Related papers: Modeling Biological Problems in Computer Science: …
In systems biology, it is becoming increasingly common to measure biochemical entities at different levels of the same biological system. Hence, data fusion problems are abundant in the life sciences. With the availability of a multitude of…
Although reproducibility is a core tenet of the scientific method, it remains challenging to reproduce many results. Surprisingly, this also holds true for computational results in domains such as systems biology where there have been…
Biology is at the precipice of a new era where AI accelerates and amplifies the ability to study how cells operate, organize, and work as systems, revealing why disease happens and how to correct it. Organizations globally are prioritizing…
Bacteria have been a source of inspiration for the design of evolutionary algorithms. At the beginning of the 20th century synthetic biology was born, a discipline whose goal is the design of biological systems that do not exist in nature,…
A substantial fraction of the time that computational modellers dedicate to developing their models is actually spent trouble-shooting and debugging their code. However, how this process unfolds is seldom spoken about, maybe because it is…
Programming is ubiquitous in applied biostatistics; adopting software engineering skills will help biostatisticians do a better job. To explain this, we start by highlighting key challenges for software development and application in…
In an effort to overcome the data deluge in computational biology and bioinformatics and to facilitate bioinformatics research in the era of big data, we identify some of the most influential algorithms that have been widely used in the…
We develop a mathematical and numerical framework to solve state estimation problems for applications that present variations in the shape of the spatial domain. This situation arises typically in a biomedical context where inverse problems…
Biological engineering, the convergence between engineering and biology, is at the forefront of significant advances in healthcare, agriculture, and environmental sustainability, making it highly relevant to current scientific and societal…
The reproduction and replication of research results has become a major issue for a number of scientific disciplines. In computer science and related computational disciplines such as systems biology, the challenges closely revolve around…
The Turing machine, as it was presented by Turing himself, models the calculations done by a person. This means that we can compute whatever any Turing machine can compute, and therefore we are Turing complete. The question addressed here…
The vast majority of scientific contributions in the field of computational systems biology are based on mathematical models. These models can be broadly classified as either dynamic (kinetic) models or steady-state (constraint-based)…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
Temporal evolution of a clonal bacterial population is modelled taking into account reversible mutation and selection mechanisms. For the mutation model, an efficient algorithm is proposed to verify whether experimental data can be…
In computer science, we can theoretically neatly separate transmission and processing of information, hardware and software, and programs and their inputs. This is much more intricate in biology, Nevertheless, I argue that Shannon's concept…
We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently…
In medicine, visualizing chromosomes is important for medical diagnostics, drug development, and biomedical research. Unfortunately, chromosomes often overlap and it is necessary to identify and distinguish between the overlapping…
Formal methods apply algorithms based on mathematical principles to enhance the reliability of systems. It would only be natural to try to progress from verification, model checking or testing a system against its formal specification into…
Testing provides means pertaining to assuring software performance. The total aim of software industry is actually to make a certain start associated with high quality software for the end user. However, associated with software testing has…
Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to…