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The common techniques to study protein-protein proximity in vivo are not well-adapted to the capabilities and the expertise of a standard proteomics laboratory, typically based on the use of mass spectrometry. With the aim of closing this…
Sequence coverage in MS analysis of protein digestion-derived peptides is a key issue for detailed characterization of proteins or identification at low quantities. In gel-based proteomics studies, the sequence coverage greatly depends on…
Identifying disease-associated changes in DNA methylation can help to gain a better understanding of disease etiology. Bisulfite sequencing technology allows the generation of methylation profiles at single base of DNA. We previously…
As in many other scientific domains, we face a fundamental problem when using machine learning to identify proteins from mass spectrometry data: large ground truth datasets mapping inputs to correct outputs are extremely difficult to…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…
Identification of nearly all proteins in a system using data-dependent acquisition (DDA) mass spectrometry has become routine for simple organisms, such as bacteria and yeast. Still, quantification of the identified proteins may be a…
Optical microscopy provides rich spatio-temporal information characterizing in vivo molecular motion. However, effective forces and other parameters used to summarize molecular motion change over time in live cells due to latent state…
Crosslinking mass spectrometry (Crosslinking MS) has substantially matured as a method over the last two decades through parallel development in multiple labs, demonstrating its applicability for protein structure determination,…
DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA "breathing") play a central role in such…
We investigate whether synthetic images generated by diffusion models can enhance multi-label classification of protein subcellular localization. Specifically, we implement a simplified class-conditional denoising diffusion probabilistic…
Drug discovery projects entail cycles of design, synthesis, and testing that yield a series of chemically related small molecules whose properties, such as binding affinity to a given target protein, are progressively tailored to a…
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…
DNA methylation is an epigenetic mechanism whose important role in development has been widely recognized. This epigenetic modification results in heritable changes in gene expression not encoded by the DNA sequence. The underlying…
Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design.…
DNA methylation is an important epigenetic mark that has been studied extensively for its regulatory role in biological processes and diseases. WGBS allows for genome-wide measurements of DNA methylation up to single-base resolutions, yet…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
3D fluorescence microscopy of living organisms has increasingly become an essential and powerful tool in biomedical research and diagnosis. An exploding amount of imaging data has been collected, whereas efficient and effective…
Motivation: Bisulphite sequencing enables the detection of cytosine methylation. The sequence of the methylation states of cytosines on any given read forms a methylation pattern that carries substantially more information than merely…
Accurate protein structural ensembles can be determined with metainference, a Bayesian inference method that integrates experimental information with prior knowledge of the system and deals with all sources of uncertainty and errors as well…
Protein interaction networks (PIN) are popular means to visualize the proteome. However, PIN datasets are known to be noisy, incomplete and biased by the experimental protocols used to detect protein interactions. This paper aims at…