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Super paramagnetic clustering of protein sequences

Igor V Tetko, Axel Facius, Andreas Ruepp, Hans-Werner Mewes
<span title="2005-04-01">2005</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Detection of sequence homologues represents a challenging task that is important for the discovery of protein families and the reliable application of automatic annotation methods. The presence of domains in protein families of diverse function, inhomogeneity and different sizes of protein families create considerable difficulties for the application of published clustering methods. Our work analyses the Super Paramagnetic Clustering (SPC) and its extension, global SPC (gSPC) algorithm. These
more &raquo; ... gorithms cluster input data based on a method that is analogous to the treatment of an inhomogeneous ferromagnet in physics. For the SwissProt and SCOP databases we show that the gSPC improves the specificity and sensitivity of clustering over the original SPC and Markov Cluster algorithm (TRIBE-MCL) up to 30%. The three algorithms provided similar results for the MIPS FunCat 1.3 annotation of four bacterial genomes, Bacillus subtilis, Helicobacter pylori, Listeria innocua and Listeria monocytogenes. However, the gSPC covered about 12% more sequences compared to the other methods. The SPC algorithm was programmed in house using C++ and it is available at http://mips.gsf.de/proj/spc. The FunCat annotation is available at http://mips.gsf.de. The gSPC calculated to a higher accuracy or covered a larger number of sequences than the TRIBE-MCL algorithm. Thus it is a useful approach for automatic detection of protein families and unsupervised annotation of full genomes.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-6-82">doi:10.1186/1471-2105-6-82</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15804359">pmid:15804359</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1084344/">pmcid:PMC1084344</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sbnc6pfuu5btnnpmvlk2dqvpby">fatcat:sbnc6pfuu5btnnpmvlk2dqvpby</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427173730/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-6-82" 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/23/82/23822605c5bbafb22125d36a7c0f8ee251b69b99.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-6-82"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1084344" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Tissue-Specific Target Analysis of Disease-Associated MicroRNAs in Human Signaling Pathways

Andreas Kowarsch, Carsten Marr, Daniel Schmidl, Andreas Ruepp, Fabian J. Theis, Richard James Morris
<span title="2010-06-30">2010</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;
MicroRNAs are a large class of post-transcriptional regulators that bind to the 39 untranslated region of messenger RNAs. They play a critical role in many cellular processes and have been linked to the control of signal transduction pathways. Recent studies indicate that microRNAs can function as tumor suppressors or even as oncogenes when aberrantly expressed. For more general insights of disease-associated microRNAs, we analyzed their impact on human signaling pathways from two perspectives.
more &raquo; ... On a global scale, we found a core set of signaling pathways with enriched tissue-specific microRNA targets across diseases. The function of these pathways reflects the affinity of microRNAs to regulate cellular processes associated with apoptosis, proliferation or development. Comparing cancer and non-cancer related microRNAs, we found no significant differences between both groups. To unveil the interaction and regulation of microRNAs on signaling pathways locally, we analyzed the cellular location and process type of disease-associated microRNA targets and proteins. While disease-associated proteins are highly enriched in extracellular components of the pathway, microRNA targets are preferentially located in the nucleus. Moreover, targets of disease-associated microRNAs preferentially exhibit an inhibitory effect within the pathways in contrast to disease proteins. Our analysis provides systematic insights into the interaction of disease-associated microRNAs and signaling pathways and uncovers differences in cellular locations and process types of microRNA targets and disease-associated proteins.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0011154">doi:10.1371/journal.pone.0011154</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20614023">pmid:20614023</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2894853/">pmcid:PMC2894853</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uepsbg7nhnh27igfhfzvr7lrdi">fatcat:uepsbg7nhnh27igfhfzvr7lrdi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170925184716/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0011154&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/94/2e/942eb642fb3310450d94dd1a065b0b9bde20af8d.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.0011154"> <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/PMC2894853" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

MicroRNAs coordinately regulate protein complexes

Steffen Sass, Sabine Dietmann, Ulrike Burk, Simone Brabletz, Dominik Lutter, Andreas Kowarsch, Klaus F Mayer, Thomas Brabletz, Andreas Ruepp, Fabian Theis, Yu Wang
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
In animals, microRNAs (miRNAs) regulate the protein synthesis of their target messenger RNAs (mRNAs) by either translational repression or deadenylation. miRNAs are frequently found to be co-expressed in different tissues and cell types, while some form polycistronic clusters on genomes. Interactions between targets of co-expressed miRNAs (including miRNA clusters) have not yet been systematically investigated. Results: Here we integrated information from predicted and experimentally verified
more &raquo; ... RNA targets to characterize protein complex networks regulated by human miRNAs. We found striking evidence that individual miRNAs or coexpressed miRNAs frequently target several components of protein complexes. We experimentally verified that the miR-141-200c cluster targets different components of the CtBP/ZEB complex, suggesting a potential orchestrated regulation in epithelial to mesenchymal transition. Conclusions: Our findings indicate a coordinate posttranscriptional regulation of protein complexes by miRNAs. These provide a sound basis for designing experiments to study miRNA function at a systems level.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-5-136">doi:10.1186/1752-0509-5-136</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21867514">pmid:21867514</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3170341/">pmcid:PMC3170341</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4nftjleyc5cvxpt3qz45wynbea">fatcat:4nftjleyc5cvxpt3qz45wynbea</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830054651/https://bmcsystbiol.biomedcentral.com/track/pdf/10.1186/1752-0509-5-136?site=http://bmcsystbiol.biomedcentral.com" 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/c7/25/c72503b21f7abb71555fdc845e186866dacc8c6f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-5-136"> <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> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170341" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

OREST: the online resource for EST analysis

Brigitte Waegele, Thorsten Schmidt, H. Werner Mewes, Andreas Ruepp
<span title="2008-05-08">2008</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;
The generation of expressed sequence tag (EST) libraries offers an affordable approach to investigate organisms, if no genome sequence is available. OREST (http://mips.gsf.de/genre/proj/orest/index. html) is a server-based EST analysis pipeline, which allows the rapid analysis of large amounts of ESTs or cDNAs from mammalia and fungi. In order to assign the ESTs to genes or proteins OREST maps DNA sequences to reference datasets of gene products and in a second step to complete genome
more &raquo; ... Mapping against genome sequences recovers additional 13% of EST data, which otherwise would escape further analysis. To enable functional analysis of the datasets, ESTs are functionally annotated using the hierarchical FunCat annotation scheme as well as GO annotation terms. OREST also allows to predict the association of gene products and diseases by Morbid Map (OMIM) classification. A statistical analysis of the results of the dataset is possible with the included PROMPT software, which provides information about enrichment and depletion of functional and disease annotation terms. OREST was successfully applied for the identification and functional characterization of more than 3000 EST sequences of the common marmoset monkey (Callithrix jacchus) as part of an international collaboration.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn253">doi:10.1093/nar/gkn253</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18463135">pmid:18463135</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2447738/">pmcid:PMC2447738</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jct5mqmdknhc7niiznrhkrqwkm">fatcat:jct5mqmdknhc7niiznrhkrqwkm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224164053/http://pdfs.semanticscholar.org/5821/937c577812bb7e5f4a65de785802426a394a.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/58/21/5821937c577812bb7e5f4a65de785802426a394a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkn253"> <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/PMC2447738" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Internal Backpressure for Terabit Switch Fabrics

Anna V. Manolova, Sarah Ruepp, Andreas Rytlig, Michael Berger, Henrik Wessing, Lars Dittmann
<span title="">2012</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/64g2ddfw6bhmnktwtxqy44u534" style="color: black;">IEEE Communications Letters</a> </i> &nbsp;
Ruepp [5] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/lcomm.2011.112311.111791">doi:10.1109/lcomm.2011.112311.111791</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zw6smbaikzcmhmefl5636okbnu">fatcat:zw6smbaikzcmhmefl5636okbnu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190413174328/https://core.ac.uk/download/pdf/13791019.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/b6/e4/b6e4604c1b140a8f789d989d808f9dcf7045790e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/lcomm.2011.112311.111791"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

An evolutionary and structural characterization of mammalian protein complex organization

Philip Wong, Sonja Althammer, Andrea Hildebrand, Andreas Kirschner, Philipp Pagel, Bernd Geissler, Pawel Smialowski, Florian Blöchl, Matthias Oesterheld, Thorsten Schmidt, Normann Strack, Fabian J Theis (+2 others)
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
We have recently released a comprehensive, manually curated database of mammalian protein complexes called CORUM. Combining CORUM with other resources, we assembled a dataset of over 2700 mammalian complexes. The availability of a rich information resource allows us to search for organizational properties concerning these complexes. Results: As the complexity of a protein complex in terms of the number of unique subunits increases, we observed that the number of such complexes and the mean
more &raquo; ... ynonymous to synonymous substitution ratio of associated genes tend to decrease. Similarly, as the number of different complexes a given protein participates in increases, the number of such proteins and the substitution ratio of the associated gene also tends to decrease. These observations provide evidence relating natural selection and the organization of mammalian complexes. We also observed greater homogeneity in terms of predicted protein isoelectric points, secondary structure and substitution ratio in annotated versus randomly generated complexes. A large proportion of the protein content and interactions in the complexes could be predicted from known binary protein-protein and domain-domain interactions. In particular, we found that large proteins interact preferentially with much smaller proteins.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-9-629">doi:10.1186/1471-2164-9-629</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19108706">pmid:19108706</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2645396/">pmcid:PMC2645396</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h2pqnjqdqfgyzjfqrpi2sbzqjy">fatcat:h2pqnjqdqfgyzjfqrpi2sbzqjy</a> </span>
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HoPaCI-DB: host-PseudomonasandCoxiellainteraction database

Sophie Bleves, Irmtraud Dunger, Mathias C. Walter, Dimitrios Frangoulidis, Gabi Kastenmüller, Romé Voulhoux, Andreas Ruepp
<span title="2013-10-16">2013</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;
Bacterial infectious diseases are the result of multifactorial processes affected by the interplay between virulence factors and host targets. The host-Pseudomonas and Coxiella interaction database (HoPaCI-DB) is a publicly available manually curated integrative database (http://mips.helmholtzmuenchen.de/HoPaCI/) of host-pathogen interaction data from Pseudomonas aeruginosa and Coxiella burnetii. The resource provides structured information on 3585 experimentally validated interactions between
more &raquo; ... olecules, bioprocesses and cellular structures extracted from the scientific literature. Systematic annotation and interactive graphical representation of disease networks make HoPaCI-DB a versatile knowledge base for biologists and network biology approaches.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt925">doi:10.1093/nar/gkt925</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24137008">pmid:24137008</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3965080/">pmcid:PMC3965080</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tjskvii7djfc5mtkkucwgiuqge">fatcat:tjskvii7djfc5mtkkucwgiuqge</a> </span>
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Edgetic perturbation signatures represent known and novel cancer biomarkers

Evans Kataka, Jan Zaucha, Goar Frishman, Andreas Ruepp, Dmitrij Frishman
<span title="2020-03-09">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
edgetic perturbation signatures represent known and novel cancer biomarkers evans Kataka 1 , Jan Zaucha 1 , Goar frishman 3 , Andreas Ruepp 3 & Dmitrij frishman 1,2* isoform switching is a recently characterized  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-020-61422-3">doi:10.1038/s41598-020-61422-3</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32152446">pmid:32152446</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7062722/">pmcid:PMC7062722</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ezuyuxtimbc4xh5y4pyk63auhm">fatcat:ezuyuxtimbc4xh5y4pyk63auhm</a> </span>
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PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes

Andreas Ruepp, Andreas Kowarsch, Daniel Schmidl, Felix Bruggenthin, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Fabian J Theis
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
Genome Biology 2010, 11:R6 http://genomebiology.com/2010/11/1/R6 Page 6 of 11 Ruepp et al. Genome Biology 2010, 11:R6 http://genomebiology.com/2010/11/1/R6 Ruepp et al.  ...  Click here for file [ http://www.biomedcentral.com/content/supplementary/gb-2010-11-1-r6-S3.pdf ] Ruepp et al.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2010-11-1-r6">doi:10.1186/gb-2010-11-1-r6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20089154">pmid:20089154</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2847718/">pmcid:PMC2847718</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ang2ncikwbaadn6xwu2xaijzh4">fatcat:ang2ncikwbaadn6xwu2xaijzh4</a> </span>
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CIDeR: multifactorial interaction networks in human diseases

Martin Lechner, Veit Höhn, Barbara Brauner, Irmtraud Dunger, Gisela Fobo, Goar Frishman, Corinna Montrone, Gabi Kastenmüller, Brigitte Waegele, Andreas Ruepp
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
The pathobiology of common diseases is influenced by heterogeneous factors interacting in complex networks. CIDeR http://mips.helmholtz-muenchen.de/cider/ is a publicly available, manually curated, integrative database of metabolic and neurological disorders. The resource provides structured information on 18,813 experimentally validated interactions between molecules, bioprocesses and environmental factors extracted from the scientific literature. Systematic annotation and interactive
more &raquo; ... representation of disease networks make CIDeR a versatile knowledge base for biologists, analysis of large-scale data and systems biology approaches.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2012-13-7-r62">doi:10.1186/gb-2012-13-7-r62</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22809392">pmid:22809392</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3491383/">pmcid:PMC3491383</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/okq7fid6l5hsxpzod6b3nozwce">fatcat:okq7fid6l5hsxpzod6b3nozwce</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171010020423/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/22f/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvZ2ItMjAxMi0xMy03LXI2Mi5wZGY%3D.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/38/94/3894d4222017c9cb06fb885499130fd473ca4b07.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2012-13-7-r62"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491383" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CRONOS: the cross-reference navigation server

Brigitte Waegele, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Corinna Montrone, H.-Werner Mewes, Andreas Ruepp
<span title="2008-11-13">2008</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;
Cross-mapping of gene and protein identifiers between different databases is a tedious and time-consuming task. To overcome this, we developed CRONOS, a cross-reference server that contains entries from five mammalian organisms presented by major gene and protein information resources. Sequence similarity analysis of the mapped entries shows that the cross-references are highly accurate. In total, up to 18 different identifier types can be used for identification of cross-references. The
more &raquo; ... of the mapping could be improved substantially by exclusion of ambiguous gene and protein names which were manually validated. Organismspecific lists of ambiguous terms, which are valuable for a variety of bioinformatics applications like text mining are available for download. Availability: CRONOS is freely available to non-commercial users at
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btn590">doi:10.1093/bioinformatics/btn590</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19010804">pmid:19010804</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2638938/">pmcid:PMC2638938</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/asaoknrz6nc2ndfcsltmyv7isi">fatcat:asaoknrz6nc2ndfcsltmyv7isi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200312211024/https://watermark.silverchair.com/btn590.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAnMwggJvBgkqhkiG9w0BBwagggJgMIICXAIBADCCAlUGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMmmNLh1Ts-OzwuuJYAgEQgIICJiJhKJEPiJrMba5k5xU4RnjbW_2zLTt2gqAJ5Nbclqr7Fn3k3eXu_jaTgnVf3hYquVLkhrttQtiC7pr0MSn5Ra0fYDE1cIRYtIvqBgtai52-crHLm7T-OyxURMaqKkcoYh_WP9D_whWeg6m11_yu_GHJLLsifmr4dNOnV52qHBwGGNDKya0tVXQBqSSpIX0XTTx4i9P63kn3sfl1TXitEMB4koRE4AjbGrI-Jtcapw4FXjeCCfG0Q_mSv4OGuNdHjPwf5FuwXRxAQP9BsgEt4lhqiTHZ2OzHTsDjVUOyaM5sMre7gjRo7Pk60LV9jLgAbN2phchTpVYvd4SSyzNAaTFfFGEYvbYt5JkyYoDTU-jl1NifnpHM5wlovDznkngYVyunlPZA2vQcGgGDHVb72w5eAt7ZzEjVaP20_69oQXd92bQpHBpiXcW48GJ7gTFeyV282YXZmSel3Y_o1X7hcu3l6_WCP-74KxACIeVjO1bBN2tEoPbPZ6ujycAqd5WL1juIT575L7NPlBxV3fOB_k5EBRKEKQ65YR1FUWjbYn6ziqLi0DK3cxLh236qe7TdsdafFegdPyblGoNT0VFR8CiDyYfvHxeJf_bP6Bdy3PmWctSfBxWO2nDZb5D2kWJYauddbb8yIm8AZF_fhAf-b181wmGcmD8q1I7_hFg4NyyVOlUByK3ecPdpzhgdsEagYIHuxy3NjuOjUljxnRY7zxzZar-7mZo" 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/3f/85/3f851694037d46a226d56e8e226886e893faadae.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btn590"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638938" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

HSC-Explorer: A Curated Database for Hematopoietic Stem Cells

Corinna Montrone, Konstantinos D. Kokkaliaris, Dirk Loeffler, Martin Lechner, Gabi Kastenmüller, Timm Schroeder, Andreas Ruepp, Kevin D. Bunting
<span title="2013-07-30">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;
HSC-Explorer (http://mips.helmholtz-muenchen.de/HSC/) is a publicly available, integrative database containing detailed information about the early steps of hematopoiesis. The resource aims at providing fast and easy access to relevant information, in particular to the complex network of interacting cell types and molecules, from the wealth of publications in the field through visualization interfaces. It provides structured information on more than 7000 experimentally validated interactions
more &raquo; ... ween molecules, bioprocesses and environmental factors. Information is manually derived by critical reading of the scientific literature from expert annotators. Hematopoiesis-relevant interactions are accompanied with context information such as model organisms and experimental methods for enabling assessment of reliability and relevance of experimental results. Usage of established vocabularies facilitates downstream bioinformatics applications and to convert the results into complex networks. Several predefined datasets (Selected topics) offer insights into stem cell behavior, the stem cell niche and signaling processes supporting hematopoietic stem cell maintenance. HSC-Explorer provides a versatile web-based resource for scientists entering the field of hematopoiesis enabling users to inspect the associated biological processes through interactive graphical presentation. Citation: Montrone C, Kokkaliaris KD, Loeffler D, Lechner M, Kastenmü ller G, et al. (2013) HSC-Explorer: A Curated Database for Hematopoietic Stem Cells. PLoS ONE 8(7): e70348.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0070348">doi:10.1371/journal.pone.0070348</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23936191">pmid:23936191</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3728102/">pmcid:PMC3728102</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/35wt2urndzaw7oeahv2nbiomim">fatcat:35wt2urndzaw7oeahv2nbiomim</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171007224939/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0070348&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/b4/22/b42295ff9b3967363d18d7d2735476fdad645708.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0070348"> <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/PMC3728102" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CORUM: the comprehensive resource of mammalian protein complexes—2019

Madalina Giurgiu, Julian Reinhard, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone, Andreas Ruepp
<span title="2018-10-24">2018</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;
CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (67%), mouse (15%) and rat (10%). Given the vital functions of these macromolecular machines, their identification and functional characterization is foundational to our understanding of normal and disease biology. The new CORUM 3.0 release encompasses 4274 protein complexes offering the largest and most comprehensive publicly available dataset
more &raquo; ... of mammalian protein complexes. The CORUM dataset is built from 4473 different genes, representing 22% of the protein coding genes in humans. Protein complexes are described by a protein complex name, subunit composition, cellular functions as well as the literature references. Information about stoichiometry of subunits depends on availability of experimental data. Recent developments include a graphical tool displaying known interactions between subunits. This allows the prediction of structural interconnections within protein complexes of unknown structure. In addition, we present a set of 58 protein complexes with alternatively spliced subunits. Those were found to affect cellular functions such as regulation of apoptotic activity, protein complex assembly or define cellular localization. CORUM is freely accessible at http://mips.helmholtz-muenchen.de/corum/.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky973">doi:10.1093/nar/gky973</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30357367">pmid:30357367</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6323970/">pmcid:PMC6323970</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l6sjbhejtbebdcjlsagorffj4a">fatcat:l6sjbhejtbebdcjlsagorffj4a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190223113657/http://pdfs.semanticscholar.org/4ed9/1b8d37215bf3be6ac1f979868127237b80a1.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/4e/d9/4ed91b8d37215bf3be6ac1f979868127237b80a1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky973"> <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/PMC6323970" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Proteasome function is dispensable under normal but not under heat shock conditions inThermoplasma acidophilum

Andreas Ruepp, Christoph Eckerskorn, Matthew Bogyo, Wolfgang Baumeister
<span title="1998-03-20">1998</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kn6dhptylrb77b5atyiom5ysjm" style="color: black;">FEBS Letters</a> </i> &nbsp;
Hitherto the biology of proteolysis in prokaryotes, particularly in archaea, is only poorly understood. We have used the tri-peptide vinyl sulfone inhibitor carboxybenzyl-leucylleucyl-leucine vinyl sulfone (Z-L Q VS) to study the in vivo function of proteasomes in Thermoplasma acidophilum. Z-L Q VS is a potent inhibitor of the Thermoplasma proteasome and is capable of modifying 75 to 80% of the proteasomal L L-subunits in cell cultures. Inhibition of proteasomes has only marginal effects under
more &raquo; ... ormal growth conditions. Under heat shock conditions, however, the effects of proteasome inhibition are much more severe, to the extent of complete cell growth arrest. These data suggest that other proteolytic systems may exist that can compensate for the loss of proteasome function in T. acidophilum. z 1998 Federation of European Biochemical Societies.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0014-5793(98)00205-1">doi:10.1016/s0014-5793(98)00205-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/9541012">pmid:9541012</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x2h35t3fwzamtdqjhetvbqjxkm">fatcat:x2h35t3fwzamtdqjhetvbqjxkm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170925190132/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/2eb/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMDAxNDU3OTM5ODAwMjA1MQ%3D%3D.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/d7/90/d7907c2b20fd9ebd3197190145db1af7ce5bcfb0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0014-5793(98)00205-1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

CORUM: the comprehensive resource of mammalian protein complexes—2009

Andreas Ruepp, Brigitte Waegele, Martin Lechner, Barbara Brauner, Irmtraud Dunger-Kaltenbach, Gisela Fobo, Goar Frishman, Corinna Montrone, H.-Werner Mewes
<span title="2009-10-31">2009</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;
CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The new CORUM 2.0 release encompasses 2837 protein complexes offering the largest and most comprehensive publicly available dataset of mammalian protein complexes. The CORUM dataset is built from
more &raquo; ... 8 different genes, representing 16% of the protein coding genes in humans. Each protein complex is described by a protein complex name, subunit composition, function as well as the literature reference that characterizes the respective protein complex. Recent developments include mapping of functional annotation to Gene Ontology terms as well as cross-references to Entrez Gene identifiers. In addition, a 'Phylogenetic Conservation' analysis tool was implemented that analyses the potential occurrence of orthologous protein complex subunits in mammals and other selected groups of organisms. This allows one to predict the occurrence of protein complexes in different phylogenetic groups. CORUM is freely accessible at
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp914">doi:10.1093/nar/gkp914</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19884131">pmid:19884131</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2808912/">pmcid:PMC2808912</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d4tg33cdbzevdgzzafsvlia2nu">fatcat:d4tg33cdbzevdgzzafsvlia2nu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302025659/http://pdfs.semanticscholar.org/9cb6/0adaee8ac6500c17f84a6cd5634a45aef1d0.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/9c/b6/9cb60adaee8ac6500c17f84a6cd5634a45aef1d0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkp914"> <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/PMC2808912" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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