Author

A. A. Chen

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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Biochemistry· 2 Cancer Biology· 2

Signature Assays, Organisms & Methods

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Research Focus:differential expression· 2 Approach:experimental assay· 2 Organism:human· 2 Assay:spatial transcriptomics· 2 Organism:bacteria (other)· 1 Assay:bulk RNA-seq· 1 Research Focus:cell type annotation· 1 Research Focus:cell-cell communication· 1

Frequent Co-Authors

A. J. Nirmal· 2 shared A. M. Yu· 2 shared C. G. Lian· 2 shared G. F. Murphy· 2 shared J. B. Lucks· 2 shared P. K. Sorger· 2 shared S. Santagata· 2 shared Y.-A. Chen· 2 shared

Activity by Year

2018-2021 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersCancer Biology

A. J. Nirmal

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4 papers

Recent·Most cited

Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch

L. Cheng, E. N. White, N. L. Brandt, A. M. Yu, A. A. Chen, J. B. Lucks

The paper investigates how ligand binding induces conformational changes in a purine-sensing riboswitch by stabilizing intermediate structures through strand exchange processes.

bioRxiv · Oct 25, 2021Biochemistry

The spatial landscape of progression and immunoediting in primary melanoma at single cell resolution

A. J. Nirmal, Z. Maliga, T. Vallius, B. Quattrochi, A. A. Chen, C. A. Jacobson, R. J. Pelletier, C. Yapp, R. Arias-Camison, Y.-A. Chen, C. G. Lian, G. F. Murphy, S. Santagata, P. K. Sorger

The paper uses spatial techniques to study immune evasion and immunoediting in primary melanoma, finding localized immunosuppressive environments and coexistence of invasion and regression.

bioRxiv · May 23, 2021Cancer Biology

Micro-region transcriptomics of fixed human tissue using Pick-Seq

Z. Maliga, A. J. Nirmal, N. G. Ericson, S. A. Boswell, L. U'Ren, R. Podyminogin, J. Chow, Y.-A. Chen, A. A. Chen, D. M. Weinstock, C. G. Lian, G. F. Murphy, E. P. Kaldjian, S. Santagata, P. K. Sorger

Pick-Seq enables deep spatial transcriptomic profiling of fixed human tissue, revealing transcriptional differences in tumor invasion, proliferation, and immuno-editing.

bioRxiv · Mar 18, 2021 · PreprintCancer Biology

Computationally Reconstructing Cotranscriptional RNA Folding Pathways from Experimental Data Reveals Rearrangement of Non-Native Folding Intermediates

A. M. Yu, P. M. Gasper, E. J. Strobel, K. E. Watters, A. A. Chen, J. B. Lucks

This paper introduces R2D2, a method to predict RNA folding pathways from cotranscriptional SHAPE-Seq data, revealing non-native intermediates in E. coli SRP RNA folding.

bioRxiv · Jul 28, 2018Biochemistry