Author

Nicholas Van Wittenberghe

Broad InstituteORCID 0000-0002-7653-9729Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 5 Research Focus:differential expression· 4 Organism:human· 4 Research Focus:clustering· 3 Approach:experimental assay· 3 Organism:mouse· 3 Research Focus:gene regulatory network inference· 2 Assay:scRNA-seq· 2

Frequent Co-Authors

Aviv RegeviD· 5 shared Eugene DrokhlyanskyiD· 5 shared Orit Rozenblatt–RoseniD· 4 shared Danielle Ashley DionneiD· 3 shared Julia WaldmaniD· 3 shared Andrew J. AguirreiD· 2 shared Cristin AubiniD· 2 shared Gabriel Kenneth GriffiniD· 2 shared

Activity by Year

2019-2025 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 40 mutual co-author links

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5 shared papersGenomics

Aviv RegevORCID

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5 papers

Recent·Most cited

Tissue and cellular spatiotemporal dynamics in colon aging

Aidan C. Daly, Francesco Cambuli, Tarmo Äijö, Britta Lötstedt, Nemanja Despot Marjanovic, Sara Fernandez, Olena Kuksenko, Matthew Smith-Erb, Daniel Domovic, Nicholas Van Wittenberghe, Eugene Drokhlyansky, Gabriel Kenneth Griffin, Hemali P. Phatnani, Richard Bonneau, Aviv Regev, Sanja Vicković

This study creates a spatial and cellular atlas of the colon across age groups using spatial transcriptomics and single nucleus RNA-seq, identifying age-related molecular gradients and multicellular programs.

Nature Biotechnology · Oct 22, 2025Peer-reviewedSystems Biology

SnFFPE-Seq: towards scalable single nucleus RNA-Seq of formalin-fixed paraffin-embedded (FFPE) tissue

Hattie Chung, Alexandre Melnikov, Cristin Aubin, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Emma M. Magee, Julia Waldman, Avrum E. Spira, Fei Chen, Sarah A. Mazzilli, Orit Rozenblatt–Rosen, Aviv Regev

The paper develops a method for single nucleus RNA-Seq from FFPE tissues and applies it to a human lung adenocarcinoma sample.

bioRxiv · Aug 25, 2022 · PreprintGenomics

Single-nucleus and spatial transcriptomics of archival pancreatic cancer reveals multi-compartment reprogramming after neoadjuvant treatment

William L. Hwang, Karthik A. Jagadeesh, Jimmy A. Guo, Hannah I. Hoffman, Payman Yadollahpour, Rahul R. Mohan, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Orr Ashenberg, Samouil L. Farhi, Denis Schapiro, Jason Reeves, Daniel R. Zollinger, George M. Eng, Jason M. Schenkel, , Aviv Regev

This study uses single-nucleus and spatial transcriptomics to analyze pancreatic cancer before and after neoadjuvant treatment, revealing changes in cell states and immune infiltration that may inform therapy.

bioRxiv · Aug 25, 2020 · PreprintGenomics

The enteric nervous system of the human and mouse colon at a single-cell resolution

Eugene Drokhlyansky, Christopher S. Smillie, Nicholas Van Wittenberghe, Maria Ericsson, Gabriel Kenneth Griffin, Danielle Ashley Dionne, Michael S. Cuoco, Max N. Goder-Reiser, Tatyana Y. Sharova, Andrew J. Aguirre, Genevieve Marie Boland, Daniel B. Graham, Orit Rozenblatt–Rosen, Ramnik J. Xavier, Aviv Regev

The paper profiles the enteric nervous system of human and mouse colon at single-cell resolution, revealing diverse neuron subsets and shared transcriptional programs between species.

bioRxiv · Sep 4, 2019 · PreprintGenomics

Nuclei multiplexing with barcoded antibodies for single-nucleus genomics

Jellert T. Gaublomme, Bo Li, Cristin Aubin, Abigail Knecht, Yiming Yang, Eugene Drokhlyansky, Nicholas Van Wittenberghe, Julia Waldman, Danielle Ashley Dionne, Lan Nguyễn, Philip L. De Jager, Bertrand Z. Yeung, Xinfang Zhao, Naomi Habib, Orit Rozenblatt–Rosen, Aviv Regev

The paper introduces a method to multiplex single-nucleus RNA-seq using barcoded antibodies, reducing costs and enabling large-scale studies.

Nature Communications · Jul 2, 2019Peer-reviewedGenomics