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SLiM is an efficient forward population genetic simulation designed for studying the effects of linkage and selection on a chromosome-wide scale. The program can incorporate complex scenarios of demography and population substructure,…
Each living species carries a complex DNA sequence that determines their unique features and functionalities. It is generally assumed that life started from a random pool of oligonucleotides sequences, generated by a prebiotic…
We construct a model of cell reprogramming (the conversion of fully differentiated cells to a state of pluripotency, known as induced pluripotent stem cells, or iPSCs) which builds on key elements of cell biology viz. cell cycles and cell…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
The reverse engineering problem with probabilities and sequential behavior is introducing here, using the expression of an algorithm. The solution is partially founded, because we solve the problem only if we have a Probabilistic Sequential…
Alternative splicing is crucial in gene regulation, with significant implications in clinical settings and biotechnology. This review article compiles bioinformatics RNA-seq tools for investigating differential splicing; offering a detailed…
Dynamical sampling refers to a class of problems in which space-time samples are taken from a signal evolving under an underlying dynamical system. The goal is to use these samples to recover relevant information about the system, such as…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Clustering is a well-known unsupervised machine learning approach capable of automatically grouping discrete sets of instances with similar characteristics. Constrained clustering is a semi-supervised extension to this process that can be…
Probabilistic clustering models (or equivalently, mixture models) are basic building blocks in countless statistical models and involve latent random variables over discrete spaces. For these models, posterior inference methods can be…
We experimentally demonstrate that information replication by templated ligation of DNA strands inherits a kinetic proofreading mechanism and achieves significant error suppression through cascade replication. A simple simulation model…
In this paper, we propose applying semantic embedding to learn the range of behaviors exhibited by molecular swarms, thereby providing a richer set of features to optimize such systems. Specifically, we consider a standard molecular swarm…
Cryptography is the science that secures data and communication over the network by applying mathematics and logic to design strong encryption methods. In the modern era of e-business and e-commerce the protection of confidentiality,…
Phase separation has recently emerged as an important organizational principle in the dense and heterogeneous environment within living cells. Here, we use a synthetic system to show that compressive stresses in a polymer network suppress…
DNA plays a special role in polymer science not just because of the highly selective recognition of complementary single DNA strands but also because bacteria can express DNA chains that are very long yet perfectly monodisperse. The latter…
Despite the apparent ease with which a sheet of paper is crumpled and tossed away, crumpling dynamics are often considered a paradigm of complexity. This complexity arises from the infinite number of configurations a disordered crumpled…
We present a phenomenological dynamical model able to describe the stretching features of the curve of DNA length vs applied force. As concerns the chain, the model is based on the discrete wormlike chain model with elastic modifications,…
Clustering of molecules on biological membranes is a widely observed phenomenon. In some cases, such as the clustering of Ras proteins on the membranes of mammalian cells, proper cell signaling is critically dependent on the maintenance of…
The Exact Circular Pattern Matching (ECPM) problem consists of reporting every occurrence of a rotation of a pattern $P$ in a text $T$. In many real-world applications, specifically in computational biology, circular rotations are of…
Computer-based modelling and simulation have become useful tools to facilitate humans to understand systems in different domains, such as physics, astrophysics, chemistry, biology, economics, engineering and social science. A complex system…