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Egon Willighagen › Comments

Egon Willighagen
A New Publicly Available Chemical Query Language, CSRML, to support Chemotype Representations for Application to Data Mining and Modeling - http://www.citeulike.org/user...
J. Chem. Inf. Model. (3 February 2015), doi:10.1021/ci500667v Chemotypes are a new approach for representing molecules, chemical substructures and patterns, reaction rules, and reactions. Chemotypes are capable of integrating types of information beyond what is possible using current representation methods (e.g., SMARTS patterns) or reaction transformations (e.g., SMIRKS, reaction SMILES). Chemotypes are expressed in the XML-based Chemical Subgraphs and Reactions Mark-up Language (CSRML), and can be encoded not only with connectivity and topology, but also with properties of atoms, bonds, electronic systems, or molecules. The CSRML language has been developed in parallel with a public set of chemotypes, i.e., the ToxPrint chemotypes, which are designed to provide excellent coverage of environmental, regulatory and commercial-use chemical space, as well as to represent chemical patterns and properties especially relevant to various toxicity concerns. A software application, ChemoTyper... - Egon Willighagen
Egon Willighagen
A M.Sc. thesis can be cited too, if stored and available! +Samuel Lampa's thesis resulted in this reuse... - https://plus.google.com/1041867...
A M.Sc. thesis can be cited too, if stored and available! +Samuel Lampa's thesis resulted in this reuse from Jan Wielemaker et al. in Amsterdam: "The Blipkit [18] system is a comprehensive system for querying and transforming data in bioinformatics. Blipkit’s RDF support in terms of performance and expressiveness was evaluated by Lampa [15]. Lampa stresses the enhanced maintainability of Prolog queries due to reuse of query fragments represented as predicates (Figure 18 in [15])." http://uu.diva-portal.org/smash... BTW, did you see those download counts?? If only DIVA used DOIs... Lampa, Samuel. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. (Prof. Jarl Wikberg, Bioclipse group). 2010 (English)Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis ... - Egon Willighagen
Egon Willighagen
Well, clearly the +American Chemical Society hasn't solved the cookie issue with their journals yet,... - https://plus.google.com/1041867...
Well, clearly the +American Chemical Society hasn't solved the cookie issue with their journals yet, but this is a paper by a large group of well-known cheminformaticians. The work seems interesting and will get back on the details. This is certainly a paper I like to review (in my blog and probably +Publons... it's about a proposed standard for substructure search specification. The CDK is used via the +KNIMETV nodes for the MACCS keys. The CDK website is cited, but none of the papers. Not for KNIME either, BTW. An Error Occurred Setting Your User Cookie. Your browser is currently set to not accept cookies. Please enable cookies in your web browser to continue. How do I enable cookies? For most browsers, the cookies settings are located under Preferences or Internet Options. - Egon Willighagen
Egon Willighagen
Reshared post from Egon Willighagen: - https://plus.google.com/1041867...
Original Post from Egon Willighagen: Well, clearly the +American Chemical Society hasn't solved the cookie issue with their journals yet, but this is a paper by a large group of well-known cheminformaticians. The work seems interesting and will get back on the details. This is certainly a paper I like to review (in my blog and probably +Publons... it's about a proposed standard for substructure search specification. The CDK is used via the +KNIMETV nodes for the MACCS keys. The CDK website is cited, but none of the papers. Not for KNIME either, BTW. An Error Occurred Setting Your User Cookie. Your browser is currently set to not accept cookies. Please enable cookies in your web browser to continue. How do I enable cookies? For most browsers, the cookies settings are located under Preferences or Internet Options. - Egon Willighagen
Egon Willighagen
A Quick Guide for Building a Successful Bioinformatics Community - http://www.citeulike.org/user...
PLoS Comput Biol, Vol. 11, No. 2. (5 February 2015), e1003972, doi:10.1371/journal.pcbi.1003972 “Scientific community” refers to a group of people collaborating together on scientific-research-related activities who also share common goals, interests, and values. Such communities play a key role in many bioinformatics activities. Communities may be linked to a specific location or institute, or involve people working at many different institutions and locations. Education and training is typically an important component of these communities, providing a valuable context in which to develop skills and expertise, while also strengthening links and relationships within the community. Scientific communities facilitate: (i) the exchange and development of ideas and expertise; (ii) career development; (iii) coordinated funding activities; (iv) interactions and engagement with professionals from other fields; and (v) other activities beneficial to individual participants, communities, and... - Egon Willighagen
Egon Willighagen
Programming: Pick up Python - http://www.citeulike.org/user...
Nature, Vol. 518, No. 7537. (4 February 2015), pp. 125-126, doi:10.1038/518125a Jeffrey Perkel - Egon Willighagen
Egon Willighagen
Our research school has a new logo. - https://plus.google.com/1041867...
Our research school has a new logo. As of January 2015 NUTRIM's name was changed into NUTRIM School of Nutrition and Translational Research in Metabolism. - Egon Willighagen
Egon Willighagen
Reshared post from Greg Landrum: - https://plus.google.com/1041867...
I like the $$$$ at the end... pharma product, I assume? :) Original Post from Greg Landrum: The new ChEMBL is here. Excellent! We are pleased to announce the release of ChEMBL_20. This version of the database was prepared on 14th January 2015 and contains: 1715135 compound records; 1463270 compounds (of which 1456020 have mol files); 13520737 activities; 1148942 assays; 10774 targets; 59610 source documents ... - Egon Willighagen
Egon Willighagen
Pathway databases and tools for their exploitation: benefits, current limitations and challenges - http://www.citeulike.org/user...
Molecular Systems Biology, Vol. 5, No. 1. (28 July 2009), doi:10.1038/msb.2009.47 In past years, comprehensive representations of cell signalling pathways have been developed by manual curation from literature, which requires huge effort and would benefit from information stored in databases and from automatic retrieval and integration methods. Once a reconstruction of the network of interactions is achieved, analysis of its structural features and its dynamic behaviour can take place. Mathematical modelling techniques are used to simulate the complex behaviour of cell signalling networks, which ultimately sheds light on the mechanisms leading to complex diseases or helps in the identification of drug targets. A variety of databases containing information on cell signalling pathways have been developed in conjunction with methodologies to access and analyse the data. In principle, the scenario is prepared to make the most of this information for the analysis of the dynamics of... - Egon Willighagen
Egon Willighagen
MetNetAPI: A flexible method to access and manipulate biological network data from MetNet - http://www.citeulike.org/user...
BMC Research Notes, Vol. 3, No. 1. (18 November 2010), 312, doi:10.1186/1756-0500-3-312 Convenient programmatic access to different biological databases allows automated integration of scientific knowledge. Many databases support a function to download files or data snapshots, or a webservice that offers "live" data. However, the functionality that a database offers cannot be represented in a static data download file, and webservices may consume considerable computational resources from the host server. Yves Sucaet, Eve Wurtele - Egon Willighagen
Egon Willighagen
Pathway Analysis for Drug Repositioning Based on Public Database Mining - http://www.citeulike.org/user...
J. Chem. Inf. Model., Vol. 54, No. 2. (26 January 2014), pp. 407-418, doi:10.1021/ci4005354 Sixteen FDA-approved drugs were investigated to elucidate their mechanisms of action (MOAs) and clinical functions by pathway analysis based on retrieved drug targets interacting with or affected by the investigated drugs. Protein and gene targets and associated pathways were obtained by data-mining of public databases including the MMDB, PubChem BioAssay, GEO DataSets, and the BioSystems databases. Entrez E-Utilities were applied, and in-house Ruby scripts were developed for data retrieval and pathway analysis to identify and evaluate relevant pathways common to the retrieved drug targets. Pathways pertinent to clinical uses or MOAs were obtained for most drugs. Interestingly, some drugs identified pathways responsible for other diseases than their current therapeutic uses, and these pathways were verified retrospectively by in vitro tests, in vivo tests, or clinical trials. The pathway... - Egon Willighagen
Egon Willighagen
#OpenDay   Brains Unlimited will have an Open Day! 27th January 2015. Take a look at the best scanners in the world, meet researchers, meet Brightlands Maastricht Health Campus and take a look at their plans for this Campus. Kids could take part in fun activities with Mad Science! Plus there will be more. - Egon Willighagen
Egon Willighagen
Cheminformatics for genome-scale metabolic reconstructions - http://www.citeulike.org/user...
(June 2014) JW May - Egon Willighagen
Egon Willighagen
eNanoMapper is well on its way to make a difference! This webinar is about the data storage component... - https://plus.google.com/1041867...
eNanoMapper is well on its way to make a difference! This webinar is about the data storage component. WEBINAR: The first eNanoMapper prototype: a substance database to support a safe innovation approach - Egon Willighagen
Egon Willighagen
The Dutch Techcentre for Life Sciences: Enabling data-intensive life science research in the Netherlands - http://www.citeulike.org/user...
F1000Research (2 February 2015), doi:10.12688/f1000research.6009.1 Lars Eijssen, Chris Evelo, Ruben Kok, Barend Mons, Rob Hooft - Egon Willighagen
Egon Willighagen
Enhancer Evolution across 20 Mammalian Species - http://www.citeulike.org/user...
Cell, Vol. 160, No. 3. (1 January 2015), pp. 554-566, doi:10.1016/j.cell.2015.01.006 The mammalian radiation has corresponded with rapid changes in noncoding regions of the genome, but we lack a comprehensive understanding of regulatory evolution in mammals. Here, we track the evolution of promoters and enhancers active in liver across 20 mammalian species from six diverse orders by profiling genomic enrichment of H3K27 acetylation and H3K4 trimethylation. We report that rapid evolution of enhancers is a universal feature of mammalian genomes. Most of the recently evolved enhancers arise from ancestral DNA exaptation, rather than lineage-specific expansions of repeat elements. In contrast, almost all liver promoters are partially or fully conserved across these species. Our data further reveal that recently evolved enhancers can be associated with genes under positive selection, demonstrating the power of this approach for annotating regulatory adaptations in genomic sequences. These... - Egon Willighagen
Egon Willighagen
Cytokines as biomarkers of nanoparticle immunotoxicity - http://www.citeulike.org/user...
Chemical Society Reviews, Vol. 42, No. 12. (2013), 5552, doi:10.1039/c3cs60064e Mahmoud Elsabahy, Karen Wooley - Egon Willighagen
Egon Willighagen
CLO: The cell line ontology - http://www.citeulike.org/user...
Journal of Biomedical Semantics In Journal of Biomedical Semantics, Vol. 5, No. 1. (2014), pp. 1-10, doi:10.1186/2041-1480-5-37 Background Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO consortium, new cell line cells, upper level alignment with the Cell Ontology (CL) and the Ontology for Biomedical Investigation, and logical extensions. Construction and content Collaboration among the CLO, CL, and OBI has established consensus definitions of cell line-specific terms such as ‘cell line’, ‘cell line cell’, ‘cell line culturing’, and ‘mortal’ vs. ‘immortal cell line cell’. A cell line is a genetically stable cultured cell population that contains individual cell line cells. The hierarchical structure of the CLO is built based on the hierarchy of the... - Egon Willighagen
Egon Willighagen
SPARQL-enabled identifier conversion with Identifiers.org - http://www.citeulike.org/user...
Bioinformatics (31 January 2015), btv064, doi:10.1093/bioinformatics/btv064 Motivation: On the Semantic Web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own IRI (International Resource Identifier) for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data.Results: We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data.Availability: The SPARQL-based identifier conversion service is available... - Egon Willighagen
Egon Willighagen
Clustering of crystal structures with a (true) supervised self-organizing map. It nicely shows that ... - https://plus.google.com/1041867...
Clustering of crystal structures with a (true) supervised self-organizing map. It nicely shows that the then popular energy-density plots do not show clustering of, basically, identical crystal structures. Willighagen, E. L., Wehrens, R., Melssen, W., de Gelder, R., Buydens, L. M. C., Sep. 2007. Supervised Self-Organizing maps in crystal property and structure prediction. Crystal Growth & Design 7 (9), 1738-1745. URL http://dx.doi.org/10... pubs.acs.org/appl/literatum/publisher/achs/journals/content/cgdefu/2007/cgdefu.2007.7.issue-9/cg060872y/production/images/medium/cg060872yn00001.gif - Egon Willighagen
Egon Willighagen
Metabolomics for Biomarker Discovery in Gastroenterological Cancer - http://www.citeulike.org/user...
Metabolites, Vol. 4, No. 3. (07 July 2014), pp. 547-571, doi:10.3390/metabo4030547 The study of the omics cascade, which involves comprehensive investigations based on genomics, transcriptomics, proteomics, metabolomics, etc., has developed rapidly and now plays an important role in life science research. Among such analyses, metabolome analysis, in which the concentrations of low molecular weight metabolites are comprehensively analyzed, has rapidly developed along with improvements in analytical technology, and hence, has been applied to a variety of research fields including the clinical, cell biology, and plant/food science fields. The metabolome represents the endpoint of the omics cascade and is also the closest point in the cascade to the phenotype. Moreover, it is affected by variations in not only the expression but also the enzymatic activity of several proteins. Therefore, metabolome analysis can be a useful approach for finding effective diagnostic markers and examining... - Egon Willighagen
Egon Willighagen
Acute Exercise Remodels Promoter Methylation in Human Skeletal Muscle - http://www.citeulike.org/user...
Cell Metabolism, Vol. 15, No. 3. (31 January 2015), pp. 405-411, doi:10.1016/j.cmet.2012.01.001 DNA methylation is a covalent biochemical modification controlling chromatin structure and gene expression. Exercise elicits gene expression changes that trigger structural and metabolic adaptations in skeletal muscle. We determined whether DNA methylation plays a role in exercise-induced gene expression. Whole genome methylation was decreased in skeletal muscle biopsies obtained from healthy sedentary men and women after acute exercise. Exercise induced a dose-dependent expression of PGC-1α, PDK4, and PPAR-δ, together with a marked hypomethylation on each respective promoter. Similarly, promoter methylation of PGC-1α, PDK4, and PPAR-δ was markedly decreased in mouse soleus muscles 45 min after ex vivo contraction. In L6 myotubes, caffeine exposure induced gene hypomethylation in parallel with an increase in the respective mRNA content. Collectively, our results provide evidence that acute... - Egon Willighagen
Egon Willighagen
System Model Network for Adipose Tissue Signatures Related to Weight Changes in Response to Calorie Restriction and Subsequent Weight Maintenance - http://www.citeulike.org/user...
PLoS Comput Biol, Vol. 11, No. 1. (2015), doi:10.1371/journal.pcbi.1004047 <title>Author Summary</title> <p>Obesity is an excess fat mass leading to metabolic diseases. Dietary management is a conve ntional strategy to promote weight loss. As energy buffering, in the form of esterified fatty acids, and secretory organ, the adipose tissu e has a pivotal role in obesity and its related complications. A comprehensive insight of adipose tissue response during and after calorie restriction might improve obesity management. Modern nutrition research study the impact of diet on health by combining multiple datasets t o provide an holistic view of tissue physiopathology. To identify significant clusters of fatty acids, transcripts or bio-clinical paramete rs related to weight change along calorie restriction and subsequent weight follow-up in obese individuals, the issue of different datasets integration must be resolved. Here, we implemented an innovative multistep approach to infer... - Egon Willighagen
Egon Willighagen
I cannot help but wonder why people do not just require exact specification of chemicals in drugs on... - https://plus.google.com/1041867...
I cannot help but wonder why people do not just require exact specification of chemicals in drugs on the market... it's insane this has to be done manually... The (probable) drugs of 2014 in PubChem and GtoPdb - Egon Willighagen
Egon Willighagen
Rare and Common Genetic Events in Type 2 Diabetes: What Should Biologists Know? - http://www.citeulike.org/user...
Cell Metabolism (January 2015), doi:10.1016/j.cmet.2014.12.020 Amélie Bonnefond, Philippe Froguel - Egon Willighagen
Egon Willighagen
(2003) Nutrient Metabolism defines the molecular fate of nutrients and other dietary compounds in humans, as well as outlining the molecular basis of processes supporting nutrition, such as chemical sensing and appetite control. It focuses on the presentation of nutritional biochemistry and the reader is given a clear and specific perspective on the events that control utilization of dietary compounds. Slightly over 100 self-contained chapters cover all essential and important nutrients as well as many other dietary compounds with relevance for human health. An essential read for healthcare professionals and researchers in all areas of health and nutrition who want to access the wealth of nutrition knowledge available today in one single source. Key Features: Highly illustrated with relevant chemical structures and metabolic pathways. Foreword by Steven Zeisel, Editor-in-chief of the Journal of Nutritional Biochemistry. First comprehensive work on the subject. Martin Kohlmeier - Egon Willighagen
Egon Willighagen
Transitive Credit as a Means to Address Social and Technological Concerns Stemming from Citation and Attribution of Digital Products - http://www.citeulike.org/user...
Journal of Open Research Software, Vol. 2, No. 1. (07 September 2014), e20, doi:10.5334/jors.be The pursuit of science and engineering research increasingly relies on activities that facilitate research but are not currently rewarded or recognized, such as development of products and infrastructure. In research publications, citations are used to credit previous works. This paper suggests that a modified citation system that includes the technological idea of transient credit could be used to recognize the developers of products other than research publications and that if this were done in a systematic manner, it would lead to social and cultural changes that would provide incentives for the further development of such products, accelerating overall scientific and engineering advances. Daniel Katz - Egon Willighagen
Egon Willighagen
Proteomics. Tissue-based map of the human proteome. - http://www.citeulike.org/user...
Science, Vol. 347, No. 6220. (23 January 2015), 1260419, doi:10.1126/science.1260419 Resolving the molecular details of proteome variation in the different tissues and organs of the human body will greatly increase our knowledge of human biology and disease. Here, we present a map of the human tissue proteome based on an integrated omics approach that involves quantitative transcriptomics at the tissue and organ level, combined with tissue microarray-based immunohistochemistry, to achieve spatial localization of proteins down to the single-cell level. Our tissue-based analysis detected more than 90% of the putative protein-coding genes. We used this approach to explore the human secretome, the membrane proteome, the druggable proteome, the cancer proteome, and the metabolic functions in 32 different tissues and organs. All the data are integrated in an interactive Web-based database that allows exploration of individual proteins, as well as navigation of global expression patterns, in... - Egon Willighagen
Egon Willighagen
Metabolic regulation : a human perspective - http://www.citeulike.org/user...
(2003) This new edition of a successful book conveys a modern and integrated picture of metabolism and metabolic regulation. Important additions include a full coverage of leptin and its role, and regulation of gene expression by nutrients, particularly covering the PPAR and SREBP systems. KN Frayn - Egon Willighagen
Egon Willighagen
Materials Cartography: Representing and Mining Materials Space Using Structural and Electronic Fingerprints - http://www.citeulike.org/user...
Chem. Mater. (15 December 2014), doi:10.1021/cm503507h As the proliferation of high-throughput approaches in materials science is increasing the wealth of data in the field, the gap between accumulated-information and derived-knowledge widens. We address the issue of scientific discovery in materials databases by introducing novel analytical approaches based on structural and electronic materials fingerprints. The framework is employed to (i) query large databases of materials using similarity concepts, (ii) map the connectivity of materials space (i.e., as a materials cartograms) for rapidly identifying regions with unique organizations/properties, and (iii) develop predictive Quantitative Materials Structure?Property Relationship models for guiding materials design. In this study, we test these fingerprints by seeking target material properties. As a quantitative example, we model the critical temperatures of known superconductors. Our novel materials fingerprinting and materials... - Egon Willighagen
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