Author

I. De Vlaminck

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

Click to filter author papers

Microbiology· 5 Cell Biology· 2

Signature Assays, Organisms & Methods

Click to filter · or open tag

Organism:human· 5 Research Focus:cell type annotation· 3 Approach:experimental assay· 3 Assay:metagenomics· 3 Approach:deep learning· 2 Organism:mouse· 2 Research Focus:spatial domain detection· 2 Approach:statistical model· 2

Frequent Co-Authors

A. C. Vill· 2 shared H. Shi· 2 shared I. L. Brito· 2 shared J. Okamoto· 2 shared N. D. Wolfe· 2 shared S. R. Quake· 2 shared A. J. De Micheli· 1 shared A. Melnick· 1 shared

Activity by Year

2017-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 10 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

2 shared papersMicrobiology

A. C. Vill

Mutual co-authors in cluster

Author profile →

7 papers

Recent·Most cited

Spatial Mapping of Mobile Genetic Elements and their Cognate Hosts in Complex Microbiomes

B. Grodner, H. Shi, O. Farchione, A. C. Vill, I. Ntekas, P. J. Diebold, W. R. Zipfel, I. L. Brito, I. De Vlaminck

The paper develops an imaging method to map mobile genetic elements and their bacterial hosts in human oral biofilms, revealing spatial clusters of AMR plasmids and prophage.

bioRxiv · Jun 9, 2023 · PreprintMicrobiology

Run-on sequencing reveals nascent transcriptomics of the human microbiome

A. C. Vill, C. G. Danko, E. J. Rice, I. De Vlaminck, I. L. Brito

This study applies PRO-seq to the human microbiome to profile nascent transcription, revealing taxon-specific RNAP pause motifs and concurrent transcription and cleavage of guide RNAs and tRNA fragments.

bioRxiv · Apr 22, 2022 · PreprintMicrobiology

Cell-free DNA (cfDNA) and exosome profiling from a year-long humanspaceflight reveals circulating biomarkers

D. Bezdan, K. Grigorev, C. Meydan, F. Pelissier Vatter, M. Ciofi, V. Rao, K. Nakahira, P. Burnham, E. Afshinnekoo, C. Westover, D. Butler, C. Moszary, M. MacKay, J. Foox, T. Mishra, , C. Mason

This study profiles cfDNA and exosomes from an astronaut during a year-long spaceflight, identifying increased cf-mtDNA and exosomal brain-derived peptides as potential biomarkers of spaceflight-related stress.

bioRxiv · Nov 8, 2020Cell Biology

Highly Multiplexed Spatial Mapping of Microbial Communities

H. Shi, W. Zipfel, I. Brito, I. De Vlaminck

The paper introduces HiPR-FISH, a method to map microbial communities with high spatial and taxonomic resolution, demonstrating its ability to distinguish multiple E. coli strains and reveal spatial structures in human and mouse microbiomes.

bioRxiv · Jun 21, 2019Microbiology

Single-cell analysis of the muscle stem cell hierarchy identifies heterotypic communication signals involved in skeletal muscle regeneration

A. J. De Micheli, P. Fraczek, S. Soueid-Baumgarten, H. Ravichandran, I. De Vlaminck, O. Elemento, B. D. Cosgrove

This study uses scRNA-seq to map muscle stem cell hierarchy and identifies heterotypic communication signals during skeletal muscle regeneration.

bioRxiv · Jun 17, 2019Cell Biology

Cell-free DNA Reveals Potential Zoonotic Reservoirs in Non-Human Primates

M. Kowarsky, I. De Vlaminck, J. Okamoto, N. F. Neff, M. LeBreton, J. Nwobegabay, U. Tamoufe, J. D. Ledoux, B. Tafon, J. Kiyang, K. Saylors, N. D. Wolfe, S. R. Quake

The paper uses cell-free DNA sequencing to identify microbial taxa in non-human primates, revealing potential zoonotic pathogens and their association with host species.

bioRxiv · Nov 29, 2018 · PreprintMicrobiology

Humans are colonized by many uncharacterized and highly divergent microbes

M. A. Kowarsky, J. Camunas-Soler, M. Kertesz, I. De Vlaminck, L. C. W. Koh, W. Pan, L. Martin, N. Neff, J. Okamoto, R. J. Wong, S. Kharbanda, Y. El-Sayed, Y. Blumenfeld, D. K. Stevenson, G. M. Shaw, , S. R. Quake

The paper identifies hundreds of new bacteria and viruses in the human microbiome using blood-based shotgun sequencing and validates their existence through independent experiments and PCR.

bioRxiv · Mar 4, 2017Microbiology