Author

Fabio Boniolo

Broad Institute

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

Biology Disciplines

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Cancer Biology· 2 Systems Biology· 1

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 2 Research Focus:cell type annotation· 2 Research Focus:differential expression· 2 Approach:experimental assay· 2 Research Focus:gene regulatory network inference· 2 Organism:human· 2 Assay:proteomics· 2 Approach:statistical model· 2

Frequent Co-Authors

Dieter SauriD· 2 shared A Gordon Robertson· 1 shared Allen Thayakumar BasanthakumariD· 1 shared Anantharamanan RajamaniiD· 1 shared Antonio Enrico ZauritoiD· 1 shared Aritra MahapatraiD· 1 shared Ashleigh MeyeriD· 1 shared Audrey TailloniD· 1 shared

Activity by Year

2023-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 15 mutual co-author links

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2 shared papersCancer Biology

Dieter SaurORCID

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3 papers

Recent·Most cited

Distinct colorectal cancer genotypes shape microbial ecosystems and reveal stage-specific microbiota dependencies

Valentina Brunner, Nicholas Bodenstein, Antonio Enrico Zaurito, M Silva, Frederic Saab, Fabian Springer, Fabio Boniolo, Moritz Jesinghaus, Anantharamanan Rajamani, Aritra Mahapatra, Tanja Groll, Nicole A Schmid, Rupert Oellinger, Chen Meng, Sabine Schwamberger, , Markus Tschurtschenthaler

This study shows that different colorectal cancer genotypes create distinct microbial ecosystems and that microbiota dependence decreases as tumors progress.

bioRxiv · Jul 7, 2026 · PreprintCancer Biology

Chromatin Perturbation Promotes Susceptibility to Hypomethylating Agents

Constanze Schneider, Gabriela Alexe, Lucy A. Merickel, Ashleigh Meyer, Michelle L. Swift, Rodolfo Bortolozo Serafim, Allen Thayakumar Basanthakumar, Audrey Taillon, Silvi Salhotra, Fabio Boniolo, Sander Lambo, Yara Rodríguez, Björn Häupl, Rani E. George, David E. Root, , Kimberly Stegmaier

The paper identifies USP48 as a regulator of chromatin stability and DNA damage response to hypomethylating agents, showing its loss increases susceptibility to these drugs in AML.

bioRxiv · Jul 28, 2025 · PreprintCancer Biology

spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape

Fabio Boniolo, Markus Hoffmann, Norman Roggendorf, Bahar Tercan, Jan Baumbach, Mauro A. A. Castro, A Gordon Robertson, Dieter Saur, Markus List

spongEffects identifies patient-specific ceRNA modules to provide insights into miRNA regulatory activity using gene expression data alone.

Bioinformatics · Apr 21, 2023Peer-reviewedSystems Biology