Related papers: Organelle proteomics
We introduce a simple physical picture to explain the process of molecular sorting, whereby specific proteins are concentrated and distilled into submicrometric lipid vesicles in eukaryotic cells. To this purpose, we formulate a model based…
This chapter deals with approaches for protein three-dimensional structure prediction, starting out from a single input sequence with unknown struc- ture, the 'query' or 'target' sequence. Both template based and template free modelling…
We survey and analyze different ways in which bornologies, coarse structures and uniformities on a group agree with the group operations.
Nucleosome positioning is an important process required for proper genome packing and its accessibility to execute the genetic program in a cell-specific, timely manner. In the recent years hundreds of papers have been devoted to the…
This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene…
The study of organoids, artificially grown cell aggregates with the functionality and small-scale anatomy of real organs, is one of the most active areas of research in biology and biophysics, yet the basic physical origins of their…
With the increasing availability and size of multi-omics datasets, investigating the casual relationships between molecular phenotypes has become an important aspect of exploring underlying biology and genetics. This paper aims to introduce…
Modern spatial microscopy has provided developmental biology with powerful research tools. However, the recent significant technological breakthroughs have inevitably led to technical "bottlenecks" for the application of the new procedures…
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,…
Classification of proteins based on their structure provides a valuable resource for studying protein structure, function and evolutionary relationships. With the rapidly increasing number of known protein structures, manual and…
Sound data analysis is essential to retrieve meaningful biological information from single-cell proteomics experiments. This analysis is carried out by computational methods that are assembled into workflows, and their implementations…
We focus on the biological problem of tracking organelles as they move through cells. In the past, most intracellular movements were recorded manually, however, the results are too incomplete to capture the full complexity of organelle…
Many pressing medical challenges - such as diagnosing disease, enhancing directed stem cell differentiation, and classifying cancers - have long been hindered by limitations in our ability to quantify proteins in single cells.…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Models which allow an explicit application to structurally modulated substances are reviewed within the frame of a symmetry-based approach starting from discrete lattice theory. Focus is set on models formulated in terms of local variables…
We review the status of protein-based molecular electronics. First we discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of…
In the post-genome era, biologists have sought to measure the complete complement of proteins, termed proteomics. Currently, the most effective method to measure the proteome is with shotgun, or bottom-up, proteomics, in which the proteome…
To understand the system-wide organization of metabolism, different lines of study have devised different categorizations of metabolites. The relationship and difference between categories can provide new insights for a more detailed…
Various structures in human physiology follow a treelike morphology, which often expresses complexity at very fine scales. Examples of such structures are intrathoracic airways, retinal blood vessels, and hepatic blood vessels. Large…
The cell nucleus is increasingly recognized as a mechanosensitive organelle whose mesoscale mechanical heterogeneity (100 nm 10 um) is inseparable from genome regulation yet remains weakly integrated into systems biology and omics…