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Feedback is ubiquitous in both biological and engineered control systems. In biology, in addition to typical feedback between plant and controller, we observe feedback pathways within control systems, which we call internal feedback…
For more than two decades, advances in personalised medicine and precision healthcare have largely been based on genomics and other omics data. These strategies aim to tailor interventions to individual patient profiles, promising greater…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
Monoclonal antibodies constitute one of the most important strategies to treat patients suffering from cancers such as hematological malignancies and solid tumors. In order to guarantee the quality of those preparations prepared at…
The canine lymphoma blood test detects the levels of two biomarkers, the acute phase proteins (C-Reactive Protein and Haptoglobin). This test can be used for diagnostics, for screening, and for remission monitoring as well. We analyze…
We present a symbolic algorithmic approach that allows to compute invariant manifolds and corresponding reduced systems for differential equations modeling biological networks which comprise chemical reaction networks for cellular…
One of the most puzzling and unsolved challenges in molecular biology is understanding how proteins fold. Despite having advanced predictive tools that can accurately estimate the native structures of proteins, we still lack a comprehensive…
Conventional histopathology has long been essential for disease diagnosis, relying on visual inspection of tissue sections. Immunohistochemistry aids in detecting specific biomarkers but is limited by its single-marker approach, restricting…
Background: In the field of radiology and radiotherapy, accurate delineation of tissues and organs plays a crucial role in both diagnostics and therapeutics. While the gold standard remains expert-driven manual segmentation, many automatic…
Immunoaffinity-based liquid biopsies of circulating tumor cells (CTCs) hold great promise for cancer management, but typically suffer from low throughput, relative complexity and post-processing limitations. Here we address these issues…
This article surveys the literature over the period 2003-2021 on heart-based biometric protocols. In particular, we focus on how the heart signal is transformed from a continuous wave to discrete values to be used afterwards in…
A novel approach to protein multiple sequence alignment is discussed: substantially this method counterparts with substitution matrix based methods (like Blosum or PAM based methods), and implies a more deterministic approach to…
A protocol for the identification of ancestry informative markers (AIMs) from genome-wide single nucleotide polymorphism (SNP) data is proposed. The protocol consists of three main steps: (a) identification of potential positive selection…
A method is described where the aminoacyl-tRNA synthetase system is used to create very small devices for quantitative analysis of the amino acids that occur in proteins. The basis of the method is that each of the 20 synthetases and/or a…
Mass spectrometry-based proteomics has become the tool of choice for identifying and quantifying the proteome of an organism. Though recent years have seen a tremendous improvement in instrument performance and the computational tools used,…
One of the most powerful techniques to study protein structures is to look for recurrent fragments (also called substructures or spatial motifs), then use them as patterns to characterize the proteins under study. An emergent trend consists…
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a high level of structural heterogeneity and are best described by ensembles consisting of multiple conformations with associated thermodynamic…
We present a molecular simulation method to simultaneously find multiple transition pathways, and their associated free-energy profiles. The scheme extends path-metadynamics (PMD) [Phys. Rev. Lett. 109, 020601 (2012)] with multiple paths…
The rules that specify how the information contained in DNA codes amino acids, is called "the genetic code". Using a simplified version of the Penna nodel, we are using computer simulations to investigate the importance of the genetic code…
The high arithmetic performance and intrinsic parallelism of recent graphical processing units (GPUs) can offer a technological edge for molecular dynamics simulations. ACEMD is a production-class bio-molecular dynamics (MD) simulation…