Friedrich-Schiller-Universität Jena, Institut für Angewandte Physik (IAP), Max-Wien-Platz 1, D-07743 Jena Lectures during Corona. CoVex is a unique online network and systems medicine platform for data analysis that integrates virus-human interactions for SARS-CoV-2 and SARS-CoV-1. Er koordiniert die Einsätze dieser Freiwilligen mit medizinischer Ausbildung. Corona virus: Availability and Restrictions at Graduate Academy. Visit the SARS-CoV-2 data portal in ViPR. The COVID-19 portal enables community crowdsourcing of publications via the “Add a publication” feature within any entry. The IUPred2A server is a biophysics-based prediction to identify intrinsically disordered protein regions (IDRs) and binding sites inside IDRs. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries. I look forward to meeting you â online and in person. ��-�X+�rO��4��L`-�K���L��Z2( �}���`�d���W�~Lp"��th�z�'�4����ǂ@$��r��7j�L�^3�(�"�9�=����h� �;%� �BI�$*�9.�XF�Ordք� �����! This heavy usage might lead to bottlenecks when it comes to setting up new meetings, or to disruptions when starting meetings. the Fundamentals of Modern Optics and the Structure of Matter courses. In response to the SARS-CoV-2 outbreak, Rfam produced a special release 14.2 that includes 10 new and 4 revised families that can be used to annotate the SARS-CoV-2 and other Coronavirus genomes with RNA families. UniProt also hosted webinars to describe the portal and publication submission system. VirHostNet is a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. The Master's programme starts in the winter semester 2020. The Pfam protein families database is widely used in the field of molecular biology for large-scale functional annotation of proteins. DisGeNET COVID-19 data collection shows the results of applying text mining tools to the LitCovid dataset, to identify mentions of diseases, signs and symptoms. DisGeNET is a discovery platform containing one of the largest publicly available collections of genes and variants associated with human diseases. This includes genetic sequence and related clinical and epidemiological data to help researchers understand how viruses evolve and spread during epidemics and pandemics. Die Seite wird regelmäßig aktualisiert und erweitert. Restrictions due to Corona virus: Regulations for PhD and habilitation procedures. 07743 Jena. A research team from the Chair of Economic Geography at the University of Jena has been examining the severity of the consequences. And we will overcome them, together. The information provided is for research only and we cannot guarantee the correctness of the data. GISAID data Submitters and Curators ensure real-time data sharing of hCoV-19 remains reliable, to enable rapid progress in the understanding of the new COVID-19 disease and in the research and development of candidate medical countermeasures. It is based on the GLUE data-centric bioinformatics environment and provides a browsable database of amino acid replacements and coding region indels that have been observed in sequences from the pandemic. The GISAID Initiative promotes the rapid sharing of data from the coronavirus causing COVID-19. Informieren Sie bitte auch das Internationale Büro der Universität Jena: international@uni-jena.de This also applies to the exams. Since the start of the COVID-19 outbreak and the identification of the pandemic virus, laboratories around the world are generating viral genome sequence data with unprecedented speed, enabling real-time progress in the understanding of the new disease and in the research and development of candidate medical countermeasures. Nextstrain is incorporating SARS-CoV-2 genomes as soon as they are shared and provides analyses and situation reports. Hidden Markov models are used to classify sequences by determining the RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleotide alignment of the full sequence to a covariance model. The Welcome and Service Desk for Doctoral Candidates and Postdocs will be closed for face-to-face contacts until further notice. Explore the virus-host interactome. Our team is mostly working online. ViralZone project is handled by the virus program of SwissProt group. We are curating a list of bioinformatics tools designed explicitly for SARS-CoV-2 and coronaviruses. The ELM resource offers a collection of short linear motifs that mediate interactions crucial in both native cell regulation and pathogenic interference. Indeed, this tree has never borne so much fruit, and so superb. The release contains manual biocuration of experimentally validated physical Coronaviridae / host protein-protein interactions and is complementary to functional and in silico interactions shared by viruses.string. Jena, July 2-3, 2020. P-HIPSTer contains predicted viral-host PPIs for 15 human-infecting coronaviruses. For a detailed description of the tools, check our review preprint: We are curious to know which tools you have developed to advance the field. Sequence data are essential to design and evaluate diagnostic tests, to track and trace the ongoing outbreak, and to identify potential intervention options. RNAcentral has launched a new tool to help scientists studying Coronaviruses to search thousands of viral genomes and explore results by virus, host, country, and more. VADR (Viral Annotation DefineR) validates and annotates viral sequences in GenBank submissions. Tools by EVBC members are marked ★. For the third year Bachelor Biology course âVom Molekül zu komplexen Gemeinschaften (BB3.Ö13)â at FSU Jena, PhD student Jennifer Gabriel and research group leader Nicole van Dam, Molecular Interaction Ecology designed a Corona proof âbrown bagâ practicum. ELM and IUPred2A mutually include each other’s predictions, and both methods utilize the newest data from UniProt and Pfam. The LitCovid dataset contains a selection of papers referring to Coronavirus 19 disease. Further you can analyze the data online using sequence alignment, phylogenetic tree reconstruction, sequence variation (SNP), metadata-driven comparative analysis and BLAST. The new search uses nhmmer and enables the users to explore the results using facets powered by the EBI Search. You can search the comprehensive database for sequences & strains, immune epitopes, 3D protein structures, host factor data, antiviral drugs, plasmid data. This way users can get a fully annotated report on candidate disordered interaction sites, highlighting their relationships with Pfam domains, for any protein of interest. PriSeT finds a primer set P balancing both: high taxonomic coverage and high resolution. Service hours of the hotline: daily 10:00 - 14:00. ��K���އ�������% These primer sets would be suitable for empirical testing. ������4�v K�W\-�z0�d�]��� ��ӌ{u�Ē�J��a �b�;%�F*�����Ql��(�E������6ٹ����%�0:�w���ѐK!��Ժ�xi atm�5A�=5�YƝ�=M���};�J��qgMĤ\�����+������8�����.�,~|�0�;����*uh���v}�i �R��ƛ��m�ʽ���&�KD��6�,�+�3/n�P��%Bi�d�۾Go��Z�������q6���N�ŧx����Uc8��ۯ���Hf�h��_���F/Rs:Ѹ��_·��p_�6B:�g"a You can find more information at: iocm.uni-jena.de. Powered by WordPress. Sites that undergo positive selection can give you insights in the evolutionary history of your sequences, for example showing you important mutation hot spots, accumulated as results of virus-host arms races during evolution. We will meet the challenges head-on. When I called him to say thank you, he calmly said: âAh, thatâs the radiation. While the search uses the same sequences as NCBI BLAST, there are several important differences: The search is produced and maintained by the RNAcentral team, repurposing the infrastructure of the RNAcentral sequence similarity search to query betacoronavirus sequences instead of non-coding RNAs. All tools are freely available online, either through web applications or public code repositories. Präsidium und Senat der Friedrich-Schiller-Universität Jena haben sich zum Ziel gesetzt, alle Nachteile, die Studierenden durch Corona entstehen, auszugleichen. Bulgariaâs Corona-Drama in Three Acts. 3TrophoSYS GmbH, Botzstrasse 5, 07743 Jena. 4Institute for Pharmaceutical Technology and Biopharmacy, Friedrich Schiller University Jena, Lessingstrasse 8, 07743 Jena. The Coronavirus typing tool is designed to use Blast and phylogenetic methods in order to identify the Coronavirus types and genotypes of a nucleotide sequence. Mai, findet der Hochschulinformationstag (HIT) der Universität Jena erstmals digital statt. p�$F�l�m����A U��t��S?��)��ͻZ�ݺc�������3�{ϥSGR�. In the autumn of 1986, I got a box of apples from my uncle. Our team is mostly working online. r�F�32� 9W The tool allows users to highlight and prioritize the most frequent mutations in specific protein regions, and to monitor their frequency in the population over time. Corona News. Die Browser-basierte Lösun The Data Portal brings together and continuously updates the relevant COVID-19 datasets and tools. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results. COPASI supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie’s stochastic simulation algorithm; arbitrary discrete events can be included in such simulations. The Data Portal brings together and continuously updates the relevant COVID-19 datasets and tools. This can capture longer and more specialized disordered interaction regions complementing linear motifs captured by ELM. Coronavirus COVID-19 Global Cases by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU) Thuringiaâs economy has been hit hard by the corona pandemic, plunging the state into a deep recession. PriSeT has been applied to 19 SARS-CoV-2 genomes and computed 114 new primer pairs with the additional constraint that the sequences have no co-occurrences in other taxa. The Friedrich Schiller University Jena has equipped several lecture halls to provide live streaming of lectures and seminars. However, we are still available for you via email. The nationwide survey "Studying in Germany in Corona Times" aims to examine the effects of the crisis on students at German universities and to shed light on the special features, challenges and opportunities of the largely digital summer semester 2020. Appropriate PCR primer pairs for DNA metabarcoding would match to a broad evolutionary range of taxa, such that we only need a few to achieve high taxonomic coverage. The latest release (March 2020) is dedicated to helping researchers to fight against the COVID-19 pandemic and is registered as a COVID-19 fair share resource. Increase of test capacities for suspected corona cases Researchers at the Friedrich Schiller University of Jena and the University Hospital Jena find an alternative to scarce buffer solutions when testing for the novel corona virus. We are happy to answer your enquiries via our contact form. Handlungsempfehlungen an Lehrende und Prüfungsämter kommuniziert, auf die sich Studierende berufen können. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. They provide a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. ORCID is used as a mechanism to validate user credentials as well as recognition for contribution. Please also have a look at our general list of virus bioinformatics tools. the reliable analysis of sequencing data. Find putative drug targets. Please also use the e-mail address corona@jena.de. CoVPipe is a highly optimized and fully automated workflow for the reference-based reconstruction of SARS-CoV-2 genomes based on next generation amplicon sequencing data using CleanPlex SARS-CoV-2 Panel (Paragon Genomics, Hayward, CA, USA) from swab samples. It allows for the detection of within-host genetic variation of SARS-CoV-2 from viral NGS data. CoV-GLUE is an online web application for the interpretation and analysis of SARS-CoV-2 virus genome sequences, with a focus on amino acid sequence variation. We cover workflows and tools for. �dj��N�cswdQ�.^�)�2 Y3 kRrT�U�,a��f&�$��ɬ���䭪c�� "��";2�]���"���]���'- In Thuringia, the first corona cases occurred at the beginning of March, and in mid-March the first infections were also confirmed in Jena. Oral examinations in the context of doctoral and habilitation procedures (disputations, colloquia, scientific lectures and talks) are currently not to be held. With sadness, we regret to inform you that we have to cancel our 7 th pairfam international interdisciplinary conference on "Personality and relationships across the life span in Jena", July 2-3 2020, due to the evolving corona virus situation. Apoptosed cells release some or all of their internal contents, notably including virions. �:M�l��Μق��D�;];��#�%2�T�t��z$ ��M�l�H�h���F]��*Vwb�C�GܲCE�V�q���e�!����� SD}��ٌ[:/�*F�Л��q�֙Xp�;��p�l�2�����Q/>~j�ܒcGIDP�?��u���B.S BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. The viral sequences are regularly extracted from the NCBI BLAST database and the metadata is retrieved from the associated INSDC entries. Vigor4 uses the VIGOR_DB project which currently has databases for the following viruses: Influenza (A & B for human, avian, and swine, and C for human), West Nile Virus, Zika Virus, Chikungunya Virus, Eastern Equine Encephalitis Virus, Respiratory Syncytial Virus, Rotavirus, Enterovirus, Lassa Mammarenavirus. SARS-CoV-2 release is coming (May, 1st). ViralZone is a web-resource from the Swiss Institute of Bioinformatics for all viral genus and families, providing general molecular and epidemiological information, along with virion and genome figures. Currently, it supports FMDV and SARS-Cov-2 viral sequences. The annotation system is based on the analysis of the input nucleotide sequence using models built from curated RefSeqs. Please contact Marco Cacciabue, Pangolin assigns a global lineage to query SARS-CoV-2 genomes by estimating the most likely placement within a phylogenetic tree of representative sequences from all currently defined global SARS-CoV-2 lineages based on the lineage nomenclature proposed by. And our most important services will continue: We are processing all incoming applications including your mail. Assembled virions are exported to the environment, where they can diffuse and infect other cells. The COVID-19 UniProt portal advances SARS-CoV-2 research by providing the latest knowledge on proteins relevant to the disease for both the virus and human host. Letzter Stand: 16. Due to the corona virus, Graduate Academy has to reduce some of its offers. information on gene functions from Gene Ontology, Support for facets and keyword searches for exploring results, Explore up to 1,000 top hits (compared to 100 in BLAST), Integration with Rfam to annotate structured RNA elements. H���C�bTB���I1�\�Œ��g��v�H��[6v3y�-���� �2m�B��kħ��3�0ϸ��q�q�ʘ�n�Oڸ������-2ѸMΰ'Аr�|9�J���딶�k7��S���z�T�:ǔ���.e�B�+�j��9� ��]�����7UZBݮ�3�����X5����� ����,���ϻ��9uļ�����]o��#>5)p��6�������y���r����l�C��n���������?�����l?t7t���]��$k�}W8x��sS���6Ѻߦ���m¡ߖX5n�>]l�@�)�˟6J��'". This is a fast-paced project with the COVID-19 Data Portal featuring relevant ⦠the discovery of potential drug targets and development of therapeutic strategies. In the extracellular space, virions adhere to ACE2 receptors and get internalized through endocytosis. The P-HIPSTer database, comprised of ∼282,000 PPIs, represents a comprehensive catalog of virus-human PPIs that spans the Baltimore classification system and is a major expansion on previously available or reported pathogen-host interactions. For example, it is possible to search for a fragment of a SARS-CoV-2 genome, select similar sequences identified in COVID-19 patients, and browse sequence variants from different countries. 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