Browse by CSHL Author

Paper

Liu, Lingjie, Zhao, Yixin, Hassett, Rebecca, Toneyan, Shushan, Koo, Peter K, Siepel, Adam (February 2025) Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data. Nucleic Acids Research (NAR), 53 (4). ISSN 1362-4962 (Public Dataset)

Liu, Lingjie, Zhao, Yixin, Siepel, Adam (December 2023) DNA-sequence and epigenomic determinants of local rates of transcription elongation. bioRxiv. (Submitted)

Zhao, Yixin, Liu, Lingjie, Hassett, Rebecca, Siepel, Adam (October 2023) Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. Nucleic Acids Research. ISSN 0305-1048

Yao, Min, Preall, Jonathan, Yeh, Johannes, Pappin, Darryl J, Cifani, Paolo, Zhao, Yixin, Shen, Sophia, Moresco, Philip, He, Brian, Patel, Hardik, Habowski, Amber N, King, Daniel A, Raphael, Kara L, Rishi, Arvind, Sejpal, Divyesh V, Weiss, Matthew, Tuveson, David, Fearon, Douglas T (September 2023) Plasma cells in human pancreatic ductal adenocarcinoma secrete antibodies to self-antigens. JCI Insight. e172449. ISSN 2379-3708 (Public Dataset)

Lu, Guang-An, Zhang, Jinning, Zhao, Yixin, Chen, Qingjian, Lin, Pei, Tang, Tian, Tang, Zhixiong, Wen, Haijun, Liufu, Zhongqi, Wu, Chung-I (January 2023) Canalization of Phenotypes-When the Transcriptome is Constantly but Weakly Perturbed. Molecular Biology and Evolution, 40 (1). msad005. ISSN 0737-4038

Abuhashem, Abderhman, Chivu, Alexandra G, Zhao, Yixin, Rice, Edward J, Siepel, Adam, Danko, Charles G, Hadjantonakis, Anna-Katerina (August 2022) RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription. Genes and Development. ISSN 0890-9369

Zhao, Yixin, Liu, Lingjie, Siepel, Adam (2022) Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. bioRxiv. (Submitted)

Siepel, Adam, Zhao, Yixin, Liu, Lingjie (2022) Model-based characterization of the equilibrium dynamics of transcription initiation and promoter-proximal pausing in human cells. Research Square. (Submitted)

Abuhashem, Abderhman, Chivu, Alexandra, Zhao, Yixin, Rice, Edward, Siepel, Adam, Danko, Charles, Hadjantonakis, Anna-Katerina (2022) RNA Pol II pausing facilitates phased pluripotency transitions by buffering transcription. bioRxiv. (Submitted)

Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles G, Siepel, Adam (August 2021) Deconvolution of Expression for Nascent RNA sequencing data (DENR) highlights pre-RNA isoform diversity in human cells. Bioinformatics. ISSN 1367-4803

Henry, Samantha, Trousdell, Marygrace C, Cyrill, Samantha L, Zhao, Yixin, Feigman, Mary J, Bouhuis, Julia M, Aylard, Dominik A, Siepel, Adam, Dos Santos, Camila O (May 2021) Characterization of Gene Expression Signatures for the Identification of Cellular Heterogeneity in the Developing Mammary Gland. Journal of Mammary Gland Biology and Neoplasia. ISSN 1083-3021

Zhao, Yixin, Lu, Guang-An, Yang, Hao, Lin, Pei, Liufu, Zhongqi, Tang, Tian, Xu, Jin (April 2021) Run or Die in the Evolution of New MicroRNAs-Testing the Red Queen Hypothesis on De Novo New Genes. Molecular Biology and Evolution, 38 (4). pp. 1544-1553. ISSN 0737-4038

Zhao, Yixin, Dukler, Noah, Barshad, Gilad, Toneyan, Shushan, Danko, Charles, Siepel, Adam (March 2021) Deconvolution of Expression for Nascent RNA Sequencing Data (DENR) Highlights Pre-RNA Isoform Diversity in Human Cells. BioRxiv. (Unpublished)

Blumberg, Amit, Zhao, Yixin, Huang, Yi-Fei, Dukler, Noah, Rice, Edward J, Chivu, Alexandra G, Krumholz, Katie, Danko, Charles G, Siepel, Adam (February 2021) Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BMC Biology, 19 (1). p. 30. ISSN 1741-7007

Blumberg, Amit, Zhao, Yixin, Huang, Yi-Fei, Dukler, Noah, Rice, Edward, Chivu, Alexandra, Krumholz, Katie, Danko, Charles, Siepel, Adam (July 2019) Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data. BioRxiv. (Unpublished)

Zhao, Y., Shen, X., Tang, T., Wu, C. I. (July 2019) Weak Regulation of Many Targets Is Cumulatively Powerful-A Reply to Seitz on microRNA Functionality. Mol Biol Evol, 36 (7). pp. 1598-1599. ISSN 0737-4038

Zhao, Y., Lin, P., Liufu, Z., Yang, H., Lyu, Y., Shen, X., Wu, C. I., Tang, T. (April 2018) Regulation of large number of weak targets - New insights from twin-microRNAs. Genome Biology and Evolution, 10 (5). pp. 1255-1264. ISSN 17596653 (ISSN)

Conference or Workshop Item

Sun, Lijuan, Liu, Bodu, Zhao, Yixin, Egeblad, Mikala (November 2024) MPLA plus IFNg-activated tumor-associated macrophages alter fibroblast composition. In: Proceedings of the AACR Special Conference in Cancer Research: Tumor-body Interactions: The Roles of Micro- and Macroenvironment in Cancer, 2024 Nov 17-20, Boston, Massachusetts.