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. 07743 Jena Telefon: Telefax: E-Mail: 0 36 41 9-431 70 0 36 41 9-431 72 studiendekanat-wiwi@uni-jena.de Jena, March 18, 2020 To the students and lecturers at the Faculty of Economics and Business Administration Information and Regulations Concerning the Corona Pandemic (last updated 18/03/2020) Dear Sir or Madam, 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. There may be longer waiting times. This tool is a work in progress and any suggestions would be greatly appreciated. DisGeNET is a discovery platform containing one of the largest publicly available collections of genes and variants associated with human diseases. �: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 Mai, findet der Hochschulinformationstag (HIT) der Universität Jena erstmals digital statt. It is capable of processing large libraries and is robust against mislabeled or low quality references. The pipeline is designed for reproducibility and scalability in order to ensure reliable and fast data analysis of SARS-CoV2 data. In Thuringia, the first corona cases occurred at the beginning of March, and in mid-March the first infections were also confirmed in Jena. This can capture longer and more specialized disordered interaction regions complementing linear motifs captured by ELM. Public life had largely come to a standstill. The Welcome and Service Desk for Doctoral Candidates and Postdocs will be closed for face-to-face contacts until further notice. p�$F�l�m����A U��t��S?��)��ͻZ�ݺc�������3�{ϥSGR�. Visit the SARS-CoV-2 data portal in ViPR. Barrierefreiheit. 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. The Pfam profile hidden Markov model (HMM) library in combination with the HMMER software facilitates rapid search and annotation of coronaviruses and can be used to generate multiple sequence alignments that allow the identification of mutations and clusters of related sequences, particularly useful for outbreak tracking and studying the evolution of Coronaviruses. Covidex is an alignment-free machine learning subtyping tool for viral species, based on a random forest model trained over a kmer database. Despite the fact that first facilities are re-opening under strict conditionshis, we ask you to learn and to work from home whenever possible and, in your personal behaviour, take into account that great efforts are still needed to contain the corona virus. 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. Sequence data are essential to design and evaluate diagnostic tests, to track and trace the ongoing outbreak, and to identify potential intervention options. VADR (Viral Annotation DefineR) validates and annotates viral sequences in GenBank submissions. 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. This also applies to the exams. On 20 March, the Friedrich Schiller University Jena went into emergency operation. However, we are still available for you via email. Restrictions due to Corona virus: Regulations for PhD and habilitation procedures. Corona News. Nextstrain is an open-source project to harness the scientific and public health potential of pathogen genome data. ��$�i��D`��ATV��@������ZWʲ]��ض PoSeiDon is a pipeline to detect significant positively selected sites and possible recombination events in an alignment of multiple coding sequences. 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. Powered by WordPress. These primer sets would be suitable for empirical testing. We cover workflows and tools for. We are curating a list of bioinformatics tools designed explicitly for SARS-CoV-2 and coronaviruses. 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. It allows for the detection of within-host genetic variation of SARS-CoV-2 from viral NGS data. And our most important services will continue: We are processing all incoming applications including your mail. Medizin-Studierende oder Personen mit medizinischer Vorbildung, die sich engagieren möchten, können sich an Karsten Krohn vom Universitätsklinikum Jena Krohn@med.uni-jena.de wenden. The University of Jena, officially the Friedrich Schiller University Jena (German: Friedrich-Schiller-Universität Jena, abbreviated FSU, shortened form Uni Jena) is a public research university located in Jena, Thuringia, Germany.. Encountering Covid-19: Jamais vu or Déjà vu? Through a review of the most relevant scientific literature, and considering different levels of experimental evidence, over 150 compounds have been identified that are potentially active against COVID-19. 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. I look forward to meeting you â online and in person. 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. 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. We are happy to answer your enquiries via our contact form. E-Mail: Please write an email to LehreLernen@uni-jena.de. ��-�X+�rO��4��L`-�K���L��Z2(
�}���`�d���W�~Lp"��th�z�'�4����ǂ@$��r��7j�L�^3�(�"�9�=����h� �;%� �BI�$*�9.�XF�Ordք� �����! Es werden keine Daten im Hintergrund erhoben, jeder Scan-Vorgang ist für den Nutzer vollständig nachvollziehbar. E-mail: stefanie.deinhardt-emmer@med.uni-jena.de Internalized ACE2 receptors release their virus cargo and are recycled back to the surface. On average the observed changes would be expected to have no or minimal consequence on virus biology. 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. Präsidium und Senat der Friedrich-Schiller-Universität Jena haben sich zum Ziel gesetzt, alle Nachteile, die Studierenden durch Corona entstehen, auszugleichen. They provide a continually-updated view of publicly available data alongside powerful analytic and visualization tools for use by the community. Lectures during Corona. Predicted proteins encoded by the sequence are validated with nucleotide-to-protein alignments using BLAST. 5Institute for Medical Microbiology, University Hospital Jena, Am Klinikum 1, 07747 Jena. International organizations take action in order to prevent a further spread of the virusâwith the World Health Organization (WHO) leading the ⦠The European COVID-19 Data Portal was launched by EMBL-EBI in conjunction with the European Commission, the European Open Science Cloud and ELIXIR, as part of the wider European COVID-19 Data Platform. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries. Corona-News: Thüringer mit medizinischer Erfahrung gesucht - Jena meldet Rekordwert 36 Menschen, die mit dem Coronavirus infiziert waren, sind innerhalb eines Tages in Thüringen verstorben. Step-by-step guide. 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. Welcome to the Chair of International Relations at Friedrich Schiller University Jena! Informatik II (B.Sc. UniProt also hosted webinars to describe the portal and publication submission system. And our most important services will continue: We are processing all incoming applications including your mail. With great discipline we have all contributed to keep the number of sick people in Jena low. [�{�I�)�$ ʚ3;tA!paTB�>XZL���z��P� ]� ��T�ˀ�{���� �6ׂcPYp�C �ǘ���Ys4*8��d�¦��B�֚S�1ơĴ��3`���TCDy�U^@�:�Y�x�ЁZ�����h�ᅌ0�yf���I��v�l���7��t�O��ȌJ�����W��q�i\�
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"Bc�.��K��'�(hF�Eޔ���Fk��5����AGg�ӷ!Fiz��ʺ�Ԇ{�k���i�8 �oSS|\�@� �A�i�\�C�nh�D��Ê�\�I=���= 2m|��P������u�ɍ����mp+25�yR*�$?%T�gX�;ɲ>Snʖ&�k�V��o:yY�I�m��l��i+k wo�k���ך@M��5��Si� 0n���t��.u��xԥP�szi dr+���e��o2SV�$�&5b�0��b�[��*�^C�3~���h`R��/��� �;�D>��_���+��Y7�C=���;��� �u�mXr���ң�*��h�\�&�$�LݰҶf�c�˱k+譱l��|?�~�dS� Please also use the e-mail address corona@jena.de. The model includes a basic pharmacodynamic response (to assembled virions) to cause cell apoptosis. Thus, the community can assist in associating new or missing publications to relevant UniProt entries. coronapp is a web application to annotate and monitor SARS-CoV-2 mutations, both worldwide and in user-selected countries. This is a fast-paced project with the COVID-19 Data Portal featuring relevant datasets from EMBL-EBI Data Resources including the European Nucleotide Archive (ENA), UniProt, Protein Data Bank in Europe (PDBe), the Electron Microscopy Data Bank (EMDB), Expression Atlas, ChEMBL, and Europe PMC. Dezember 2020 . This includes genetic sequence and related clinical and epidemiological data to help researchers understand how viruses evolve and spread during epidemics and pandemics. Further you can analyze the data online using sequence alignment, phylogenetic tree reconstruction, sequence variation (SNP), metadata-driven comparative analysis and BLAST. The virus is uncoated to explose viral RNA, which synthesizes viral proteins that are assembled into a virion. "doc-in" is the online administration for doctoral procedures at the Friedrich Schiller University Jena and accompanies you through the entire PhD phase. It tackles the computationally expensive steps with linear runtime filters and efficient encodings. Tools by EVBC members are marked ★. (raumverwaltung@uni-jena.de) in good time â one week in advance as a rule â to discuss arrangements. V-Pipe has released a new version specifically adapted to analyze high-throughput sequencing data of SARS-CoV-2. Hier finden Sie wichtige Informationen, die Sie im Zusammenhang mit dem Coronavirus wissen sollten. Letzter Stand: 16. The corona pandemic is fundamentally changing the everyday life of many people â this naturally also affects students. 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. Henceforth, it is possible to proceed the studies or to start the studies without being physically in Jena. 07743 Jena. Photonics course are held, e.g. The Pfam protein families database is widely used in the field of molecular biology for large-scale functional annotation of proteins. 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. In the autumn of 1986, I got a box of apples from my uncle. ������4�v
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��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 The LitCovid dataset contains a selection of papers referring to Coronavirus 19 disease. If anything, the Corona crisis forces us to be creative about our teaching. This literature curation effort is now, Complete the online application form providing answers as directed Ensure you add relevant information to the “Application submission” section where you are asked to provide three 100-word paragraphs that cover your: scientific biography work history current research interests Upload a letter of support from your supervisor or a senior colleague, Complete the online application form Ensure you add relevant information to the “application submission” section where you are asked to provide three 100-word paragraphs that cover your: scientific biography work history current research interests Upload a letter of support from your supervisor or a senior colleague detailing reasons why you should be selected, International Virus Bioinformatics Meeting 2020, SARS-CoV-2 genome browser and related resources, Phylogeographic reconstruction using air transportation data. BEAST 2 uses Markov chain Monte Carlo (MCMC) to average over tree space, so that each tree is weighted proportional to its posterior probability. We will meet the challenges head-on. 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. Both ELM and IUPred2A identify functional regions that are disordered and generally less conserved due to rapid evolvability, and hence their outputs complement the well conserved functional regions identified by Pfam. Among them is the ACP auditorium, where main lectures in the M.Sc. The latest release of Pfam, version 33.1, contains an updated set of models that comprehensively cover the proteins encoded by SARS-CoV-2. COVID-19 UniProt portal provides early pre-release access to (i) SARS-CoV-2 annotated protein sequences, (ii) closest SARS proteins from SARS 2003, (iii) human proteins relevant to the biology of viral infection, like receptors and enzymes, (iv) ProtVista visualisation of sequence features for each protein, (v) links to sequence analysis tools, (vi) access to collated community-contributed publications relevant to COVID-19, as well as (vii) links to relevant resources. ViralZone project is handled by the virus program of SwissProt group. However, tracking these changes will help us better understand the virus pandemic. I will strive to reduce this impact and to ensure the high quality of teaching you can expect from the University of Jena. It will determine the reliable analysis of sequencing data. Die Browser-basierte Lösun You can find more information at: iocm.uni-jena.de. BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. And we will overcome them, together. 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. Service hours of the hotline: daily 10:00 - 14:00. The latest 2020 release of ELM includes updated motif definitions and new instances covering nearly 300 motif classes based on over 3,400 publications. CORDITE (CORona Drug InTEractions database) collects and aggregates data from PubMed, MedRxiv, BioRxiv, and ChemRxiv for SARS-CoV-2. The European COVID-19 Data Portal was launched by EMBL-EBI in conjunction with the European Commission, the European Open Science Cloud and ELIXIR, as part of the wider European COVID-19 Data Platform. Currently, it supports FMDV and SARS-Cov-2 viral sequences. 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. Ten publication submissions have been received so far, contributing to our understanding of the virus biology. Oral examinations in the context of doctoral and habilitation procedures (disputations, colloquia, scientific lectures and talks) are currently not to be held. 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. 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. P-HIPSTer contains predicted viral-host PPIs for 15 human-infecting coronaviruses. The new search uses nhmmer and enables the users to explore the results using facets powered by the EBI Search. the discovery of potential drug targets and development of therapeutic strategies. Repurpose drugs. VirHostNet is a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks. ELM and IUPred2A mutually include each other’s predictions, and both methods utilize the newest data from UniProt and Pfam. The IUPred2A server is a biophysics-based prediction to identify intrinsically disordered protein regions (IDRs) and binding sites inside IDRs. BEAST 2 includes a graphical user-interface for setting up standard analyses and a suit of programs for analysing the results. 4Institute for Pharmaceutical Technology and Biopharmacy, Friedrich Schiller University Jena, Lessingstrasse 8, 07743 Jena. In this model, SARS-CoV-2 infects a single cell, or a solution of virions is administered to the extracellular space. 14.3k Followers, 294 Following, 894 Posts - See Instagram photos and videos from Universität Jena (@unijena) Find putative drug targets. PriSeT finds a primer set P balancing both: high taxonomic coverage and high resolution. The political actors therefore donât stop at their borders on the search for solutions. This heavy usage might lead to bottlenecks when it comes to setting up new meetings, or to disruptions when starting meetings. In the extracellular space, virions adhere to ACE2 receptors and get internalized through endocytosis. � �]{s�F��ۮ�w���Yr�|ʒE�ϖ��[��=)��Km��� ��3R��~���A"H�q��� ������|�7ή���̵�>q��;���j����3�w�k6�pay��9�˥J�;��^��bԆ��4�:貏!_�;��5�uW�T�ݸ�٭���5�R1=���m�E'��S$�LY���/�4eS*~�VK!m�IY)�BW���n�΄�eY!���
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�-!u�h�m0���b]s�p�kNݮ�����N�)�������|���xw>>��T�vɇ�/���vO��RL�ո#�cW���O�ݩ.��`e��*}�~�.� �sen��M�$W\���O���5�=΄��=[��(�8Z�)�wG�P���hKu��/��B���{�|ڳY�2���wKt�=�ܻ����T|�1��>��w\��]Z Essential information concerning this matter is ⦠the routine detection of SARS-CoV-2 infection. The Data Portal brings together and continuously updates the relevant COVID-19 datasets and tools. This also applies if you are using rooms for the examination that are not centrally managed. Designed using Hoot Business. The tool allows users to highlight and prioritize the most frequent mutations in specific protein regions, and to monitor their frequency in the population over time. [8r�vJ�b���������/9����b_�R�ͅkcz���׃�/��0M�o}yi���R�ɚ
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�_��F���jU� The ELM resource offers a collection of short linear motifs that mediate interactions crucial in both native cell regulation and pathogenic interference. International Organizations and Crisis Management - IOCM in short - is the masters degree in political science of the Chair for International Relations at the Friedrich-Schiller-University Jena. /� ��lJ�4��s����2�����7���a)h��D�u��s�f�N?�}=��B��t2c}��'@ҟ�@Ճ_/�������h��d��ejΘ��+��!T��;�)a�������7S��̉*-����p��/!�`����к/�fȋ�����/`
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�*�y+9�%���Қs�e���s0���0�&(��/����3�M��8�(��:U:OLp�u�lad�q���0g6�M}��˭�q�����v�=|� �/��77�$ Er koordiniert die Einsätze dieser Freiwilligen mit medizinischer Ausbildung. uni-assist has already taken comprehensive protective measures for the staff in its Berlin office. Person working on a computer Image: Glenn Carstens-Peters Despite the official case numbers of Covid-19 in Jena and Thuringia being very low (as of 23.06.2020), the coming winter semester will nevertheless take place online. Ъn�������K����o���h��E{ׁ�rθ3��燏"`G�A]
���G�p>�vw�}��O Users may also analyse their own SARS-CoV-2 sequences by submitting them to the web application to receive an interactive report containing visualisations of phylogenetic classification and highlighting genomic variation of potentially high impact, for example, linked to primer mismatches. If you wish to start a PhD at the University of Jena you have to register in the portal with your personal data. The Data Portal brings together and continuously updates the relevant COVID-19 datasets and tools. First Act. 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�
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����,���ϻ��9uļ�����]o��#>5)p��6�������y���r����l�C��n���������?�����l?t7t���]��$k�}W8x��sS���6Ѻߦ���m¡ߖX5n�>]l�@�)�˟6J��'". Beautiful, sweet-smelling, delicious apples. Thuringiaâs economy has been hit hard by the corona pandemic, plunging the state into a deep recession. COPASI is a software application for simulation and analysis of biochemical networks and their dynamics. 3TrophoSYS GmbH, Botzstrasse 5, 07743 Jena. The ViPR database integrates various types of data for multiple virus families. The opening page has been updated to give references to an overview of motif hijacking in viruses in general, and an application to detecting SARS-CoV-2 motif usage in host cell attachment and modulation. Due to the corona virus, Graduate Academy has to reduce some of its offers. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. 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. ... âThe corona crisis is the epitome of a transboundary crisisâ 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. SARS-CoV-2 genome browser and related resources, including the following data: Like for all Ensembl data, no restrictions on the use of the COVID-19 resources are placed. It collects and provides up-to-date information on computational predictions, in vitro, as well as in vivo study data. r�F�32� 9W Schools and daycare centres in Thuringia closed from 17 March. 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. the tracking of the COVID-19 pandemic and evaluation of containment measures. The COVID-19 portal enables community crowdsourcing of publications via the “Add a publication” feature within any entry. The Friedrich Schiller University Jena has equipped several lecture halls to provide live streaming of lectures and seminars. Informieren Sie bitte auch das Internationale Büro der Universität Jena: international@uni-jena.de 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. Please also have a look at our general list of virus bioinformatics tools. The goal is to aid epidemiological understanding and improve outbreak response. 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. 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. 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. The Master's programme starts in the winter semester 2020. Explore the virus-host interactome. SARS-CoV-2 release is coming (May, 1st). Die Seite wird regelmäßig aktualisiert und erweitert. Physik): Course takes place: Yes: Multimedia support: PDF (lecture slides), Video for the PDF (explanations of slides) Interaction: video conference, Discussion and feedback via discussion boards in Moodle (every week) This applies initially until the start of the summer semester lecture period on 4 ⦠�dj��N�cswdQ�.^�)�2 Y3
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"��";2�]���"���]���'- Nextstrain is incorporating SARS-CoV-2 genomes as soon as they are shared and provides analyses and situation reports. Friedrich-Schiller-Universität Jena, Institut für Angewandte Physik (IAP), Max-Wien-Platz 1, D-07743 Jena Corona virus: Availability and Restrictions at Graduate Academy. SARS-CoV-2 will naturally accumulate nucleotide mutations in its RNA genome as the pandemic progresses.
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