Explanipedia

MERFISH+, a large-scale, multi-omics spatial technology resolves the molecular holograms of the 3D human developing heart Open

Colin Kern, Qingquan Zhang, Yifan Lu, Jacqueline Eschbach, Zehua Zeng , et al. · 2025

Summary Hybridization-based spatial transcriptomics technologies have advanced our ability to map cellular and subcellular organization in complex tissues. However, existing methods remain constrained in gene coverage, multimodal compatibi…

Charting the cardiac landscape: Advances in spatial transcriptomics for heart biology Open

Elie N. Farah, Jessyka T. Diaz, Joshua Bloomekatz, C. Neil · 2025

The heart is the first organ to form in the developing embryo. Throughout development, it continues to grow and function to support the maturing fetus by circulating nutrients to all of the developing organs. Defects in the spatial organiz…

Single cell multiomics reveals drivers of metabolic dysfunction-associated steatohepatitis Open

Weston Elison, Lei Chang, Yang Xie, Charlene Miciano, Qian Yang , et al. · 2025

Metabolic dysfunction-associated steatotic liver disease (MASLD) has limited treatments, and cell type-specific regulatory networks driving MASLD represent therapeutic avenues. We assayed five transcriptomic and epigenomic modalities in 2.…

Single cell multiomics and 3D genome architecture reveal novel pathways of human heart failure Open

Yang Xie, Luca Tucciarone, Elie N. Farah, Lei Chang, Qian Yang , et al. · 2025

Heart failure is a leading cause of morbidity and mortality; yet gene regulatory mechanisms driving cell type-specific pathologic responses remain undefined. Here, we present the cell type-resolved transcriptomes, chromatin accessibility, …

CXCL12 drives natural variation in coronary artery anatomy across diverse populations Open

Pamela E. Rios Coronado, Jiayan Zhou, Xiaochen Fan, Daniela Zanetti, Jeffrey A. Naftaly , et al. · 2025

Coronary arteries have a specific branching pattern crucial for oxygenating heart muscle. Among humans, there is natural variation in coronary anatomy with respect to perfusion of the inferior/posterior left heart, which can branch from ei…

Single-cell multi-modal integrative analyses highlight functional dynamic gene regulatory networks directing human cardiac development Open

Alyssa R. Holman, Shaina Tran, Eugin Destici, Elie N. Farah, Ting Li , et al. · 2024

Illuminating the precise stepwise genetic programs directing cardiac development provides insights into the mechanisms of congenital heart disease and strategies for cardiac regenerative therapies. Here, we integrate in vitro and in vivo h…

Spatially organized cellular communities form the developing human heart Open

Elie N. Farah, Robert Hu, Colin Kern, Qingquan Zhang, Tingyu Lu , et al. · 2024

The heart, which is the first organ to develop, is highly dependent on its form to function 1,2 . However, how diverse cardiac cell types spatially coordinate to create the complex morphological structures that are crucial for heart functi…

<i>CXCL12</i>drives natural variation in coronary artery anatomy across diverse populations Open

Pamela E. Rios Coronado, Daniela Zanetti, Jiayan Zhou, Jeffrey A. Naftaly, Pratima Prabala , et al. · 2023

To efficiently distribute blood flow to cardiac muscle, the coronary artery tree must follow a specific branching pattern over the heart. How this pattern arises in humans is unknown due to the limitations of studying human heart developme…

Author Correction: Human-gained heart enhancers are associated with species-specific cardiac attributes Open

Eugin Destici, Fugui Zhu, Shaina Tran, Sebastian Preißl, Elie N. Farah , et al. · 2022

Human-gained heart enhancers are associated with species-specific cardiac attributes Open

Eugin Destici, Fugui Zhu, Shaina Tran, Sebastian Preißl, Elie N. Farah , et al. · 2022

Cell Layers: uncovering clustering structure in unsupervised single-cell transcriptomic analysis Open

Andrew P. Blair, Robert Hu, Elie N. Farah, C. Neil, Katherine S. Pollard , et al. · 2022

Motivation Unsupervised clustering of single-cell transcriptomics is a powerful method for identifying cell populations. Static visualization techniques for single-cell clustering only display results for a single resolution parameter. Ana…

Cardiac cell type–specific gene regulatory programs and disease risk association Open

James D. Hocker, Olivier Poirion, Fugui Zhu, Justin Buchanan, Kai Zhang , et al. · 2021

A human heart cell type–specific cis-regulatory element atlas reveals gene regulatory mechanisms of cardiovascular diseases.

Cell Layers: Uncovering clustering structure and knowledge in unsupervised single-cell transcriptomic analysis Open

Andrew P. Blair, Robert Hu, Elie N. Farah, C. Neil, Katherine S. Pollard , et al. · 2020

Motivation Unsupervised clustering of single-cell transcriptomics is a powerful method for identifying cell populations. Static visualization techniques for single-cell clustering only display results for a single resolution parameter. Ana…

Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association Open

James D. Hocker, Olivier Poirion, Fugui Zhu, Justin Buchanan, Kai Zhang , et al. · 2020

Background Cis -regulatory elements such as enhancers and promoters are crucial for directing gene expression in the human heart. Dysregulation of these elements can result in many cardiovascular diseases that are major leading causes of m…

Canonical Wnt5b Signaling Directs Outlying Nkx2.5+ Mesoderm into Pacemaker Cardiomyocytes Open

Jie Ren, Peidong Han, Xuanyi Ma, Elie N. Farah, Joshua Bloomekatz , et al. · 2019

Combinatorial interactions of genetic variants in human cardiomyopathy Open

Dekker C. Deacon, Cassandra Happe, Chao Chen, Neil Tedeschi, Ana Maria Manso , et al. · 2019

Dilated cardiomyopathy (DCM) is a leading cause of morbidity and mortality worldwide; yet how genetic variation and environmental factors impact DCM heritability remains unclear. Here, we report that compound genetic interactions between D…

3D Chromatin Architecture Remodeling during Human Cardiomyocyte Differentiation Reveals A Role Of HERV-H In Demarcating Chromatin Domains Open

Yanxiao Zhang, Ting Li, Sebastian Preißl, Jonathan D. Grinstein, Elie N. Farah , et al. · 2018

Dynamic restructuring of chromatin architecture has been implicated in cell-type specific gene regulatory programs; yet, how chromatin remodels during lineage specification remains to be elucidated. Through interrogating chromatin reorgani…

mRNAs and lncRNAs intrinsically form secondary structures with short end-to-end distances Open

Wan-Jung C. Lai, Mohammad Kayedkhordeh, Erica V. Cornell, Elie N. Farah, Stanislav Bellaousov , et al. · 2018

The 5′ and 3′ termini of RNA play important roles in many cellular processes. Using Förster resonance energy transfer (FRET), we show that mRNAs and lncRNAs have an intrinsic propensity to fold in the absence of proteins into structures in…

Cell-Surface Marker Signature for Enrichment of Ventricular Cardiomyocytes Derived from Human Embryonic Stem Cells Open

Jennifer Veevers, Elie N. Farah, Mirko Corselli, Alec Witty, Karina Palomares , et al. · 2018

The formation of intramolecular secondary structure brings mRNA ends in close proximity Open

Wan-Jung C. Lai, Mohammad Kayedkhordeh, Erica V. Cornell, Elie N. Farah, Stanislav Bellaousov , et al. · 2018

A number of protein factors regulate protein synthesis by bridging mRNA ends or untranslated regions (UTRs). Using experimental and computational approaches, we show that mRNAs from various organisms, including humans, have an intrinsic pr…

EF-G Activation by Phosphate Analogs Open

Enea Salsi, Elie N. Farah, Dmitri N. Ermolenko · 2016

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