Stefan Solbrig
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View article: Integration of high-throughput proteomic data and complementary omics layers with PriOmics
Integration of high-throughput proteomic data and complementary omics layers with PriOmics Open
High-throughput bottom-up proteomic data cover thousands of proteins and related co- and post-translational modifications (CTMs/PTMs). Yet, it remains an open question how to holistically explore such data and their relationship to complem…
View article: Spatial Cellular Networks from omics data with SpaCeNet
Spatial Cellular Networks from omics data with SpaCeNet Open
Advances in omics technologies have allowed spatially resolved molecular profiling of single cells, providing a window not only into the diversity and distribution of cell types within a tissue, but also into the effects of interactions be…
View article: PriOmics: integration of high-throughput proteomic data with complementary omics layers using mixed graphical modeling with group priors
PriOmics: integration of high-throughput proteomic data with complementary omics layers using mixed graphical modeling with group priors Open
Mass spectrometry (MS)-based high-throughput proteomics data cover abundances of 1,000s of proteins and facilitate the study of co- and post-translational modifications (CTMs/PTMs) such as acetylation, ubiquitination, and phosphorylation. …
View article: SpaCeNet: Spatial Cellular Networks from omics data
SpaCeNet: Spatial Cellular Networks from omics data Open
Advances in omics technologies have allowed spatially resolved molecular profiling of single cells, providing a window not only into the diversity and distribution of cell types within a tissue, but also into the effects of interactions be…
View article: Grid on QPACE 4
Grid on QPACE 4 Open
In 2020 we deployed QPACE 4, which features 64 Fujitsu A64FX model FX700 processors interconnected by InfiniBand EDR. QPACE 4 runs an open-source software stack. For Lattice QCD simulations we ported the Grid LQCD framework to support the …
View article: BITES: Balanced Individual Treatment Effect for Survival data
BITES: Balanced Individual Treatment Effect for Survival data Open
Estimating the effects of interventions on patient outcome is one of the key aspects of personalized medicine. Their inference is often challenged by the fact that the training data comprises only the outcome for the administered treatment…
View article: Supplementary Material for: Evaluation of the Dementia Apraxia Test in Parkinson’s Disease Patients
Supplementary Material for: Evaluation of the Dementia Apraxia Test in Parkinson’s Disease Patients Open
Introduction: Ideomotor apraxia, a disorder of skilled movements affecting limbs and/or face, can be seen in patients with Parkinson’s disease (PD), yet tests of apraxia in PD are rare. The aim of this project was to evaluate the psychomet…
View article: Grid on QPACE 4
Grid on QPACE 4 Open
In 2020 we deployed QPACE 4, which features 64 Fujitsu A64FX model FX700 processors interconnected by InfiniBand EDR. QPACE 4 runs an open-source software stack. For Lattice QCD simulations we ported the Grid LQCD framework to support the …
View article: DTD: An R Package for Digital Tissue Deconvolution
DTD: An R Package for Digital Tissue Deconvolution Open
Digital tissue deconvolution (DTD) estimates the cellular composition of a tissue from its bulk gene-expression profile. For this, DTD approximates the bulk as a mixture of cell-specific expression profiles. Different tissues have differen…
View article: Modelling cancer progression using Mutual Hazard Networks
Modelling cancer progression using Mutual Hazard Networks Open
Motivation Cancer progresses by accumulating genomic events, such as mutations and copy number alterations, whose chronological order is key to understanding the disease but difficult to observe. Instead, cancer progression models use co-o…
View article: Lattice QCD on upcoming ARM architectures
Lattice QCD on upcoming ARM architectures Open
Recently Arm introduced a new instruction set called Scalable Vector Extension (SVE), which supports vector lengths up to 2048 bits. While SVE hardware will not be generally available until about 2021, we believe that future SVE-based arch…
View article: Modelling cancer progression using Mutual Hazard Networks
Modelling cancer progression using Mutual Hazard Networks Open
Motivation Cancer progresses by accumulating genomic events, such as mutations and copy number alterations, whose chronological order is key to understanding the disease but difficult to observe. Instead, cancer progression models use co-o…
View article: Fully integrative data analysis of NMR metabolic fingerprints with comprehensive patient data: a case report based on the German Chronic Kidney Disease (GCKD) study
Fully integrative data analysis of NMR metabolic fingerprints with comprehensive patient data: a case report based on the German Chronic Kidney Disease (GCKD) study Open
Omics data facilitate the gain of novel insights into the pathophysiology of diseases and, consequently, their diagnosis, treatment, and prevention. To that end, it is necessary to integrate omics data with other data types such as clinica…