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Proteomics

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Knowledge-Based Analysis for Detecting Key Signaling Events from Time-Series Phosphoproteomics Data.

PLoS computational biology
Cell signaling underlies transcription/epigenetic control of a vast majority of cell-fate decisions. A key goal in cell signaling studies is to identify the set of kinases that underlie key signaling events. In a typical phosphoproteomics study, phos...

ProCon - PROteomics CONversion tool.

Journal of proteomics
With the growing amount of experimental data produced in proteomics experiments and the requirements/recommendations of journals in the proteomics field to publicly make available data described in papers, a need for long-term storage of proteomics d...

Machine learning reveals sex-specific 17β-estradiol-responsive expression patterns in white perch (Morone americana) plasma proteins.

Proteomics
With growing abundance and awareness of endocrine disrupting compounds (EDCs) in the environment, there is a need for accurate and reliable detection of EDC exposure. Our objective in the present study was to observe differences within and between th...

Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study.

Database : the journal of biological databases and curation
The evidence that two molecules interact in a living cell is often inferred from multiple different experiments. Experimental data is captured in multiple repositories, but there is no simple way to assess the evidence of an interaction occurring in ...

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data.

BMC genomics
BACKGROUND: Investigations into novel biomarkers using omics techniques generate large amounts of data. Due to their size and numbers of attributes, these data are suitable for analysis with machine learning methods. A key component of typical machin...

Functional annotation and biological interpretation of proteomics data.

Biochimica et biophysica acta
Proteomics experiments often generate a vast amount of data. However, the simple identification and quantification of proteins from a cell proteome or subproteome is not sufficient for the full understanding of complex mechanisms occurring in the bio...

[Serum proteomics and machine learning unveil new diagnostic biomarkers for tuberculosis in adolescents and young adults].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Adolescents and young adults (AYAs) are one of the major populations susceptible to tuberculosis. However, little is known about the unique characteristics and diagnostic biomarkers of tuberculosis in this population. In this study, 81 AYAs were recr...

Graph neural networks for single-cell omics data: a review of approaches and applications.

Briefings in bioinformatics
Rapid advancement of sequencing technologies now allows for the utilization of precise signals at single-cell resolution in various omics studies. However, the massive volume, ultra-high dimensionality, and high sparsity nature of single-cell data ha...