms

Cited by 1,261

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

Maynard, K. R., Collado-Torres, L., Weber, L. M., Uytingco, C., Barry, B. K., Williams, S. R., Catallini, J. L., Tran, M. N., Besich, Z., Tippani, M., et al. (2021) · Nature Neuroscience

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 1,222

Shared molecular neuropathology across major psychiatric disorders parallels polygenic overlap

Gandal, M. J., Haney, J. R., Parikshak, N. N., Leppa, V., Ramaswami, G., Hartl, C., Schork, A. J., Appadurai, V., Buil, A., Werge, T. M., et al. (2018) · Science

Genetic Associations and EpidemiologySchizophrenia research and treatment

Cited by 1,095

Accounting for cellular heterogeneity is critical in epigenome-wide association studies

Jaffe, A. E., & Irizarry, R. A. (2014) · Genome Biology

Epigenetics and DNA MethylationGenetic Associations and Epidemiology

Cited by 1,067

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

Li, M., Santpere, G., Imamura Kawasawa, Y., Evgrafov, O. V., Gulden, F. O., Pochareddy, S., Sunkin, S. M., Li, Z., Shin, Y., Zhu, Y., et al. (2018) · Science

Genetics and Neurodevelopmental DisordersGenomics and Chromatin Dynamics

Cited by 810

Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex

Jaffe, A. E., Gao, Y., Deep-Soboslay, A., Tao, R., Hyde, T. M., Weinberger, D. R., & Kleinman, J. E. (2016) · Nature Neuroscience

Epigenetics and DNA MethylationSchizophrenia research and treatment

Cited by 511

The PsychENCODE project

Akbarian, S., Liu, C., Knowles, J. A., Vaccarino, F. M., Farnham, P. J., Crawford, G. E., Jaffe, A. E., Pinto, D., Dracheva, S., Geschwind, D. H., et al. (2015) · Nature Neuroscience

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 451

Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis

The BrainSeq Consortium, Jaffe, A. E., Straub, R. E., Shin, J. H., Tao, R., Gao, Y., Collado-Torres, L., Kam-Thong, T., Xi, H. S., Quan, J., et al. (2018) · Nature Neuroscience

Schizophrenia research and treatmentGenetic Associations and Epidemiology

Cited by 364

Polyester : simulating RNA-seq datasets with differential transcript expression

Frazee, A. C., Jaffe, A. E., Langmead, B., & Leek, J. T. (2015) · Bioinformatics

Genomics and Phylogenetic StudiesGene expression and cancer classification

Cited by 313

Intersection of diverse neuronal genomes and neuropsychiatric disease: The Brain Somatic Mosaicism Network

McConnell, M. J., Moran, J. V., Abyzov, A., Akbarian, S., Bae, T., Cortes-Ciriano, I., Erwin, J. A., Fasching, L., Flasch, D. A., Freed, D., et al. (2017) · Science

Genomic variations and chromosomal abnormalitiesGenetics and Neurodevelopmental Disorders

Cited by 262

Single-nucleus transcriptome analysis reveals cell-type-specific molecular signatures across reward circuitry in the human brain

Tran, M. N., Maynard, K. R., Spangler, A., Huuki, L. A., Montgomery, K. D., Sadashivaiah, V., Tippani, M., Barry, B. K., Hancock, D. B., Hicks, S. C., et al. (2021) · Neuron

Single-cell and spatial transcriptomicsNeurotransmitter Receptor Influence on Behavior

Cited by 219

Association of DNA methylation differences with schizophrenia in an Epigenome-Wide association study

Montano, C., Taub, M. A., Jaffe, A., Briem, E., Feinberg, J. I., Trygvadottir, R., Idrizi, A., Runarsson, A., Berndsen, B., Gur, R. C., et al. (2016) · JAMA Psychiatry

Epigenetics and DNA MethylationSchizophrenia research and treatment

Cited by 180

Developmental regulation of human cortex transcription and its clinical relevance at single base resolution

Jaffe, A. E., Shin, J., Collado-Torres, L., Leek, J. T., Tao, R., Li, C., Gao, Y., Jia, Y., Maher, B. J., Hyde, T. M., et al. (2015) · Nature Neuroscience

Single-cell and spatial transcriptomicsGenomics and Chromatin Dynamics

Cited by 156

Longitudinal analyses of the DNA methylome in deployed military servicemen identify susceptibility loci for post-traumatic stress disorder

Rutten, B. P. F., Vermetten, E., Vinkers, C. H., Ursini, G., Daskalakis, N. P., Pishva, E., de Nijs, L., Houtepen, L. C., Eijssen, L., Jaffe, A. E., et al. (2018) · Molecular Psychiatry

Posttraumatic Stress Disorder ResearchEpigenetics and DNA Methylation

Cited by 142

qSVA framework for RNA quality correction in differential expression analysis

Jaffe, A. E., Tao, R., Norris, A. L., Kealhofer, M., Nellore, A., Shin, J. H., Kim, D., Jia, Y., Hyde, T. M., Kleinman, J. E., et al. (2017) · Proceedings of the National Academy of Sciences

Gene expression and cancer classificationSingle-cell and spatial transcriptomics

Cited by 114

Neuronal and glial 3D chromatin architecture informs the cellular etiology of brain disorders

Hu, B., Won, H., Mah, W., Park, R. B., Kassim, B., Spiess, K., Kozlenkov, A., Crowley, C. A., Pochareddy, S., The PsychENCODE Consortium, et al. (2021) · Nature Communications

Genomics and Chromatin DynamicsGenetic Associations and Epidemiology

Cited by 103

Comprehensive assessment of multiple biases in small RNA sequencing reveals significant differences in the performance of widely used methods

Wright, C., Rajpurohit, A., Burke, E. E., Williams, C., Collado-Torres, L., Kimos, M., Brandon, N. J., Cross, A. J., Jaffe, A. E., Weinberger, D. R., et al. (2019) · BMC Genomics

Genomics and Phylogenetic StudiesSingle-cell and spatial transcriptomics

Cited by 99

Prenatal Expression Patterns of Genes Associated With Neuropsychiatric Disorders

Birnbaum, R., Jaffe, A. E., Hyde, T. M., Kleinman, J. E., & Weinberger, D. R. (2014) · American Journal of Psychiatry

Genetics and Neurodevelopmental DisordersSchizophrenia research and treatment

Cited by 97

Molecularly Defined Hippocampal Inputs Regulate Population Dynamics in the Prelimbic Cortex to Suppress Context Fear Memory Retrieval

Hallock, H. L., Quillian, H. M., Maynard, K. R., Mai, Y., Chen, H.-Y., Hamersky, G. R., Shin, J. H., Maher, B. J., Jaffe, A. E., & Martinowich, K. (2020) · Biological Psychiatry

Memory and Neural MechanismsNeuroscience and Neuropharmacology Research

Cited by 25

Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex

Perzel Mandell, K. A., Price, A. J., Wilton, R., Collado-Torres, L., Tao, R., Eagles, N. J., Szalay, A. S., Hyde, T. M., Weinberger, D. R., Kleinman, J. E., et al. (2021) · Epigenetics

Epigenetics and DNA MethylationGenetic Syndromes and Imprinting

Cited by 21

Postmortem human brain genomics in neuropsychiatric disorders — how far can we go?

Jaffe, A. E. (2016) · Current Opinion in Neurobiology

Genetic Associations and EpidemiologySingle-cell and spatial transcriptomics

Cited by 19