Journal Article - page 3

Image-based computational quantification and visualization of genetic alterations and tumour heterogeneity

Recent large-scale genome analyses of human tissue samples have uncovered a high degree of genetic alterations and tumour heterogeneity in most tumour entities, independent of morphological phenotypes and histopathological characteristics. Assessment of genetic copy-number variation (CNV) and tumour heterogeneity by fluorescence in situ hybridization (ISH) provides additional tissue morphology at single-cell resolution, but it is labour intensive with limited throughput and high inter-observer variability. We present an integrative method combining bright-field dual-colour chromogenic and silver ISH assays with an image-based...

Active learning based segmentation of Crohns disease from abdominal MRI

Prediction of colorectal cancer diagnosis based on circulating plasma proteins

Non‐invasive detection of colorectal cancer with blood‐based markers is a critical clinical need. Here we describe a phased mass spectrometry‐based approach for the discovery, screening, and validation of circulating protein biomarkers with diagnostic value. Initially, we profiled human primary tumor tissue epithelia and characterized about 300 secreted and cell surface candidate glycoproteins. These candidates were then screened in patient systemic circulation to identify detectable candidates in blood plasma. An 88‐plex targeting method was established to systematically monitor these proteins in...

Inversion of hierarchical Bayesian models using Gaussian processes

Inferring causal metabolic signals that regulate the dynamic TORC1-dependent transcriptome

Cells react to nutritional cues in changing environments via the integrated action of signaling, transcriptional, and metabolic networks. Mechanistic insight into signaling processes is often complicated because ubiquitous feedback loops obscure causal relationships. Consequently, the endogenous inputs of many nutrient signaling pathways remain unknown. Recent advances for system‐wide experimental data generation have facilitated the quantification of signaling systems, but the integration of multi‐level dynamic data remains challenging. Here, we co‐designed dynamic experiments and a probabilistic, model‐based method to infer causal...

Crowdsourcing the creation of image segmentation algorithms for connectomics

To stimulate progress in automating the reconstruction of neural circuits, we organized the first international challenge on 2D segmentation of electron microscopic (EM) images of the brain. Participants submitted boundary maps predicted for a test set of images, and were scored based on their agreement with a consensus of human expert annotations. The winning team had no prior experience with EM images, and employed a convolutional network. This “deep learning” approach has since become accepted as a standard for segmentation...

Automatic single cell segmentation on highly multiplexed tissue images

Asymptotic analysis of estimators on multi-label data

Multi-label classification extends the standard multi-class classification paradigm by dropping the assumption that classes have to be mutually exclusive, i.e., the same data item might belong to more than one class. Multi-label classification has many important applications in e.g. signal processing, medicine, biology and information security, but the analysis and understanding of the inference methods based on data with multiple labels are still underdeveloped. In this paper, we formulate a general generative process for multi-label data, i.e. we associate each...

A model-based approach to predicting graduate-level performance using indicators of undergraduate-level performance

Prostate MRI Segmentation Using Learned Semantic Knowledge and Graph Cuts