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Colonoscopy is the most widely used medical technique for preventing Colorectal Cancer, by detecting and removing polyps before they become malignant. Recent studies show that around one quarter of the existing polyps are routinely missed.…
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…
Protein identification is one of the major task of Proteomics researchers. Protein identification could be resumed by searching the best match between an experimental mass spectrum and proteins from a database. Nevertheless this approach…
This study investigates the convergence properties of a collection of iterative electron ptychography methods, under low electron doses ($<$ 10$^3$ $e^-/A^2$) and gives particular attention to the impact of the user-defined update…
Super-resolution imaging techniques have largely improved our capabilities to visualize nanometric structures in biological systems. Their application further enables one to potentially quantitate relevant parameters to determine the…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
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…
Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repetitions within a single repeat protein can be extremely variable at the sequence level. We propose a mathematical…
We present a new approach for improving motif scanning accuracy, based on analysis of in-between similarity. Given a set of motifs obtained from a scanning process, we construct an associated weighted graph. We also compute the expected…
Designing protein sequences that fold into a target 3D structure, known as protein inverse folding, is a fundamental challenge in protein engineering. While recent deep learning methods have achieved impressive performance by recovering…
Deep generative models have achieved tremendous success in designing novel drug molecules in recent years. A new thread of works have shown the great potential in advancing the specificity and success rate of in silico drug design by…
Purpose: To demonstrate a proton imaging system based on well-established fast scintillator technology to achieve high performance with low cost and complexity, with the potential of a straightforward translation into clinical use. Methods:…
We theorize that phylogenetic profiles provide a quantitative method that can relate the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of phylogenetic profiles is the…
Feature extraction is an unavoidable task, especially in the critical step of preprocessing biological sequences. This step consists for example in transforming the biological sequences into vectors of motifs where each motif is a…
Gene finding is the task of identifying the locations of coding sequences within the vast amount of genetic code contained in the genome. With an ever increasing quantity of raw genome sequences, gene finding is an important avenue towards…
Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where the bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many…
The repeat content and heterozygosity rate of a target genome are important factors in determining the feasibility of achieving a complete telomere-to-telomere assembly. The mathematical relationship between the required coverage and read…
Proteins perform nearly all cellular functions and constitute most drug targets, making their analysis fundamental to understanding human biology in health and disease. Tandem mass spectrometry (MS$^2$) is the major analytical technique in…
Protein inverse folding, the design of an amino acid sequence based on a target protein structure, is a fundamental problem of computational protein engineering. Existing methods either generate sequences without leveraging external…
Accurate detection of individual intake gestures is a key step towards automatic dietary monitoring. Both inertial sensor data of wrist movements and video data depicting the upper body have been used for this purpose. The most advanced…