Annika Röhl
A5026954665- Chronic Obstructive Pulmonary Disease (COPD) Research
- Neonatal Respiratory Health Research
- Childhood Cancer Survivors' Quality of Life
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- COVID-19 Clinical Research Studies
- SARS-CoV-2 and COVID-19 Research
- Enzyme Catalysis and Immobilization
- COVID-19 diagnosis using AI
- Biofuel production and bioconversion
- Advanced Proteomics Techniques and Applications
- Gene Regulatory Network Analysis
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- Fungal and yeast genetics research
- Congenital Diaphragmatic Hernia Studies
- Gene expression and cancer classification
- Asthma and respiratory diseases
- Sepsis Diagnosis and Treatment
- Genetic Associations and Epidemiology
- RNA modifications and cancer
- Eosinophilic Disorders and Syndromes
- Ubiquitin and proteasome pathways
- Long-Term Effects of COVID-19
Charité - Universitätsmedizin Berlin
2020-2023
The Francis Crick Institute
2022
Brigham and Women's Hospital
2019-2022
Harvard University
2019-2022
Freie Universität Berlin
2017-2019
COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. We characterized the time-dependent progression of disease 139 inpatients by measuring 86 accredited diagnostic parameters, such as blood cell counts enzyme activities, well untargeted plasma proteomes at 687 sampling points. report an initial spike a systemic inflammatory response, which gradually alleviated followed protein signature indicative tissue repair,...
Functional genomic strategies have become fundamental for annotating gene function and regulatory networks. Here, we combined functional genomics with proteomics by quantifying protein abundances in a genome-scale knockout library Saccharomyces cerevisiae, using data-independent acquisition mass spectrometry. We find that global expression is driven complex interplay of (1) general biological properties, including translation rate, turnover, the formation complexes, growth genome...
Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such SOFA APACHE II scores show only limited performance for predicting survival severely ill patients. Additional tools also needed monitor treatment, including experimental therapies clinical trials. Comprehensively capturing human physiology, we speculated that proteomics combination with new...
Constraint-based analysis has become a widely used method to study metabolic networks. While some of the associated algorithms can be applied genome-scale network reconstructions with several thousands reactions, others are limited small or medium-sized models. In 2015, Erdrich et al. introduced called NetworkReducer, which reduces large networks smaller subnetworks, while preserving set biological requirements that specified by user. Already in 2001, Burgard developed mixed-integer linear...
Summary Functional genomic strategies help to address the genotype phenotype problem by annotating gene function and regulatory networks. Here, we demonstrate that combining functional genomics with proteomics uncovers general principles of protein expression, provides new avenues annotate function. We recorded precise proteomes for all non-essential knock-outs in Saccharomyces cerevisiae. find abundance is driven a complex interplay i) biological properties, including translation rate,...
Abstract COVID-19 is highly variable in its clinical presentation, ranging from asymptomatic infection to severe organ damage and death. There an urgent need for predictive markers that can guide decision-making, inform about the effect of experimental therapies, point novel therapeutic targets. Here, we characterize time-dependent progression through different stages disease, by measuring 86 accredited diagnostic parameters plasma proteomes at 687 sampling points, a cohort 139 patients...
Chronic obstructive pulmonary disease (COPD) is a leading cause of death in adults that may have origins early lung development. It complex disease, influenced by multiple factors including genetic variants and environmental factors. Maternal smoking during pregnancy influence the risk for diseases adulthood, potentially through epigenetic modifications methylation.In this work, we explore fetal COPD utilizing DNA methylation marks associated with utero smoke (IUS) exposure, evaluate network...
Minimal cut sets (MCSs) for metabolic networks are of reactions which, if they removed from the network, prevent a target reaction carrying flux. To compute MCSs different methods exist, which may fail to find sufficiently many larger genome-scale networks.Here we introduce irreversible minimal (iMCSs). These that consist only. The advantage iMCSs is can be computed by projecting flux cone network on set reactions, usually leads smaller cone. Using oriented matroid theory, show how projected...
There is an acute need for advances in pharmacologic therapies and a better understanding of novel drug targets severe asthma. Imatinib, tyrosine kinase inhibitor, has been shown to improve forced expiratory volume 1 s (FEV1) clinical trial patients with In pilot study, we applied systems biology approaches epithelium gene expression from these treated imatinib understand lung function response treatment. Bronchial brushings ten imatinib-treated patient samples 14 placebo-treated were...
Abstract Global healthcare systems are challenged by the COVID-19 pandemic. There is a need to optimize allocation of treatment and resources in intensive care, as clinically established risk assessments such SOFA APACHE II scores show only limited performance for predicting survival severely ill patients. Comprehensively capturing host physiology, we speculated that proteomics combination with new data-driven analysis strategies could produce generation prognostic discriminators. We studied...
Abstract Understanding the connectivity patterns of genes in a localized disease neighborhood or module molecular interaction network (interactome) is key step toward advancing knowledge about mechanisms underlying complex disease. In this work, we introduce framework that detects peripheral and core regions human interactome. We leverage gene expression data on 104 diseases analyze differentially expressed (quantified by p-value < 0.05) their topological membership to distinguish between...
Abstract Metabolic network reconstructions are widely used in computational systems biology for silico studies of cellular metabolism. A common approach to analyse these models elementary flux modes (EFMs), which correspond minimal functional units the network. Already medium-sized networks, it is often impossible compute set all EFMs, due their huge number. From a practical point view, this might also not be necessary because subset EFMs may already sufficient answer relevant biological...