Journal of proteome research
Jun 10, 2022
In their recent review ( 2022, 21 (4), 849-864), Crook et al. diligently discuss the basics (and less basics) of Bayesian modeling, survey its various applications to proteomics, and highlight its potential for the improvement of computational prote...
Science (New York, N.Y.)
Jun 10, 2022
INTRODUCTION The eukaryotic nucleus pro-tects the genome and is enclosed by the two membranes of the nuclear envelope. Nuclear pore complexes (NPCs) perforate the nuclear envelope to facilitate nucleocytoplasmic transport. With a molecular weight of ...
Analytical chemistry
May 24, 2022
Peptide fragmentation spectra contain critical information for the identification of peptides by mass spectrometry. In this study, we developed an algorithm that more accurately predicts the high-intensity peaks among the peptide spectra. The trainin...
Analytical chemistry
May 12, 2022
The prediction of fragment ion intensities and retention time of peptides has gained significant attention over the past few years. However, the progress shown in the accurate prediction of such properties focused primarily on unlabeled peptides. Tan...
Molecules (Basel, Switzerland)
May 8, 2022
Humans are exposed to numerous compounds daily, some of which have adverse effects on health. Computational approaches for modeling toxicological data in conjunction with machine learning algorithms have gained popularity over the last few years. Mac...
Journal of proteome research
Apr 12, 2022
Machine learning has been an integral part of interpreting data from mass spectrometry (MS)-based proteomics for a long time. Relatively recently, a machine-learning structure appeared successful in other areas of bioinformatics, Transformers. Furthe...
Immunology letters
Apr 2, 2022
Mass spectrometry proteomics has become an important part of modern immunology, making major contributions to understanding protein expression levels, subcellular localizations, posttranslational modifications, and interactions in various immune cell...
Proceedings of the National Academy of Sciences of the United States of America
Mar 11, 2022
SignificanceDeep profiling of the plasma proteome at scale has been a challenge for traditional approaches. We achieve superior performance across the dimensions of precision, depth, and throughput using a panel of surface-functionalized superparamag...
Journal of proteome research
Mar 8, 2022
Proteomics is a data-rich science with complex experimental designs and an intricate measurement process. To obtain insights from the large data sets produced, statistical methods, including machine learning, are routinely applied. For a quantity of ...
Journal of molecular biology
Mar 5, 2022
Proteome-wide identification of protein-protein interactions is a formidable task which has yet to be sufficiently addressed by experimental methodologies. Many computational methods have been developed to predict proteome-wide interaction networks, ...