Publications

Nature Methods: DiMeLo-seq: a long-read, single-molecule method for mapping protein-DNA interactions genome wide Icon
April 8, 2022
We optimized and benchmarked DiMeLo-seq by mapping chromatin-binding proteins and histone modifications across the human genome.
bioRxiv: Comparative analysis of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing Icon
March 7, 2022
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.
Nature: Early prediction of preeclampsia in pregnancy with cell-free RNA Icon
February 9, 2022
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.
Cell Host & Microbe: Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota Icon
February 9, 2022
These findings demonstrate that stool-derived in vitro communities can serve as a powerful system for microbiota research.
medRxiv: A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants Icon
January 7, 2022
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.
PNAS: Single-cell quantification of a broad RNA spectrum reveals unique noncoding patterns associated with cell types and states Icon
December 15, 2021
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.
Cell: Gut-microbiota-targeted diets modulate human immune status Icon
August 5, 2021
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.
bioRxiv: The Tabula Sapiens: a single cell transcriptomic atlas of multiple organs from individual human donors Icon
July 20, 2021
We used single cell transcriptomics to create a molecularly defined phenotypic reference of human cell types which spans 24 human tissues and organs.
Microbiome: Genetic and behavioral adaptation of Candida parapsilosis to the microbiome of hospitalized infants revealed by in situ genomics, transcriptomics, and proteomics Icon
June 21, 2021
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.
Cell Reports: Sexual and asexual development: two distinct programs producing the same tunicate. Icon
January 26, 2021
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.
Nature: A molecular cell atlas of the human lung from single-cell RNA sequencing Icon
November 18, 2020
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.
Nature: Upper airway gene expression reveals suppressed immune responses to SARS-CoV-2 compared with other respiratory viruses Icon
November 17, 2020
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).
Cell: Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing Icon
August 20, 2020
This study highlights how therapy-induced adaptation of the multi-cellular ecosystem of metastatic cancer shapes clinical outcomes.
Nature: A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Icon
July 15, 2020
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.
Cell Host & Microbe: A Genomic Toolkit for the Mechanistic Dissection of Intractable Human Gut Bacteria Icon
April 28, 2020
We report a comparative genomics platform for Eggerthella lenta and other Coriobacteriia, a neglected taxon broadly relevant to human health and disease.
Cell Host & Microbe: Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs. Icon
November 13, 2019
Our findings highlight deterministic microbiota adaptations to perturbations and the translational potential for modulating diet, sanitation, and microbiota composition during antibiotics.
PNAS: Nucleic acid cleavage with a hyperthermophilic Cas9 from an uncultured Ignavibacterium Icon
October 28, 2019
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.
Adv Biosystems: Single Cell Transcriptomes Derived from Human Cervical and Uterine Tissue during Pregnancy Icon
May 15, 2019
This work presents the workflow for generating single cell transcriptomes derived from primary human uterine and cervical tissue obtained during planned cesarean hysterectomies.
PNAS: Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens Icon
February 27, 2019
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.
Nature; Complex mammalian-like haematopoietic system found in a colonial chordate Icon
December 5, 2018
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.
bioRxiv: Cell-free DNA Reveals Potential Zoonotic Reservoirs in Non-Human Primates Icon
November 29, 2018
Blood from non-human primates provides insight into potential pathogens which might eventually infect humans.
Stem Cell Research & Therapy: Identifying deer antler uhrf1 proliferation and s100a10 mineralization genes using comparative RNA-seq Icon
October 31, 2018
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.
Nature: Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris Icon
October 3, 2018
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.
Science: Noninvasive blood tests for fetal development predict gestational age and preterm delivery Icon
June 8, 2018
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.
PLOS: Single-cell RNA sequencing reveals intrinsic and extrinsic regulatory heterogeneity in yeast responding to stress Icon
December 24, 2017
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.
Cell Rep: Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma Icon
October 31, 2017
Our data provide a detailed dissection of GBM cell types, revealing an abundance of information about tumor formation and migration.
PNAS: Numerous uncharacterized and highly divergent microbes which colonize humans are revealed by circulating cell-free DNA Icon
August 22, 2017
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.
Elife: Microfluidic-based mini-metagenomics enables discovery of novel microbial lineages from complex environmental samples Icon
July 5, 2017
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.
BMC Biology: Long-term microfluidic tracking of coccoid cyanobacterial cells reveals robust control of division timing Icon
February 14, 2017
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.
Adv Biosyst: Mini-Metagenomics and Nucleotide Composition Aid the Identification and Host Association of Novel Bacteriophage Sequences Icon
August 19, 2016
Results of this work demonstrate the value of combining viral sequence identification with mini-metagenomic experimental methods to understand the microbial ecosystem.