Publications

We optimized and benchmarked DiMeLo-seq by mapping chromatin-binding proteins and histone modifications across the human genome.

We conclude that compared to scRNA-seq, MERFISH provides a quantitatively comparable method for measuring single-cell gene expression, and that efficient gene panel design allows for robust identification of cell types with intact spatial information without the need for computational integration with scRNA-seq reference atlases.

e find that changes in cfRNA gene expression between normotensive and preeclamptic mothers are marked and stable early in gestation, well before the onset of symptoms. These changes are enriched for genes specific to neuromuscular, endothelial and immune cell types and tissues that reflect key aspects of preeclampsia physiology6,7,8,9, suggest new hypotheses for disease progression and correlate with maternal organ health.

These findings demonstrate that stool-derived in vitro communities can serve as a powerful system for microbiota research.

We leverage nasopharyngeal swab RNA-seq data from patients with COVID-19, other viral acute respiratory illnesses and non-viral conditions (n=318) to develop support vector machine classifiers that rely on a parsimonious 2-gene host signature to predict COVID-19.

Using Smart-seq-total, we analyzed the content of hundreds of human and mouse cells and showed that the noncoding RNA content of cells significantly differs across cell types and dynamically changes throughout the vital processes of a cell, such as cell cycle and cell differentiation.

Here, we determined how two microbiota-targeted dietary interventions, plant-based fiber and fermented foods, influence the human microbiome and immune system in healthy adults.

We used single cell transcriptomics to create a molecularly defined phenotypic reference of human cell types which spans 24 human tissues and organs.

The results reveal potentially medically relevant differences in Candida function in gut vs. laboratory environments, and constrain evolutionary processes that could contribute to hospital strain persistence and transfer into premature infant microbiomes.

Our findings demonstrate that convergent morphology need not imply convergent molecular mechanisms but that it showcases the importance that tissue-specific stem cells and transcription factors play in producing the same mature body through different pathways.

This atlas provides the molecular foundation for investigating how lung cell identities, functions and interactions are achieved in development and tissue engineering and altered in disease and evolution.

Here, we examine the upper airway host transcriptional response in patients with COVID-19 (n = 93), other viral (n = 41) or non-viral (n = 100) acute respiratory illnesses (ARIs).

This study highlights how therapy-induced adaptation of the multi-cellular ecosystem of metastatic cancer shapes clinical outcomes.

This transcriptomic atlas—which we denote Tabula Muris Senis, or ‘Mouse Ageing Cell Atlas’—provides molecular information about how the most important hallmarks of ageing are reflected in a broad range of tissues and cell types.

We report a comparative genomics platform for Eggerthella lenta and other Coriobacteriia, a neglected taxon broadly relevant to human health and disease.

Our findings highlight deterministic microbiota adaptations to perturbations and the translational potential for modulating diet, sanitation, and microbiota composition during antibiotics.

Through mini-metagenomic sequencing of hot spring samples from Yellowstone National Park, we discovered and characterized a novel hyperthermophilic Cas9 protein from an unculturable Ignavibacterium.

This work presents the workflow for generating single cell transcriptomes derived from primary human uterine and cervical tissue obtained during planned cesarean hysterectomies.

We discovered hydrogenotrophic methanogenesis in a thermophilic order of the Verstraetearchaeota, a noneuryarchaeote. The Verstraetearchaeota, hitherto known as methylotrophs, unify the origins of methanogenesis and shed light on how organisms can evolve to adapt from hydrogenotrophic to methylotrophic methane metabolism.

Our results show that HSC and myeloid lineage immune cells emerged in a common ancestor of tunicates and vertebrates, and also suggest that haematopoietic bone marrow and the B. schlosseri endostyle niche evolved from a common origin.

Blood from non-human primates provides insight into potential pathogens which might eventually infect humans.

Deer antlers are bony structures that re-grow at very high rates, making them an attractive model for studying rapid bone regeneration. To identify the genes that are involved in this fast pace of bone growth, an in vitro RNA-seq model that paralleled the sharp differences in bone growth between deer antlers and humans was established.

Here we present a compendium of single-cell transcriptomic data from the model organism Mus musculus that comprises more than 100,000 cells from 20 organs and tissues.

In a pilot study of 31 healthy pregnant women, we found that measurement of nine cell-free RNA (cfRNA) transcripts in maternal blood predicted gestational age with comparable accuracy to ultrasound but at substantially lower cost.

ere, we used single-cell RNA sequencing (scRNA-seq) to measure cell-to-cell heterogeneity in the transcriptome of budding yeast (Saccharomyces cerevisiae). We find surprising patterns of variation across known sets of transcription factor targets, indicating that cells vary in their transcriptome profile both before and after stress exposure.

Our data provide a detailed dissection of GBM cell types, revealing an abundance of information about tumor formation and migration.

Through massive shotgun sequencing of circulating cell-free DNA from the blood of more than 1,000 independent samples, we identified hundreds of new bacteria and viruses which represent previously unidentified members of the human microbiome.

Here we present a microfluidic-based mini-metagenomic method which offers a statistically rigorous approach to extract novel microbial genomes while preserving single-cell resolution.

Our findings suggest that by monitoring the growth kinetics of individual cells we can build testable models of circadian control of the cell cycle in cyanobacteria.

Results of this work demonstrate the value of combining viral sequence identification with mini-metagenomic experimental methods to understand the microbial ecosystem.