Explanipedia

Orchestrating Spatial Transcriptomics Analysis with Bioconductor Open

Ilaria Billato, Peiying Cai, Martin Emons, Boyi Guo, Mengbo Li , et al. · 2025

Spatial transcriptomics technologies provide spatially-resolved measurements of gene expression through assays that can either target selected genes or capture transcriptome-wide expression profiles. The complexity and variability of these…

Spherical PCA: a transparent and scalable approach to quantifying the Waddington Landscape in single-cell RNA-seq data 3144 Open

Long Yuan, Xuyang Li, Stephanie C. Hicks, Alexander S. Szalay · 2025

Description Understanding cell fate decisions in developmental landscapes is a key challenge in single-cell biology. We present spherical principal component analysis (PCA), an interpretable method for visualizing and quantifying these tra…

Impact of Alzheimer’s disease risk factors and local neuromelanin content on the transcriptomic landscape of the human locus coeruleus Open

Bernard Mulvey, Heena R. Divecha, Madhavi Tippani, Svitlana V. Bach, Rahul Bharadwaj , et al. · 2025

The locus coeruleus (LC) is a small noradrenergic nucleus in the dorsal pons that sends projections across the brain regulating sleep, arousal, attention, stress responses, and some forms of cognition. LC neurons show pathology in the earl…

Transcriptomic diversity of amygdalar subdivisions across humans and nonhuman primates Open

Michael S. Totty, Rita Cervera‐Juanes, Svitlana V. Bach, Lamya Ben Ameur, Madeline R. Valentine , et al. · 2025

The amygdaloid complex mediates learning, memory, and emotions. Understanding cellular and anatomical features specialized in the primate amygdala versus other mammals requires a systematic, anatomically resolved molecular analysis of neur…

Characterizing intra- and inter-tumor heterogeneity in Ovarian high-grade serous carcinoma subtypes using single-cell and spatial transcriptomics Open

Weishan Li, Laurie Grieshober, Jason Gertz, Adriana Ivich, J.A. Doherty , et al. · 2025

Ovarian high-grade serous carcinoma (HGSC) is an aggressive ovarian cancer with a heterogeneous tumor microenvironment (TME). Advances in single-cell RNA sequencing (scRNA-seq) and spatially-resolved transcriptomics have enabled the study …

Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens Open

Prashanthi Ravichandran, Svitlana V. Bach, Robert A. Phillips, Madeline R. Valentine, Nicholas J. Eagles , et al. · 2025

The nucleus accumbens (NAc) is a key component of the mesolimbic dopamine system that critically regulates many behaviors related to reward and motivation. The NAc is implicated in several neuropsychiatric disorders, including major depres…

Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain Open

Kinnary Shah, Michael S. Totty, Svitlana V. Bach, Madeline R. Valentine, A. Chandra , et al. · 2025

In the human brain, the dorsal anterior cingulate cortex (dACC) plays key roles in various components of cognitive control, and is particularly relevant for reward processing and conflict monitoring. The dACC regulates expression of fear a…

Spatial mutual nearest neighbors for spatial transcriptomics data Open

Haowen Zhou, Pratibha Panwar, Boyi Guo, Caleb Hallinan, Shila Ghazanfar , et al. · 2025

Motivation Mutual nearest neighbors (MNN) is a widely used computational tool to perform batch correction for single-cell RNA-sequencing data. However, in applications such as spatial transcriptomics, it fails to take into account the 2D s…

Spatial domain detection using contrastive self-supervised learning for spatial multi-omics technologies Open

Jianing Yao, Jinglun Yu, Brian Caffo, Stephanie C. Page, Keri Martinowich , et al. · 2025

Recent advances in spatially resolved single-omic and multi-omics technologies have led to the emergence of computational tools to detect and predict spatial domains. Additionally, histological images and immunofluorescence (IF) staining o…

Transcriptional dynamics of sleep deprivation and subsequent recovery sleep in the male mouse cortex Open

Alexander Popescu, C. A. Ottaway, Kaitlyn Ford, E Medina, Taylor Wintler , et al. · 2025

This study investigates different time points of sleep deprivation and recovery sleep to better understand the molecular processes influenced by sleep and lack of sleep. This study highlights redox metabolism, chromatin regulation, and DNA…

lute: estimating the cell composition of heterogeneous tissue with varying cell sizes using gene expression Open

Sean K. Maden, Louise A. Huuki-Myers, Sang Ho Kwon, Leonardo Collado‐Torres, Kristen R. Maynard , et al. · 2025

0061 Transcriptional Dynamics of Sleep Deprivation and Subsequent Recovery Sleep in the Male Mouse Cortex Open

C. A. Ottaway, Alexander Popescu, Kaitlyn Ford, Taylor Wintler, Ashley M. Ingiosi , et al. · 2025

Introduction Sleep is a critical physiological process governed by circadian and homeostatic mechanisms. The circadian clock controls sleep timing, while the sleep homeostat regulates sleep need (sleep pressure), which increases with wakef…

Benchmark of cellular deconvolution methods using a multi-assay dataset from postmortem human prefrontal cortex Open

Louise A. Huuki-Myers, Kelsey D. Montgomery, Sang Ho Kwon, Sophia Cinquemani, Nicholas J. Eagles , et al. · 2025

Missing cell types in single-cell references impact deconvolution of bulk data but are detectable Open

Adriana Ivich, Natalie R. Davidson, Laurie Grieshober, Weishan Li, Stephanie C. Hicks , et al. · 2025

Background Advancements in RNA sequencing have expanded our ability to study gene expression profiles of biological samples in bulk tissue and single cells. Deconvolution of bulk data with single-cell references provides the ability to stu…

Can AI reveal the next generation of high-impact bone genomics targets? Open

Casey S. Greene, Christopher R. Gignoux, Marc Subirana-Granés, Milton Pividori, Stephanie C. Hicks , et al. · 2025

Genetic studies have revealed hundreds of loci associated with bone-related phenotypes, including bone mineral density (BMD) and fracture risk. However, translating discovered loci into effective new therapies remains challenging. We revie…

Integrating Spatially‐Resolved Transcriptomics Data Across Tissues and Individuals: Challenges and Opportunities Open

Boyi Guo, Wodan Ling, Sang Ho Kwon, Pratibha Panwar, Shila Ghazanfar , et al. · 2025

Advances in spatially‐resolved transcriptomics (SRT) technologies have propelled the development of new computational analysis methods to unlock biological insights. The lowering cost of SRT data generation presents an unprecedented opport…

Spatiotemporal analysis of gene expression in the human dentate gyrus reveals age-associated changes in cellular maturation and neuroinflammation Open

Anthony D. Ramnauth, Madhavi Tippani, Heena R. Divecha, Alexis R. Papariello, Ryan A. Miller , et al. · 2025

The dentate gyrus of the hippocampus is important for many cognitive functions, including learning, memory, and mood. Here, we present transcriptome-wide spatial gene expression maps of the human dentate gyrus and investigate age-associate…

Transcriptomic characterization of human lateral septum neurons reveals conserved and divergent marker genes across species Open

Robert A. Phillips, Seyun Oh, Svitlana V. Bach, Yufeng Du, Ryan A. Miller , et al. · 2025

Quantifying the Alignment of a Data Analysis Between Analyst and Audience Open

Lucy D’Agostino McGowan, Roger D. Peng, Stephanie C. Hicks · 2025

A challenge that data scientists face is building an analytic product that is useful and trustworthy for a given audience. Previously, a set of principles for describing data analyses were defined that can be used to create a data analysis…

Addressing the mean–variance relationship in spatially resolved transcriptomics data with <i>spoon</i> Open

Kinnary Shah, Boyi Guo, Stephanie C. Hicks · 2024

An important task in the analysis of spatially resolved transcriptomics (SRT) data is to identify spatially variable genes (SVGs), or genes that vary in a 2D space. Current approaches rank SVGs based on either $ P $-values or an effect siz…

HuBMAPR : an R client for the HuBMAP data portal Open

Christine Hou, Shila Ghazanfar, Fédérico Marini, Martin Morgan, Stephanie C. Hicks · 2024

Summary The Human BioMolecular Atlas Program (HuBMAP) constructs the worldwide available platform to research the human body at the cellular level. The HuBMAP Data Portal encompasses a wide range of data resources measured on emerging expe…

Spatially-resolved molecular sex differences at single cell resolution in the adult human ventromedial and arcuate hypothalamus Open

Bernard Mulvey, Yi Wang, Heena R. Divecha, Svitlana V. Bach, Kelsey D. Montgomery , et al. · 2024

The hypothalamus contains multiple regions, including the ventromedial hypothalamus (VMH) and arcuate (ARC), which are responsible for sex-differentiated functions such as endocrine signaling, metabolism, and reproductive behaviors. While …

Addressing the mean-variance relationship in spatially resolved transcriptomics data with spoon Open

Kinnary Shah, Boyi Guo, Stephanie C. Hicks · 2024

An important task in the analysis of spatially resolved transcriptomics data is to identify spatially variable genes (SVGs), or genes that vary in a 2D space. Current approaches rank SVGs based on either p-values or an effect size, such as…

GeneCover: A Combinatorial Approach for Label-free Marker Gene Selection Open

An Wang, Stephanie C. Hicks, Donald Geman, Laurent Younès · 2024

The selection of marker gene panels is critical for capturing the cellular and spatial hetero-geneity in the expanding atlases of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics data. Most current approaches to marker ge…

Transcriptomic diversity of amygdalar subdivisions across humans and nonhuman primates Open

Michael S. Totty, Rita Cervera‐Juanes, Svitlana V. Bach, Lamya Ben Ameur, Madeline R. Valentine , et al. · 2024

The amygdaloid complex mediates learning, memory, and emotions. Understanding the cellular and anatomical features that are specialized in the amygdala of primates versus other vertebrates requires a systematic, anatomically-resolved molec…

Spatial mutual nearest neighbors for spatial transcriptomics data Open

Haowen Zhou, Pratibha Panwar, Boyi Guo, Caleb Hallinan, Shila Ghazanfar , et al. · 2024

Mutual nearest neighbors (MNN) is a widely used computational tool to perform batch correction for single-cell RNA-sequencing data. However, in applications such as spatial transcriptomics, it fails to take into account the 2D spatial info…

HuBMAPR: an R Client for the HuBMAP Data Portal Open

Christine Hou, Shila Ghazanfar, Fédérico Marini, Martin Morgan, Stephanie C. Hicks · 2024

Summary The Human BioMolecular Atlas Program (HuBMAP) constructs the worldwide available platform to research the human body at the cellular level. The HuBMAP Data Portal encompasses a wide range of data resources measured on emerging expe…

Open Case Studies: Statistics and Data Science Education through Real-World Applications Open

Carrie Wright, Qier Meng, Michael R. Breshock, Lyla Atta, Margaret A. Taub , et al. · 2024

With unprecedented and growing interest in data science education, there are limited educator materials that provide meaningful opportunities for learners to practice statistical thinking, as defined by Wild and Pfannkuch, with mess…

Transcriptional dynamics of sleep deprivation and subsequent recovery sleep in the male mouse cortex Open

Alexander Popescu, C. A. Ottaway, Kaitlyn Ford, Taylor Wintler, Ashley M. Ingiosi , et al. · 2024

Sleep is an essential, tightly regulated biological function. Sleep is also a homeostatic process, with the need to sleep increasing as a function of being awake. Acute sleep deprivation (SD) increases sleep need, and subsequent recovery s…

A global transcriptional atlas of the effect of acute sleep deprivation in the mouse frontal cortex Open

Kaitlyn Ford, Elena Zuin, Dario Righelli, E Medina, Hannah Schoch , et al. · 2024

Stephanie C. Hicks YOU? Author Swipe