Related papers: TraianProt: a user-friendly R shiny application fo…
Large-scale proteomic analysis is emerging as a powerful technique in biology and relies heavily on data acquired by state-of-the-art mass spectrometers. As with any other field in Systems Biology, computational tools are required to deal…
Single-cell proteomics (SCP) is transforming our understanding of biological complexity by shifting from bulk proteomics, where signals are averaged over thousands of cells, to the proteome analysis of individual cells. This granular…
Mass Spectrometry (MS) is a largely used analytical technique in biology with applications such as the determination of molecule masses or the elucidation of structural data. Fourier Transform Ion Cyclotron Resonance MS is one…
Prostate cancer is one of the most prevalent and deadly cancers among men, motivating the development of accurate and accessible imaging technologies for early detection. Ultrasound computed tomography (USCT) reconstructs quantitative…
Magnetic resonance spectroscopy (MRS) is an important clinical imaging method for diagnosis of diseases. MRS spectrum is used to observe the signal intensity of metabolites or further infer their concentrations. Although the magnetic…
Mass spectrometry based clinical proteomics has emerged as a powerful tool for highthroughput protein profiling and biomarker discovery. Recent improvements in mass spectrometry technology have boosted the potential of proteomic studies in…
Melanoma detection is vital for early diagnosis and effective treatment. While deep learning models on dermoscopic images have shown promise, they require specialized equipment, limiting their use in broader clinical settings. This study…
Over the last years, the SWATH data-independent acquisition protocol (Sequential Window acquisition of All THeoretical mass spectra) has become a cornerstone for the worldwide proteomics community. In this approach, a high-resolution…
High throughput metabolomics data are fraught with both non-ignorable missing observations and unobserved factors that influence a metabolite's measured concentration, and it is well known that ignoring either of these complications can…
Background and objective: Cell migration is essential for many biological phenomena with direct impact on human health and disease. One conventional approach to study cell migration involves the quantitative analysis of individual cell…
Synthetic tabular data is used for privacy-preserving data sharing and data-driven model development. Its effectiveness, however, depends heavily on the used Tabular Data Synthesis (TDS) tool. Recent studies have shown that…
The integration of spatial multi-omics data from single tissues is crucial for advancing biological research. However, a significant data imbalance impedes progress: while spatial transcriptomics data is relatively abundant, spatial…
Compound identification from tandem mass spectrometry (MS/MS) data is a critical step in the analysis of complex mixtures. Typical solutions for the MS/MS spectrum to compound (MS2C) problem involve comparing the unknown spectrum against a…
Proteomic matrix-assisted laser desorption/ionisation (MALDI) linear time-of-flight (TOF) mass spectrometry (MS) may be used to produce protein profiles from biological samples with the aim of discovering biomarkers for disease. However,…
Domain adaptation (DA) is an important technique for modern machine learning-based medical data analysis, which aims at reducing distribution differences between different medical datasets. A proper domain adaptation method can…
Multiplexed imaging data are revolutionizing our understanding of the composition and organization of tissues and tumors. A critical aspect of such tissue profiling is quantifying the spatial relationship relationships among cells at…
Mammalian cells have about 30,000-fold more protein molecules than mRNA molecules. This larger number of molecules and the associated larger dynamic range have major implications in the development of proteomics technologies. We examine…
The Connectivity Map (CMap) is a large publicly available database of cellular transcriptomic responses to chemical and genetic perturbations built using a standardized acquisition protocol known as the L1000 technique. Databases such as…
X-ray absorption spectroscopy (XAS) is a powerful technique to probe the electronic and structural properties of materials. With the rapid growth in both the volume and complexity of XAS datasets driven by advancements in synchrotron…
Shotgun proteomics is a high-throughput technology used to identify unknown proteins in a complex mixture. At the heart of this process is a prediction task, the spectrum identification problem, in which each fragmentation spectrum produced…