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Sequential Monte Carlo (SMC) methods are widely used to draw samples from intractable target distributions. Particle degeneracy can hinder the use of SMC when the target distribution is highly constrained or multimodal. As a motivating…
It is becoming clear that traditional, single-structure models of proteins are insufficient for understanding their biological function. Here, we outline one method for inferring, from experiments, not only the most common structure a…
Proteomics is the large-scale analysis of the proteins. The common method for identifying proteins and characterising their amino acid sequences is to digest the proteins into peptides, analyse the peptides using mass spectrometry and…
Gene expression profiling technologies have been used in various applications such as cancer biology. The development of gene expression profiling has expanded the scope of target discovery in transcriptomic studies, and each technology…
In recent years, there has been remarkable progress in machine learning for protein-protein interactions. However, prior work has predominantly focused on improving learning algorithms, with less attention paid to evaluation strategies and…
In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different…
The application of single-cell molecular profiling coupled with spatial technologies has enabled charting cellular heterogeneity in reference tissues and in disease. This new wave of molecular data has highlighted the expected diversity of…
A plethora of protein language models have been released in recent years. Yet comparatively little work has addressed how to best sample from them to optimize desired biological properties. We fill this gap by proposing a flexible,…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
Two-dimensional gel electrophoresis has been instrumental in the development of proteomics. Although it is no longer the exclusive scheme used for proteomics, its unique features make it a still highly valuable tool, especially when…
Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous, and have complicated dependency structures, making…
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…
Understanding how protein mutations affect protein-nucleic acid binding is critical for unraveling disease mechanisms and advancing therapies. Current experimental approaches are laborious, and computational methods remain limited in…
Generative modeling has become a central paradigm in protein research, extending machine learning beyond structure prediction toward sequence design, backbone generation, inverse folding, and biomolecular interaction modeling. However, the…
Single-molecule pulling techniques have emerged as versatile tools for probing the noncovalent forces holding together the secondary and tertiary structure of macromolecules. They also constitute a way to study at the single-molecule level…
In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through…
This study investigates the current landscape and future directions of protein foundation model research. While recent advancements have transformed protein science and engineering, the field lacks a comprehensive benchmark for fair…
Mitochondria are complex organelles, and their proteomics analysis requires a combination of techniques. The emphasis in this chapter is made first on mitochondria preparation from cultured mammalian cells, then on the separation of the…
Alignment of molecules through electric fields minimizes the averaging over orientations, e. g., in single particle imaging experiments. The response of molecules to external ac electric fields is governed by their polarizability tensor,…
Protein footprinting is a new methodology that is based on probing, typically with the use of mass spectrometry, of reactivity of different aminoacid residues to a modifying reagent. Data thus obtained allow one to make inferences about…