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The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
A unified approach is applied in the consideration of the multi-parametric (colored) Yang-Baxter equations (YBE) and the usual YBE with two-parametric R-matrices, relying on the existence of the arbitrary functions in the general solutions.…
This work exposes which mechanisms and procesess in the Nature of evolution compute a function not computable by Turing machine. The computer with intelligence that is not higher than one bacteria population could have, but with efficency…
To reduce experimental effort associated with directed protein evolution and to explore the sequence space encoded by mutating multiple positions simultaneously, we incorporate machine learning in the directed evolution workflow.…
Artificial intelligence methods are being increasingly applied across various domains, but their often opaque nature has raised concerns about accountability and trust. In response, the field of explainable AI (XAI) has emerged to address…
We propose a model of chemostat where the bacterial population is individually-based, each bacterium is explicitly represented and has a mass evolving continuously over time. The substrate concentration is represented as a conventional…
The automatic generation of computer programs is one of the main applications with practical relevance in the field of evolutionary computation. With program synthesis techniques not only software developers could be supported in their…
Escherichia coli has long been used as a model organism due to the extensive experimental characterization of its pathways and molecular components. Take chemotaxis as an example, which allows bacteria to sense and swim in response to…
Discrete mixture models provide a well-known basis for effective clustering algorithms, although technical challenges have limited their scope. In the context of gene-expression data analysis, a model is presented that mixes over a finite…
Can a micron sized sack of interacting molecules understand, and adapt to a constantly-fluctuating environment? Cellular life provides an existence proof in the affirmative, but the principles that allow for life's existence are far from…
Cybersecurity attacks on embedded devices for industrial control systems and cyber-physical systems may cause catastrophic physical damage as well as economic loss. This could be achieved by infecting device binaries with malware that…
Data for several applications in diverse fields can be represented as multiple matrices that are linked across rows or columns. This is particularly common in molecular biomedical research, in which multiple molecular "omics" technologies…
Complex systems can be described at myriad different scales, and their causal workings often have multiscale structure (e.g., a computer can be described at the microscale of its hardware circuitry, the mesoscale of its machine code, and…
We introduce an algorithm to generate (not solve) spin-glass instances with planted solutions of arbitrary size and structure. First, a set of small problem patches with open boundaries is solved either exactly or with a heuristic, and then…
Four chapters of the synthesis represent four major areas of my research interests: 1) data analysis in molecular biology, 2) mathematical modeling of biological networks, 3) genome evolution, and 4) cancer systems biology. The first…
Neural networks have proven to be effective at solving machine learning tasks but it is unclear whether they learn any relevant causal relationships, while their black-box nature makes it difficult for modellers to understand and debug…
The matrix chain problem consists in finding the parenthesization of a matrix product $M := A_1 A_2 \cdots A_n$ that minimizes the number of scalar operations. In practical applications, however, one frequently encounters more complicated…
We present a new algorithm based on a Cartesian mesh for the numerical approximation of kinetic models for chemosensitive movements set in an arbitrary geometry. We investigate the influence of the geometry on the collective behavior of…
External information propagates in the cell mainly through signaling cascades and transcriptional activation, allowing it to react to a wide spectrum of environmental changes. High throughput experiments identify numerous molecular…
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach…