A5082415138- Single-cell and spatial transcriptomics
- Advanced Thermodynamics and Statistical Mechanics
- stochastic dynamics and bifurcation
- Gene Regulatory Network Analysis
- Neural dynamics and brain function
- Molecular Communication and Nanonetworks
- Epigenetics and DNA Methylation
- Nonlinear Dynamics and Pattern Formation
- Bioinformatics and Genomic Networks
- Cancer Genomics and Diagnostics
- Protein Structure and Dynamics
- Hematopoietic Stem Cell Transplantation
- Bacterial Identification and Susceptibility Testing
- CRISPR and Genetic Engineering
- Evolution and Genetic Dynamics
- Sepsis Diagnosis and Treatment
- Knowledge Management and Sharing
- Healthcare Policy and Management
- Streptococcal Infections and Treatments
- Slime Mold and Myxomycetes Research
- thermodynamics and calorimetric analyses
- Cellular Automata and Applications
- Global Health Care Issues
- Extenics and Innovation Methods
- Animal Behavior and Reproduction
Westlake University
2023-2025
Boston VA Research Institute
2021-2022
Harvard University
2018-2022
Center for Systems Biology
2018-2020
Tsinghua University
2013-2019
Princeton University
2018-2019
Beijing Computational Science Research Center
2016-2019
Harvard University Press
2018
National Cheng Kung University Hospital
2015-2016
Huazhong University of Science and Technology
2012-2013
Energy flows in biomolecular motors and machines are vital to their function. Yet experimental observations often limited a small subset of variables that participate energy transport dissipation. Here we show, through solvable Langevin model, the seemingly hidden entropy production is measurable violation spectrum fluctuation-response relation slow observable. For general Markov systems with time scale separation, prove exhibits characteristic plateau intermediate frequency region. Despite...
Summary Cellular lineage histories along with their molecular states encode fundamental principles of tissue development and homeostasis. Current lineage-recording mouse models have limited barcode diversity poor single-cell coverage, thus precluding use in tissues composed millions cells. Here, we developed DARLIN, an improved Cas9 barcoding line that utilizes terminal deoxynucleotidyl transferase (TdT) to enhance insertion events over 30 CRISPR target sites, stably integrated into 3...
Statistical analysis of alignments large numbers protein sequences has revealed "sectors" collectively coevolving amino acids in several families. Here, we show that selection acting on any functional property a protein, represented by an additive trait, can give rise to such sector. As illustration selected consider the elastic energy important conformational change within network model, and this leads correlations among residues. For concrete example more generally, demonstrate main...
Background Blood culture contamination in emergency departments (ED) that experience a high volume of patients has negative impacts on optimal patient care. It is therefore important to identify risk factors associated with blood EDs. Methodology/Principal Findings A prospectively observational study university-affiliated hospital were conducted between August 2011 and December 2012. Positive monomicrobial cultures drawn from adult the ED analyzed evaluate possible for contamination. total...
The ability to monitor nutrient and other environmental conditions with high sensitivity is crucial for cell growth survival.Sensory adaptation allows a recover its after transient response shift in the strength of extracellular stimulus.The working principles have been established previously based on rate equations which do not consider fluctuations thermal environment.Recently, G. Lan et al. (Nature Phys., 8:422-8, 2012) performed detailed analysis stochastic model E. coli sensory...
Abstract Collective oscillations of cells in a population appear under diverse biological contexts. Here, we establish set common principles by categorising the response individual against time-varying signal. A positive intracellular signal relay sufficient gain from participating is required to sustain oscillations, together with phase matching. The two conditions yield quantitative predictions for onset cell density and frequency terms measured single-cell functions. Through mathematical...
The Harada-Sasa equality elegantly connects the energy dissipation rate of a moving object with its measurable violation Fluctuation-Dissipation Theorem (FDT). Although proven for Langevin processes, validity remains unclear discrete Markov systems whose forward and backward transition rates respond asymmetrically to external perturbation. A typical example is motor protein called kinesin. Here we show generally that FDT persists surprisingly in high-frequency limit due asymmetry, resulting...
We present a theoretical framework to analyze the violation of fluctuation-response relation (FRR) for any observable from finite Markov system with two well-separated time scales. find that, generally both slow and fast observables, broad plateau exists in intermediate frequency region, which contributes hidden entropy production. Assuming that non-equilibrium behavior arises only coupling processes, we at large observation scae, effective temperature deviates slightly bath temperature,...
Abstract Statistical analysis of alignments large numbers protein sequences has revealed “sectors” collectively coevolving amino acids in several families. Here, we show that selection acting on any functional property a protein, represented by an additive trait, can give rise to such sector. As illustration selected consider the elastic energy important conformational change within network model, and this leads correlations among residues. For concrete example more generally, demonstrate...
Abstract A goal of single cell genome-wide profiling is to reconstruct dynamic transitions during differentiation, disease onset, and drug response. Single assays have recently been integrated with lineage tracing, a set methods that identify cells common ancestry establish bona fide relationships between states. These revealed unappreciated dynamics, but their analysis faces recurrent challenges arising from noisy, dispersed data. Here, we develop coherent, sparse optimization (CoSpar) as...
Human immunodeficiency virus (HIV) tests are commonly performed in emergency departments (EDs) the United States (US), but experience and effectiveness of conducting rapid HIV EDs regions with low seroprevalence outside US have seldom been reported. An observational cross-sectional opt-in test counseling program was conducted at an ED a teaching hospital Taiwan, country seroprevalence, to determine acceptance as well risky behaviors illness presentations people who agreed undergo tests....
In this paper, we propose a new model of the Kuramoto type to study nonlinear wave generation and propagation on circle network with excitable node dynamics, reveal certain common features traveling solutions, which are independent local dynamics but strongly related diffusive coupling neighboring nodes. view stability size basin attraction, regular waves and, in case large number nodes, circulating pulses most important ones. The period T functional expression for computed analytically,...
Abstract A goal of single cell genome-wide profiling is to reconstruct dynamic transitions during differentiation, disease onset, and drug response. Single assays have recently been integrated with lineage tracing, a set methods that identify cells common ancestry establish bona fide relationships between states. These revealed unappreciated dynamics, but their analysis faces recurrent challenges arising from noisy, dispersed data. Here, we develop coherent, sparse optimization (CoSpar) as...
Extracting energy from fluctuations has been an everlasting endeavor. An important strategy is to use information-based operation, which allows extraction even thermal fluctuations. However, it remains unclear whether a blind external ignorant of such fluctuations, will also work. Assuming small we find that requires negative response spectrum in certain frequency region, inevitably internal power source maintain. Energy then extracted by operating the system at these frequencies. Negative...