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Large-scale transcriptomic analyses of major depressive disorder reveal convergent dysregulation of synaptic pathways in excitatory neurons

Major Depressive Disorder (MDD) is a heritable psychiatric disorder whose biological basis remains poorly understood. This large-scale postmortem brain study identified extensive gene expression changes associated with genetic risk, highlighting disrupted glutamatergic signaling and synaptic vesicle function in MDD.

Fernando S. Goes
Leonardo Collado-Torres
Thomas M. Hyde
ResearchOpen Access28 Apr 2025
Nature Communications

Volume: 16, P: 1-15
Correction: Corrigendum: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Cole Trapnell
Adam Roberts
Lior Pachter
Amendments and Corrections25 Sept 2014
Nature Protocols

Volume: 9, P: 2513
StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

Using a network flow algorithm from optimization theory enables improved assembly of transcriptomes from RNA-seq reads.

Mihaela Pertea
Geo M Pertea
Steven L Salzberg
Research18 Feb 2015
Nature Biotechnology

Volume: 33, P: 290-295
Gene Index analysis of the human genome estimates approximately 120,000 genes

Feng Liang
Ingeborg Holt
John Quackenbush
Research01 Jun 2000
Nature Genetics

Volume: 25, P: 239-240
Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

Pertea et al. describe a protocol to analyze RNA-seq data using HISAT, StringTie and Ballgown (the ‘new Tuxedo’ package). The protocol can be used for assembly of transcripts, quantification of gene expression levels and differential expression analysis.

Mihaela Pertea
Daehwan Kim
Steven L Salzberg
Protocols11 Aug 2016
Nature Protocols

Volume: 11, P: 1650-1667
Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry

Studying gene expression in admixed Black Americans, Benjamin et al. reveal genetic ancestry-linked differences impacting immune and vascular genes and potentially influencing neurological disease risk. These findings highlight the importance of considering ancestry in brain research.

Kynon J. M. Benjamin
Qiang Chen
Daniel R. Weinberger
ResearchOpen Access20 May 2024
Nature Neuroscience

Volume: 27, P: 1064-1074
Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus

Schizophrenia research has traditionally overlooked sex differences. Here, the authors show the importance of sex-based analysis across multi-brain regions by identifying sex-specific genes and genetic interactions in schizophrenia and sex-specific risk.

Kynon J. M. Benjamin
Ria Arora
Jennifer A. Erwin
ResearchOpen Access10 May 2024
Nature Communications

Volume: 15, P: 1-16
Ballgown bridges the gap between transcriptome assembly and expression analysis

Alyssa C Frazee
Geo Pertea
Jeffrey T Leek
Correspondence06 Mar 2015
Nature Biotechnology

Volume: 33, P: 243-246
Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

A combination of advanced sequencing and mapping techniques is used to produce a reference genome of Aegilops tauschii, progenitor of the wheat D genome, providing a valuable resource for comparative genetic studies.

Ming-Cheng Luo
Yong Q. Gu
Jan Dvořák
ResearchOpen Access01 Nov 2017
Nature

Volume: 551, P: 498-502
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

RNA-Seq enables rapid sequencing of total cellular RNA and should allow the reconstruction of spliced transcripts in a cell population. Trapnell et al. achieve this and transcript quantification using only paired-end RNA-Seq data and an unannotated genome sequence, and apply the approach to characterize isoform switching over a developmental time course.

Cole Trapnell
Brian A Williams
Lior Pachter
Research02 May 2010
Nature Biotechnology

Volume: 28, P: 511-515
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

Cole Trapnell
Adam Roberts
Lior Pachter
Protocols01 Mar 2012
Nature Protocols

Volume: 7, P: 562-578

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Large-scale transcriptomic analyses of major depressive disorder reveal convergent dysregulation of synaptic pathways in excitatory neurons

Correction: Corrigendum: Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

Gene Index analysis of the human genome estimates approximately 120,000 genes

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

Analysis of gene expression in the postmortem brain of neurotypical Black Americans reveals contributions of genetic ancestry

Sex affects transcriptional associations with schizophrenia across the dorsolateral prefrontal cortex, hippocampus, and caudate nucleus

Ballgown bridges the gap between transcriptome assembly and expression analysis

Genome sequence of the progenitor of the wheat D genome Aegilops tauschii

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

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