WANG LAB Where Machine Learning Meets Single-Cell Genomics

Publications

* Corresponding authors

Published

2023

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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 tracingMouse modelMultiomicsCell fateClonal memoryMigration
Manuscript30min videoCode-analysisCode-preprocessing

2022

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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 tracingCell fate predictionTrajectory inference
Main textSupplement methodsDocumentationCode1 hour video20min video

2020

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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 tracingSerial clonal analysisGraphic modeling
Supplement methods

2019

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Emergence of collective oscillations in adaptive cells
Shou-Wen Wang*, and Lei-Han Tang*
Nature Communications  ·  01 Dec 2019
Collective oscillationsSensory adaptationNon-equilibirum statistical physics
Main textSupplemental methods
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Revealing evolutionary constraints on proteins through sequence analysis
Shou-Wen Wang, Anne-Florence Bitbol, Ned S. Wingreen
PLOS Computational Biology  ·  24 Apr 2019
Protein evolutionSingle-site mutation effectElastic network modeling
Main textSupplemental methods

2018

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Inferring energy dissipation from violation of the fluctuation-dissipation theorem
Shou-Wen Wang
Physical Review E  ·  18 May 2018
Non-equilibirum statistical physicsAsymmetric transitions
Main text

2016

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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 physicsEntropy productionTime-scale separationCoarse-graining
Main textSupplemental methods

2015

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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 physicsSensory adaptation
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2013

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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 dynamicsSynchronization
Main text