Publications

2024

1. 

   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

1. 

   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

2. 

   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

3. 

   An econometric lens resolves cell-state parallax

   Alexander P Wu*, Rohit Singh*, Christopher A Walsh, and Bonnie Berger

   bioRxiv, 2023

2022

1. 

   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

1. 

   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

1. 

   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

2. 

   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

1. 

   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

1. 

   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