Related papers: Multiple Lac-mediated loops revealed by Bayesian s…
We use a nanofluidic system to investigate the emergence of thermally driven collective phenomena along a single polymer chain. In our approach, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded…
We show how the tracer motion of tagged, distinguishable particles can effectively describe transport in various homogeneous quantum many-body systems with constraints. We consider systems of spinful particles on a one-dimensional lattice…
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…
We analyze the structure of DNA molecules of different organisms by using the additive Markov chain approach. Transforming nucleotide sequences into binary strings, we perform statistical analysis of the corresponding "texts". We develop…
The interaction between proteins and DNA is a key driving force in a significant number of biological processes such as transcriptional regulation, repair, recombination, splicing, and DNA modification. The identification of DNA-binding…
Involved in mitotic condensation, interaction of transcriptional regulatory elements or isolation of structural domains, understanding loop formation is becoming a paradigm in the deciphering of chromatin architecture and its functional…
Recent literature has shown how linear time-invariant (LTI) systems can be represented by trajectories features, that is relying on a single input-output (IO) data dictionary to span all possible system trajectories, as long as the input is…
Transcriptional noise, or heterogeneity, is important in cellular development and in disease. The molecular mechanisms driving it are, however, elusive and ill-understood. Here, we use computer simulations to explore the role of 3D…
We consider integrative modeling of multiple gene networks and diverse genomic data, including protein-DNA binding, gene expression and DNA sequence data, to accurately identify the regulatory target genes of a transcription factor (TF).…
The study of transcription remains one of the centerpieces of modern biology with implications in settings from development to metabolism to evolution to disease. Precision measurements using a host of different techniques including…
DNA-based storage has emerged as a promising alternative to traditional data storage methods, offering unmatched advantages in data density, longevity, and sustainability. Two main approaches have developed: in-vitro storage, where…
We show the existence of a high interrelation between the different loops that may appear in a DNA segment. Conformational changes in a chain segment caused by the formation of a particular loop may either promote or prevent the appearance…
At the heart of the structured architecture and complex dynamics of biological systems are specific and timely interactions operated by biomolecules. In many instances, biomolecular agents are spatially confined to flexible lipid membranes…
Measuring the electrophoretic mobility of molecules is a powerful experimental approach for investigating biomolecular processes. A frequent challenge in the context of single-particle measurements is throughput, limiting the obtainable…
We propose a Bayesian hidden Markov model for analyzing time series and sequential data where a special structure of the transition probability matrix is embedded to model explicit-duration semi-Markovian dynamics. Our formulation allows…
Random feature latent variable models (RFLVMs) represent the state-of-the-art in latent variable models, capable of handling non-Gaussian likelihoods and effectively uncovering patterns in high-dimensional data. However, their heavy…
Particles with ligand-receptor contacts bind and unbind fluctuating "legs" to surfaces, whose fluctuations cause the particle to diffuse. Quantifying the diffusion of such "nanoscale caterpillars" is a challenge, since binding events often…
Motivated by experimental results on the interplay between molecular motors and tau proteins, we extend lattice-based models of intracellular transport to include a second species of particle which locally influences the motor-filament…
We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are…
Tracking cells in time-lapse videos is an essential technique for monitoring cell population dynamics at a single-cell level. Current methods for cell tracking are developed on videos with mostly single, constant signals and do not detect…