Author

Alexandra G. Chivu

Cornell UniversityORCID 0000-0001-8875-3530Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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

Frequent Co-Authors

Charles G. DankoiD· 4 shared Edward J. Rice· 4 shared Abderhman AbuhashemiD· 2 shared Adam C. SiepeliD· 2 shared Anna‐Katerina HadjantonakisiD· 2 shared Yixin ZhaoiD· 2 shared Amit BlumbergiD· 1 shared Carrie J. FinnoiD· 1 shared

Activity by Year

2020-2023 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 28 mutual co-author links

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4 shared papersGenomics

Charles G. DankoORCID

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4 papers

Recent·Most cited

RNA polymerase II and PARP1 shape enhancer-promoter contacts

Gilad Barshad, James J. Lewis, Alexandra G. Chivu, Abderhman Abuhashem, Nils Krietenstein, Edward J. Rice, Yitian Ma, Zhong Wang, Oliver J. Rando, Anna‐Katerina Hadjantonakis, Charles G. Danko

This study investigates enhancer-promoter contact architecture and communication, finding that RNA polymerase II and PARP1 activity stabilize these contacts.

Nature Genetics · Jul 10, 2023Peer-reviewedGenomics

RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription

Abderhman Abuhashem, Alexandra G. Chivu, Yixin Zhao, Edward J. Rice, Adam C. Siepel, Charles G. Danko, Anna‐Katerina Hadjantonakis

The paper shows that RNA Pol II pausing is essential for proper pluripotency transitions in mouse embryos by maintaining balance between gene expression states.

bioRxiv · Apr 21, 2022Molecular Biology

Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data

Amit Blumberg, Yixin Zhao, Yi-Fei Huang, Noah Dukler, Edward J. Rice, Alexandra G. Chivu, Katie Krumholz, Charles G. Danko, Adam C. Siepel

The paper introduces a method to estimate RNA half-lives using PRO-seq and RNA-seq data, finding correlations between RNA stability and splicing, miRNA binding, DNA methylation, and histone modifications.

BMC Biology · Feb 15, 2021Peer-reviewedGenomics

Interdependence between histone marks and steps in Pol II transcription

Zhong Wang, Alexandra G. Chivu, Lauren A. Choate, Edward J. Rice, Donald C. Miller, Tinyi Chu, Shao‐Pei Chou, Nicole B. Kingsley, Jessica L. Petersen, Carrie J. Finno, Rebecca R. Bellone, Douglas F. Antczak, John T. Lis, Charles G. Danko

The paper uses machine learning to show that transcription predicts histone marks and chromatin states, and that transcription is required for maintaining active and repressive histone modifications.

bioRxiv · Apr 8, 2020 · PreprintGenomics