Author
Harvard UniversityORCID 0000-0003-0796-3232Unclaimed ORCID profile · follow to get notified of new preprints
5 papers
Recent·Most cited
Allen W. Lynch, S W Lee, Jan P. Hummel, Benedikt Geiger, Michael S. Lawrence, Hu Jin, D. Gulhan, Peter J. Park
The paper introduces MuTopia, a framework that identifies topographic archetypes of mutagenesis in cancer genomes, revealing that mutational processes are constrained by replication timing and chromatin state.
bioRxiv · Apr 21, 2026 · PreprintBioinformatics
Yija Jiang, Zhirui Hu, Feng Lu, Allen W. Lynch, Junchen Jiang, Alexander Zhu, Ziqi Zeng, Yi Zhang, Gongwei Wu, Yingtian Xie, Rong Li, Ningxuan Zhou, Clifford A. Meyer, Paloma Cejas, Myles A Brown, , Xintao Qiu
scATAnno automatically annotates scATAC-seq data using reference atlases, outperforming existing methods across multiple datasets.
Genomics Proteomics & Bioinformatics · Nov 24, 2025Peer-reviewedBioinformatics
Pratik Narendra Pratap Singh, Wei Gu, Shariq Madha, Allen W. Lynch, Paloma Cejas, Ruiyang He, Swarnabh Bhattacharya, Miguel Muñoz Gomez, Matthew G. Oser, Myles A Brown, Henry W. Long, Clifford A. Meyer, Qiao Zhou, Ramesh A. Shivdasani
This study investigates transcription factor dynamics during human enteroendocrine cell differentiation, finding that oscillations of ASCL1 and NEUROD1 enable accurate cell type diversification.
Cell stem cell · May 10, 2024Peer-reviewedMolecular Biology
Yi Zhang, Guanjue Xiang, Alva Yijia Jiang, Allen W. Lynch, Zexian Zeng, Chenfei Wang, Wubing Zhang, Jing‐Yu Fan, Jiajinlong Kang, Shengqing Stan Gu, Changxin Wan, Boning Zhang, X. Shirley Liu, Myles A Brown, Clifford A. Meyer
MetaTiME identifies data-driven meta-components in tumor immune microenvironment scRNA-seq data to annotate cell states and reveal transcriptional regulators.
Nature Communications · May 6, 2023Peer-reviewedGenomics
Allen W. Lynch, Christina V. Theodoris, Henry W. Long, Myles A Brown, X. Shirley Liu, Clifford A. Meyer
MIRA jointly models gene expression and chromatin accessibility in single cells to infer regulatory circuits and lineage trees during development.
Nature Methods · Sep 1, 2022Peer-reviewedBioinformatics