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Author: Andrew E Jaffe

Rankings

  • All-time downloads: 65,518 (rank: 2,897 )
  • Categories:
    • bioinformatics: 15,606 (rank: 499 )
    • cell biology: 442 (rank: 27,817 (tie) )
    • developmental biology: 1,123 (rank: 4,701 (tie) )
    • genetics: 1,179 (rank: 15,737 (tie) )
    • genomics: 21,010 (rank: 653 )
    • immunology: 499 (rank: 24,213 (tie) )
    • neuroscience: 25,056 (rank: 278 )
    • psychiatry and clinical psychology: 603 (rank: 2,699 (tie) )

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Preprints

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

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recount: A large-scale resource of analysis-ready RNA-seq expression data

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Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

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Polyester: simulating RNA-seq datasets with differential transcript expression

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Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation

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A Bayesian Framework for Multiple Trait Colocalization from Summary Association Statistics

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Addressing confounding artifacts in reconstruction of gene co-expression networks

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Flexible expressed region analysis for RNA-seq with derfinder

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dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues

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

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A framework for RNA quality correction in differential expression analysis

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    • In bioinformatics: 1,323
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Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs

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    • In genomics: 1,202
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recount3: summaries and queries for large-scale RNA-seq expression and splicing

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    • In genomics: 1,220
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Single-nucleus transcriptome analysis reveals cell type-specific molecular signatures across reward circuitry in the human brain

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    • Site-wide: 15,363
    • In neuroscience: 1,712
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    • Site-wide: 5,073
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Strategies for cellular deconvolution in human brain RNA sequencing data

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    • In genomics: 1,598
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recount-brain: a curated repository of human brain RNA-seq datasets metadata

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    • Site-wide: 18,114
    • In genomics: 1,729
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Defects of myelination are common pathophysiology in syndromic and idiopathic autism spectrum disorders

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    • Site-wide: 18,110
    • In neuroscience: 2,131
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Recounting the FANTOM Cage Associated Transcriptome

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Placental gene expression mediates the interaction between obstetrical history and genetic risk for schizophrenia

genetics more details view paper
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Integrated DNA methylation and gene expression profiling across multiple brain regions implicate novel genes in Alzheimer's disease

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    • Site-wide: 23,587
    • In genomics: 2,174
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The methylome of the human frontal cortex across development

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    • In developmental biology: 413
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Divergent neuronal DNA methylation patterns across human cortical development: Critical periods and a unique role of CpH methylation

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Identification and prioritization of gene sets associated with schizophrenia risk by co-expression network analysis in human brain

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    • In neuroscience: 3,281
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Regional heterogeneity in gene expression, regulation and coherence in hippocampus and dorsolateral prefrontal cortex across development and in schizophrenia

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    • Site-wide: 28,137
    • In neuroscience: 3,544
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Correcting For Cell-Type Heterogeneity In Epigenome-Wide Association Studies: Premature Analyses And Conclusions

bioinformatics more details view paper
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    • Site-wide: 33,003
    • In bioinformatics: 3,595
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Incomplete annotation of disease-associated genes is limiting our understanding of Mendelian and complex neurogenetic disorders

bioinformatics more details view paper
  • Downloaded 840 times
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    • Site-wide: 36,815
    • In bioinformatics: 3,963
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Cell type-specific genetic regulation of expression in the granule cell layer of the human dentate gyrus

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    • Site-wide: 38,424
    • In neuroscience: 5,128
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Brain expressed FKBP5 delineates a therapeutic subtype of severe mental illness

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    • In neuroscience: 6,127
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Integrating brain methylome with GWAS for psychiatric risk gene discovery

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  • Downloaded 725 times
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    • Site-wide: 45,493
    • In bioinformatics: 4,735
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BDNF-TrkB signaling in oxytocin neurons contributes to maternal behavior

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    • In neuroscience: 6,568
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spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

bioinformatics more details view paper
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    • In bioinformatics: 4,962
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Decoding shared versus divergent transcriptomic signatures across cortico-amygdala circuitry in PTSD and depressive disorders

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    • In neuroscience: 6,996
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SUFI: An automated approach to spectral unmixing of fluorescent multiplex images captured in mouse and postmortem human brain tissues

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

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Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome

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    • Site-wide: 63,132
    • In neuroscience: 9,117
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regionReport: Interactive reports for region-based analyses

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    • Site-wide: 65,269
    • In bioinformatics: 6,252
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Association of a lincRNA postmortem with suicide by violent means and in vivo with aggressive phenotypes

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  • Downloaded 547 times
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    • In neuroscience: 9,548
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SPEAQeasy: a Scalable Pipeline for Expression Analysis and Quantification for R/Bioconductor-powered RNA-seq analyses

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Genetic and environmental regulation of caudate nucleus transcriptome: insight into schizophrenia risk and the dopamine system

psychiatry and clinical psychology more details view paper
  • Downloaded 526 times
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Non-coding Class Switch Recombination-related transcription in human normal and pathological immune responses

immunology more details view paper
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Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex

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Strong Components of Epigenetic Memory in Cultured Human Fibroblasts Related to Site of Origin and Donor Age

cell biology more details view paper
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Genome-wide DNA methylation differences in nucleus accumbens of smokers vs. nonsmokers

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Widespread methylation quantitative trait loci and their role in schizophrenia risk

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VistoSeg: a MATLAB pipeline to process, analyze and visualize high resolution histology images for Visium spatial transcriptomics data

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Epigenome-wide study of brain DNA methylation among opioid users and controls

genomics more details view paper
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Differential Expression of NPAS4 in the Dorsolateral Prefrontal Cortex Following Acute Opioid Intoxication

genomics more details view paper
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    • In genomics: 7,153
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CaPTure: Calcium Peak Toolbox for analysis of in vitro calcium imaging data

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Expression of brain-derived neurotrophic factor in basolateral amygdala inputs to lateral septum is necessary for mice to identify socially novel individuals

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Developmental profile of psychiatric risk associated with voltage-gated cation channel activity

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Induction of Bdnf from promoter I following electroconvulsive seizures contributes to structural plasticity in neurons of the piriform cortex

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Molecular phenotypes associated with antipsychotic drugs in the human caudate nucleus

psychiatry and clinical psychology more details view paper
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