Piotr Grabowski

Piotr Grabowski
AstraZeneca | AZ

Doctor of Philosophy

About

28
Publications
1,891
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218
Citations
Citations since 2016
27 Research Items
218 Citations
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20162017201820192020202120220102030405060
20162017201820192020202120220102030405060
20162017201820192020202120220102030405060

Publications

Publications (28)
Article
Full-text available
The mechanisms of coordinated changes in proteome composition and their relevance for the differentiation of neutrophil granulocytes are not well studied. Here, we discover two novel human genetic defects in SRPRA and SRP19, constituents of the mammalian co-translational targeting machinery and characterize their role in neutrophil granulocyte diff...
Preprint
Full-text available
Artificial intelligence recently experienced a renaissance with the advancement of convolutional neural networks (CNNs). CNNs require spatially meaningful matrices (e.g., image data) with recurring patterns, limiting its applicability to high-throughput omics data. We present GIM, a simple, CNN-ready framework for omics data to detect both individu...
Preprint
Full-text available
High dimensionality omics and hyperspectral imaging datasets present difficult challenges for feature extraction and data mining due to huge numbers of features that cannot be simultaneously examined. The sample numbers and variables of these methods are constantly growing as new technologies are developed, and computational analysis needs to evolv...
Article
Background Novel computational algorithms for multi-omics analysis bear great potential to highlight pathomechanisms of monogenic diseases. We recently defined the in-depth proteome of primary human neutrophil granulocytes (PMID 30630937). Here, we ask the question whether proteotypic patterns differ between defined genetic subtypes associated with...
Article
Full-text available
Neutrophil granulocyte play pivotal roles in inflammatory responses, immune defence, tissue remodeling, and cancer control. Studying rare patients with defects in differentiation and/or function of neutrophil granulocytes highlights genes and pathways orchestrating these important cellular functions. A previously not appreciated role of the signal...
Article
Full-text available
Assigning functions to the vast array of proteins present in eukaryotic cells remains challenging. To identify relationships between proteins, and thereby enable functional annotation of proteins, we determined changes in abundance of 10,323 human proteins in response to 294 biological perturbations using isotope-labeling mass spectrometry. We appl...
Preprint
Full-text available
The annotation of protein function is a longstanding challenge of cell biology that suffers from the sheer magnitude of the task. Here we present ProteomeHD, which documents the response of 10,323 human proteins to 294 biological perturbations, measured by isotope-labelling mass spectrometry. Using this data matrix and robust machine learning we cr...
Preprint
Full-text available
Gene co-expression analysis is a widespread method to identify the potential biological function of uncharacterised genes. Recent evidence suggests that proteome profiling may provide more accurate results than transcriptome profiling. However, it is unclear which statistical measure is best suited to detect proteins that are co-regulated. We have...
Article
Full-text available
Neutrophil granulocytes are critical mediators of innate immunity and tissue regeneration. Rare diseases of neutrophil granulocytes may affect their differentiation and/or functions. However, there are very few validated diagnostic tests assessing the functions of neutrophil granulocytes in these diseases. Here, we set out to probe omics analysis a...
Article
Full-text available
High-throughput methodologies and machine learning have been central in developing systems-level perspectives in molecular biology. Unfortunately, performing such integrative analyses has traditionally been reserved for bioinformaticians. This is now changing with the appearance of resources to help bench-side biologists become skilled at computati...
Article
Background and objective Neutrophil granulocytes (NG) are critical mediators of innate immunity and tissue regeneration. Few monogenic diseases affecting their differentiation and/or function have been described, yet a systems-biology perspective has not yet been opened. We set out to define the proteome and transcriptome of NG from healthy individ...
Article
Full-text available
Genes are often co-expressed with their genomic neighbors, even if these are functionally unrelated. For small expression changes driven by genetic variation within the same cell type, non-functional mRNA co-expression is not propagated to the protein level. However, it is unclear if protein levels are also buffered against any non-functional mRNA...
Article
Full-text available
Genes are not randomly distributed in the genome. In humans, 10% of protein-coding genes are transcribed from bidirectional promoters and many more are organised in larger clusters. Intriguingly, neighbouring genes are frequently coexpressed but rarely functionally related. Here we show that coexpression of bidirectional gene pairs, and closeby gen...
Article
Full-text available
Subcellular localisation is an important aspect of protein function, but the protein composition of many intracellular compartments is poorly characterised. For example, many nuclear bodies are challenging to isolate biochemically and thus remain inaccessible to proteomics. Here we explore covariation in proteomics data as an alternative route to s...

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