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A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with highthroughput data…
A method for the optimisation and advanced studies of a laser-plasma electron injector is presented, based on a truncated ionisation injection scheme for high quality beam production. The SMILEI code is used with laser envelope…
The high-throughput data generated by microarray experiments provides complete set of genes being expressed in a given cell or in an organism under particular conditions. The analysis of these enormous data has opened a new dimension for…
Generating a novel and optimized molecule with desired chemical properties is an essential part of the drug discovery process. Failure to meet one of the required properties can frequently lead to failure in a clinical test which is costly.…
Histone modifications play a critical role in gene regulation. Consequently, predicting gene expression from histone modification signals is a highly motivated problem in epigenetics. We build upon the work of DeepChrome by Singh et al.…
Many methods to computationally predict red blood cell damage have been introduced, and among these are Lagrangian methods which track the cells along their pathlines. Such methods typically do not explicitly include cell-cell interactions.…
Atomic-level simulations are widely used to study biomolecules and their dynamics. A common goal in such studies is to compare simulations of a molecular system under several conditions -- for example, with various mutations or bound…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
A key challenge in segmentation in digital histopathology is inter- and intra-stain variations as it reduces model performance. Labelling each stain is expensive and time-consuming so methods using stain transfer via CycleGAN, have been…
We discuss a detailed weak scaling analysis of GEM, a 3D MPI-parallelised gyrofluid code used in theoretical plasma physics at the Max Planck Institute of Plasma Physics, IPP at Garching b. M\"unchen, Germany. Within a PRACE Preparatory…
A high-order accurate implicit-mesh discontinuous Galerkin framework for wave propagation in single-phase and bi-phase solids is presented. The framework belongs to the embedded-boundary techniques and its novelty regards the spatial…
To enable personalized cancer treatment, machine learning models have been developed to predict drug response as a function of tumor and drug features. However, most algorithm development efforts have relied on cross validation within a…
How cells regulate the number of organelles is a fundamental question in cell biology. While decades of experimental work have uncovered four fundamental processes that regulate organelle biogenesis, namely, de novo synthesis, fission,…
The present paper studies existence and distributional uniqueness of subclasses of stationary hard-core particle systems arising as thinnings of stationary particle processes. These subclasses are defined by natural maximality criteria. We…
The Cell Formation Problem has been studied as an optimization problem in manufacturing for more than 90 years. It consists of grouping machines and parts into manufacturing cells in order to maximize loading of cells and minimize movement…
Segmentation of enhancement in LGE cardiac MRI is critical for diagnosing various ischemic and non-ischemic cardiomyopathies. However, creating pixel-level annotations for these images is challenging and labor-intensive, leading to limited…
An important occurrence in many cellular contexts is the crossing of a prescribed threshold by a regulatory protein. The timing of such events is stochastic as a consequence of the innate randomness in gene expression. A question of…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
For particle filters and ensemble Kalman filters it is of practical importance to understand how and why data assimilation methods can be effective when used with a fixed small number of particles, since for many large-scale applications it…