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1. Ok Google or Not Ok Google?—Voice Assistants and the Protection of Privacy in Families

Author

Backes, Christina, Jungfleisch, Julia, Pültz, Sebastian, Bungenberg, Marc, Series Editor, Fröhlich, Mareike, Series Editor, Giegerich, Thomas, Series Editor, Zdraveva, Neda, Series Editor, Baysal, Başak, Advisory Editor, Chi, Manjiao, Advisory Editor, Guckelberger, Annette, Advisory Editor, Jelić, Ivana, Advisory Editor, Kurdadze, Irine, Advisory Editor, Lažetić, Gordana, Advisory Editor, Mekelberg, Yossi, Advisory Editor, Meškić, Zlatan, Advisory Editor, Perišin, Tamara, Advisory Editor, Petrov, Roman, Advisory Editor, Popović, Dušan V., Advisory Editor, Ziegler, Andreas R., Advisory Editor, Gstrein, Oskar J., editor, and van den Berg, Caspar, editor

Published
2023
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2. Deep sequencing of sncRNAs reveals hallmarks and regulatory modules of the transcriptome during Parkinson’s disease progression

Author

Kern, Fabian, Fehlmann, Tobias, Violich, Ivo, Alsop, Eric, Hutchins, Elizabeth, Kahraman, Mustafa, Grammes, Nadja L., Guimarães, Pedro, Backes, Christina, Poston, Kathleen L., Casey, Bradford, Balling, Rudi, Geffers, Lars, Krüger, Rejko, Galasko, Douglas, Mollenhauer, Brit, Meese, Eckart, Wyss-Coray, Tony, Craig, David W., Van Keuren-Jensen, Kendall, and Keller, Andreas

Published
2021
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5. Common diseases alter the physiological age-related blood microRNA profile

Author

Fehlmann, Tobias, Lehallier, Benoit, Schaum, Nicholas, Hahn, Oliver, Kahraman, Mustafa, Li, Yongping, Grammes, Nadja, Geffers, Lars, Backes, Christina, Balling, Rudi, Kern, Fabian, Krüger, Rejko, Lammert, Frank, Ludwig, Nicole, Meder, Benjamin, Fromm, Bastian, Maetzler, Walter, Berg, Daniela, Brockmann, Kathrin, Deuschle, Christian, von Thaler, Anna-Katharina, Eschweiler, Gerhard W., Milman, Sofiya, Barziliai, Nir, Reichert, Matthias, Wyss-Coray, Tony, Meese, Eckart, and Keller, Andreas

Published
2020
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10. TRPC1- and TRPC3-dependent Ca2+ signaling in mouse cortical astrocytes affects injury-evoked astrogliosis in vivo

Author

Belkacemi, Thabet, Niermann, Alexander, Hofmann, Laura, Wissenbach, Ulrich, Birnbaumer, Lutz, Leidinger, Petra, Backes, Christina, Meese, Eckart, Keller, Andreas, Bai, Xianshu, Scheller, Anja, Kirchhoff, Frank, Philipp, Stephan E., Weissgerber, Petra, Flockerzi, Veit, and Beck, Andreas

Subjects
Male, Mice, 129 Strain, CIENCIAS MÉDICAS Y DE LA SALUD, MIGRATION, glia, proliferation, Inmunología, Brain Edema, Wounds, Stab, migration, Article, MEMBRANE CURRENTS, STAB WOUND INJURY, Cell Movement, CEREBRO, TRPC6 Cation Channel, ION CHANNELS, Animals, Humans, Calcium Signaling, Gliosis, Cell Proliferation, TRPC Cation Channels, Cerebral Cortex, Mice, Knockout, CELULAS, PROLIFERATION, CORTEZA CEREBRAL, ion channels, HERIDAS, Mice, Inbred C57BL, Disease Models, Animal, Medicina Básica, HEK293 Cells, TEJIDO NERVIOSO, Astrocytes, GLIA, stab wound injury, membrane currents
Abstract

Fil: Belkacemi, Thabet. Universität des Saarlandes. Experimentelle und Klinische Pharmakologie und Toxikologie; Alemania Fil: Niermann, Alexander. Universität des Saarlandes. Experimentelle und Klinische Pharmakologie und Toxikologie; Alemania Fil: Hofmann, Laura. Universität des Saarlandes. Experimentelle und Klinische Pharmakologie und Toxikologie; Alemania Fil: Wissenbach, Ulrich. Universität des Saarlandes. Experimentelle und Klinische Pharmakologie und Toxikologie; Alemania Fil: Birnbaumer, Lutz. National Institute of Environmental Health Sciences. Research Triangle Park. Neurobiology Laboratory; Estados Unidos Fil: Birnbaumer, Lutz. Pontificia Universidad Católica Argentina. Facultad de Ciencias Médicas. Instituto de Investigaciones Biomédicas; Argentina Fil: Leidinger, Petra. Universität des Saarlandes. Institut für Humangenetik; Alemania Fil: Backes, Christina. Universität des Saarlandes. Klinische Bioinformatik; Alemania Fil: Meese, Eckart. Universität des Saarlandes. Institut für Humangenetik; Alemania Fil: Keller, Andreas. Universität des Saarlandes. Klinische Bioinformatik; Alemania Fil: Bai, Xianshu. Universität des Saarlandes. Molekulare Physiologie; Alemania Fil: Scheller, Anja. Universität des Saarlandes. Molekulare Physiologie; Alemania Fil: Kirchhoff, Frank. Universität des Saarlandes. Molekulare Physiologie; Alemania Fil: Philipp, Stephan E. Universität des Saarlandes. Experimentelle und Klinische Pharmakologie und Toxikologie; Alemania Fil: Weissgerber, Petra. Universität des Saarlandes. Experimentelle und Klinische Pharmakologie und Toxikologie; Alemania Fil: Flockerzi, Veit. Universität des Saarlandes. Experimentelle und Klinische Pharmakologie und Toxikologie; Alemania Fil: Beck, Andreas. Universität des Saarlandes. Experimentelle und Klinische Pharmakologie und Toxikologie; Alemania Fil: Beck, Andreas. Universität des Saarlandes. Molekulare Physiologie; Alemania Abstract: Following brain injury astrocytes change into a reactive state, proliferate and grow into the site of lesion, a process called astrogliosis, initiated and regulated by changes in cytoplasmic Ca2+ . Transient receptor potential canonical (TRPC) channels may contribute to Ca2+ influx but their presence and possible function in astrocytes is not known. By RT-PCR and RNA sequencing we identified transcripts of Trpc1, Trpc2, Trpc3, and Trpc4 in FACS-sorted glutamate aspartate transporter (GLAST)-positive cultured mouse cortical astrocytes and subcloned full-length Trpc1 and Trpc3 cDNAs from these cells. Ca2+ entry in cortical astrocytes depended on TRPC3 and was increased in the absence of Trpc1. After co-expression of Trpc1 and Trpc3 in HEK-293 cells both proteins co-immunoprecipitate and form functional heteromeric channels, with TRPC1 reducing TRPC3 activity. In vitro, lack of Trpc3 reduced astrocyte proliferation and migration whereas the TRPC3 gain-of-function moonwalker mutation and Trpc1 deficiency increased astrocyte migration. In vivo, astrogliosis and cortex edema following stab wound injury were reduced in Trpc3-/- but increased in Trpc1-/- mice. In summary, our results show a decisive contribution of TRPC3 to astrocyte Ca2+ signaling, which is even augmented in the absence of Trpc1, in particular following brain injury. Targeted therapies to reduce TRPC3 channel activity in astrocytes might therefore be beneficial in traumatic brain injury.

Published
2023
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15. Deep characterization of blood cell miRNomes by NGS

Author

Schwarz, Eva C., Backes, Christina, Knörck, Arne, Ludwig, Nicole, Leidinger, Petra, Hoxha, Cora, Schwär, Gertrud, Grossmann, Thomas, Müller, Sabine C., Hart, Martin, Haas, Jan, Galata, Valentina, Müller, Isabelle, Fehlmann, Tobias, Eichler, Hermann, Franke, Andre, Meder, Benjamin, Meese, Eckart, Hoth, Markus, and Keller, Andreas

Published
2016
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22. An estimate of the total number of true human miRNAs

Author

Alles, Julia, Fehlmann, Tobias, Fischer, Ulrike, Backes, Christina, Galata, Valentina, Minet, Marie, Hart, Martin, Abu-Halima, Masood, Gr��sser, Friedrich A., Lenhof, Hans-Peter, Keller, Andreas, Meese, Eckart, and Brunner, Marie-Louise

Published
2022
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28. BN++ – A Biological Information System

Author

Küntzer Jan, Blum Torsten, Gerasch Andreas, Backes Christina, Hildebrandt Andreas, Kaufmann Michael, Kohlbacher Oliver, and Lenhof Hans-Peter

Subjects
Biotechnology, TP248.13-248.65
Abstract

Recent years have seen an explosive growth in the amount of biochemical data available. Numerous databases have been established and are being used as an essential resource by biologists around the world. The sheer amount and heterogeneity of these data poses a major challenge: data integration and, based thereupon, the integrative analysis of these data. We present BN++, the biochemical network library, a powerful software package for integrating, analyzing, and visualizing biochemical data in the context of networks. BN++ is based on a comprehensive and extensible object model (BioCore), which has been implemented as a C++ framework, a Java class library, and a relational database. The C++ framework is used to efficiently import, integrate, and analyze the data, which is stored in a data warehouse. The Java-based viewer (BiNA) provides a powerful platform-independent visualization of the data using sophisticated graph layout algorithms. Currently, the data warehouse imports and integrates data from about a dozen important databases including, among others, sequence data, metabolic and regulatory networks, and protein interaction data. We illustrate the usefulness of BN++ with a few select example applications.

Published
2006
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32. Paleoproteomic study of the Iceman’s brain tissue

Author

Maixner, Frank, Overath, Thorsten, Linke, Dennis, Janko, Marek, Guerriero, Gea, van den Berg, Bart H. J., Stade, Bjoern, Leidinger, Petra, Backes, Christina, Jaremek, Marta, Kneissl, Benny, Meder, Benjamin, Franke, Andre, Egarter-Vigl, Eduard, Meese, Eckart, Schwarz, Andreas, Tholey, Andreas, Zink, Albert, and Keller, Andreas

Published
2013
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33. Contemporary scientometric analyses using a novel web application: the science performance evaluation (SciPE) approach

Author

Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Scholz, Sean S, Dillmann, Markus, Flohr, Alexander, Backes, Christina, Fehlmann, Tobias, Millenaar, Dominic, Ukena, Christian, Böhm, Michael, Keller, Andreas, Mahfoud, Felix, Massachusetts Institute of Technology. Institute for Medical Engineering & Science, Scholz, Sean S, Dillmann, Markus, Flohr, Alexander, Backes, Christina, Fehlmann, Tobias, Millenaar, Dominic, Ukena, Christian, Böhm, Michael, Keller, Andreas, and Mahfoud, Felix

Abstract

Aims We aimed at developing a structured study protocol utilizing the bibliographic web-application science performance evaluation (SciPE) to perform comprehensive scientometric analyses. Methods and results Metadata related to publications derived from online databases were processed and visualized by transferring the information to an undirected multipartite graph and distinct partitioned sets of nodes. Also, institution-specific data were normalized and merged allowing precise geocoordinate positioning, to enable heatmapping and valid identification. As a result, verified, processed data regarding articles, institutions, journals, authors gender, nations and subject categories can be obtained. We recommend including the total number of publications, citations, the population, research institutions, gross domestic product, and the country-specific modified Hirsch Index and to form corresponding ratios (e.g., population/publication). Also, our approach includes implementation of bioinformatical methods such as heatmapping based on exact geocoordinates, simple chord diagrams, and the central implementation of specific ratios with plain visualization techniques. Conclusion This protocol allows precise conduction of contemporaneous scientometric analyses based on bioinformatic and meta-analytical techniques, allowing to evaluate and contextualize scientific efforts. Data presentation with the depicted visualization techniques is mandatory for transparent and consistent analyses of research output across different nations and topics. Research performance can then be discussed in a synopsis of all findings. Graphic abstract

Published
2021

36. Deep sncRNA-seq of the PPMI cohort to study Parkinson’s disease progression

Author

Kern, Fabian, Fehlmann, Tobias, Violich, Ivo, Alsop, Eric, Hutchins, Elizabeth, Kahraman, Mustafa, Grammes, Nadja Liddy, Guimarães, Pedro, Backes, Christina, Poston, Kathleen, Casey, Bradford, Balling, Rudolf, Geffers, Lars, Krüger, Rejko, Galasko, Douglas, Mollenhauer, Brit, Meese, Eckart, Wyss-Coray, Tony, Craig, David Wesley, Van Keuren-Jensen, Kendall, Keller, Andreas, and Michael J. Fox Foundation [sponsor]

Subjects
sncRNA-seq, Biochemistry, biophysics & molecular biology [F05] [Life sciences], Biochimie, biophysique & biologie moléculaire [F05] [Sciences du vivant], Parkinson’s diseases, RNAs
Abstract

Coding and non-coding RNAs have diagnostic and prognostic importance in Parkinson’s diseases (PD). We studied circulating small non-coding RNAs (sncRNAs) in 7, 003 samples from two longitudinal PD cohorts (Parkinson’s Progression Marker Initiative (PPMI) and Luxembourg Parkinson’s Study (NCER-PD)) and modelled their influence on the transcriptome. First, we sequenced sncRNAs in 5, 450 blood samples of 1, 614 individuals in PPMI. The majority of 323 billion reads (59 million reads per sample) mapped to miRNAs. Other covered RNA classes include piRNAs, rRNAs, snoRNAs, tRNAs, scaRNAs, and snRNAs. De-regulated miRNAs were associated with the disease and disease progression and occur in two distinct waves in the third and seventh decade of live. Originating mostly from a characteristic set of immune cells they resemble a systemic inflammation response and mitochondrial dysfunction, two hallmarks of PD. By profiling 1, 553 samples from 1, 024 individuals in the NCER-PD cohort using an independent technology, we validate relevant findings from the sequencing study. Finally, network analysis of sncRNAs and transcriptome sequencing of the original cohort identified regulatory modules emerging in progressing PD patients.Competing Interest StatementThe authors have declared no competing interest.

Published
2020

40. Evaluating the Use of Circulating MicroRNA Profiles for Lung Cancer Detection in Symptomatic Patients

Author

Fehlmann, Tobias, Kahraman, Mustafa, Backes, Christina, Galata, Valentina, Keller, Verena, Geffers, Lars, Mercaldo, Nathaniel, Hornung, Daniela, Keller, Andreas, Krüger, Rejko, Balling, Rudolf, Fehlmann, Tobias, Kahraman, Mustafa, Backes, Christina, Galata, Valentina, Keller, Verena, Geffers, Lars, Mercaldo, Nathaniel, Hornung, Daniela, Keller, Andreas, Krüger, Rejko, and Balling, Rudolf

Abstract

Importance The overall low survival rate of patients with lung cancer calls for improved detection tools to enable better treatment options and improved patient outcomes. Multivariable molecular signatures, such as blood-borne microRNA (miRNA) signatures, may have high rates of sensitivity and specificity but require additional studies with large cohorts and standardized measurements to confirm the generalizability of miRNA signatures. Objective To investigate the use of blood-borne miRNAs as potential circulating markers for detecting lung cancer in an extended cohort of symptomatic patients and control participants. Design, Setting, and Participants This multicenter, cohort study included patients from case-control and cohort studies (TREND and COSYCONET) with 3102 patients being enrolled by convenience sampling between March 3, 2009, and March 19, 2018. For the cohort study TREND, population sampling was performed. Clinical diagnoses were obtained for 3046 patients (606 patients with non–small cell and small cell lung cancer, 593 patients with nontumor lung diseases, 883 patients with diseases not affecting the lung, and 964 unaffected control participants). No samples were removed because of experimental issues. The collected data were analyzed between April 2018 and November 2019. Main Outcomes and Measures Sensitivity and specificity of liquid biopsy using miRNA signatures for detection of lung cancer. Results A total of 3102 patients with a mean (SD) age of 61.1 (16.2) years were enrolled. Data on the sex of the participants were available for 2856 participants; 1727 (60.5%) were men. Genome-wide miRNA profiles of blood samples from 3046 individuals were evaluated by machine-learning methods. Three classification scenarios were investigated by splitting the samples equally into training and validation sets. First, a 15-miRNA signature from the training set was used to distinguish patients diagnosed with lung cancer from all other individuals in the validation

Published
2020

41. Deep sncRNA-seq of the PPMI cohort to study Parkinson’s disease progression

Author

Michael J. Fox Foundation [sponsor], Kern, Fabian, Fehlmann, Tobias, Violich, Ivo, Alsop, Eric, Hutchins, Elizabeth, Kahraman, Mustafa, Grammes, Nadja Liddy, Guimarães, Pedro, Backes, Christina, Poston, Kathleen, Casey, Bradford, Balling, Rudolf, Geffers, Lars, Krüger, Rejko, Galasko, Douglas, Mollenhauer, Brit, Meese, Eckart, Wyss-Coray, Tony, Craig, David Wesley, Van Keuren-Jensen, Kendall, Keller, Andreas, Michael J. Fox Foundation [sponsor], Kern, Fabian, Fehlmann, Tobias, Violich, Ivo, Alsop, Eric, Hutchins, Elizabeth, Kahraman, Mustafa, Grammes, Nadja Liddy, Guimarães, Pedro, Backes, Christina, Poston, Kathleen, Casey, Bradford, Balling, Rudolf, Geffers, Lars, Krüger, Rejko, Galasko, Douglas, Mollenhauer, Brit, Meese, Eckart, Wyss-Coray, Tony, Craig, David Wesley, Van Keuren-Jensen, Kendall, and Keller, Andreas

Abstract

Coding and non-coding RNAs have diagnostic and prognostic importance in Parkinson’s diseases (PD). We studied circulating small non-coding RNAs (sncRNAs) in 7, 003 samples from two longitudinal PD cohorts (Parkinson’s Progression Marker Initiative (PPMI) and Luxembourg Parkinson’s Study (NCER-PD)) and modelled their influence on the transcriptome. First, we sequenced sncRNAs in 5, 450 blood samples of 1, 614 individuals in PPMI. The majority of 323 billion reads (59 million reads per sample) mapped to miRNAs. Other covered RNA classes include piRNAs, rRNAs, snoRNAs, tRNAs, scaRNAs, and snRNAs. De-regulated miRNAs were associated with the disease and disease progression and occur in two distinct waves in the third and seventh decade of live. Originating mostly from a characteristic set of immune cells they resemble a systemic inflammation response and mitochondrial dysfunction, two hallmarks of PD. By profiling 1, 553 samples from 1, 024 individuals in the NCER-PD cohort using an independent technology, we validate relevant findings from the sequencing study. Finally, network analysis of sncRNAs and transcriptome sequencing of the original cohort identified regulatory modules emerging in progressing PD patients.Competing Interest StatementThe authors have declared no competing interest.

Published
2020

42. Validation of human microRNA target pathways enables evaluation of target prediction tools

Author

Kern, Fabian, primary, Krammes, Lena, additional, Danz, Karin, additional, Diener, Caroline, additional, Kehl, Tim, additional, Küchler, Oliver, additional, Fehlmann, Tobias, additional, Kahraman, Mustafa, additional, Rheinheimer, Stefanie, additional, Aparicio-Puerta, Ernesto, additional, Wagner, Sylvia, additional, Ludwig, Nicole, additional, Backes, Christina, additional, Lenhof, Hans-Peter, additional, von Briesen, Hagen, additional, Hart, Martin, additional, Keller, Andreas, additional, and Meese, Eckart, additional

Published
2020
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44. Genome-wide miRNA signatures of human longevity

Author

ElSharawy, Abdou, Keller, Andreas, Flachsbart, Friederike, Wendschlag, Anke, Jacobs, Gunnar, Kefer, Nathalie, Brefort, Thomas, Leidinger, Petra, Backes, Christina, Meese, Eckart, Schreiber, Stefan, Rosenstiel, Philip, Franke, Andre, and Nebel, Almut

Published
2012
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47. Deep sncRNA-seq of the PPMI cohort to study Parkinson’s disease progression

Author

Kern, Fabian, primary, Fehlmann, Tobias, additional, Violich, Ivo, additional, Alsop, Eric, additional, Hutchins, Elizabeth, additional, Kahraman, Mustafa, additional, Grammes, Nadja Liddy, additional, Guimarães, Pedro, additional, Backes, Christina, additional, Poston, Kathleen, additional, Casey, Bradford, additional, Balling, Rudi, additional, Geffers, Lars, additional, Krüger, Rejko, additional, Galasko, Douglas, additional, Mollenhauer, Brit, additional, Meese, Eckart, additional, Wyss-Coray, Tony, additional, Craig, David Wesley, additional, Van Keuren-Jensen, Kendall, additional, and Keller, Andreas, additional

Published
2020
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49. Evaluating the Use of Circulating MicroRNA Profiles for Lung Cancer Detection in Symptomatic Patients

Author

Fehlmann, Tobias, primary, Kahraman, Mustafa, additional, Ludwig, Nicole, additional, Backes, Christina, additional, Galata, Valentina, additional, Keller, Verena, additional, Geffers, Lars, additional, Mercaldo, Nathaniel, additional, Hornung, Daniela, additional, Weis, Tanja, additional, Kayvanpour, Elham, additional, Abu-Halima, Masood, additional, Deuschle, Christian, additional, Schulte, Claudia, additional, Suenkel, Ulrike, additional, von Thaler, Anna-Katharina, additional, Maetzler, Walter, additional, Herr, Christian, additional, Fähndrich, Sebastian, additional, Vogelmeier, Claus, additional, Guimaraes, Pedro, additional, Hecksteden, Anne, additional, Meyer, Tim, additional, Metzger, Florian, additional, Diener, Caroline, additional, Deutscher, Stephanie, additional, Abdul-Khaliq, Hashim, additional, Stehle, Ingo, additional, Haeusler, Sebastian, additional, Meiser, Andreas, additional, Groesdonk, Heinrich V, additional, Volk, Thomas, additional, Lenhof, Hans-Peter, additional, Katus, Hugo, additional, Balling, Rudi, additional, Meder, Benjamin, additional, Kruger, Rejko, additional, Huwer, Hanno, additional, Bals, Robert, additional, Meese, Eckart, additional, and Keller, Andreas, additional

Published
2020
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