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Gene clusters involved in anaerobic benzoate degradation of Geobacter metallireducens

Simon Wischgoll, Dimitri Heintz, Franziska Peters, Anika Erxleben, Eric Sarnighausen, Ralf Reski, Alain Van Dorsselaer, Matthias Boll
<span title="2005-10-27">2005</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/f55g362z2zdsnfvbumwdj3b53i" style="color: black;">Molecular Microbiology</a> </i> &nbsp;
The degradation of aromatic compounds follows different biochemical principles in aerobic and anaerobic microorganisms. While aerobes dearomatize and cleave the aromatic ring by oxygenases, facultative anaerobes utilize an ATP-dependent ring reductase for the dearomatization of the activated key intermediate benzoyl-coenzyme A (CoA). In this work, the aromatic metabolism was studied in the obligately anaerobic model organism Geobacter metallireducens . The gene coding for a putative carboxylic
more &raquo; ... cid-CoA ligase was heterologously overexpressed and the gene product was characterized as a highly specific benzoate-CoA ligase catalysing the initial step of benzoate metabolism. However, no evidence for the presence of an ATP-dependent benzoyl-CoA reductase as observed in facultative anaerobes was obtained. In a proteomic approach benzoate-induced proteins were identified; the corresponding genes are organized in two clusters comprising 44 genes. Induction of representative genes during growth on benzoate was confirmed by reverse transcription polymerase chain reaction. The results obtained suggest that benzoate is activated to benzoyl-CoA, which is then reductively dearomatized to cyclohexa-1,5diene-1-carbonyl-CoA, followed by β β β β -oxidation reactions to acetyl-CoA units, as in facultatively anaerobic bacteria. However, in G. metallireducens the process of reductive benzene ring dearomatization appears to be catalysed by a set of completely different protein components comprising putative molybdenum and selenocysteine containing enzymes.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1365-2958.2005.04909.x">doi:10.1111/j.1365-2958.2005.04909.x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16313613">pmid:16313613</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ni5ls476lbfszlquux5dkchn7m">fatcat:ni5ls476lbfszlquux5dkchn7m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060114172644/http://www.plant-biotech.net:80/paper/MolecularMicrobiology_2005_Wischgoll_pageproof.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/79/86/79866b9fa7a2fd15c6baabbdd361044d39bea18b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1365-2958.2005.04909.x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Mining and evaluation of molecular relationships in literature

Christian Senger, Björn A. Grüning, Anika Erxleben, Kersten Döring, Hitesh Patel, Stephan Flemming, Irmgard Merfort, Stefan Günther
<span title="2012-01-13">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Motivation: Specific information on newly discovered proteins is often difficult to find in literature. Particularly if only sequences and no common names of proteins or genes are available, preceding sequence similarity searches can be crucial for the process of information collection. In drug research, it is important to know whether a small molecule targets only one specific protein or whether similar or homologous proteins are also influenced that may account for possible side effects.
more &raquo; ... ts: prolific (protein-literature investigation for interacting compounds) provides a one-step solution to investigate available information on given protein names, sequences, similar proteins or sequences on the gene level. Co-occurrences of UniProtKB/Swiss-Prot proteins and PubChem compounds in all PubMed abstracts are retrievable. Concise 'heat-maps' and tables display frequencies of co-occurrences. They provide links to processed literature with highlighted found protein and compound synonyms. Evaluation with manually curated drug-protein relationships showed that up to 69% could be discovered by automatic text-processing. Examples are presented to demonstrate the capabilities of prolific. Availability: The web-application is available at http://prolific .pharmaceutical-bioinformatics.de and a web service at http://www .pharmaceutical-bioinformatics.de/prolific/soap/
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts026">doi:10.1093/bioinformatics/bts026</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22247277">pmid:22247277</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/477n4tdtc5gwlfctflgv42vvzy">fatcat:477n4tdtc5gwlfctflgv42vvzy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224112449/http://pdfs.semanticscholar.org/551c/b7aa6b909540f351005658bf34755ed7699b.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/55/1c/551cb7aa6b909540f351005658bf34755ed7699b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts026"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

StreptomeDB 2.0—an extended resource of natural products produced by streptomycetes

Dennis Klementz, Kersten Döring, Xavier Lucas, Kiran K. Telukunta, Anika Erxleben, Denise Deubel, Astrid Erber, Irene Santillana, Oliver S. Thomas, Andreas Bechthold, Stefan Günther
<span title="2015-11-28">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Over the last decades, the genus Streptomyces has stirred huge interest in the scientific community as a source of bioactive compounds. The majority of all known antibiotics is isolated from these bacterial strains, as well as a variety of other drugs such as antitumor agents, immunosuppressants and antifungals. To the best of our knowledge, Strep-tomeDB was the first database focusing on compounds produced by streptomycetes. The new version presented herein represents a major step forward: its
more &raquo; ... content has been increased to over 4000 compounds and more than 2500 host organisms. In addition, we have extended the background information and included hundreds of new manually curated references to literature. The latest update features a unique scaffold-based navigation system, which enables the exploration of the chemical diversity of StreptomeDB on a structural basis. We have included a phylogenetic tree, based on 16S rRNA sequences, which comprises more than two-thirds of the included host organisms. It enables visualizing the frequency, appearance, and persistence of compounds and scaffolds in an evolutionary context. Additionally, we have included predicted MS-and NMRspectra of thousands of compounds for assignment of experimental data. The database is freely accessible via http://www.pharmaceutical-bioinformatics. org/streptomedb.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1319">doi:10.1093/nar/gkv1319</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26615197">pmid:26615197</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4702922/">pmcid:PMC4702922</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/u7svsg52wbcutnipkbzzzz6hom">fatcat:u7svsg52wbcutnipkbzzzz6hom</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722143410/https://discovery.dundee.ac.uk/ws/files/9834021/Nucl._Acids_Res._2016_Klementz_D509_14.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6b/6c/6b6c30fc6ec97bb1523a9f8b882e8e725b13ad49.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkv1319"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702922" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome Sequence of the Fungus Glarea lozoyensis: the First Genome Sequence of a Species from the Helotiaceae Family

Loubna Youssar, Björn Andreas Grüning, Anika Erxleben, Stefan Günther, Wolfgang Hüttel
<span title="">2012</span> <i title="American Society for Microbiology"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6ec5x3ljznbijf2rtf6dn2u5ta" style="color: black;">Eukaryotic Cell</a> </i> &nbsp;
The anamorphic fungus Glarea lozoyensis mutant strain 74030 is an overproducer of pneumocandin B 0 , which is chemically converted into Cancidas, a potent antibiotic against clinically important fungal pathogens. Pneumocandins are acylated, cyclic hexapeptides with unusual hydroxylated amino acids. With the Glarea lozoyensis genome, the first species from the large polyphyletic family Helotiaceae has been sequenced.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/ec.05302-11">doi:10.1128/ec.05302-11</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22302591">pmid:22302591</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3272893/">pmcid:PMC3272893</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yqhv27u4ibcsdafb42fk3a32ue">fatcat:yqhv27u4ibcsdafb42fk3a32ue</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429033455/https://ec.asm.org/content/eukcell/11/2/250.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8e/cc/8ecc418bc1a48e8dcf803e1f2f7552ee313738f1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1128/ec.05302-11"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> asm.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272893" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Combinatorial Omics Analysis Reveals Perturbed Lysosomal Homeostasis in Collagen VII-deficient Keratinocytes

Kerstin Thriene, Björn Andreas Grüning, Olivier Bornert, Anika Erxleben, Juna Leppert, Ioannis Athanasiou, Ekkehard Weber, Dimitra Kiritsi, Alexander Nyström, Thomas Reinheckel, Rolf Backofen, Cristina Has (+2 others)
<span title="2018-01-11">2018</span> <i title="American Society for Biochemistry &amp; Molecular Biology (ASBMB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/63atlvwyorhorfip35rcvk6bey" style="color: black;">Molecular &amp; Cellular Proteomics</a> </i> &nbsp;
The extracellular matrix protein collagen VII is part of the microenvironment of stratified epithelia and critical in organismal homeostasis. Mutations in the encoding gene COL7A1 lead to the skin disorder dystrophic epidermolysis bullosa (DEB), are linked to skin fragility and progressive inflammation-driven fibrosis that facilitates aggressive skin cancer. So far, these changes have been linked to mesenchymal alterations, the epithelial consequences of collagen VII loss remaining
more &raquo; ... d. As epithelial dysfunction is a principal initiator of fibrosis, we performed a comprehensive transcriptome and proteome profiling of primary human keratinocytes from DEB and control subjects to generate global and detailed images of dysregulated epidermal molecular pathways linked to loss of collagen VII. These revealed downregulation of interaction partners of collagen VII on mRNA and protein level, but also increased abundance of S100 pro-inflammatory proteins in primary DEB keratinocytes. Increased TGF-␤ signaling because of loss of collagen VII was associated with enhanced activity of lysosomal proteases in both keratinocytes and skin of collagen VII-deficient individuals. Thus, loss of a single structural protein, collagen VII, has extra-and intracellular consequences, resulting in inflammatory processes that enable tissue destabilization and promote keratinocyte-driven, progressive fibrosis. Molecular & Cellular
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/mcp.ra117.000437">doi:10.1074/mcp.ra117.000437</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29326176">pmid:29326176</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ftyzhgxiarae5gyvqus2zrn2nq">fatcat:ftyzhgxiarae5gyvqus2zrn2nq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190226215949/http://pdfs.semanticscholar.org/77ea/a97832514c6471631c42a40bbbf91ed09a45.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/77/ea/77eaa97832514c6471631c42a40bbbf91ed09a45.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1074/mcp.ra117.000437"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

Fostering accessible online education using Galaxy as an e-learning platform

Beatriz Serrano-Solano, Melanie C. Föll, Cristóbal Gallardo-Alba, Anika Erxleben, Helena Rasche, Saskia Hiltemann, Matthias Fahrner, Mark J. Dunning, Marcel H. Schulz, Beáta Scholtz, Dave Clements, Anton Nekrutenko (+3 others)
<span title="2021-05-13">2021</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
The COVID-19 pandemic is shifting teaching to an online setting all over the world. The Galaxy framework facilitates the online learning process and makes it accessible by providing a library of high-quality community-curated training materials, enabling easy access to data and tools, and facilitates sharing achievements and progress between students and instructors. By combining Galaxy with robust communication channels, effective instruction can be designed inclusively, regardless of the students' environments.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1008923">doi:10.1371/journal.pcbi.1008923</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33983944">pmid:33983944</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xe5lwcf66fbpbpqixfs5ok7a6e">fatcat:xe5lwcf66fbpbpqixfs5ok7a6e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210514062528/https://storage.googleapis.com/plos-corpus-prod/10.1371/journal.pcbi.1008923/1/pcbi.1008923.pdf?X-Goog-Algorithm=GOOG4-RSA-SHA256&amp;X-Goog-Credential=wombat-sa%40plos-prod.iam.gserviceaccount.com%2F20210514%2Fauto%2Fstorage%2Fgoog4_request&amp;X-Goog-Date=20210514T062528Z&amp;X-Goog-Expires=3600&amp;X-Goog-SignedHeaders=host&amp;X-Goog-Signature=44f712e57df20cef0d3b5d7648a1f577cf6f123600a04fef8fae8e640677197ba458ac8765699b37bf503ef87678e781c16f0a4b51401ba3946a3e9b8df0643728901840d3272fa8f6f092586995bd5e8dd4addc88263a4b349144f693d9408014c854ad6507247a006374ae052178b12424e08f46b5f4e60eab583712908ba3b18f26f8dac16f9e0acf8e84412cb29a046aa3a81252b52baeea938dcb720adda1332014d4988c38299abf6fa5c6ff9846d3d208ec432edf6028c7c099cd96b0e1a5fb60e29cc6da06525a14f7740d6f32644d052241344edcd4e94b3f66e5e563080b79efd75e13ccba895891f8dd1c2de0539932985ac0b98e22a367db35f3" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/9b/e7/9be7230d01ece98d3399ffa4eb36b2dfbff44140.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1008923"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a>

Thiopental Inhibits Global Protein Synthesis by Repression of Eukaryotic Elongation Factor 2 and Protects from Hypoxic Neuronal Cell Death

Christian I. Schwer, Cornelius Lehane, Timo Guelzow, Simone Zenker, Karl M. Strosing, Sashko Spassov, Anika Erxleben, Bernd Heimrich, Hartmut Buerkle, Matjaz Humar, Ferenc Gallyas
<span title="2013-10-22">2013</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Ischemic and traumatic brain injury is associated with increased risk for death and disability. The inhibition of penumbral tissue damage has been recognized as a target for therapeutic intervention, because cellular injury evolves progressively upon ATP-depletion and loss of ion homeostasis. In patients, thiopental is used to treat refractory intracranial hypertension by reducing intracranial pressure and cerebral metabolic demands; however, therapeutic benefits of thiopental-treatment are
more &raquo; ... roversially discussed. In the present study we identified fundamental neuroprotective molecular mechanisms mediated by thiopental. Here we show that thiopental inhibits global protein synthesis, which preserves the intracellular energy metabolite content in oxygen-deprived human neuronal SK-N-SH cells or primary mouse cortical neurons and thus ameliorates hypoxic cell damage. Sensitivity to hypoxic damage was restored by pharmacologic repression of eukaryotic elongation factor 2 kinase. Translational inhibition was mediated by calcium influx, activation of the AMP-activated protein kinase, and inhibitory phosphorylation of eukaryotic elongation factor 2. Our results explain the reduction of cerebral metabolic demands during thiopental treatment. Cycloheximide also protected neurons from hypoxic cell death, indicating that translational inhibitors may generally reduce secondary brain injury. In conclusion our study demonstrates that therapeutic inhibition of global protein synthesis protects neurons from hypoxic damage by preserving energy balance in oxygen-deprived cells. Molecular evidence for thiopental-mediated neuroprotection favours a positive clinical evaluation of barbiturate treatment. The chemical structure of thiopental could represent a pharmacologically relevant scaffold for the development of new organ-protective compounds to ameliorate tissue damage when oxygen availability is limited.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0077258">doi:10.1371/journal.pone.0077258</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24167567">pmid:24167567</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3805597/">pmcid:PMC3805597</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pnkwx5y2efcrfp5pljmvkj6fde">fatcat:pnkwx5y2efcrfp5pljmvkj6fde</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171008190636/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0077258&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ec/6b/ec6b42cda011ddf944a60dbcaa5db798ec4124f2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0077258"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3805597" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

Björn A. Grüning, Jörg Fallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, Florian Eggenhofer, Torsten Houwaart, Bérénice Batut, Pavankumar Videm, Andrea Bagnacani, Markus Wolfien, Steffen C. Lott (+8 others)
<span title="2017-06-05">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNAbased regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to
more &raquo; ... ombine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target predic-tion. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis. Availability: The RNA workbench is available at https: //github.com/bgruening/galaxy-rna-workbench.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx409">doi:10.1093/nar/gkx409</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28582575">pmid:28582575</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5570170/">pmcid:PMC5570170</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qhl5knnpazd3noomvloekfefsy">fatcat:qhl5knnpazd3noomvloekfefsy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429141812/https://repub.eur.nl/pub/108108/REPUB_108108_OA.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2e/36/2e36584c011a6ff5c95bdb1e522dbe1fe522fd67.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx409"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570170" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Community-driven data analysis training for biology [article]

Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, Clemens Blank, Anthony Bretaudeau, Loraine Guéguen, Martin Čech, John Chilton, Dave Clements, Olivia Doppelt-Azeroual (+24 others)
<span title="2017-11-29">2017</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The primary problem with the explosion of biomedical datasets is not the data itself, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training
more &raquo; ... erials. The key feature of our system is that it is not a static but a continuously improved collection of tutorials. By coupling tutorials with a web-based analysis framework, biomedical researchers can learn by performing computation themselves through a web-browser without the need to install software or search for example datasets. Our ultimate goal is to expand the breadth of training materials to include fundamental statistical and data science topics and to precipitate a complete re-engineering of undergraduate and graduate curricula in life sciences.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/225680">doi:10.1101/225680</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bbgha6r4rbhifp5zx3mdj6tt6e">fatcat:bbgha6r4rbhifp5zx3mdj6tt6e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502181111/https://www.biorxiv.org/content/biorxiv/early/2018/04/05/225680.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/86/3c/863c4fe77fdd4884e611bbd3536b3fc8ca5386ea.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/225680"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

The ChemicalToolbox: reproducible, user-friendly cheminformatics analysis on the Galaxy platform

Simon A. Bray, Xavier Lucas, Anup Kumar, Björn A. Grüning
<span title="2020-06-01">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5aubiwi6v5beng6iqzj577kiaa" style="color: black;">Journal of Cheminformatics</a> </i> &nbsp;
Acknowledgements The authors would like to thank the following for discussions and instructive comments: Rolf Backofen, Chris Barnett, Leo Biscassi, Stefan Bleher, Andrew Dalke, Anika Erxleben, Stefan  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13321-020-00442-7">doi:10.1186/s13321-020-00442-7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33431029">pmid:33431029</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cuyfjffoefeb7ajt2mpusoiqua">fatcat:cuyfjffoefeb7ajt2mpusoiqua</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200603104907/https://jcheminf.biomedcentral.com/track/pdf/10.1186/s13321-020-00442-7" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/85/f2/85f26020b0f48336aa745f3535451f1a8085c639.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13321-020-00442-7"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

La banque à Athènes au IVe siècle avant J.-C. : état de la question

Raymond Bogaert
<span title="">1986</span>
Erxleben n'a pas remarque.  ...  Erxleben, Klio 55 (1973)133. Voir notre critique supra p. 32sq. E. Erxleben, Klio 55 (1973) 131-132.144 Voir supra p. 4L 145 E. Erxleben, Klio 55 (1973) 130. 146 Voir R.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5169/seals-33386">doi:10.5169/seals-33386</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4xzzre7ciff2xa2oskcvxiwy5i">fatcat:4xzzre7ciff2xa2oskcvxiwy5i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211210104033/https://www.e-periodica.ch/cntmng?pid=mhl-001:1986:43::305" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/25/9f/259ffdaafe44067b0f4b520918ffdf986fdcad0a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5169/seals-33386"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Annotated catalogue of primate type specimens in the mammal collection of the Museum of Natural History Vienna

Simon Engelberger
<span title="">2010</span> <span class="release-stage">unpublished</span>
Tang[anika].; iv.1910; R. Grauer (no.68) leg., P.v. Oberländer don.; NMW 4478/B 3943 ♂ ad., skull, skin: Urwald hinter den Randbergen des Nordwestufers des Tanganika; iii.1910; R.  ...  Papio ERXLEBEN, 1777 Contrary to authors who classified the fife traditionally recognized baboon types as separate species (e.g. GROVES 2001 (e.g.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.25365/thesis.9962">doi:10.25365/thesis.9962</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cg6wcm52f5bynjfbwdpprkgj24">fatcat:cg6wcm52f5bynjfbwdpprkgj24</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20181005055840/http://othes.univie.ac.at/9962/1/2010-05-31_0600472.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2f/7f/2f7fc6e469229a49ef3fde390ddb3de39fd5ed2c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.25365/thesis.9962"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

2006 Sommersemester SS 2006

Universität, Technische Universität Dortmund, Technische Universität Dortmund
<span title="2011-08-12">2011</span>
Erxleben Jurkschat N.N. Erxleben Jurkschat N.N. Titel/ Nr.  ...  MA Erxleben Zachwie ja Costisella Keller/N.N. Costisella Keller/N.N. Erxleben Titel/ Nr.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17877/de290r-14122">doi:10.17877/de290r-14122</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/puuk3ers6rgbjniat4r4ghp52a">fatcat:puuk3ers6rgbjniat4r4ghp52a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200221220733/https://eldorado.tu-dortmund.de/bitstream/2003/28992/1/Vorlesungsverzeichnis_SoSe_2006.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.17877/de290r-14122"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Bibliographie critique

<span title="">2011</span> <i title="CAIRN"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/oqwh6tqr3jhyzj3wzpk7cfyvdq" style="color: black;">Etudes germaniques</a> </i> &nbsp;
Unter Mitarb. von Anika Meier. spectrum Literaturwissenschaft/ spectrum Literature. Komparatistische Studien/Comparative Studies 21.  ...  Après le tome 1 des cours de Lichtenberg sur les « sciences de la nature » (Lichtenbergs annotiertes Handexemplar der vierten Aufl age von Johann Christian Polykarp Erxleben : Anfangsgründe der Naturlehre  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3917/eger.261.0177">doi:10.3917/eger.261.0177</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/grah73opv5hfdfkihoy4lq4574">fatcat:grah73opv5hfdfkihoy4lq4574</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201214155414/https://www.cairn.info/load_pdf.php?ID_ARTICLE=EGER_261_0177&amp;download=1" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b0/cb/b0cb75a62c04002bf0dd1d87580331f0a0761553.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3917/eger.261.0177"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a>

A comparative study of the male genital tract in some species of shrews
Badania porównawcze układu płciowego męskiego niektórych gatunków ryjówek

Alina Kowalska-Dyrcz
<span title="1966-10-30">1966</span> <i title="Mammal Research Institute"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nrcmdz2qtrf25odiqzzc7lfzl4" style="color: black;">ACTA THERIOLOGICA</a> </i> &nbsp;
Z anika on p raw dopodobnie pod k on iec ży cia em brionalnego. E X P L A N A T IO N OF PLA T ES P la te V.  ...  ., K a udern (1911) in num erous Insectívora, M o s sm a n (1932) in Tamiasciurus hudsonicus (Erxleben, 1777), S z a r s k i (1935) in Mus musculus Linnaeus, 1758, and Raynaud (1951) in Microtus agrestis  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4098/at.arch.66-4">doi:10.4098/at.arch.66-4</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vuyzmmp6sfel3eoe3weyqpedxa">fatcat:vuyzmmp6sfel3eoe3weyqpedxa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428064505/http://rcin.org.pl/ibs/Content/9412/BI002_2613_Cz-40-2_Acta-T11-nr4-69-127_o.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fd/89/fd896a08f56cbf1aa33c18d2b727c46df3de371c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4098/at.arch.66-4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>
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