Author

Vivek Bhardwaj

Hubrecht Institute for Developmental Biology and Stem Cell ResearchORCID 0000-0002-5570-9338Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Genomics· 6 Bioinformatics· 3 Cell Biology· 1 Developmental Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:experimental assay· 7 Research Focus:gene regulatory network inference· 6 Assay:ChIP-seq· 5 Research Focus:benchmarking· 4 Research Focus:cell type annotation· 4 Assay:scRNA-seq· 4 Research Focus:differential expression· 3 Research Focus:software / tool· 3

Frequent Co-Authors

Alexander van OudenaardeniD· 4 shared Peter J. ZelleriD· 4 shared Thomas MankeiD· 3 shared Asifa AkhtariD· 2 shared Björn Andreas GrüningiD· 2 shared Buys de BarbansoniD· 2 shared Devon Patrick RyaniD· 2 shared Fidel RamíreziD· 2 shared

Activity by Year

2018-2026 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 19 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

4 shared papersGenomics

Alexander van OudenaardenORCID

Mutual co-authors in cluster

Author profile →

11 papers

Recent·Most cited

Single-cell co-mapping reveals relationship between chromatin state and gene expression in early zebrafish development

Vivek Bhardwaj, Alberto Griffa, Helena Viñas Gaza, Peter J. Zeller, Alexander van Oudenaarden

The paper uses single-cell multimodal data to show how chromatin states and gene expression interact during early zebrafish development, revealing lineage-specific transcription factor regulation.

eLife · Apr 21, 2026Peer-reviewedGenomics

Acute multi-level response to defective de novo chromatin assembly in S-phase

Jan Dreyer, Giulia Ricci, Jeroen van den Berg, Vivek Bhardwaj, Janina Funk, Claire Armstrong, Vincent van Batenburg, Chance C. Sine, Michael A. VanInsberghe, Rinskje B. Tjeerdsma, Richard Marsman, Imke K. Mandemaker, Simone Di Sanzo, Juliette Costantini, Stefano Giustino Manzo, , Francesca Mattiroli

This study investigates the acute effects of CAF-1 loss on chromatin assembly during S-phase, revealing multi-level responses including replication slowdown and histone modification changes.

Molecular Cell · Nov 12, 2024Peer-reviewedCell Biology

User-friendly exploration of epigenomic data in single cells using sincei

Vivek Bhardwaj, Soufiane M. C. Mourragui

The paper introduces sincei, a command-line toolkit for exploring single-cell epigenomic data from aligned reads, aiming to improve accessibility and flexibility in data analysis.

bioRxiv · Jul 27, 2024 · PreprintBioinformatics

Stem cell culture conditions affect in vitro differentiation potential and efficiency of mouse gastruloid development

Marloes Blotenburg, Lianne C Suurenbroek, Vivek Bhardwaj, Peter J. Zeller

This study shows that optimizing mouse embryonic stem cell pluripotency state improves the consistency and complexity of gastruloid development.

bioRxiv · May 9, 2024 · PreprintDevelopmental Biology

Detection of histone modifications and full-length transcriptome in single cells identifies sequential epigenetic perceptiveness to lineage commitment

Marloes Blotenburg, Vivek Bhardwaj, Buys de Barbanson, Fredrik Salmén, Peter J. Zeller, Alexander van Oudenaarden

The paper develops T-ChIC to detect histone modifications and full-length transcripts in single cells, revealing sequential epigenetic changes during lineage commitment in gastruloids.

bioRxiv · May 9, 2024 · PreprintGenomics

Hierarchical chromatin regulation during blood formation uncovered by single cell sortChIC

Peter J. Zeller, Jake Yeung, Helena Viñas Gaza, Buys de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, Alexander van Oudenaarden

The paper develops sortChIC to map histone modifications in mouse hematopoietic cells, revealing hierarchical chromatin regulation during blood formation.

Nature Genetics · Dec 20, 2022Peer-reviewedGenomics

Creating Clear and Informative Image-based Figures for Scientific Publications

Helena Klara Jambor, Alberto Antonietti, Bradly Alicea, Tracy Lynn Audisio, Susann Auer, Vivek Bhardwaj, Steven Burgess, Iuliia Ferling, Małgorzata Anna Gazda, Luke H. Hoeppner, Vinodh Ilangovan, Hung Lo, Mischa A. Olson, Salem Yousef Mohamed, Sarvenaz Sarabipour, , Tracey Lynn Weissgerber

The paper evaluates image quality in scientific publications, identifying common issues and providing guidelines to improve clarity and accessibility.

PLoS Biology · Mar 31, 2021Peer-reviewedBioinformatics

snakePipes enable flexible, scalable and integrative epigenomic analysis

Vivek Bhardwaj, Steffen Heyne, Katarzyna Sikora, Leily Rabbani, Michael Rauer, Fabian Kilpert, Andreas S. Richter, Devon Patrick Ryan, Thomas Manke

snakePipes provides a flexible, scalable pipeline for integrative epigenomic analysis across multiple assays, simplifying reproducibility and extending existing studies.

Bioinformatics · May 23, 2019Peer-reviewedGenomics

The NSL complex mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise

Kin Chung Lam, Ho‐Ryun Chung, Giuseppe Semplicio, Shantanu S. Iyer, Aline Gaub, Vivek Bhardwaj, Herbert Holz, Plamen Georgiev, Asifa Akhtar

This study shows the NSL complex maintains nucleosome organization at promoters, ensuring transcription fidelity and suppressing noise by preventing nucleosome invasion into NDRs.

Genes & Development · Apr 1, 2019Peer-reviewedGenomics

Community-driven data analysis training for biology

Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Brillet-Guéguen, Martin Čech, John M. Chilton, Dave Clements, Olivia Doppelt‐Azeroual, Anika Erxleben, Mallory Freeberg, Simon L. Gladman, , Björn Andreas Grüning

The paper presents a community-driven framework for interactive data analytics training in life sciences, enabling researchers to learn through web-based computation without software installation.

Cell Systems · Jun 1, 2018Peer-reviewedBioinformatics

High-resolution TADs reveal DNA sequences underlying genome organization in flies

Fidel Ramírez, Vivek Bhardwaj, Laura Arrigoni, Kin Chung Lam, Björn Andreas Grüning, Jose M. Villaveces, Bianca Hermine Habermann, Asifa Akhtar, Thomas Manke

The paper identifies DNA motifs at TAD boundaries in flies and shows they encode 3D genome architecture, with an online database for exploration.

Nature Communications · Jan 9, 2018Peer-reviewedGenomics