qSVA framework for RNA quality correction in differential expression analysis

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RSeQC: quality control of RNA-seq experiments

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The RIN: an RNA integrity number for assigning integrity values to RNA measurements

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Tackling the widespread and critical impact of batch effects in high-throughput data

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Normalization of RNA-seq data using factor analysis of control genes or samples

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Capturing Heterogeneity in Gene Expression Studies by Surrogate Variable Analysis

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Transcriptomic Analysis of Autistic Brain Reveals Convergent Molecular Pathology

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Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

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A survey of human brain transcriptome diversity at the single cell level

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Gene expression elucidates functional impact of polygenic risk for schizophrenia

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

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A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

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Removing technical variability in RNA-seq data using conditional quantile normalization

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Remarks on Parallel Analysis

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

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Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples

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RNA-seq: impact of RNA degradation on transcript quantification

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Critical Factors in Gene Expression in Postmortem Human Brain: Focus on Studies in Schizophrenia

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Measure transcript integrity using RNA-seq data

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bwtool: a tool for bigWig files

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Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

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Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study

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Detecting and correcting systematic variation in large-scale RNA sequencing data

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

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Flexible expressed region analysis for RNA-seq with derfinder

Collado‐Torres, L., Nellore, A., Frazee, A. C., Wilks, C., Love, M. I., Langmead, B., Irizarry, R. A., Leek, J. T., & Jaffe, A. E. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw852 · Cited by 63 · see citing works

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

Jaffe, A. E. (2016) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2015.11.002 · Cited by 19 · see citing works

Developmental and genetic regulation of the human cortex transcriptome in schizophreniaPreprint

Jaffe, A. E., Straub, R. E., Shin, J. H., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/124321 · Cited by 13 · see citing works

Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder

Gandal, M. J., Zhang, P., Hadjimichael, E., Walker, R. L., Chen, C., Liu, S., Won, H., van Bakel, H., Varghese, M., Wang, Y., et al. (2018) · Science · doi:10.1126/science.aat8127 · Cited by 1,247 · see citing works

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 · doi:10.1126/science.aad6469 · Cited by 1,095 · see citing works

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 · doi:10.1038/s41593-018-0197-y · Cited by 364 · see citing works

Truncated stathmin-2 is a marker of TDP-43 pathology in frontotemporal dementia

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Supplementary Table 3 from Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq

Beane, J., Vick, J. L., Schembri, F. M., et al. (2023) · doi:10.1158/1940-6207.22524413

Identification of Salt Stress Response Genes in Rosa chinensis Leaves by Comparative RNA-seq Analysis of Transcriptome Dynamics

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Supplementary Table 9 from Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq

Beane, J., Vick, J. L., Schembri, F. M., et al. (2023) · doi:10.1158/1940-6207.22524395

Supplementary Table 10 from Characterizing the Impact of Smoking and Lung Cancer on the Airway Transcriptome Using RNA-Seq

Beane, J., Vick, J. L., Schembri, F. M., et al. (2023) · doi:10.1158/1940-6207.22524419

Collembola Regulate Biological Processes of a Plant: Evidence from a Rna-Seq-Based Transcriptome AnalysisPreprint

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