A5081672760- Gene Regulatory Network Analysis
- stochastic dynamics and bifurcation
- CRISPR and Genetic Engineering
- Nonlinear Dynamics and Pattern Formation
- Animal Genetics and Reproduction
- Neural dynamics and brain function
- Single-cell and spatial transcriptomics
- Advanced Thermodynamics and Statistical Mechanics
- Opinion Dynamics and Social Influence
- RNA Research and Splicing
- Chaos control and synchronization
- Stellar, planetary, and galactic studies
- Probabilistic and Robust Engineering Design
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- Advanced Memory and Neural Computing
- Evolutionary Algorithms and Applications
- Bioinformatics and Genomic Networks
- Pluripotent Stem Cells Research
- Neural Networks and Reservoir Computing
- Complex Network Analysis Techniques
- Neural Networks Stability and Synchronization
- Ecosystem dynamics and resilience
- Cancer Cells and Metastasis
- Immune cells in cancer
Jackson Laboratory
2017-2023
North Carolina State University
2016-2018
Indian Institute of Science Education and Research Mohali
2011-2017
Carl von Ossietzky Universität Oldenburg
2017
Potsdam Institute for Climate Impact Research
2014-2017
Humboldt-Universität zu Berlin
2017
University of Hawaiʻi at Mānoa
2015-2016
Indian Institute of Science Bangalore
2013-2015
We study the stability of synchronized state in time-varying complex networks using concept basin stability, which is a nonlocal and nonlinear measure that can be easily applied to high-dimensional systems [P. J. Menck, Heitzig, N. Marwan, Kurths, Nature Phys. 9, 89 (2013)]. The character included by stochastically rewiring each link with average frequency f. find time taken reach synchronization lowered range increases considerably dynamic networks. Further we uncover small-world are much...
The unprecedented light curves of the Kepler space telescope document how brightness some stars pulsates at primary and secondary frequencies whose ratios are near golden mean, most irrational number. A nonlinear dynamical system driven by an ratio generically exhibits a strange but nonchaotic attractor. For Kepler's "golden" stars, we present evidence first observation dynamics in nature outside laboratory. This discovery could aid classification detailed modeling variable stars.
Abstract A major question in systems biology is how to identify the core gene regulatory circuit that governs decision-making of a biological process. Here, we develop computational platform, named NetAct, for constructing transcription factor networks using both transcriptomics data and literature-based factor-target databases. NetAct robustly infers regulators’ activity target expression, constructs based on transcriptional activity, integrates mathematical modeling validation. Our silico...
Stochasticity in gene expression impacts the dynamics and functions of regulatory circuits. Intrinsic noises, including those that are caused by low copy number molecules transcriptional bursting, usually studied stochastic simulations. However, role extrinsic factors, such as cell-to-cell variability heterogeneity microenvironment, is still elusive. To evaluate effects both intrinsic we develop a method, named sRACIPE, integrating analysis with random circuit perturbation (RACIPE) method....
A two-state system driven by two inputs has been found to consistently produce a response mirroring logic function of the inputs, in an optimal window moderate noise. This phenomenon is called logical stochastic resonance (LSR). We extend conventional LSR paradigm implement higher-level architecture or typical digital electronic structures via carefully crafted coupling schemes. Further, we examine intriguing possibility obtaining reliable outputs from noise-free bistable system, subject...
The phenomena of logical stochastic resonance (LSR) was demonstrated recently [Phys. Rev. Lett. 102, 104101 (2009)]: namely, when a bistable system is driven by two inputs it consistently yields response mirroring logic function the in an optimal window moderate noise. Here we examine intriguing possibility obtaining dynamical behavior equivalent to LSR noise-free system, subjected only periodic forcing, such as sinusoidal driving or rectangular pulse trains. We find that despite having no...
Epithelial-mesenchymal transition (EMT) is well established as playing a crucial role in cancer progression and being potential therapeutic target. To elucidate the gene regulation that drives decision making of EMT, many previous studies have been conducted to model EMT regulatory circuits (GRCs) using interactions from literature. While this approach can depict generic interactions, it falls short capturing context-specific features. Here, we explore effectiveness combined bioinformatics...
Abstract Background Gene disruption in mouse embryonic stem cells or zygotes is a conventional genetics approach to identify gene function vivo. However, because different strategies use mechanisms disrupt genes, the can result diverse phenotypes resulting model. To determine whether affect phenotype of mutant mice, we characterized Rhbdf1 strains generated by three commonly used strategies—definitive-null, targeted knockout (KO)-first, and CRISPR/Cas9. Results We find that responds...
We study the dynamics of a collection nonlinearly coupled limit cycle oscillators, relevant to systems ranging from neuronal populations electrical circuits, under coupling topologies varying regular ring random network. find that trajectories this system escape infinity coupling, for sufficiently strong strengths. However, when some fraction connections are dynamically randomized, unbounded growth is suppressed and always remains bounded. Further we determine critical links necessary...
Certain nonlinear systems can switch between dynamical attractors occupying different regions of phase space, under variation parameters or initial states. In this work we exploit feature to obtain reliable logic operations. With output 0 1 mapped bounded in distinct and inputs encoded by a very small bias parameter, explicitly demonstrate that the system hops consistently response an external input stream, operating effectively as gate. This offers advantage low-amplitude yield highly...
Many biological processes involve precise cellular state transitions controlled by complex gene regulation. Here, we use budding yeast cell cycle as a model system and explore how regulatory circuit encodes essential information of transitions. We present generalized random perturbation method for circuits containing heterogeneous regulation types its usage to analyze both steady oscillatory states from an ensemble models with kinetic parameters. The stable form robust clusters circular...
Although epithelial-mesenchymal transition (EMT) is a common feature of fibrotic lung disease, its role in fibrogenesis controversial. Recently, aberrant basaloid cells were identified tissue as novel epithelial cell type displaying partial EMT phenotype. The developmental origin these remains unknown. To elucidate the development from bronchial epithelium, we mapped EMT-induced transcriptional changes at population and single-cell levels. Human grown submerged or air-liquid interface (ALI)...
As Moore's Law winds down, we look to do more with less---more computing fewer components, that is. One approach is ``chaos computing'', in which nonlinear dynamics exploited create any type of logic gate on the fly, almost instantly, from a single generic setup. Starting super-stable initial conditions robust noise, authors combine conventional digital circuit an analog just three transistors, implement arbitrary Boolean functions...
We report the phenomenon of temporally intermittently synchronized and desynchronized dynamics in Watts-Strogatz networks chaotic Rössler oscillators. consider topologies for which master stability function (MSF) predicts stable behaviour, as rewiring probability (p) is tuned from 0 to 1. MSF essentially utilizes largest non-zero Lyapunov exponent transversal synchronization manifold making considerations, thereby ignoring other exponents. However, an N-node networked dynamical system, we...
Abstract Automated detection of complex animal behavior remains a challenge in neuroscience. Developments computer-vision have greatly advanced automated and allow high-throughput pre-clinical studies. An integrated hardware software solution is necessary to facilitate the adoption these advances field behavioral neurogenetics, particularly for non-computational labs. We published series papers using an open arena annotate behaviors such as grooming, posture, gait well higher level...
Abstract A major question in systems biology is how to identify the core gene regulatory circuit that governs decision-making of a biological process. Here, we develop computational platform, named NetAct, for constructing transcription-factor networks using both transcriptomics data and literature-based transcription factor-target databases. NetAct robustly infers regulators’ activity target expression, constructs based on transcriptional activity, integrates mathematical modeling...
We study the effect of additive colored noise on evolution maps and demonstrate that deviations caused by such can be reduced using coupled dynamics. consider both Ornstein–Uhlenbeck process as well [Formula: see text] in our numerical simulations. observe though variance depends correlations noise, under optimal coupling strength, it decreases a factor equal to number elements array compared single isolated map. This reduction levels occurs chaotic periodic regime maps. Lastly, we examine...