A5101567547- Advanced Thermodynamics and Statistical Mechanics
- Gene Regulatory Network Analysis
- Protein Structure and Dynamics
- stochastic dynamics and bifurcation
- thermodynamics and calorimetric analyses
- Statistical Mechanics and Entropy
- Evolution and Genetic Dynamics
- Single-cell and spatial transcriptomics
- RNA and protein synthesis mechanisms
- DNA and Nucleic Acid Chemistry
- Research in Cotton Cultivation
- Bacterial Genetics and Biotechnology
- Spectroscopy and Quantum Chemical Studies
- Nonlinear Dynamics and Pattern Formation
- Phase Equilibria and Thermodynamics
- Coccidia and coccidiosis research
- Diffusion and Search Dynamics
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Laser-Matter Interactions and Applications
- Quantum Mechanics and Applications
- Bioinformatics and Genomic Networks
- Stochastic processes and statistical mechanics
- Mathematical Biology Tumor Growth
- Veterinary medicine and infectious diseases
Peking University
2016-2025
Robert Bosch (Germany)
2024
Peking University International Hospital
2013-2024
Sichuan Agricultural University
2023-2024
Xinjiang University
2023-2024
Dalian Polytechnic University
2024
Hunan Agricultural University
2024
Nanjing University of Chinese Medicine
2024
Guangzhou University of Chinese Medicine
2023
East China University of Science and Technology
2023
Natural variations in gene expression provide a mechanism for multiple phenotypes to arise an isogenic bacterial population. In particular, sub-group termed persisters show high tolerance antibiotics. Previously, their formation has been attributed cell dormancy. Here we demonstrate that persisters, under β-lactam antibiotic treatment, less cytoplasmic drug accumulation as result of enhanced efflux activity. Consistently, number multi-drug genes, particularly the central component TolC,...
The placenta is crucial for a successful pregnancy and the health of both fetus pregnant woman. However, how human trophoblast lineage regulated, including categorization placental cell subtypes poorly understood. Here we performed single-cell RNA sequencing (RNA-seq) on sorted cells from first- second-trimester placentas. New known cytotrophoblast (CTBs), extravillous (EVTs), Hofbauer cells, mesenchymal stromal were identified cell-type-specific gene signatures defined. Functionally, this...
Allostery is well documented for proteins but less recognized DNA-protein interactions. Here, we report that specific binding of a protein on DNA substantially stabilized or destabilized by another bound nearby. The ternary complex's free energy oscillates as function the separation between two with periodicity ~10 base pairs, helical pitch B-form DNA, and decay length ~15 pairs. affinity near hairpin similarly dependent their separation, which-together molecular dynamics...
Abstract Background Colorectal cancer (CRC) ranks as the second-leading cause of cancer-related death worldwide with metastases being main death. Here, we investigated genomic and transcriptomic alterations in matching adjacent normal tissues, primary tumors, metastatic tumors CRC patients. Methods We performed whole genome sequencing (WGS), multi-region exome (WES), simultaneous single-cell RNA-Seq, targeted cDNA Sanger on from 12 colorectal patients ( n =84 for genomes, =81 exomes, =9120...
A unifying mathematical theory of nonequilibrium thermodynamics stochastic systems in terms master equations is presented. As generalizations isothermal entropy and free energy, two functions state play central roles: the Gibbs $S$ relative $F$, which are related via stationary distribution dynamics. satisfies fundamental balance equation $dS/dt={e}_{p}\ensuremath{-}{h}_{d}/T$ with production rate ${e}_{p}\ensuremath{\ge}0$ heat dissipation ${h}_{d}$, while...
Despite advances in DNA methylome analyses of cells and tissues, current techniques for genome-scale profiling methylation circulating cell-free (ccfDNA) remain limited. Here we describe a methylated CpG tandems amplification sequencing (MCTA-Seq) method that can detect thousands hypermethylated islands simultaneously ccfDNA. This highly sensitive technique work with genomic as little 7.5 pg, which is equivalent to 2.5 copies the haploid genome. We have analyzed cohort tissue plasma samples...
Multiple phenotypic states often arise in a single cell with different gene-expression that undergo transcription regulation positive feedback. Recent experiments show that, at least E. coli, the gene state switching can be neither extremely slow nor exceedingly rapid as many previous theoretical treatments assumed. Rather, it is intermediate region which difficult to handle mathematically. Under this condition, from full chemical-master-equation description we derive model protein copy...
Gibbs' macroscopic chemical thermodynamics is one of the most important theories in chemistry. Generalizing it to mesoscaled nonequilibrium systems essential biophysics. The stochastic reaction kinetics suggested a free energy balance equation $d{F}^{(\text{meso})}/dt={E}_{\text{in}}\ensuremath{-}{e}_{p}$ which input rate ${E}_{\text{in}}$ and dissipation ${e}_{p}$ are both non-negative, ${E}_{\text{in}}\ensuremath{\le}{e}_{p}$. We prove that limit by merely allowing molecular numbers be...
In 2018, by Ramsey and Hoffman theory, Koolen, Yang, Yang presented a structural result on graphs with smallest eigenvalue at least $-3$ large minimum degree. this study, we depart from the conventional use of theory instead employ novel approach that combines Bose-Laskar type argument to derive insights into $\mu$-bounded fixed eigenvalue. Our method establishes reasonable bound Note local distance-regular are $\mu$-bounded. We apply these results characterize structure for any graph...
Unveiling the complexities of gene expression regulation, study explores intricate DNA-binding mechanisms transcription factors (TFs). By employing KaScape method previously developed to measure both bound and unbound populations at thermodynamic equilibrium, "anchoring elements" (AEs), 3-4 base pair sequences, are identified in Arabidopsis WRKY human PU.1 TFs crucial for binding affinity. Building on BEESEM method, introduces AEEscape algorithm, which advances AE concept by creating a...
Landscape is one of the key notions in literature on biological processes and physics complex systems with both deterministic stochastic dynamics. The large deviation theory (LDT) provides a possible mathematical basis for scientists' intuition. In terms Freidlin-Wentzell's LDT, we discuss explicitly two issues singularly perturbed stationary diffusion arisen from nonlinear differential equations: (1) For process whose corresponding ordinary equation has stable limit cycle, solution exhibits...
Organ formation relies on the orchestration of pattern formation, proliferation and growth during development. How these processes are integrated at individual cell level remains unclear. Studies using Drosophila wing imaginal discs as a model system have provided valuable insights into control regeneration in past decades. Here we single transcriptomic landscapes discs. We found that patterning information is robustly maintained data can provide reference matrices to computationally map...
A theory for an non-equilibrium phase transition in a driven biochemical network is presented. The based on the chemical master equation (CME) formulation of mesoscopic reactions and mathematical method large deviations. deviations provides analytical tool connecting macroscopic multi-stability open system with multi-scale dynamics its counterpart. It shows corresponding among multiple stochastic attractors. As example, canonical phosphorylation–dephosphorylation feedback that exhibits...
Markov models are widely used to describe stochastic dynamics. Here, we show that follow directly from the dynamical principle of maximum caliber (Max Cal). Max Cal is a method deriving based on maximizing path entropy subject constraints. We give three different cases. First, if constraints (or data) given in form singlet statistics (average occupation probabilities), then predicts time-independent process modeled by identical, independently distributed random variables. Second, sequential...
Nonequilibrium thermodynamics of a system situated in sustained environment with influx and efflux is usually treated as subsystem larger, closed ``universe.'' A question remains regard to what the minimally required description for surrounding such an open driven so that its nonequilibrium can be established solely based on internal stochastic kinetics. We provide solution this problem using insights from studies molecular motors chemical steady state (NESS) external drive through...