Publications

DNA methylation meets lineage tracing: History, recent progress, and future directions

Ruijiang Fu, Mengyang Chen, Shou-Wen Wang*

Quantitative Biology · 21 Sep 2025

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DARLIN mouse for in vivo lineage tracing at high efficiency and clonal diversity

Li Li, Sarah Bowling, Hongying Lin, Daolong Chen, Shou-Wen Wang* & Fernando D. Camargo*

Nature Protocols · 21 Mar 2025

Lineage tracing Protocol

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MethylTree: exploring epimutations for accurate and non-invasive lineage tracing

Nature Methods · 16 Jan 2025

Research Briefing

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High-resolution, noninvasive single-cell lineage tracing in mice and humans based on DNA methylation epimutations

Mengyang Chen, Ruijiang Fu, Yiqian Chen, Li Li* & Shou-Wen Wang*

Nature Methods · 16 Jan 2025

Lineage tracing Multiomics Clonal memory

Main text Code Video

A mouse model with high clonal barcode diversity for joint lineage, transcriptomic, and epigenomic profiling in single cells

L. Li, ..., Shou-Wen Wang*, Fernando D. Camargo*

Cell · 17 Oct 2023

Lineage tracing Mouse model Multiomics Cell fate Clonal memory Migration

Manuscript 30min video Code-analysis Code-preprocessing

CoSpar identifies early cell fate biases from single-cell transcriptomic and lineage information

Shou-Wen Wang*, Michael J. Herriges, Kilian Hurley, Darrell N. Kotton, Allon M. Klein*

Nature Biotechnology · 21 Feb 2022

Lineage tracing Cell fate prediction Trajectory inference

Main text Supplement methods Documentation Code 1 hour video 20min video

Single-cell lineage tracing unveils a role for TCF15 in haematopoiesis

Alejo E. Rodriguez-Fraticelli, Caleb Weinreb, Shou-Wen Wang, Rosa P. Migueles, Maja Jankovic, Marc Usart, Allon M. Klein, Sally Lowell, Fernando D. Camargo

Nature · 15 Jul 2020

Lineage tracing Serial clonal analysis Graphic modeling

Supplement methods

Emergence of collective oscillations in adaptive cells

Shou-Wen Wang*, and Lei-Han Tang*

Nature Communications · 01 Dec 2019

Collective oscillations Sensory adaptation Non-equilibirum statistical physics

Main text Supplemental methods

Revealing evolutionary constraints on proteins through sequence analysis

Shou-Wen Wang, Anne-Florence Bitbol, Ned S. Wingreen

PLOS Computational Biology · 24 Apr 2019

Protein evolution Single-site mutation effect Elastic network modeling

Main text Supplemental methods

Inferring energy dissipation from violation of the fluctuation-dissipation theorem

Shou-Wen Wang

Physical Review E · 18 May 2018

Non-equilibirum statistical physics Asymmetric transitions

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Entropy Production of Nanosystems with Time Scale Separation

Shou-Wen Wang, Kyogo Kawaguchi, Shin-ichi Sasa, Lei-Han Tang

Physical Review Letters · 10 Aug 2016

Non-equilibrium statistical physics Entropy production Time-scale separation Coarse-graining

Main text Supplemental methods

Energy dissipation in an adaptive molecular circuit

Shou-Wen Wang, Yueheng Lan, Lei-Han Tang

Journal of Statistical Mechanics: Theory and Experiment · 21 Jul 2015

Non-equilibirum statistical physics Sensory adaptation

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Nonlinear waves on circle networks with excitable nodes

Shouwen Wang, Yueheng Lan

Journal of Physics A: Mathematical and Theoretical · 14 Aug 2013

Nonlinear dynamics Synchronization

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