Members » Maximilian Collatz

@article{nokey_89,

title = {AssayBLAST: A Bioinformatic Tool for In Silico Analysis of Molecular Multiparameter Assays},

author = {Maximilian Collatz and Sascha D. Braun and Martin Reinicke and Elke Müller and Stefan Monecke and Ralf Ehricht},

doi = {10.3390/applbiosci4020018},

year  = {2025},

date = {2025-04-01},

journal = {Applied Biosciences},

volume = {4},

abstract = {Accurate primer and probe design is essential for molecular applications, including PCR, qPCR, and molecular multiparameter assays like microarrays. The novel software tool AssayBLAST addresses this need by simulating interactions between oligonucleotides and target sequences. AssayBLAST handles large sets of primer and probe sequences simultaneously and supports comprehensive assay designs by allowing users to identify off-target binding, calculate melting temperatures, and ensure strand specificity, a critical but often overlooked aspect. AssayBLAST performs two optimized BLAST-based searches for each primer or probe sequence, checking the forward and reverse strands for off-target interactions and strand-specific binding accuracy. The results are compiled into a mapping table containing binding sites, mismatches, and strand orientation, allowing users to validate large sets of oligonucleotides across predefined custom databases for a complete and optimal theoretical assay design. AssayBLAST was evaluated against experimental Staphylococcus aureus microarray data, achieving 97.5% accuracy in predicting probe–target hybridization outcomes. This high accuracy demonstrates the method’s effectiveness in reliably using BLAST hits and mismatch counts to predict microarray results. AssayBLAST provides a reliable, scalable solution for in silico primer and probe validation, effectively supporting large-scale assay designs and optimizations. Its accurate prediction of hybridization outcomes demonstrates its utility in enhancing the efficiency and reliability of molecular assays.},

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@article{nokey_95,

title = {Multiplex Real-Time Polymerase Chain Reaction and Recombinase Polymerase Amplification: Methods for Quick and Cost-Effective Detection of Vancomycin-Resistant Enterococci (VRE)},

author = {Ibukun Elizabeth Osadare and Abdinasir Abdilahi and Martin Reinicke and Celia Diezel and Maximilian Collatz and Annett Reissig and Stefan Monecke and Ralf Ehricht},

doi = {10.3390/antibiotics14030295},

year  = {2025},

date = {2025-03-12},

journal = {Antibiotics},

volume = {14},

abstract = {Background/Objectives: Vancomycin-resistant enterococci (VRE) are one of the leading causes of antibiotic-resistant infections in the hospital setting worldwide, and this has become a major issue, because most patients infected with this strain are difficult to treat. Multiplex real-time polymerase chain reaction (RT PCR) is an advantageous technique that can amplify multiple targets in a single reaction, and can be used to quickly detect specific targets in VRE within two hours, starting from suspected colonies of bacterial cultures, without sample preparation. Methods: In this study, we selected the glycopeptide/vancomycin resistance genes that are most common in clinical settings, vanA and vanB, in combination with the species markers ddl_faecium and ddl_faecalis for the most common VRE species—Enterococcus faecium and Enterococcus faecalis. Results: DNA from forty clinical VRE strains was prepared using a fast and economic heat lysis method, and a multiplex real-time PCR assay was optimized and carried out subsequently. The results were in concordance with the results from recombinase polymerase amplification (RPA) of the same VRE samples. Conclusions: Multiplex RT PCR and RPA for VRE detection proffers a second method for the confirmation of vancomycin resistance, and it can be developed as a fast screening assay for patients before admission into high-risk settings.},

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@article{nokey_94,

title = {Fast and Economic Microarray-Based Detection of Species-, Resistance-, and Virulence-Associated Genes in Clinical Strains of Vancomycin-Resistant Enterococci (VRE)},

author = {Ibukun Elizabeth Osadare and Stefan Monecke and Abdinasir Abdilahi and Elke Müller and Maximilian Collatz and Sascha Braun and Annett Reissig and Wulf Schneider-Brachert and Bärbel Kieninger and Anja Eichner and Anca Rath and Jürgen Fritsch and Dominik Gary and Katrin Frankenfeld and Thomas Wellhöfer and Ralf Ehricht},

doi = {10.3390/s24196476},

year  = {2024},

date = {2024-10-08},

journal = {Sensors},

volume = {24},

abstract = {Today, there is a continuous worldwide battle against antimicrobial resistance (AMR) and that includes vancomycin-resistant enterococci (VRE). Methods that can adequately and quickly detect transmission chains in outbreaks are needed to trace and manage this problem fast and cost-effectively. In this study, DNA-microarray-based technology was developed for this purpose. It commenced with the bioinformatic design of specific oligonucleotide sequences to obtain amplification primers and hybridization probes. Microarrays were manufactured using these synthesized oligonucleotides. A highly parallel and stringent labeling and hybridization protocol was developed and employed using isolated genomic DNA from previously sequenced (referenced) clinical VRE strains for optimal sensitivity and specificity. Microarray results showed the detection of virulence, resistance, and species-specific genes in the VRE strains. Theoretical predictions of the microarray results were also derived from the sequences of the same VRE strain and were compared to array results while optimizing protocols until the microarray result and theoretical predictions were a match. The study concludes that DNA microarray technology can be used to quickly, accurately, and economically detect specifically and massively parallel target genes in enterococci.},

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@article{nokey_93,

title = {ConsensusPrime—A Bioinformatic Pipeline for Efficient Consensus Primer Design—Detection of Various Resistance and Virulence Factors in MRSA—A Case Study},

author = {Maximilian Collatz and Martin Reinicke and Celia Diezel and Sascha D. Braun and Stefan Monecke and Annett Reissig and Ralf Ehricht},

doi = {10.3390/biomedinformatics4020068},

year  = {2024},

date = {2024-05-10},

urldate = {2024-05-10},

journal = {BioMedInformatics},

volume = {4},

abstract = {Background: The effectiveness and reliability of diagnostic tests that detect DNA sequences largely hinge on the quality of the used primers and probes. This importance is especially evident when considering the specific sample being analyzed, as it affects the molecular background and potential for cross-reactivity, ultimately determining the test’s performance.

Methods: Predicting primers based on the consensus sequence of the target has multiple advantages, including high specificity, diagnostic reliability, broad applicability, and long-term validity. Automated curation of the input sequences ensures high-quality primers and probes.

Results: Here, we present a use case for developing a set of consensus primers and probes to identify antibiotic resistance and virulence genes in Staphylococcus (S.) aureus using the ConsensusPrime pipeline. Extensive qPCR experiments with several S. aureus strains confirm the exceptional quality of the primers designed using the pipeline.

Conclusions: By improving the quality of the input sequences and using the consensus sequence as a basis, the ConsensusPrime pipeline pipeline ensures high-quality primers and probes, which should be the basis of molecular assays.},

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@article{nokey_91,

title = {ConsensusPrime—A Bioinformatic Pipeline for Ideal Consensus Primer Design},

author = {Maximilian Collatz and Sascha D. Braun and Stefan Monecke and Ralf Ehricht},

doi = {10.3390/biomedinformatics2040041},

year  = {2022},

date = {2022-11-24},

urldate = {2022-11-24},

journal = {BioMedInformatics},

volume = {2},

abstract = {Background: High-quality oligonucleotides for molecular amplification and detection procedures of diverse target sequences depend on sequence homology. Processing input sequences and identifying homogeneous regions in alignments can be carried out by hand only if they are small and contain sequences of high similarity. Finding the best regions for large and inhomogeneous alignments needs to be automated.

Results: The ConsensusPrime pipeline was developed to sort out redundant and technical interfering data in multiple sequence alignments and detect the most homologous regions from multiple sequences. It automates the prediction of optimal consensus primers for molecular analytical and sequence-based procedures/assays.

Conclusion: ConsensusPrime is a fast and easy-to-use pipeline for predicting optimal consensus primers that is executable on local systems without depending on external resources and web services. An implementation in a Docker image ensures platform-independent executability and installability despite the combination of multiple programs. The source code and installation instructions are publicly available on GitHub.},

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@article{nokey_90,

title = {Description of Staphylococcal Strains from Straw-Coloured Fruit Bat (Eidolon helvum) and Diamond Firetail (Stagonopleura guttata) and a Review of their Phylogenetic Relationships to Other Staphylococci},

author = {Stefan Monecke and Frieder Schaumburg and Adebayo O. Shittu and Stefan Schwarz and Kristin Mühldorfer and Christian Brandt and Sascha D. Braun and Maximilian Collatz and Celia Diezel and Darius Gawlik and Dennis Hanke and Helmut Hotzel and Elke Müller and Martin Reinicke and Andrea T. Feßler and Ralf Ehricht},

doi = {10.3389/fcimb.2022.878137},

year  = {2022},

date = {2022-05-11},

urldate = {2022-05-11},

journal = {Frontiers in Cellular and Infection Microbiology},

volume = {12},

abstract = {The phylogenetic tree of the Staphylococcus aureus complex consists of several distinct clades and the majority of human and veterinary S. aureus isolates form one large clade. In addition, two divergent clades have recently been described as separate species. One was named Staphylococcus argenteus, due to the lack of the “golden” pigment staphyloxanthin. The second one is S. schweitzeri, found in humans and animals from Central and West Africa. In late 2021, two additional species, S. roterodami and S. singaporensis, have been described from clinical samples from Southeast Asia.

In the present study, isolates and their genome sequences from wild Straw-coloured fruit bats (Eidolon helvum) and a Diamond firetail (Stagonopleura guttata, an estrildid finch) kept in a German aviary are described. The isolates possessed staphyloxanthin genes and were closer related to S. argenteus and S. schweitzeri than to S. aureus. Phylogenetic analysis revealed that they were nearly identical to both, S. roterodami and S. singaporensis.

We propose considering the study isolates, the recently described S. roterodami and S. singaporensis as well as some Chinese strains with MLST profiles stored in the PubMLST database as different clonal complexes within one new species. According to the principle of priority we propose it should be named S. roterodami. 

This species is more widespread than previously believed, being observed in Western Africa, Southeast Asia and Southern China. It has a zoonotic connection to bats and has been shown to be capable of causing skin and soft tissue infections in humans. It is positive for staphyloxanthin, and it could be mis-identified as S. aureus (or S. argenteus) using routine procedures. However, it can be identified based on distinct MLST alleles, and “S. aureus” sequence types ST2470, ST3135, ST3952, ST3960, ST3961, ST3963, ST3965, ST3980, ST4014, ST4075, ST4076, ST4185, ST4326, ST4569, ST6105, ST6106, ST6107, ST6108, ST6109, ST6999 and ST7342 belong to this species.},

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@article{Christ2021,

title = {Hepatectomy-Induced Alterations in Hepatic Perfusion and Function - Toward Multi-Scale Computational Modeling for a Better Prediction of Post-hepatectomy Liver Function},

author = {Bruno Christ and Maximilian Collatz and Uta Dahmen and Karl-Heinz Herrmann and Sebastian Höpfl and Matthias König and Lena Lambers and Manja Marz and Daria Meyer and Nicole Radde and Jürgen R. Reichenbach and Tim Ricken and Hans-Michael Tautenhahn},

doi = {10.3389/fphys.2021.733868},

year  = {2021},

date = {2021-11-18},

urldate = {2021-11-18},

journal = {Front Physiol},

volume = {12},

pages = {733868},

abstract = {Liver resection causes marked perfusion alterations in the liver remnant both on the organ scale (vascular anatomy) and on the microscale (sinusoidal blood flow on tissue level). These changes in perfusion affect hepatic functions via direct alterations in blood supply and drainage, followed by indirect changes of biomechanical tissue properties and cellular function. Changes in blood flow impose compression, tension and shear forces on the liver tissue. These forces are perceived by mechanosensors on parenchymal and non-parenchymal cells of the liver and regulate cell-cell and cell-matrix interactions as well as cellular signaling and metabolism. These interactions are key players in tissue growth and remodeling, a prerequisite to restore tissue function after PHx. Their dysregulation is associated with metabolic impairment of the liver eventually leading to liver failure, a serious post-hepatectomy complication with high morbidity and mortality. Though certain links are known, the overall functional change after liver surgery is not understood due to complex feedback loops, non-linearities, spatial heterogeneities and different time-scales of events. Computational modeling is a unique approach to gain a better understanding of complex biomedical systems. This approach allows (i) integration of heterogeneous data and knowledge on multiple scales into a consistent view of how perfusion is related to hepatic function; (ii) testing and generating hypotheses based on predictive models, which must be validated experimentally and clinically. In the long term, computational modeling will (iii) support surgical planning by predicting surgery-induced perfusion perturbations and their functional (metabolic) consequences; and thereby (iv) allow minimizing surgical risks for the individual patient. Here, we review the alterations of hepatic perfusion, biomechanical properties and function associated with hepatectomy. Specifically, we provide an overview over the clinical problem, preoperative diagnostics, functional imaging approaches, experimental approaches in animal models, mechanoperception in the liver and impact on cellular metabolism, omics approaches with a focus on transcriptomics, data integration and uncertainty analysis, and computational modeling on multiple scales. Finally, we provide a perspective on how multi-scale computational models, which couple perfusion changes to hepatic function, could become part of clinical workflows to predict and optimize patient outcome after complex liver surgery.},

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pubstate = {published},

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@article{nokey_96,

title = {Characterisation and Molecular Analysis of an Unusual Chimeric Methicillin Resistant Staphylococcus Aureus Strain and its Bacteriophages},

author = {Sindy Burgold-Voigt and Stefan Monecke and Alexandra Simbeck and Thomas Holzmann and Bärbel Kieninger and Elisabeth M. Liebler-Tenorio and Sascha D. Braun and Maximilian Collatz and Celia Diezel and Elke Müller and Wulf Schneider-Brachert and Ralf Ehricht},

doi = {10.3389/fgene.2021.723958},

year  = {2021},

date = {2021-11-18},

journal = {Frontiers in Genetics},

volume = {12},

abstract = {In the context of microarray-based epidemiological typing of the clonal organism Staphylococcus aureus/MRSA, a strain was identified that did not belong to known clonal complexes. The molecular analysis by microarray-based typing yielded signals suggesting that it was a mosaic or hybrid strain of two lineages. To verify this result, the isolate was sequenced with both, short-read Illumina and long-read Nanopore technologies and analysed in detail. This supported the hypothesis that the genome of this strain, ST6610-MRSA-IVg comprised of segments originating from two different clonal complexes (CC).

While the backbone of the strain´s genome, i.e., roughly 2 megabases, belongs to CC8, a continuous insert of 894 kb (approx. 30% of the genome) originated from CC140. Beside core genomic markers in the normal succession and orientation, this insert also included the mecA gene, coding for PbP2a and causing methicillin resistance , localised on an SCCmec IVg element. This particular SCCmec type was also previously observed in CC140 MRSA from African countries. A second conspicuous observation was the presence of the trimethoprim resistance gene dfrG within on a prophage that occupied an attachment site normally used by Panton-Valentine Leucocidin (PVL) phages. 

This observation could indicate a role of large-scale chromosomal recombination in the evolution of S. aureus as well as a role of phages in the dissemination of antibiotic resistance genes.},

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@article{Collatz:20,

title = {EpiDope: A Deep Neural Network for linear B-cell epitope prediction},

author = {Maximilian Collatz and Florian Mock and Emanuel Barth and Martin Hölzer and Konrad Sachse and Manja Marz},

editor = {Lenore Cowen},

url = {https://github.com/rnajena/EpiDope},

doi = {10.1093/bioinformatics/btaa773},

year  = {2020},

date = {2020-09-11},

urldate = {2020-09-11},

journal = {Bioinformatics},

volume = {37},

number = {4},

pages = {448–455},

publisher = {Oxford University Press (OUP)},

abstract = {By binding to specific structures on antigenic proteins, the so-called epitopes, B-cell antibodies can neutralize pathogens. The identification of B-cell epitopes is of great value for the development of specific serodiagnostic assays and the optimization of medical therapy. However, identifying diagnostically or therapeutically relevant epitopes is a challenging task that usually involves extensive laboratory work. In this study, we show that the time, cost and labor-intensive process of epitope detection in the lab can be significantly reduced using in silico prediction.

Here, we present EpiDope, a python tool which uses a deep neural network to detect linear B-cell epitope regions on individual protein sequences. With an area under the curve between 0.67 ± 0.07 in the receiver operating characteristic curve, EpiDope exceeds all other currently used linear B-cell epitope prediction tools. Our software is shown to reliably predict linear B-cell epitopes of a given protein sequence, thus contributing to a significant reduction of laboratory experiments and costs required for the conventional approach.},

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tppubtype = {article}

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@article{Mostajo:20,

title = {A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes},

author = {Nelly F. Mostajo and Marie Lataretu and Sebastian Krautwurst and Florian Mock and Daniel Desirò and Kevin Lamkiewicz and Maximilian Collatz and Andreas Schoen and Friedemann Weber and Manja Marz and Martin Hölzer},

url = {https://www.rna.uni-jena.de/supplements/bats/index.html},

doi = {10.1093/nargab/lqz006},

year  = {2019},

date = {2019-09-30},

urldate = {2019-09-30},

journal = {NAR Genomics Bioinf},

volume = {2},

number = {1},

pages = {lqz006},

abstract = {Although bats are increasingly becoming the focus of scientific studies due to their unique properties, these exceptional animals are still among the least studied mammals. Assembly quality and completeness of bat genomes vary a lot and especially non-coding RNA (ncRNA) annotations are incomplete or simply missing. Accordingly, standard bioinformatics pipelines for gene expression analysis often ignore ncRNAs such as microRNAs or long antisense RNAs. The main cause of this problem is the use of incomplete genome annotations. We present a complete screening for ncRNAs within 16 bat genomes. NcRNAs affect a remarkable variety of vital biological functions, including gene expression regulation, RNA processing, RNA interference and, as recently described, regulatory processes in viral infections. Within all investigated bat assemblies, we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and lncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Our annotations will be usable as a resource (rna.uni-jena.de/supplements/bats) for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology and important host–virus interactions.},

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@article{Riege:17,

title = {Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D},

author = {Konstantin Riege and Martin Hölzer and Tilman E Klassert and Emanuel Barth and Julia Bräuer and Maximilian Collatz and Franziska Hufsky and Nelly F. Mostajo and Magdalena Stock and Bertram Vogel and Hortense Slevogt and Manja Marz},

doi = {10.1038/srep40598},

year  = {2017},

date = {2017-01-17},

urldate = {2017-01-17},

journal = {Sci Rep},

volume = {7},

pages = {40598},

abstract = {Mycoses induced by C.albicans or A.fumigatus can cause important host damage either by deficient or exaggerated immune response. Regulation of chemokine and cytokine signaling plays a crucial role for an adequate inflammation, which can be modulated by vitamins A and D. Non-coding RNAs (ncRNAs) as transcription factors or cis-acting antisense RNAs are known to be involved in gene regulation. However, the processes during fungal infections and treatment with vitamins in terms of therapeutic impact are unknown. We show that in monocytes both vitamins regulate ncRNAs involved in amino acid metabolism and immune system processes using comprehensive RNA-Seq analyses. Compared to protein-coding genes, fungi and bacteria induced an expression change in relatively few ncRNAs, but with massive fold changes of up to 4000. We defined the landscape of long-ncRNAs (lncRNAs) in response to pathogens and observed variation in the isoforms composition for several lncRNA following infection and vitamin treatment. Most of the involved antisense RNAs are regulated and positively correlated with their sense protein-coding genes. We investigated lncRNAs with stimulus specific immunomodulatory activity as potential marker genes: LINC00595, SBF2-AS1 (A.fumigatus) and RP11-588G21.2, RP11-394l13.1 (C.albicans) might be detectable in the early phase of infection and serve as therapeutic targets in the future.},

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@article{Hoelzer:16,

title = {Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells},

author = {Martin Hölzer and Verena Krähling and Fabian Amman and Emanuel Barth and Stephan H. Bernhart and Victor A. O. Carmelo and Maximilian Collatz and Gero Doose and Florian Eggenhofer and Jan Ewald and Jörg Fallmann and Lasse M. Feldhahn and Markus Fricke and Juliane Gebauer and Andreas J. Gruber and Franziska Hufsky and Henrike Indrischek and Sabina Kanton and Jörg Linde and Nelly F. Mostajo and Roman Ochsenreiter and Konstantin Riege and Lorena Rivarola-Duarte and Abdullah H. Sahyoun and Sita J. Saunders and Stefan E. Seemann and Andrea Tanzer and Bertram Vogel and Stefanie Wehner and Michael T. Wolfinger and Rolf Backofen and Jan Gorodkin and Ivo Grosse and Ivo Hofacker and Steve Hoffmann and Christoph Kaleta and Peter F. Stadler and Stephan Becker and Manja Marz},

doi = {10.1038/srep34589},

year  = {2016},

date = {2016-10-07},

urldate = {2016-10-07},

journal = {Sci Rep},

volume = {6},

pages = {34589},

abstract = {The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections.},

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