Alexander Ullrich

Alexander Ullrich
Robert Koch Institut | RKI · Department for Infectious Disease Epidemiology

Dr. rer nat

About

37
Publications
4,494
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740
Citations
Introduction
I work in public health, especially infectious disease surveillance on developing outbreak detection systems. I used to study the spatio-temporal mechanisms of neuronal signalling processes using particle-based reaction-diffusion simulations as this is an appropriate choice given the highly coordinated nature of neurotransmission as well as the availability of single-molecule resolved experimental data from super-resolution microscopy.
Additional affiliations
October 2011 - present
Freie Universität Berlin
Position
  • Computational Molecular Biology
November 2008 - September 2011
University of Leipzig
February 2008 - October 2008
University of Vienna

Publications

Publications (37)
Article
Full-text available
Background The COVID-19 pandemic expanded the need for timely information on acute respiratory illness at population level. Aim We explored the potential of routine emergency department data for syndromic surveillance of acute respiratory illness in Germany. Methods We used routine attendance data from emergency departments, which continuously tr...
Article
German national surveillance data analysis shows that hospitalisation odds associated with Omicron lineage BA.1 or BA.2 infections are up to 80% lower than with Delta infection, primarily in ≥ 35-year-olds. Hospitalised vaccinated Omicron cases’ proportions (2.3% for both lineages) seemed lower than those of the unvaccinated (4.4% for both lineages...
Preprint
Background: During the COVID-19 pandemic and associated public health and social measures, decreasing patient numbers have been described in various healthcare settings in Germany, including emergency care. This could be explained by changes in disease burden, e.g. due to contact restrictions, but could also be a result of changes in utilization be...
Article
Background Utilising national surveillance data, we investigated the impact of the COVID-19 immunisation campaign on COVID-19 morbidity and mortality between December/2020 and October/2021 in Germany. Methods We compared patterns in immunisation coverage, incidence, hospitalisations, and deaths among 12-17, 18-59, and 60+ year-olds and examined th...
Article
Full-text available
Zusammenfassung Hintergrund Die Häufigkeit von Suizidversuchen ist ein zentraler Indikator der psychischen Gesundheit der Bevölkerung und daher Gegenstand der Mental Health Surveillance am Robert Koch-Institut. Da bisher keine Datenquellen systematisch zur kontinuierlichen Erfassung von psychiatrischen Notfällen – zu denen Suizidversuche zählen –...
Preprint
Full-text available
We report on the second and final part of a pre-registered forecasting study on COVID-19 cases and deaths in Germany and Poland. Fifteen independent research teams provided forecasts at lead times of one through four weeks from January through mid-April 2021. Compared to the first part (October--December 2020), the number of participating teams inc...
Preprint
Full-text available
Introduction: To better assess the epidemiological situation of acute respiratory illness in Germany over time, we used emergency department data for syndromic surveillance before and during the COVID-19 pandemic. Methods: We included routine attendance data from emergency departments who continuously transferred data between week 10-2017 and 10-20...
Article
Full-text available
Disease modelling has had considerable policy impact during the ongoing COVID-19 pandemic, and it is increasingly acknowledged that combining multiple models can improve the reliability of outputs. Here we report insights from ten weeks of collaborative short-term forecasting of COVID-19 in Germany and Poland (12 October–19 December 2020). The stud...
Article
Full-text available
Background The COVID-19 pandemic and associated non-pharmaceutical interventions (NPIs) affect healthcare seeking behaviour, access to healthcare, test strategies, disease notification and workload at public health authorities, but may also lead to a true change in transmission dynamics. We aimed to assess the impact of the pandemic and NPIs on oth...
Article
Full-text available
As of December 31, 2019, initial reports circulated internationally of an unusual cluster of pneumonia of unknown cause in China. By the end of January 2020, the virus affected Germany with the first case confirmed on January 27, 2020. Intensive contact tracing and infection control measures contained the first two clusters in the country. However,...
Preprint
Full-text available
We report insights from ten weeks of collaborative COVID-19 forecasting for Germany and Poland (12 October – 19 December 2020). The study period covers the onset of the second wave in both countries, with tightening non-pharmaceutical interventions (NPIs) and subsequently a decay (Poland) or plateau and renewed increase (Germany) in reported cases....
Article
Full-text available
According to the World Health Organization (WHO), around 60% of all outbreaks are detected using informal sources. In many public health institutes, including the WHO and the Robert Koch Institute (RKI), dedicated groups of public health agents sift through numerous articles and newsletters to detect relevant events. This media screening is one imp...
Article
Full-text available
In this paper, a simple yet interpretable, probabilistic model is proposed for the prediction of reported case counts of infectious diseases. A spatio-temporal kernel is derived from training data to capture the typical interaction effects of reported infections across time and space, which provides insight into the dynamics of the spread of infect...
Preprint
Full-text available
According to the World Health Organization (WHO), around 60% of all outbreaks are detected using informal sources. In many public-health institutes, including the WHO and the Robert Koch Institute (RKI), dedicated groups of epidemiologists sift through numerous articles and newsletters to detect relevant events. This media screening is one importan...
Article
Full-text available
Objective Providing an integrative tool for public health experts to rapidly assess the epidemiological situation based on data streams from different surveillance systems and relevant external factors, e.g. weather or socio-economic conditions. The efficient implementation in a modular architecture of disease- or task-specific visualisations and i...
Article
Full-text available
Objective By systematically scoring algorithms and integrating outbreak data through statistical learning, evaluate and improve the performance of automated infectious-disease-outbreak detection. The improvements should be directly relevant to the epidemiological practice. A broader objective is to explore the usefulness of machine-learning approac...
Preprint
Full-text available
In this paper, a simple yet interpretable, probabilistic model is proposed for the prediction of reported case counts of infectious diseases. A spatio-temporal kernel is derived from training data to capture the typical interaction effects of reported infections across time and space, which provides insight into the dynamics of the spread of infect...
Article
Europe received an increased number of migrants in 2015. Housing in inadequate mass accommodations (MA) made migrants prone to infectious disease outbreaks. In order to enhance awareness for infectious diseases (ID) and to detect clusters early, we developed and evaluated a syndromic surveillance system in three MA with medical centres in Berlin, G...
Article
Full-text available
Clathrin-mediated endocytosis (CME) involves membrane-associated scaffolds of the bin-amphiphysin-rvs (BAR) domain protein family as well as the GTPase dynamin, and is accompanied and perhaps triggered by changes in local lipid composition. How protein recruitment, scaffold assembly and membrane deformation is spatiotemporally controlled and couple...
Article
Full-text available
Author Summary For the communication between two nerve cells, a synaptic vesicle containing neurotransmitters has to fuse with the neuronal membrane at a specific fusion site, releasing its signaling molecules. The vesicle fusion is mediated by a specific family of proteins (SNAREs) that are located on the vesicle as well as on the neuronal membra...
Article
Full-text available
ReaDDy is a modular particle simulation package combining off-lattice reaction kinetics with arbitrary particle interaction forces. Here we present a graphical processing unit implementation of ReaDDy that employs the fast multiplatform molecular dynamics package OpenMM. A speedup of up to two orders of magnitude is demonstrated, giving us access t...
Article
Full-text available
Particle-based reaction-diffusion algorithms facilitate the modeling of the diffusional motion of individual molecules and the reactions between them in cellular environments. A physically realistic model, depending on the system at hand and the questions asked, would require different levels of modeling detail such as particle diffusion, geometric...
Article
Full-text available
Clathrin mediated endocytosis (CME) is an ubiquitous cellular pathway that regulates central aspects of cell physiology such as nutrient uptake, modulation of signal transduction, synaptic transmission and membrane turn-over. Endocytic vesicle formation depends on the timed production of specific phosphoinositides and their interactions with variou...
Article
Phosphoinositides serve crucial roles in cell physiology, ranging from cell signalling to membrane traffic. Among the seven eukaryotic phosphoinositides the best studied species is phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2), which is concentrated at the plasma membrane where, among other functions, it is required for the nucleation of endocy...
Article
Full-text available
We developed a simulation tool for investigating the evolution of early metabolism, allowing us to speculate on the formation of metabolic pathways from catalyzed chemical reactions and on the development of their characteristic properties. Our model consists of a protocellular entity with a simple RNA-based genetic system and an evolving metabolis...
Article
Full-text available
BackgroundThe metabolic architectures of extant organisms share many key pathways such as the citric acid cycle, glycolysis, or the biosynthesis of most amino acids. Several competing hypotheses for the evolutionary mechanisms that shape metabolic networks have been discussed in the literature, each of which finds support from comparative analysis...
Conference Paper
Full-text available
We extend our previous work on the exploration of static metabolic networks to evolving, and therefore dynamic, pathways. We apply our visualization software to data from a simulation of early metabolism. Thereby, we show that our technique allows us to test and argue for or against different scenarios for the evolution of metabolic pathways. This...
Article
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One important aspect of computational systems biol-ogy includes the identification and analysis of functional response networks within large biochemical networks. These functional response networks represent the response of a biological system under a particular experimental condition which can be used to pinpoint critical biological processes. For...
Conference Paper
Full-text available
We introduce a novel genotype-phenotype mapping based on the relation between RNA sequence and its secondary structure for the use in evolutionary studies. Various extensive studies concerning RNA folding in the context of neutral theory yielded insights about properties of the structure space and the mapping itself. We intend to get a better under...
Conference Paper
Full-text available
The origin and evolution of metabolism is an interesting field of research with many unsolved questions. Simulation approaches, even though mostly very abstract and specific, have proven to be helpful in explaining properties and behavior observed in real world metabolic reaction networks, such as the occurrence of hub-metabolites. We propose here...

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