[HTML][HTML] Statistical and machine learning methods for spatially resolved transcriptomics data analysis

Z Zeng, Y Li, Y Li, Y Luo - Genome biology, 2022 - Springer
The recent advancement in spatial transcriptomics technology has enabled multiplexed
profiling of cellular transcriptomes and spatial locations. As the capacity and efficiency of the …

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

KR Maynard, L Collado-Torres, LM Weber… - Nature …, 2021 - nature.com
We used the 10x Genomics Visium platform to define the spatial topography of gene
expression in the six-layered human dorsolateral prefrontal cortex. We identified extensive …

[HTML][HTML] Evaluation of the suitability of RNAscope as a technique to measure gene expression in clinical diagnostics: a systematic review

S Atout, S Shurrab, C Loveridge - Molecular Diagnosis & Therapy, 2022 - Springer
Objective To evaluate the application of RNAscope in the clinical diagnostic field compared
to the current 'gold standard'methods employed for testing gene expression levels, including …

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

MN Tran, KR Maynard, A Spangler, LA Huuki… - Neuron, 2021 - cell.com
Single-cell gene expression technologies are powerful tools to study cell types in the human
brain, but efforts have largely focused on cortical brain regions. We therefore created a …

A functional cellular framework for sex and estrous cycle-dependent gene expression and behavior

JR Knoedler, S Inoue, DW Bayless, T Yang, A Tantry… - Cell, 2022 - cell.com
Sex hormones exert a profound influence on gendered behaviors. How individual sex
hormone-responsive neuronal populations regulate diverse sex-typical behaviors is unclear …

Single-cell dissection of schizophrenia reveals neurodevelopmental-synaptic link and transcriptional resilience associated cellular state

B Ruzicka, S Mohammadi… - Biological …, 2021 - biologicalpsychiatryjournal.com
Background Schizophrenia is a severe mental illness afflicting young adults just as they
approach their full potential, often resulting in a lifetime of severe disability. While many …

[HTML][HTML] Data-driven identification of total RNA expression genes for estimation of RNA abundance in heterogeneous cell types highlighted in brain tissue

LA Huuki-Myers, KD Montgomery, SH Kwon, SC Page… - Genome biology, 2023 - Springer
We define and identify a new class of control genes for next-generation sequencing called
total RNA expression genes (TREGs), which correlate with total RNA abundance in cell …

A data-driven single-cell and spatial transcriptomic map of the human prefrontal cortex

LA Huuki-Myers, A Spangler, NJ Eagles… - Science, 2024 - science.org
The molecular organization of the human neocortex historically has been studied in the
context of its histological layers. However, emerging spatial transcriptomic technologies …

Decoding shared versus divergent transcriptomic signatures across cortico-amygdala circuitry in PTSD and depressive disorders

AE Jaffe, R Tao, SC Page, KR Maynard… - American Journal of …, 2022 - Am Psychiatric Assoc
Objective: Posttraumatic stress disorder (PTSD) is a debilitating neuropsychiatric disease
that is highly comorbid with major depressive disorder (MDD) and bipolar disorder. The …

[HTML][HTML] Klf5 defines alveolar epithelial type 1 cell lineage commitment during lung development and regeneration

DC Liberti, WA Liberti III, MM Kremp, IJ Penkala… - Developmental Cell, 2022 - cell.com
Alveolar epithelial cell fate decisions drive lung development and regeneration. Using
transcriptomic and epigenetic profiling coupled with genetic mouse and organoid models …