Biology subjects

Hennig, H.

Publications and source records attributed to Hennig, H..

3 recordsLinked to original sources

bioRxiv2024

Morphological map of under- and over-expression of genes in human cells

Cell Painting images offer valuable insights into a cells state and enable many biological applications, but publicly available arrayed datasets only include hundreds of genes perturbed. The JUMP (Joint Undertaking in Morphological Profiling) Cell Painting Consortium perturbed roughly 75% of the protein-coding genome in human U-2 OS cells, generating a rich resource of single-cell images and extracted features. These profiles capture the phenotypic impacts of perturbing 15,243 human genes, including overexpressing 12,609 genes (using open reading frames, ORFs) and knocking out 7,975 genes (using CRISPR-Cas9). We mitigated technical artifacts by rigorously evaluating data processing options and validated the datasets robustness and biological relevance. Analysis of phenotypic profiles revealed novel gene clusters and functional relationships, including those associated with mitochondrial function, cancer, and neural processes. The JUMP Cell Painting genetic dataset is a valuable resource for exploring gene relationships and uncovering novel functions.

bioinformatics↗

bioRxiv2018

Label-free assessment of red blood cell storage lesions by deep learning

Blood transfusion is a life-saving clinical procedure. With millions of units needed globally each year, it is a growing concern to improve product quality and recipient outcomes.\n\nStored red blood cells (RBCs) undergo continuous degradation, leading to structural and biochemical changes. To analyze RBC storage lesions, complex biochemical and biophysical assays are often employed.\n\nWe demonstrate that label-free imaging flow cytometry and deep learning can characterize RBC morphologies during 42-day storage, replacing the current practice of manually quantifying a blood smear from stored blood units. Based only on bright field and dark field images, our model achieved 90% accuracy in classifying six different RBC morphologies associated with storage lesions versus human-curated manual examination. A model fitted to the deep learning-extracted features revealed a pattern of morphological changes within the aging blood unit that allowed predicting the expiration date of stored blood using solely morphological assessment.\n\nDeep learning and label-free imaging flow cytometry could therefore be applied to reduce complex laboratory procedures and facilitate robust and objective characterization of blood samples.

bioinformatics↗

bioRxiv2017

Revisiting the General Concept of Network Centralities: A Propose for Centrality Analysis in Network Science

BackgroundNumerous centrality measures have been introduced to identify \"central\" nodes in large networks. The availability of a wide range of measures for ranking influential nodes leaves the user to decide which measure may best suit the analysis of a given network. The choice of a suitable measure is furthermore complicated by the impact of the network topology on ranking influential nodes by centrality measures. To approach this problem systematically, we examined the centrality profile of nodes of yeast protein-protein interaction networks (PPINs) in order to detect which centrality measure is succeeding in predicting influential proteins. We studied how different topological network features are reflected in a large set of commonly used centrality measures.\n\nResultsWe used yeast PPINs to compare 27 common of centrality measures. The measures characterize and assort influential nodes of the networks. We applied principal component analysis (PCA) and hierarchical clustering and found that the most informative measures depend on the networks topology. Interestingly, some measures had a high level of contribution in comparison to others in all PPINs, namely Latora closeness, Decay, Lin, Freeman closeness, Diffusion, Residual closeness and Average distance centralities.\n\nConclusionsThe choice of a suitable set of centrality measures is crucial for inferring important functional properties of a network. We concluded that undertaking data reduction using unsupervised machine learning methods helps to choose appropriate variables (centrality measures). Hence, we proposed identifying the contribution proportions of the centrality measures with PCA as a prerequisite step of network analysis before inferring functional consequences, e.g., essentiality of a node.

systems biology↗