Author

Alexander A. Shishkin

University of California San Diego

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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Genomics· 3 Evolutionary Biology· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Research Focus:cell type annotation· 2 Research Focus:gene regulatory network inference· 2 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Assay:ChIP-seq· 1 Approach:deep learning· 1 Research Focus:differential expression· 1

Frequent Co-Authors

Eric L. Van NostrandiD· 2 shared Gene Wei-Ming YeoiD· 2 shared Ali PallaiD· 1 shared Amy Y. ChowiD· 1 shared Aviv RegeviD· 1 shared Barbara Tabak· 1 shared Brian A. YeeiD· 1 shared Christine S. ChengiD· 1 shared

Activity by Year

2015-2022 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 14 mutual co-author links

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2 shared papersGenomics

Eric L. Van NostrandORCID

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Author profile →

4 papers

Recent·Most cited

Scalable and deep profiling of mRNA targets for individual microRNAs with chimeric eCLIP

Sergei A. Manakov, Alexander A. Shishkin, Brian A. Yee, Kylie A. Shen, Diana Cox, Samuel S. Park, Heather M Foster, Karen B. Chapman, Gene Wei-Ming Yeo, Eric L. Van Nostrand

This paper introduces chimeric eCLIP, a method to efficiently profile miRNA:mRNA interactions at scale, showing significant improvements in recovery and specificity.

bioRxiv · Feb 13, 2022 · PreprintGenomics

Unbiased identification of nanoparticle cell uptake mechanism via a genome-wide CRISPR/Cas9 knockout screen

Eric L. Van Nostrand, Sarah A. Barnhill, Alexander A. Shishkin, David A. Nelles, Eric Byeon, Thai B. Nguyen, Yiu Chueng Eric Wong, Nathan C. Gianneschi, Gene Wei-Ming Yeo

The paper uses a genome-wide CRISPR/Cas9 knockout screen to identify novel transporters involved in nanoparticle uptake, finding SLC18B1 mediates polymeric micellar nanoparticle uptake.

bioRxiv · Oct 8, 2020 · PreprintGenomics

Higher-order inter-chromosomal hubs shape 3-dimensional genome organization in the nucleus

Sofia A. Quinodoz, Noah Ollikainen, Barbara Tabak, Ali Palla, Jan Marten Schmidt, Elizabeth Detmar, Mason Lai, Alexander A. Shishkin, Prashant Bhat, Yodai Takei, Vickie Trinh, Erik I. Aznauryan, Pamela H. Russell, Christine S. Cheng, Marko Jovanović, , Mitchell Guttman

The paper introduces SPRITE, a method for detecting higher-order DNA interactions, and shows that nuclear bodies act as inter-chromosomal hubs shaping 3D genome organization.

Cell · Jun 7, 2018Peer-reviewedGenomics

Evolutionary analysis across mammals reveals distinct classes of long noncoding RNAs

Jenny Chen, Alexander A. Shishkin, Xiaopeng Zhu, Sabah Kadri, Itay Maza, Jacob H Hanna, Aviv Regev, Manuel Garber

The paper introduces a computational tool for lncRNA discovery and analysis, identifying two distinct classes of lncRNAs based on evolutionary patterns.

bioRxiv · Nov 11, 2015Evolutionary Biology