Publications

2025

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    An econometric lens resolves cell-state parallax
    Alexander P Wu*, Rohit Singh*, Christopher A Walsh, and Bonnie Berger
    Nature Communications, 2025

2024

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    Causal gene regulatory analysis with RNA velocity reveals an interplay between slow and fast transcription factors
    Rohit Singh*, Alexander P Wu*, Anish Mudide*, and Bonnie Berger
    Cell Systems, 2024

2023

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    Structural and functional properties of mSWI/SNF chromatin remodeling complexes revealed through single-cell perturbation screens
    Jordan E Otto*, Oana Ursu*, Alexander P Wu*, Evan B Winter, Michael S Cuoco, Sai Ma, Kristin Qian, Brittany C Michel, Jason D Buenrostro, Bonnie Berger, Aviv Regev†, and Cigall Kadoch†
    Molecular Cell, 2023
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    Causally-guided Regularization of Graph Attention Improves Generalizability
    Alexander P Wu, Thomas Markovich, Bonnie Berger, Nils Yannick Hammerla, and Rohit Singh
    Transactions on Machine Learning Research, 2023

2022

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    Granger causal inference on DAGs identifies genomic loci regulating transcription
    Rohit Singh*, Alexander P Wu*, and Bonnie Berger
    In International Conference on Learning Representations, 2022

2021

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    Bayesian information sharing enhances detection of regulatory associations in rare cell types
    Alexander P Wu, Jian Peng, Bonnie Berger, and Hyunghoon Cho
    Bioinformatics, 2021

2019

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    Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute
    Binbin Wang, Mei Wang, Wubing Zhang, Tengfei Xiao, Chen-Hao Chen, Alexander Wu, Feizhen Wu, Nicole Traugh, Xiaoqing Wang, Ziyi Li, and  others
    Nature Protocols, 2019
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    Deciphering essential cistromes using genome-wide CRISPR screens
    Teng Fei, Wei Li, Jingyu Peng, Tengfei Xiao, Chen-Hao Chen, Alexander Wu, Jialiang Huang, Chongzhi Zang, X Shirley Liu, and Myles Brown
    Proceedings of the National Academy of Sciences, 2019

2018

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    Reducing false positives in CRISPR/Cas9 screens from copy number variations
    Alexander Wu, Tengfei Xiao, Teng Fei, X Shirley Liu, and Wei Li
    BioRxiv, 2018

2015

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    Sec24 is a coincidence detector that simultaneously binds two signals to drive ER export
    Silvere Pagant, Alexander Wu, Samuel Edwards, Frances Diehl, and Elizabeth A Miller
    Current Biology, 2015