Author

A. Rotem

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

Cancer Biology· 4 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

Click to filter · or open tag

Research Focus:cell type annotation· 4 Organism:human· 4 Research Focus:differential expression· 3 Approach:experimental assay· 3 Research Focus:gene regulatory network inference· 3 Assay:scRNA-seq· 3 Assay:bulk RNA-seq· 2 Research Focus:spatial domain detection· 2

Frequent Co-Authors

I. Wakiro· 4 shared S. Vigneau· 3 shared A. Segerstolpe· 2 shared B. E. Johnson· 2 shared G. Grimaldi· 2 shared J. Jane-Valbuena· 2 shared J. Wang· 2 shared J. Wu· 2 shared

Activity by Year

2016-2024 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 39 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 papersCancer Biology

I. Wakiro

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

A spatial cell atlas of neuroblastoma reveals developmental, epigenetic and spatial axis of tumor heterogeneity

A. G. Patel, O. Ashenberg, N. B. Collins, A. Segerstolpe, S. Jiang, M. Slyper, X. Huang, C. Caraccio, H. Jin, H. Sheppard, K. Xu, T.-C. Chang, B. A. Orr, A. Shirinifard, R. H. Chapple, , S. J. Rodig

This paper creates a spatial cell atlas of neuroblastoma, revealing tumor heterogeneity through multi-omics data and identifying spatial compartmentalization and signaling patterns.

bioRxiv · Jan 7, 2024 · PreprintCancer Biology

A cellular and spatial atlas of TP53-associated tissue remodeling in lung adenocarcinoma

W. Zhao, B. Kepecs, N. R. Mahadevan, A. Segerstolpe, J. L. Weirather, N. R. Besson, B. Giotti, B. Y. Soong, C. Li, S. Vigneau, M. Slyper, I. Wakiro, J. Jane-Valbuena, O. Ashenberg, A. Rotem, , A. M. Tsankov

This study constructs a multi-omic atlas of TP53-mutant lung adenocarcinoma tumors, revealing altered cellular identity, gene expression programs, and spatial interactions in the tumor microenvironment.

bioRxiv · Jun 28, 2023 · PreprintCancer Biology

Intertumoral lineage diversity and immunosuppressive transcriptional programs in well-differentiated gastroenteropancreatic neuroendocrine tumors

S. E. Hoffman, T. W. Dowrey, C. V. Martin, K. Bi, B. M. Titchen, S. Johri, L. DelloStritto, M. Patel, C. Mackichan, S. Inga, J. Chen, G. Grimaldi, S. Napolitano, I. Wakiro, J. Wu, , G. J. Murphy

This study analyzes single-cell transcriptomes of gastroenteropancreatic neuroendocrine tumors to identify lineage diversity and immunosuppressive programs in tumor and immune cells.

bioRxiv · Nov 8, 2022Cancer Biology

The tumor microenvironment drives transcriptional phenotypes and their plasticity in metastatic pancreatic cancer

S. Raghavan, P. S. Winter, A. W. Navia, H. L. Williams, A. DenAdel, R. L. Kalekar, J. Galvez-Reyes, K. E. Lowder, N. Mulugeta, M. S. Raghavan, A. A. Borah, K. S. Kapner, S. A. Vayrynen, A. Dias Costa, R. W. S. Ng, , A. K. Shalek

This study identifies a transitional cancer cell state in metastatic pancreatic cancer and shows that tumor microenvironment signals drive transcriptional plasticity and subtype transitions.

bioRxiv · Aug 25, 2020 · PreprintCancer Biology

Tuning the course of evolution on the biophysical fitness landscape of an RNA virus

A. Rotem, A. Serohijos, C. Chang, J. Wolfe, A. Fischer, T. Mehoke, H. Zhang, Y. Tao, L. Ung, J.-M. Choi, A. Kolawole, S. Koehler, S. Wu, P. Thielen, N. Cui, , E. Shakhnovich

This study predicts the evolutionary pathway of norovirus escaping antibodies using a biophysical fitness model, validated by experimental evolution in bulk culture and microfluidics.

bioRxiv · Dec 8, 2016Evolutionary Biology