@article{Alfaiz2014, abstract = {TBC1D7 forms a complex with TSC1 and TSC2 that inhibits mTORC1 signaling and limits cell growth. Mutations in TBC1D7 were reported in a family with intellectual disability and macrocrania. Using exome sequencing we identified two sisters homozygote for the novel c.17_20delAGAG, p.R7TfsX21 TBC1D7 truncating mutation. In addition to the already described macrocephaly and mild intellectual disability, they share osteo-articular defects, patella dislocation, behavioral abnormalities, psychosis, learning difficulties, celiac disease, prognathism, myopia and astigmatism. Consistent with a loss-of-function of TBC1D7 the patient's cell lines show an increase in the phosphorylation of 4EBP1, a direct downstream target of mTORC1 and a delay in the initiation of the autophagy process. This second family allows enlarging the phenotypic spectrum associated with TBC1D7 mutations and defining a TBC1D7 syndrome. Our work reinforces the involvement of TBC1D7 in the regulation of mTORC1 pathways and suggests an altered control of autophagy as possible cause of this disease. This article is protected by copyright. All rights reserved.}, author = {Alfaiz, Ali Abdullah and Micale, Lucia and Mandriani, Barbara and Augello, Bartolomeo and Pellico, Maria Teresa and Chrast, Jacqueline and Xenarios, Ioannis and Zelante, Leopoldo and Merla, Giuseppe and Reymond, Alexandre}, doi = {10.1002/humu.22529}, journal = {Human Mutation: Variation, Informatics and Disease}, month = {mar}, pages = {447-451}, title = {TBC1D7Mutations are Associated with Intellectual Disability, Macrocrania, Patellar Dislocation, and Celiac Disease}, url = {https://www.researchgate.net/profile/Giuseppe_Merla/publication/260154207_TBC1D7_Mutations_are_Associated_with_Intellectual_Disability_Macrocrania_Patellar_Dislocation_and_Celiac_Disease/links/00b7d5303de1034b95000000.pdf}, volume = {35}, year = {2014} } @article{Altenhoff2016, abstract = {Achieving high accuracy in orthology inference is essential for many comparative, evolutionary and functional genomic analyses, yet the true evolutionary history of genes is generally unknown and orthologs are used for very different applications across phyla, requiring different precision-recall trade-offs. As a result, it is difficult to assess the performance of orthology inference methods. Here, we present a community effort to establish standards and an automated web-based service to facilitate orthology benchmarking. Using this service, we characterize 15 well-established inference methods and resources on a battery of 20 different benchmarks. Standardized benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimum requirement for new tools and resources, and guides the development of more accurate orthology inference methods.}, author = {Altenhoff, Adrian M. and Dalquen, Daniel A. and Huerta-Cepas, Jaime and Boeckmann, Brigitte and Bork, Peer and Capella-Gutiérrez, Salvador and Forslund, Kristoffer and Pereira, Cécile and DeLuca, Todd and Martin, Maria J. and Schreiber, Fabian and Sjölander, Kimmen and Szklarczyk, Damian and Gabaldón, Toni and Xenarios, Ioannis and da Silva, Alan Sousa and Jensen, Lars Juhl and Lewis, Suzanna E. and Linard, Benjamin and Train, Clément-Marie and Pryszcz, Leszek P. and Dessimoz, Christophe and von Mering, Christian and Lecompte, Odile and Muffato, Matthieu and Thomas, Paul D. and Consortium, Quest for Orthologs and Sonnhammer, Erik}, doi = {10.1038/nmeth.3830}, journal = {Nature Methods}, month = {apr}, pages = {425-430}, title = {Standardized benchmarking in the quest for orthologs}, url = {http://www.nature.com/nmeth/journal/v13/n5/pdf/nmeth.3830.pdf}, volume = {13}, year = {2016} } @article{Bonzanni2013, abstract = {Motivation: Combinatorial interactions of transcription factors with cis-regulatory elements control the dynamic progression through successive cellular states and thus underpin all metazoan development. The construction of network models of cis-regulatory elements, therefore, has the potential to generate fundamental insights into cellular fate and differentiation. Haematopoiesis has long served as a model system to study mammalian differentiation, yet modelling based on experimentally informed cis-regulatory interactions has so far been restricted to pairs of interacting factors. Here, we have generated a Boolean network model based on detailed cis-regulatory functional data connecting 11 haematopoietic stem/progenitor cell (HSPC) regulator genes.}, author = {Bonzanni, Nicola and Anton Feenstra, K. and Garg, Abhishek and Feenstra, K. Anton and Schütte, Judith and Kinston, Sarah and Miranda-Saavedra, Diego and Heringa, Jaap and Xenarios, Ioannis and Göttgens, Berthold}, doi = {10.1093/bioinformatics/btt243}, journal = {Bioinformatics}, month = {jun}, pages = {i80-i88}, title = {Hard-wired heterogeneity in blood stem cells revealed using a dynamic regulatory network model}, url = {http://www.ncbi.nlm.nih.gov/pubmed/23813012}, volume = {29}, year = {2013} } @article{Bugliani2013, abstract = {To shed light on islet cell molecular phenotype in human type 2 diabetes (T2D), we studied the transcriptome of non-diabetic (ND) and T2D islets to then focus on the ubiquitin-proteasome system (UPS), the major protein degradation pathway. We assessed gene expression, amount of ubiquitinated proteins, proteasome activity, and the effects of proteasome inhibition and prolonged exposure to palmitate. Microarray analysis identified more than one thousand genes differently expressed in T2D islets, involved in many structures and functions, with consistent alterations of the UPS. Quantitative RT-PCR demonstrated downregulation of selected UPS genes in T2D islets and beta cell fractions, with greater ubiquitin accumulation and reduced proteasome activity. Chemically induced reduction of proteasome activity was associated with lower glucose-stimulated insulin secretion, which was partly reproduced by palmitate exposure. These results show the presence of many changes in islet transcriptome in T2D islets and underline the importance of the association between UPS alterations and beta cell dysfunction in human T2D. © 2012 Elsevier Ireland Ltd. ; SCOPUS: ar.j ; info:eu-repo/semantics/published}, author = {Bugliani, Marco and Liechti, Robin and Cheon, Hwanju H. and Suleiman, Mara M. and Marselli, Lorella and Kirkpatrick, Clare C. and Filipponi, Franco F. and Boggi, Ugo U. and Xenarios, Ioannis and Syed, Farooq F. and Ladrière, Laurence and Wollheim, Claes C. and Lee, Myung-Shik M.-S. and Marchetti, Piero}, doi = {10.1016/j.mce.2012.12.001}, journal = {Molecular and Cellular Endocrinology}, month = {mar}, pages = {1-10}, title = {Microarray analysis of isolated human islet transcriptome in type 2 diabetes and the role of the ubiquitin-proteasome system in pancreatic beta cell dysfunction}, url = {https://dipot.ulb.ac.be/dspace/bitstream/2013/167735/1/Elsevier_151365.pdf}, volume = {367}, year = {2013} } @article{Claes2014, abstract = {Combining epidemiological information, genetic characterization and geomapping in the analysis of influenza can contribute to a better understanding and description of influenza epidemiology and ecology, including possible virus reassortment events. Furthermore, integration of information such as agroecological farming system characteristics can provide new knowledge on risk factors of influenza emergence and spread. Integrating viral characteristics into an animal disease information system is therefore expected to provide a unique tool to trace-and-track particular virus strains; generate clade distributions and spatiotemporal clusters; screen for distribution of viruses with specific molecular markers; identify potential risk factors; and analyze or map viral characteristics related to vaccines used for control and/or prevention. For this purpose, a genetic module was developed within EMPRES-i (FAO’s global animal disease information system) linking epidemiological information from influenza events with virus characteristics and enabling combined analysis. An algorithm was developed to act as the interface between EMPRES-i disease event data and publicly available influenza virus sequences in OpenfluDB. This algorithm automatically computes potential links between outbreak event and sequences, which are subsequently manually validated by experts. Subsequently, other virus characteristics such as antiviral resistance can then be associated to outbreak data. To visualize such characteristics on a geographic map, shape files with virus characteristics to overlay on other EMPRES-i map layers (e.g. animal densities) can be generated. The genetic module allows export of associated epidemiological and sequence data for further analysis. FAO has made this tool available for scientists and policy makers. Contributions are expected from users to improve and validate the number of linked influenza events and isolate information as well as the quality of information. Possibilities to interconnect with other influenza sequence databases or to expand the genetic module to other viral diseases (e.g. foot and mouth disease) are being explored.}, author = {Claes, Filip and Kuznetsov, Dmitry and Liechti, Robin and Von Dobschuetz, Sophie and Dinh Truong, Bao and Truong, Bao Dinh and Gleizes, Anne and Conversa, Daniele and Colonna, Alessandro and Demaio, Ettore and Ramazzotto, Sabina and Larfaoui, Fairouz and Pinto, Julio and Le Mercier, Philippe and Mercier, Philippe Le and Xenarios, Ioannis and Dauphin, Gwenaelle}, doi = {10.1093/database/bau008}, journal = {Database}, month = {mar}, pages = {bau008-bau008}, title = {The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses}, url = {http://dx.doi.org/10.1093/database/bau008}, volume = {2014}, year = {2014} } @article{Cruciani-Guglielmacci2017, author = {Cruciani-Guglielmacci, Céline and Bellini, Lara and Denom, Jessica and Oshima, Masaya and Fernandez, Neïké and Normandie-Levi, Priscilla and Berney, Xavier P. and Kassis, Nadim and Rouch, Claude and Dairou, Julien and Gorman, Tracy and Smith, David M. and Marley, Anna and Liechti, Robin and Kuznetsov, Dmitry and Wigger, Leonore and Burdet, Frédéric and Lefèvre, Anne-Laure and Wehrle, Isabelle and Uphues, Ingo and Hildebrandt, Tobias and Rust, Werner and Bernard, Catherine and Ktorza, Alain and Rutter, Guy A. and Scharfmann, Raphael and Xenarios, Ioannis and Le Stunff, Hervé and Thorens, Bernard and Magnan, Christophe and Ibberson, Mark}, doi = {10.1016/j.molmet.2017.01.009}, month = {jan}, title = {Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers a role for Elovl2 in glucose-induced insulin secretion}, url = {http://doi.org/10.1016/j.molmet.2017.01.009}, year = {2017} } @article{Deforges2019, author = {Deforges, Jules and Reis, Rodrigo S. and Jacquet, Philippe and Sheppard, Shaoline and Gadekar, Veerendra P. and Hart-Smith, Gene and Tanzer, Andrea and Hofacker, Ivo L. and Iseli, Christian and Xenarios, Ioannis and Poirier, Yves}, doi = {10.1104/pp.19.00043}, journal = {Plant Physiology}, month = {feb}, pages = {305-322}, title = {Control of Cognate Sense mRNA Translation by cis-Natural Antisense RNAs}, url = {https://oadoi.org/10.1104/pp.19.00043}, volume = {180}, year = {2019} } @article{Ibberson2013, abstract = {PURPOSE: Tumor-associated TIE-2-expressing monocytes (TEM) are highly proangiogenic cells critical for tumor vascularization. We previously showed that, in human breast cancer, TIE-2 and VEGFR pathways control proangiogenic activity of TEMs. Here, we examine the contribution of these pathways to immunosuppressive activity of TEMs. EXPERIMENTAL DESIGN: We investigated the changes in immunosuppressive activity of TEMs and gene expression in response to specific kinase inhibitors of TIE-2 and VEGFR. The ability of tumor TEMs to suppress tumor-specific T-cell response mediated by tumor dendritic cells (DC) was measured in vitro. Characterization of TEM and DC phenotype in addition to their interaction with T cells was done using confocal microscopic images analysis of breast carcinomas. RESULTS: TEMs from breast tumors are able to suppress tumor-specific immune responses. Importantly, proangiogenic and suppressive functions of TEMs are similarly driven by TIE-2 and VEGFR kinase activity. Furthermore, we show that tumor TEMs can function as antigen-presenting cells and elicit a weak proliferation of T cells. Blocking TIE-2 and VEGFR kinase activity induced TEMs to change their phenotype into cells with features of myeloid dendritic cells. We show that immunosuppressive activity of TEMs is associated with high CD86 surface expression and extensive engagement of T regulatory cells in breast tumors. TIE-2 and VEGFR kinase activity was also necessary to maintain high CD86 surface expression levels and to convert T cells into regulatory cells. CONCLUSIONS: These results suggest that TEMs are plastic cells that can be reverted from suppressive, proangiogenic cells into cells that are able to mediate an antitumoral immune response.}, author = {Ibberson, Mark and Bron, Sylvian and Guex, Nicolas and Faes-Van't Hull, Eveline and Ifticene-Treboux, Assia and Henry, Luc and Lehr, Ha-A. and Delaloye, Jf-F. and Coukos, George and Xenarios, Ioannis and Doucey, Marie-Agnès}, doi = {10.1158/1078-0432.ccr-12-3181}, month = {may}, title = {TIE-2 and VEGFR kinase activities drive immunosuppressive function of TIE-2-expressing monocytes in human breast tumors.}, url = {http://clincancerres.aacrjournals.org/content/clincanres/19/13/3439.full.pdf}, year = {2013} } @article{Liechti2016, author = {Liechti, Robin and George, Nancy and El-Gebali, Sara and Götz, Lou and Chasapi, Anastasia and Crespo, Isaac and Xenarios, Ioannis and Lemberger, Thomas}, doi = {10.1038/nmeth.4471}, journal = {Nature Methods}, month = {jun}, pages = {1021-1022}, title = {SourceData - a semantic platform for curating and searching figures}, url = {http://www.nature.com/articles/nmeth.4471.pdf}, volume = {14}, year = {2016} } @article{Marti-Solano2014, author = {Marti-Solano, Maria and Birney, Ewan and Bril, Antoine and Pasqua, Oscar Della and Kitano, Hiroaki and Mons, Barend and Xenarios, Ioannis and Sanz, Ferran}, doi = {10.1038/nrd4290}, journal = {Nature Reviews Drug Discovery}, month = {apr}, pages = {239-240}, title = {Integrative knowledge management to enhance pharmaceutical R&D}, url = {http://www.nature.com/articles/nrd4290.pdf}, volume = {13}, year = {2014} } @article{Ounzain2014, author = {Ounzain, Samir and Micheletti, Rudi and Beckmann, Tal and Schroen, Blanche and Alexanian, Michael and Pezzuto, Iole and Crippa, Stefania and Nemir, Mohamed and Sarre, Alexandre and Johnson, Rory and Dauvillier, Jérôme and Burdet, Frédéric and Ibberson, Mark and Guigó, Roderic and Xenarios, Ioannis and Heymans, Stephane and Pedrazzini, Thierry}, doi = {10.1093/eurheartj/ehu180}, journal = {European Heart Journal}, month = {apr}, pages = {353-368}, title = {Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs}, url = {https://academic.oup.com/eurheartj/article-pdf/36/6/353/17899392/ehu180.pdf}, volume = {36}, year = {2014} } @article{Pagni2013, abstract = {Motivation: Analysis of millions of pyro-sequences is currently playing a crucial role in the advance of environmental microbiology. Taxonomy-independent, i.e. unsupervised, clustering of these sequences is essential for the definition of Operational Taxonomic Units. For this application, reproducibility and robustness should be the most sought after qualities, but have thus far largely been overlooked.}, author = {Pagni, Marco and Niculita-Hirzel, Hélène and Pellissier, Loïc and Dubuis, Anne and Xenarios, Ioannis and Guisan, Antoine and Sanders, Ian R. and Goudet, Jérôme and Guex, Nicolas}, doi = {10.1093/bioinformatics/btt149}, journal = {Bioinformatics}, month = {mar}, pages = {1268-1274}, title = {Density-based hierarchical clustering of pyro-sequences on a large scale—the case of fungal ITS1}, url = {https://academic.oup.com/bioinformatics/article-pdf/29/10/1268/723526/btt149.pdf}, volume = {29}, year = {2013} } @article{Pellissier2013, abstract = {The distribution of plants along environmental gradients is constrained by abiotic and biotic factors. Cumulative evidence attests of the impact of biotic factors on plant distributions, but only few studies discuss the role of belowground communities. Soil fungi, in particular, are thought to play an important role in how plant species assemble locally into communities. We first review existing evidence, and then test the effect of the number of soil fungal operational taxonomic units (OTUs) on plant species distributions using a recently collected dataset of plant and metagenomic information on soil fungi in the Western Swiss Alps. Using species distribution models (SDMs), we investigated whether the distribution of individual plant species is correlated to the number of OTUs of two important soil fungal classes known to interact with plants: the Glomeromycetes, that are obligatory symbionts of plants, and the Agaricomycetes, that may be facultative plant symbionts, pathogens, or wood decayers. We show that including the fungal richness information in the models of plant species distributions improves predictive accuracy. Number of fungal OTUs is especially correlated to the distribution of high elevation plant species. We suggest that high elevation soil show greater variation in fungal assemblages that may in turn impact plant turnover among communities. We finally discuss how to move beyond correlative analyses, through the design of field experiments manipulating plant and fungal communities along environmental gradients.}, author = {Pellissier, Loïc and Pinto-Figueroa, Eric and Niculita-Hirzel, Hélène and Moora, Mari and Villard, Lucas and Goudet, Jérome and Guex, Nicolas and Pagni, Marco and Xenarios, Ioannis and Sanders, Ian and Guisan, Antoine}, doi = {10.3389/fpls.2013.00500}, journal = {Frontiers in Plant Science}, month = {jan}, title = {Plant species distributions along environmental gradients: Do belowground interactions with fungi matter?}, url = {http://dx.doi.org/10.3389/fpls.2013.00500}, volume = {4}, year = {2013} } @article{Sankar2014, abstract = {Among various advantages, their small size makes model organisms preferred subjects of investigation. Yet, even in model systems detailed analysis of numerous developmental processes at cellular level is severely hampered by their scale. For instance, secondary growth of Arabidopsis hypocotyls creates a radial pattern of highly specialized tissues that comprises several thousand cells starting from a few dozen. This dynamic process is difficult to follow because of its scale and because it can only be investigated invasively, precluding comprehensive understanding of the cell proliferation, differentiation, and patterning events involved. To overcome such limitation, we established an automated quantitative histology approach. We acquired hypocotyl cross-sections from tiled high-resolution images and extracted their information content using custom high-throughput image processing and segmentation. Coupled with automated cell type recognition through machine learning, we could establish a cellular resolution atlas that reveals vascular morphodynamics during secondary growth, for example equidistant phloem pole formation. DOI: http://dx.doi.org/10.7554/eLife.01567.001}, author = {Sankar, Martial and Nieminen, Kaisa and Ragni, Laura and Xenarios, Ioannis and Hardtke, Christian S.}, doi = {10.7554/elife.01567}, journal = {eLife}, month = {feb}, title = {Automated quantitative histology reveals vascular morphodynamics during Arabidopsis hypocotyl secondary growth}, url = {https://doi.org/10.7554/elife.01567}, volume = {3}, year = {2014} } @article{Schmitter2013, abstract = {Abstract Background The yeast Schizosaccharomyces pombe is frequently used as a model for studying the cell cycle. The cells are rod-shaped and divide by medial fission. The process of cell division, or cytokinesis, is controlled by a network of signaling proteins called the Septation Initiation Network (SIN); SIN proteins associate with the SPBs during nuclear division (mitosis). Some SIN proteins associate with both SPBs early in mitosis, and then display strongly asymmetric signal intensity at the SPBs in late mitosis, just before cytokinesis. This asymmetry is thought to be important for correct regulation of SIN signaling, and coordination of cytokinesis and mitosis. In order to study the dynamics of organelles or large protein complexes such as the spindle pole body (SPB), which have been labeled with a fluorescent protein tag in living cells, a number of the image analysis problems must be solved; the cell outline must be detected automatically, and the position and signal intensity associated with the structures of interest within the cell must be determined. Results We present a new 2D and 3D image analysis system that permits versatile and robust analysis of motile, fluorescently labeled structures in rod-shaped cells. We have designed an image analysis system that we have implemented as a user-friendly software package allowing the fast and robust image-analysis of large numbers of rod-shaped cells. We have developed new robust algorithms, which we combined with existing methodologies to facilitate fast and accurate analysis. Our software permits the detection and segmentation of rod-shaped cells in either static or dynamic (i.e. time lapse) multi-channel images. It enables tracking of two structures (for example SPBs) in two different image channels. For 2D or 3D static images, the locations of the structures are identified, and then intensity values are extracted together with several quantitative parameters, such as length, width, cell orientation, background fluorescence and the distance between the structures of interest. Furthermore, two kinds of kymographs of the tracked structures can be established, one representing the migration with respect to their relative position, the other representing their individual trajectories inside the cell. This software package, called “RodCellJ”, allowed us to analyze a large number of S. pombe cells to understand the rules that govern SIN protein asymmetry. (Continued on next page) (Continued from previous page) Conclusions “RodCellJ” is freely available to the community as a package of several ImageJ plugins to simultaneously analyze the behavior of a large .}, author = {Schmitter, Daniel and Wachowicz, Paulina and Sage, Daniel and Chasapi, Anastasia and Xenarios, Ioannis and Simanis, Viesturs and Unser, Michael}, doi = {10.1186/1747-1028-8-6}, journal = {Cell Division}, month = {jan}, pages = {6}, title = {A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis}, url = {http://dx.doi.org/10.1186/1747-1028-8-6}, volume = {8}, year = {2013} } @article{Schuepbach2013, abstract = {Summary: The PROSITE resource provides a rich and well annotated source of signatures in the form of generalized profiles that allow protein domain detection and functional annotation. One of the major limiting factors in the application of PROSITE in genome and metagenome annotation pipelines is the time required to search protein sequence databases for putative matches. We describe an improved and optimized implementation of the PROSITE search tool pfsearch that, combined with a newly developed heuristic, addresses this limitation. On a modern x86_64 hyper-threaded quad-core desktop computer, the new pfsearchV3 is two orders of magnitude faster than the original algorithm.}, author = {Schuepbach, Thierry and Pagni, Marco and Bridge, Alan and Bougueleret, Lydie and Xenarios, Ioannis and Cerutti, Lorenzo}, doi = {10.1093/bioinformatics/btt129}, journal = {Bioinformatics}, month = {mar}, pages = {1215-1217}, title = {pfsearchV3: a code acceleration and heuristic to search PROSITE profiles}, url = {https://academic.oup.com/bioinformatics/article-pdf/29/9/1215/595909/btt129.pdf}, volume = {29}, year = {2013} } @article{Stockinger2014, abstract = {The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) was created in 1998 as an institution to foster excellence in bioinformatics. It is renowned worldwide for its databases and software tools, such as UniProtKB/Swiss-Prot, PROSITE, SWISS-MODEL, STRING, etc, that are all accessible on ExPASy.org, SIB's Bioinformatics Resource Portal. This article provides an overview of the scientific and training resources SIB has consistently been offering to the life science community for more than 15 years.}, author = {Stockinger, Heinz and von Mering, Christian and van Nimwegen, Erik and Altenhoff, Adrian M. and Arnold, Konstantin and Bairoch, Amos and Bastian, Frederic and Bergmann, Sven and Bougueleret, Lydie and Bucher, Philipp and Delorenzi, Mauro and Lane, Lydie and Mercier, Philippe Le and Lisacek, Frédérique and Michielin, Olivier and Palagi, Patricia M. and Rougemont, Jacques and Schwede, Torsten and Mering, Christian von and Zavolan, Mihaela and Nimwegen, Erik van and Zdobnov, Evgeny M. and Walther, Daniel and Xenarios, Ioannis and Zoete, Vincent and Appel, Ron D.}, doi = {10.1093/nar/gku380}, journal = {Nucleic Acids Research}, month = {may}, pages = {W436-W441}, title = {Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support}, url = {https://doi.org/10.1093/nar/gku380}, volume = {42}, year = {2014} } @article{Tanyi2018, abstract = {Personalized cancer vaccines induce antitumor T cells that correlate with clinical benefit in patients with ovarian cancer.}, author = {Tanyi, Janos L. and Bobisse, Sara and Ophir, Eran and Tuyaerts, Sandra and Roberti, Annalisa and Genolet, Raphael and Baumgartner, Petra and Stevenson, Brian J. and Iseli, Christian and Dangaj, Denarda and Czerniecki, Brian and Semilietof, Aikaterini and Racle, Julien and Michel, Alexandra and Xenarios, Ioannis and Chiang, Cheryl and Monos, Dimitri S. and Torigian, Drew A. and Nisenbaum, Harvey L. and Michielin, Olivier and June, Carl H. and Levine, Bruce L. and Powell, Daniel J. and Gfeller, David and Mick, Rosemarie and Dafni, Urania and Zoete, Vincent and Harari, Alexandre and Coukos, George and Kandalaft, Lana E.}, doi = {10.1126/scitranslmed.aao5931}, journal = {Science Translational Medicine}, month = {apr}, title = {Personalized cancer vaccine effectively mobilizes antitumor T cell immunity in ovarian cancer}, url = {https://oadoi.org/10.1126/scitranslmed.aao5931}, volume = {10}, year = {2018} } @article{Vizcaíno2014, author = {Vizcaíno, Juan A. and Deutsch, Eric W. and Wang, Rui and Csordas, Attila and Reisinger, Florian and Rios, Daniel and Sun, Zhi and Pablo Albar, Juan and Dianes, José A. and Farrah, Terry and Bandeira, Nuno and Binz, Pierre-Alain and Xenarios, Ioannis and Eisenacher, Martin and Mayer, Gerhard and Gatto, Laurent and Campos, Alex and Chalkley, Robert J. and Kraus, Hans-Joachim and Albar, Juan Pablo and Martínez-Bartolomé, Salvador and Apweiler, Rolf and Omenn, Gilbert S. and Martens, Lennart and Jones, Andrew R. and Hermjakob, Henning}, doi = {10.1038/nbt.2839}, journal = {Nature Biotechnology}, month = {mar}, pages = {223-226}, title = {ProteomeXchange provides globally coordinated proteomics data submission and dissemination}, url = {http://www.nature.com/articles/nbt.2839.pdf}, volume = {32}, year = {2014} } @article{Zhang2013, abstract = {A heme-containing transmembrane ferric reductase domain (FRD) is found in bacterial and eukaryotic protein families, including ferric reductases (FRE), and NADPH oxidases (NOX). The aim of this study was to understand the phylogeny of the FRD superfamily. Bacteria contain FRD proteins consisting only of the ferric reductase domain, such as YedZ and short bFRE proteins. Full length FRE and NOX enzymes are mostly found in eukaryotic cells and all possess a dehydrogenase domain, allowing them to catalyze electron transfer from cytosolic NADPH to extracellular metal ions (FRE) or oxygen (NOX). Metazoa possess YedZ-related STEAP proteins, possibly derived from bacteria through horizontal gene transfer. Phylogenetic analyses suggests that FRE enzymes appeared early in evolution, followed by a transition towards EF-hand containing NOX enzymes (NOX5- and DUOX-like). An ancestral gene of the NOX(1-4) family probably lost the EF-hands and new regulatory mechanisms of increasing complexity evolved in this clade. Two signature motifs were identified: NOX enzymes are distinguished from FRE enzymes through a four amino acid motif spanning from transmembrane domain 3 (TM3) to TM4, and YedZ/STEAP proteins are identified by the replacement of the first canonical heme-spanning histidine by a highly conserved arginine. The FRD superfamily most likely originated in bacteria.}, author = {Zhang, Xuezhi and Krause, Karl-Heinz and Xenarios, Ioannis and Soldati, Thierry and Boeckmann, Brigitte}, doi = {10.1371/journal.pone.0058126}, journal = {PLoS ONE}, month = {mar}, pages = {e58126}, title = {Evolution of the Ferric Reductase Domain (FRD) Superfamily: Modularity, Functional Diversification, and Signature Motifs}, url = {https://doi.org/10.1371/journal.pone.0058126}, volume = {8}, year = {2013} }