Stefan Rödiger

Stefan Rödiger
Faculty of Health Sciences Brandenburg, Brandenburg University of Technology Cottbus -Senftenberg

PD Dr.

About

132
Publications
45,289
Reads
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1,953
Citations
Additional affiliations
October 2019 - present
Faculty of Health Sciences, joint Faculty of the Brandenburg University of Technology Cottbus – Senftenberg, the Brandenburg Medical School Theodor Fontane and the University of Potsdam, Berlin, Germany
Position
  • Group Leader
December 2017 - present
University of Surrey
Position
  • Group Leader
June 2017 - present
Brandenburg University of Technology Cottbus - Senftenberg
Position
  • Bioinformatician
Description
  • Applied Statistical Bioinformatics and Digital Image Analysis for Forensics

Publications

Publications (132)
Article
Full-text available
Background The CRISPR/Cas9 technology is nowadays a common tool for genome editing to achieve new insights into, for example, diagnostics and therapeutics in cancer and genetic disorders. Cell proliferation and anticancer drug response studies are widely used to evaluate the impact of editing. However, these assays are often time‐consuming, expensi...
Article
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The transition to sustainable electronics necessitates both resource conservation in hardware production and shifts in software usage. This paper investigates the contribution of Free/Libre Open-Source Software (FLOSS) towards fair, and conflict-free practices through promoting collaboration, transparency, and resource accessibility. Our study inv...
Article
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Neurodegenerative diseases (ND) are characterized by abnormalities within neurons of the brain or spinal cord that gradually lose function, eventually leading to cell death. Upon examination of affected tissue, pathological changes reveal a loss of synapses, misfolded proteins, and activation of immune cells-all indicative of disease progression- b...
Article
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NanoString nCounter is a medium-throughput technology used in mRNA and miRNA differential expression studies. It offers several advantages, including the absence of an amplification step and the ability to analyze low-grade samples. Despite its considerable strengths, the popularity of the nCounter platform in experimental research stabilized in 20...
Conference Paper
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Lens epithelium-derived growth factor-splice variant of 75kDa (LEDGF/p75) is an autoantigen over-expressed in solid tumors and acts as a stress-related transcriptional co-activator. Autoimmunity to LEDGF/p75 in the form of autoantibodies (autoAbs) against LEDGF/p75 has been shown in various diseases such as prostate cancer (PCa) and in healthy indi...
Article
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Multidrug-resistant gram-negative pathogens such as Escherichia coli have become increasingly difficult to treat and therefore alternative treatment options are needed. Targeting virulence factors like biofilm formation could be one such option. Inhibition of biofilm-related structures like curli and cellulose formation in E. coli has been shown fo...
Article
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Lens epithelium-derived growth factor splice variant of 75 kDa (LEDGF/p75) is an au- toantigen over-expressed in solid tumors and acts as a stress-related transcriptional co-activator. Participation of autoimmune responses in the pathophysiology of benign prostatic hyperplasia (PBH) and a corresponding immunosuppressive therapy by TNFalpha antagoni...
Preprint
Background Lipids and amphiphilic molecules are ubiquitous and play a central role in cell signalling, cell membrane structure, and lipid transport in the human body. However, they also appear in many diseases such as atherosclerosis, cardiovascular diseases, infections, inflammatory diseases, cancer, and autoimmune diseases. Thus, it is necessary...
Article
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Glycoprotein 2 (GP2) is an autoantigen in Crohn's (CD) and coeliac disease (CeD). We assessed GP2-isoform (GP21–4)-expression in intestinal biopsies of paediatric patients with CD, CeD, ulcerative colitis (UC), and healthy children (HC). Transcription of GP21–4 was elevated in proximal small intestine in CeD and CD patients (only GP22/4) compared t...
Article
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The discovery that certain diseases have specific miRNA signatures which correspond to disease progression opens a new biomarker category. The detection of these small non-coding RNAs is performed routinely using body fluids or tissues with real-time PCR, next-generation sequencing, or amplification-based miRNA assays. Antibody-based detection syst...
Article
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A highly sensitive detection of anti-neutrophil cytoplasmic antibodies to serine proteinase-3 (PR3-ANCAs) aids in the serological diagnosis of autoimmune liver disorders and the prediction of severity in primary sclerosing cholangitis (PSC). Here, we evaluate a novel third-generation ELISA for the detection of PR3-ANCAs. In total, 309 patients with...
Article
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Antimicrobial peptides (AMPs) are a heterogeneous group of short polypeptides that target not only microorganisms but also viruses and cancer cells. Due to their lower selection for resistance compared with traditional antibiotics, AMPs have been attracting the ever-growing attention from researchers, including bioinformaticians. Machine learning r...
Article
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Neural networks for deep-learning applications, also called artificial neural networks, are important tools in science and industry. While their widespread use was limited because of inadequate hardware in the past, their popularity increased dramatically starting in the early 2000s when it became possible to train increasingly large and complex ne...
Article
Full-text available
The discovery that certain diseases have specific miRNA signatures which correspond to disease progression opens a new biomarker category. The detection of these small non-coding RNAs is performed routinely using body fluids or tissues with real-time PCR, next-generation sequencing, or amplification-based miRNA assays. Antibody-based detection syst...
Preprint
Full-text available
Antimicrobial peptides (AMPs) are a heterogeneous group of short polypeptides that target microorganisms but also viruses and cancer cells. Due to their lower selection for resistance compared to traditional antibiotics, AMPs have been attracting the ever-growing attention from researchers, including bioinformaticians. Machine learning represents t...
Article
Full-text available
CITATIONS 0 READS 129 60 authors, including: Some of the authors of this publication are also working on these related projects: SafeConsume View project O perfil epidemiológico e demográfico dos pacientes com tumor da cabeça e pescoço HPV16+ numa instituição oncológica em Portugal View project
Article
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Background Through continuous innovation and improvement, Nanopore sequencing has become a powerful technology. Because of its fast processing time, low cost, and ability to generate long reads, this sequencing technique would be particularly suitable for clinical diagnostics. However, its raw data accuracy is inferior in contrast to other sequenci...
Article
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Pathogenic bacteria, such as enteropathogenic (EPEC) and enterotoxigenic Escherichia coli (ETEC), cause diarrhea in mammals. In particular, E. coli colonize and infect the gastrointestinal tract via type 1 fimbriae (T1F). Here the major zymogen granule membrane glycoprotein 2 (GP2) acts as host cell receptor. GP2 is also secreted by the pancreas an...
Article
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For improving aptamer-ligand binding we have developed a screening system that defines optimal binding buffer composition. Using multiplex assays, one buffer system is needed which guarantees the specific binding of all aptamers. We investigated nine peer-reviewed DNA aptamers. Non-specific binding of aptamers is an obstacle. To address this, we in...
Article
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Shortages of reverse transcriptase (RT)-polymerase chain reaction (PCR) reagents and related equipment during the COVID-19 pandemic have demonstrated the need for alternative, high-throughput methods for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-mass screening in clinical diagnostic laboratories. A robust, SARS-CoV-2 RT-loop-medi...
Article
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Background: Laboratory diagnosis of Lyme borreliosis refers to some methods with known limitations. Molecular diagnostics using specific nucleic acid probes may overcome some of these limitations. Methods: We describe the novel reporter fluorescence real-time polymerase chain reaction (PCR) probe system LoopTag for detection of Borrelia species....
Article
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To study host-virus interactions after SARS coronavirus-2 (SARS-CoV-2) infection, genetic virus characteristics and the ensued humoral immune response were investigated for the first time. Fifty-five SARS-CoV-2-infected patients from the early pandemic phase were followed up including serological testing and whole genome sequencing. Anti-spike and...
Article
Rheumatoid arthritis (RA) belongs to the most often occurring autoimmune diseases in the world. For serological diagnosis, IgM auto-antibodies directed against the Fc portion of IgG referred to as rheumatoid factor are used as biomarkers. The autoantibody detection is usually done by ELISA. Such assays are reliable but are not suitable for point-of...
Article
Full-text available
Lens epithelium-derived growth factor splice variant of 75 kDa (LEDGF/p75) plays an important role in cancer, but its DNA-damage repair (DDR)-related implications are still not completely understood. Different LEDGF model cell lines were generated: a complete knock-out of LEDGF (KO) and re-expression of LEDGF/p75 or LEDGF/p52 using CRISPR/Cas9 tech...
Article
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Background: DNA double-strand breaks can be counted as discrete foci by imaging techniques. In personalized medicine and pharmacology, the analysis of counting data is relevant for numerous applications, e.g., for cancer and aging research and the evaluation of drug efficacy. By default, it is assumed to follow the Poisson distribution. This assum...
Preprint
Background MicroRNAs (miRNAs) are small, conserved, noncoding RNAs regulating gene expression that functions in RNA silencing and post-transcriptional regulation of gene expression. Altered miRNA profiles have been implicated in many human diseases, and due to their circulating abilities, they have excited great interest in their use as clinical bi...
Article
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To increase our understanding of bacterial intestinal colonization in animal populations lacking substantial anthropogenic influence we studied the diversity of E. coli in cormorants from the pristine West-Mongolian steppe. E. coli were isolated from individual birds of two cormorant colonies located on small islands in lakes at least 100 km away f...
Article
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Digital PCR (dPCR) has developed considerably since the publication of the Minimum Information for Publication of Digital PCR Experiments (dMIQE) guidelines in 2013, with advances in instrumentation, software, applications, and our understanding of its technological potential. Yet these developments also have associated challenges; data analysis st...
Article
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Background In addition to the broad dissemination of pathogenic extended-spectrum beta-lactamase (ESBL)-producing Escherichia (E.) coli in human and veterinary medicine and the community, their occurrence in wildlife and the environment is a growing concern. Wild birds in particular often carry clinically relevant ESBL-producing E. coli. Objective...
Article
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Antimicrobial peptides (AMPs) are molecules widespread in all branches of the tree of life that participate in host defense and/or microbial competition. Due to their positive charge, hydrophobicity and amphipathicity, they preferentially disrupt negatively charged bacterial membranes. AMPs are considered an important alternative to traditional ant...
Article
Multidrug-resistant extended-spectrum beta lactamase (ESBL)-producing Escherichia coli strains are emerging globally in both humans and animals. Antimicrobial susceptibility testing and ESBL screening were performed on pure cultures of 216 E. coli isolates from human and animal fecal samples as well as beef. Polymerase chain reaction was performed...
Article
Biofilms cause complications and high costs in both industry and medicine. Of particular interest are bacterial infections of prosthetic materials, which usually cannot be eliminated due to the high antibiotic resistance known for bacteria forming biofilms. The search for new materials and coatings with lower colonization potential and antibacteria...
Article
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Antibodies are used in diagnostic tests, including enzyme-linked immunosorbent assay (ELISA) and protein arrays. They serve either as a detection molecule or target (e.g., autoantibodies). For point-of-care diagnostics it is important to develop efficient technologies for multiparametric antibody testing to simplify and accelerate the diagnostics....
Article
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The ratio between living and dead cells is an important parameter in microalgae culture and environmental monitoring. Fast, robust and automated analytical methods for monitoring microalgae growth for biotechnological and pharmaceutical applications and for optimizing production strains are needed. We developed a pipeline for the automatic binary c...
Article
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Zusammenfassung Der Beirat des Wissenschaftlichen Nachwuchses (GI-WiN) der Gesellschaft für Informatik (GI) fordert und empfiehlt Maßnahmen zur Verbesserung der Lage von Promovierenden sowie Postdoktoranden und Postdoktorandinnen in der Informatik und anderen Technikwissenschaften. Promovierende sowie Postdoktoranden und Postdoktorandinnen im Berei...
Article
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Background The enzyme-linked immunosorbent assay (ELISA) is an indispensable tool for clinical diagnostics to identify or differentiate diseases such as autoimmune illnesses, but also to monitor their progression or control the efficacy of drugs. One use case of ELISA is to differentiate between different states (e.g. healthy vs. diseased). Anothe...
Article
BACKGROUND:The 3D printing is relevant as a manufacturing technology of functional models for forensic, pharmaceutical and bioanalytical applications such as drug delivery systems, sample preparation and point-of-care tests. OBJECTIVE: Melting behavior and autofluorescence of materials are decisive for optimal printing and applicability of the pro...
Article
One of the most commonly used bonds between two biomolecules is the bond between biotin and streptavidin (SA) or streptavidin homologs (SAHs). A high dissociation constant and the consequent high-temperature stability even allows for its use in nucleic acid detection under PCR conditions. There are a number of SAHs available and for assay design, i...
Article
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The rapid and simultaneous detection of DNA and protein biomarkers is necessary to detect the outbreak of a disease or to monitor a disease. For example, cardiovascular diseases are a major cause of adult mortality worldwide. We have developed a rapidly adaptable platform to assess biomarkers using a microfluidic technology. Our model mimics autoan...
Article
Background In eukaryotic cells treated with chemotherapeutic drugs DNA double strand breaks (DSB) are the most severe form of DNA damage which usually leads to apoptotic cell death. Cytotoxic chemotherapy is still a mainstay of cancer therapy, but there are few established methods to individually predict efficacy and tolerability. In most regimens...
Article
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We evaluated prevalence and distribution of antibiotic resistant E. coli in three categories: animals (goats, pigs, poultry, cattle, sheep), humans (butchers, meat sellers, animal farm workers, buyers) and animal food products (milk, cheese, beef, chicken, yoghurt) from selected animal farms in South-West Nigeria. The biofilm formation, phylogroupi...
Article
Multiplex detection techniques are emerging within the fields of life science research and medical diagnostics where it is mandatory to analyze a great number of molecules. The detection techniques need to be highly efficient but often involve complicated and expensive fabrication procedures. Here, we present the immobilization and geometric separa...
Article
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DNA double-strand breaks (DSBs) are critical cellular lesions that represent a high risk for genetic instability. DSBs initiate repair mechanisms by recruiting sensor proteins and mediators. DSB biomarkers, like phosphorylated histone 2AX (γH2AX) and p53-binding protein 1 (53BP1), are detectable by immunofluorescence as either foci or distinct patt...
Article
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The DNA origami technique has great potential for the development of brighter and more sensitive reporters for fluorescence based detection schemes such as a microbead-based assay in diagnostic applications. The nanostructures can be programmed to include multiple dye molecules to enhance the measured signal as well as multiple probe strands to inc...
Preprint
Background: The analysis of biomedical samples requires multiplex measurement systems with which biomarkers can be sensitively detected. Preferably this should be possible without prior duplication or enrichment. We have developed an assay to quantify the binding of biomarkers to specific receptors of randomly arranged microparticles. We use a dire...
Preprint
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Background and Aims: There is an increasing incidence of inflammatory bowel disease [IBD]. Autoimmune responses are involved in the pathophysiology of IBD, but their underlying pathways and target antigens have not yet been fully elucidated. Methods: Autoantigenic targets in IBD were identified after separation of whole cell proteinsisolated from n...
Article
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Diffuse large B-cell lymphoma (DLBCL) is a highly aggressive form of non-Hodgkin’s lymphoma with a long-term survival rate of around 60% upon standard treatment with rituximab and chemotherapy. While this marks a great improvement over the pre-rituximab/pre-biologicals era, DLBCLs remain a heterogeneous disease with marked variability in clinical o...
Article
Quantitative analysis of a target molecule in a microbead-based fluorescent assay requires a specific labeling procedure. For nucleic acid analysis the hybridization with florescent labeled oligonucleotides is the most common method. However, disadvantages are the necessity for direct labeling of probes and the sensitivity to detect low amounts of...
Article
Full-text available
Amplification curves from quantitative Real-Time PCR experiments typically exhibit a sigmoidal shape. They can roughly be divided into a ground or baseline phase, an exponential amplification phase, a linear phase and finally a plateau phase, where in the latter, the PCR product concentration no longer increases. Nevertheless, in some cases the pla...
Article
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Bacterial host tropism is a primary determinant of the range of host organisms they can infect. Salmonella serotypes are differentiated into host-restricted and host-adapted specialists, and host-unrestricted generalists. In order to elucidate the underlying molecular mechanisms of host specificity in Salmonella infection, we investigated the role...
Conference Paper
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Introduction Infections by oncoviruses are an important risk factor for the development of neoplasms. Particularly, anogenital cancers are strongly associated with persistent infections by high-risk human papillomaviruses (HPV). In the case of cervical cancer the physical state of the virus seems to be an important prognostic marker. Especially the...
Poster
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Introduction Upper tract urothelial carcinoma (UTUC) is a rare malignancy in urinary system. In order to improve preoperative treatment choice and management of postoperative surveillance, identification of prognostic factors is necessarily required. To our knowledge, the elevation of systemic inflammatory markers may imply the development of an in...
Poster
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For the first time, we provide evidence that CHI3L1, overexpressed in enterocytes during inflammation of the large bowel and supporting the uptake of pathogenic intestinal bacteria, is a novel neutrophilic autoantigenic target in IBD. IgA and sIgA to CHI3L1 may serve as novel markers for CD and may facilitate the serological diagnosis of IBD.
Article
Background: DNA double strand breaks (DSBs) are the most severe form of DNA damage in eukaryotic cells treated with ionizing radiation or chemotherapeutic drugs. They can be quantitatively assessed by fluorescence imaging of phosphorylated histone protein H2AX (γH2AX), where the number of γH2AX foci represents the number of DNA DSB. Real-time asses...
Article
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Precision or personalized medicine is an aspiring but controversially discussed new paradigm in modern medicine. The individual variability of patients and their diverse responses to treatment options casts doubt on “one-fits-all” therapeutic strategies. Thus, biomarker-based stratification of patients into smaller cohorts is recommended. Indeed, t...
Article
Chemotherapy and radiation therapy are used in malignant oncological diseases to increase the level of DNA double strand breaks (DSBs) in tumor cells. Unrepaired DSBs may either kill a cell or induce terminal arrest. Those DNA damages can be detected by fluorescence imaging of phosphorylated histone protein H2AX (H2AX). Peripheral blood mononuclear...
Article
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Bacterial biofilm formation is a widespread phenomenon and a complex process requiring a set of genes facilitating the initial adhesion, maturation, and production of the extracellular polymeric matrix and subsequent dispersal of bacteria. Most studies on Escherichia coli biofilm formation have investigated nonpathogenic E. coli K-12 strains. Due t...
Poster
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Routine laboratory testing is connected with transport of samples and the testing schedule. Therefore, a time delay in obtaining test results could influence the decision for a clinical treatment. In rural areas or areas with limited laboratory equipment, Point-of-Care (POC) technologies could improve rapid diagnosis and monitoring of diseases [1]....
Poster
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Cardiovascular diseases are one of the main reasons for adult mortality in western world, leading to huge liability on healthcare system. Lifestyle, genetic disposition, deficiency of clearly defined risk assessment criteria, as well as high occurrences of misdiagnosis directly contribute to this issue [1,2]. Due to this fact a rapid and simultaneo...
Article
Full-text available
Amyloids are proteins associated with several clinical disorders, including Alzheimer’s, and Creutzfeldt-Jakob’s. Despite their diversity, all amyloid proteins can undergo aggregation initiated by short segments called hot spots. To find the patterns defining the hot spots, we trained predictors of amyloidogenicity, using n-grams and random forest...