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Egon Willighagen › Comments

Egon Willighagen
Distribution of cognitive load in Web search - http://www.citeulike.org/user...
J. Am. Soc. Inf. Sci., Vol. 61, No. 11. (1 November 2010), pp. 2167-2187, doi:10.1002/asi.21385 The search task and the system both affect the demand on cognitive resources during information search. In some situations the demands may become too high for a person. This article has a three-fold goal. First, it presents and critiques methods to measure cognitive load. Second, it explores the distribution of load across search task stages. Finally, it seeks to improve our understanding of factors affecting cognitive load levels in information search. To this end, a controlled Web search experiment with 48 participants was conducted. Interaction logs were used to segment search tasks semiautomatically into task stages. Cognitive load was assessed using a new variant of the dual-task method. Average cognitive load was found to vary by search task stages. It was significantly higher during query formulation and user description of a relevant document as compared to examining search results... - Egon Willighagen
Egon Willighagen
Is Evaluating Visual Search Interfaces in Digital Libraries Still an Issue? - http://www.citeulike.org/user...
(21 Aug 2014) Although various visual interfaces for digital libraries have been developed in prototypical systems, very few of these visual approaches have been integrated into today's digital libraries. In this position paper we argue that this is most likely due to the fact that the evaluation results of most visual systems lack comparability. There is no fix standard on how to evaluate visual interactive user interfaces. Therefore it is not possible to identify which approach is more suitable for a certain context. We feel that the comparability of evaluation results could be improved by building a common evaluation setup consisting of a reference system, based on a standardized corpus with fixed tasks and a panel for possible participants. Wilko van Hoek, Philipp Mayr - Egon Willighagen
Egon Willighagen
Ten Simple Rules of Live Tweeting at Scientific Conferences - http://www.citeulike.org/user...
PLoS Comput Biol, Vol. 10, No. 8. (21 August 2014), e1003789, doi:10.1371/journal.pcbi.1003789 Sean Ekins, Ethan Perlstein - Egon Willighagen
Egon Willighagen
Annotating the structure and components of a nanoparticle formulation using computable string expressions - http://www.citeulike.org/user...
In Bioinformatics and Biomedicine Workshops (BIBMW), 2012 IEEE International Conference on (October 2012), pp. 889-894, doi:10.1109/bibmw.2012.6470259 Nanoparticle formulations that are being developed and tested for various medical applications are typically multi-component systems that vary in their structure, chemical composition, and function. It is difficult to compare and understand the differences between the structural and chemical descriptions of hundreds and thousands of nanoparticle formulations found in text documents. We have developed a string nomenclature to create computable string expressions that identify and enumerate the different high-level types of material parts of a nanoparticle formulation and represent the spatial order of their connectivity to each other. The string expressions are intended to be used as IDs, along with terms that describe a nanoparticle formulation and its material parts, in data sharing documents and nanomaterial research databases. The... - Egon Willighagen
Egon Willighagen
History of the Harvard ChemDraw Project - http://www.citeulike.org/user...
Angewandte Chemie International Edition (08 August 2014), pp. n/a-n/a, doi:10.1002/anie.201405820 David Evans - Egon Willighagen
Egon Willighagen
Systems Toxicology: From Basic Research to Risk Assessment - http://www.citeulike.org/user...
Chem. Res. Toxicol., Vol. 27, No. 3. (9 January 2014), pp. 314-329, doi:10.1021/tx400410s Systems Toxicology is the integration of classical toxicology with quantitative analysis of large networks of molecular and functional changes occurring across multiple levels of biological organization. Society demands increasingly close scrutiny of the potential health risks associated with exposure to chemicals present in our everyday life, leading to an increasing need for more predictive and accurate risk-assessment approaches. Developing such approaches requires a detailed mechanistic understanding of the ways in which xenobiotic substances perturb biological systems and lead to adverse outcomes. Thus, Systems Toxicology approaches offer modern strategies for gaining such mechanistic knowledge by combining advanced analytical and computational tools. Furthermore, Systems Toxicology is a means for the identification and application of biomarkers for improved safety assessments. In Systems... - Egon Willighagen
Egon Willighagen
Online collaboration: Scientists and the social network - http://www.citeulike.org/user...
Nature, Vol. 512, No. 7513. (13 August 2014), pp. 126-129, doi:10.1038/512126a Richard Van Noorden - Egon Willighagen
Egon Willighagen
Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin - http://www.citeulike.org/user...
Cell, Vol. 158, No. 4. (18 August 2014), pp. 929-944, doi:10.1016/j.cell.2014.06.049 Recent genomic analyses of pathologically defined tumor types identify ?within-a-tissue? disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head and neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multiplatform classification, while correlated with tissue-of-origin, provides independent... - Egon Willighagen
Egon Willighagen
Deuterated drugs: where are we now? - http://www.citeulike.org/user...
Expert opinion on therapeutic patents (29 July 2014), pp. 1-9 Introduction: Deuterated versions of existing drugs can exhibit improved pharmacokinetic or toxicological properties due the stronger deuterium- carbon bond modifying their metabolism. There is great interest in the current state of development of this approach. Areas covered: This review covers recent US patent applications and prosecutions in this area that are based on beneficial modifications in metabolism of deuterated versions of existing drugs. The current state of 35 U.S.C. §103 'obviousness' rejections are emphasized, as is the development of strategies to overcome such rejections. Current trials and market considerations are also discussed. Expert opinion: Deuterated drugs collectively are worth at least US$1 billion. It would seem that the likelihood of obviousness rejections is increasing in this area. However, careful elucidation of metabolic outcomes from deuteration that would not be anticipated from the... - Egon Willighagen
Egon Willighagen
Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation - http://www.citeulike.org/user...
PeerJ, Vol. 2 (14 August 2014), e524, doi:10.7717/peerj.524 Alex Clark, Barry Bunin, Nadia Litterman, Stephan Schürer, Ubbo Visser - Egon Willighagen
Egon Willighagen
Cancer biomarkers: Written in blood - http://www.citeulike.org/user...
Nature, Vol. 511, No. 7511. (30 July 2014), pp. 524-526, doi:10.1038/511524a DNA circulating in the bloodstream could guide cancer treatment if researchers can work out how best to use it. Ed Yong - Egon Willighagen
Egon Willighagen
SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases. - http://www.citeulike.org/user...
BMC bioinformatics, Vol. 15, No. 1. (15 August 2014) Semantic Web has established itself as a framework for using and sharing data across applications and database boundaries. Here, we present a web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and executes it on a public endpoint. The tool integrates several publicly available Semantic Web databases, including the databases of the just recently released EBI RDF platform. Furthermore, it provides several predefined template queries for answering biological questions. Users can easily create and save new query graphs, which can also be shared with other researchers. This new graphical way of creating queries for biological Semantic Web databases considerably facilitates usability as it removes the requirement of knowing specific query languages and database structures. The system is freely... - Egon Willighagen
Egon Willighagen
Genomic-scale exchange of mRNA between a parasitic plant and its hosts - http://www.citeulike.org/user...
Science, Vol. 345, No. 6198. (15 August 2014), pp. 808-811, doi:10.1126/science.1253122 Because RNA normally functions within an individual cell, we generally think that we keep our RNAs to ourselves. Kim et al. now show that the parasitic dodder plant breaks that rule. When dodder attacks a host plant, it opens up a conduit through which messenger and perhaps other regulatory RNAs are exchanged between parasite and host. Because a single dodder plant can attack multiple hosts, such exchanges may underlie instances of genes transferring between species. Gunjune Kim, Megan LeBlanc, Eric Wafula, Claude dePamphilis, James Westwood - Egon Willighagen
Egon Willighagen
Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms. - http://www.citeulike.org/user...
BioEssays : news and reviews in molecular, cellular and developmental biology (8 August 2014) Microbes in the gastrointestinal tract are under selective pressure to manipulate host eating behavior to increase their fitness, sometimes at the expense of host fitness. Microbes may do this through two potential strategies: (i) generating cravings for foods that they specialize on or foods that suppress their competitors, or (ii) inducing dysphoria until we eat foods that enhance their fitness. We review several potential mechanisms for microbial control over eating behavior including microbial influence on reward and satiety pathways, production of toxins that alter mood, changes to receptors including taste receptors, and hijacking of the vagus nerve, the neural axis between the gut and the brain. We also review the evidence for alternative explanations for cravings and unhealthy eating behavior. Because microbiota are easily manipulatable by prebiotics, probiotics, antibiotics, fecal... - Egon Willighagen
Egon Willighagen
Practical Chemoinformatics - http://www.citeulike.org/user...
(2014) Muthukumarasamy Karthikeyan - Egon Willighagen
Egon Willighagen
The Royal Society of Chemistry and the delivery of chemistry data repositories for the community - http://www.citeulike.org/user...
In Journal of Computer-Aided Molecular Design (2014), pp. 1-8, doi:10.1007/s10822-014-9784-5 Since 2009 the Royal Society of Chemistry (RSC) has been delivering access to chemistry data and cheminformatics tools via the ChemSpider database and has garnered a significant community following in terms of usage and contribution to the platform. ChemSpider has focused only on those chemical entities that can be represented as molecular connection tables or, to be more specific, the ability to generate an InChI from the input structure. As a structure centric hub ChemSpider is built around the molecular structure with other data and links being associated with this structure. As a result the platform has been limited in terms of the types of data that can be managed, and the flexibility of its searches, and it is constrained by the data model. New technologies and approaches, specifically taking into account a shift from relational to NoSQL databases, and the growing importance of the... - Egon Willighagen
Egon Willighagen
WebProtégé: A Collaborative Ontology Editor and Knowledge Acquisition Tool for the Web. - http://www.citeulike.org/user...
Semantic web, Vol. 4, No. 1. (1 January 2013), pp. 89-99 In this paper, we present WebProtégé-a lightweight ontology editor and knowledge acquisition tool for the Web. With the wide adoption of Web 2.0 platforms and the gradual adoption of ontologies and Semantic Web technologies in the real world, we need ontology-development tools that are better suited for the novel ways of interacting, constructing and consuming knowledge. Users today take Web-based content creation and online collaboration for granted. WebProtégé integrates these features as part of the ontology development process itself. We tried to lower the entry barrier to ontology development by providing a tool that is accessible from any Web browser, has extensive support for collaboration, and a highly customizable and pluggable user interface that can be adapted to any level of user expertise. The declarative user interface enabled us to create custom knowledge-acquisition forms tailored for domain experts. We built... - Egon Willighagen
Egon Willighagen
A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes - http://www.citeulike.org/user...
Nature Communications, Vol. 5 (24 July 2014), doi:10.1038/ncomms5498 Bas Dutilh, Noriko Cassman, Katelyn McNair, Savannah Sanchez, Genivaldo Silva, Lance Boling, Jeremy Barr, Daan Speth, Victor Seguritan, Ramy Aziz, Ben Felts, Elizabeth Dinsdale, John Mokili, Robert Edwards - Egon Willighagen
Egon Willighagen
Social Studies of Science, Vol. 44, No. 4. (01 August 2014), pp. 638-654, doi:10.1177/0306312714535679 Many of the messages presented in respectable scientific publications are, in fact, based on various forms of rumors. Some of these rumors appear so frequently, and in such complex, colorful, and entertaining ways that we can think of them as academic urban legends. The explanation for this phenomenon is usually that authors have lazily, sloppily, or fraudulently employed sources, and peer reviewers and editors have not discovered these weaknesses in the manuscripts during evaluation. To illustrate this phenomenon, I draw upon a remarkable case in which a decimal point error appears to have misled millions into believing that spinach is a good nutritional source of iron. Through this example, I demonstrate how an academic urban legend can be conceived and born, and can continue to grow and reproduce within academia and beyond. Ole Rekdal - Egon Willighagen
Egon Willighagen
ALTEX, Vol. 31, No. 1. (2014), pp. 53-61, doi:10.14573/altex.1309261 Andre Kleensang - Egon Willighagen
Egon Willighagen
LECTINPred: web Server that Uses Complex Networks of Protein Structure for Prediction of Lectins with Potential Use as Cancer Biomarkers or in Parasite Vaccine Design - http://www.citeulike.org/user...
Mol. Inf., Vol. 33, No. 4. (1 April 2014), pp. 276-285, doi:10.1002/minf.201300027 Lectins (Ls) play an important role in many diseases such as different types of cancer, parasitic infections and other diseases. Interestingly, the Protein Data Bank (PDB) contains +3000 protein 3D structures with unknown function. Thus, we can in principle, discover new Ls mining non-annotated structures from PDB or other sources. However, there are no general models to predict new biologically relevant Ls based on 3D chemical structures. We used the MARCH-INSIDE software to calculate the Markov-Shannon 3D electrostatic entropy parameters for the complex networks of protein structure of 2200 different protein 3D structures, including 1200 Ls. We have performed a Linear Discriminant Analysis (LDA) using these parameters as inputs in order to seek a new Quantitative Structure-Activity Relationship (QSAR) model, which is able to discriminate 3D structure of Ls from other proteins. We implemented this... - Egon Willighagen
Egon Willighagen
weerd el jenkofiets ;) "Weird Al" Yankovic - Word Crimes - Egon Willighagen
Egon Willighagen
Finding the Right Questions: Exploratory Pathway Analysis to Enhance Biological Discovery in Large Datasets - http://www.citeulike.org/user...
PLoS Biol, Vol. 8, No. 8. (31 August 2010), e1000472, doi:10.1371/journal.pbio.1000472 This Essay discusses the role of pathways for exploratory data analysis in present-day biology. Thomas Kelder, Bruce Conklin, Chris Evelo, Alexander Pico - Egon Willighagen
Egon Willighagen
Spatial control of membrane receptor function using ligand nanocalipers - http://www.citeulike.org/user...
Nature Methods (6 July 2014), doi:10.1038/nmeth.3025 Alan Shaw, Vanessa Lundin, Ekaterina Petrova, Ferenc Fördős, Erik Benson, Abdullah Al-Amin, Anna Herland, Andries Blokzijl, Björn Högberg, Ana Teixeira - Egon Willighagen
Egon Willighagen
Synthetisch DNA is handig als biomedische meetlat. Je kunt er mee onderzoeken wat de onderlinge afstand tussen twee functionele groepen moet zijn om op een receptoreiwit te passen, schrijven onderzoekers van het Karolinska-instituut in Stockholm... - Egon Willighagen
Egon Willighagen
Mapping the Protein Interaction Landscape for Fully Functionalized Small-Molecule Probes in Human Cells - http://www.citeulike.org/user...
J. Am. Chem. Soc. (21 July 2014), doi:10.1021/ja505517t Phenotypic screening provides a means to discover small molecules that perturb cell biological processes. Discerning the proteins and biochemical pathways targeted by screening hits, however, remains technically challenging. We recently described the use of small molecules bearing photoreactive groups and latent affinity handles as fully functionalized probes for integrated phenotypic screening and target identification. The general utility of such probes, or, for that matter, any small-molecule screening library, depends on the scope of their protein interactions in cells, a parameter that remains largely unexplored. Here, we describe the synthesis of an ?60-member fully functionalized probe library, prepared from Ugi-azide condensation reactions to impart structural diversity and introduce diazirine and alkyne functionalities for target capture and enrichment, respectively. In-depth mass spectrometry-based analysis revealed a... - Egon Willighagen
Egon Willighagen
About ligand-protein interactions... - https://plus.google.com/1041867...
About ligand-protein interactions... About this Author. DBL%20Hendrix%20small.png College chemistry, 1983. Derek Lowe The 2002 Model Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . . Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in ... - Egon Willighagen
Egon Willighagen
Hypothesis: The proprietary RDF is valid and uses common ontologies. Start date: 2014-07-23 End date: 2014-07-23. Description: For obvious reasons, this experiment will not disclose all details. It will outline, however, the steps I undertook to do the validation and evaluation. Methods: ... - Egon Willighagen
Egon Willighagen
"The diverse world of citation indexing services" http://feedly.com/e/cNOyAA9Y - https://plus.google.com/1041867...
"The diverse world of citation indexing services" http://feedly.com/e/cNOyAA9Y When assessing the impact of a published research article, it might seem logical to look at the Impact Factor of the journal that you find it in. But as journals and scholars have moved online, and citation indexing has been automated, the wealth of information for citation discovery and analysis has vastly increased. Citation counts can tell a more accurate story about the scholarly impact that an individual article has made than the journal Imp... - Egon Willighagen
Egon Willighagen
"The diverse world of citation indexing services" http://feedly.com/e/cNOyAA9Y - https://plus.google.com/1041867...
"The diverse world of citation indexing services" http://feedly.com/e/cNOyAA9Y When assessing the impact of a published research article, it might seem logical to look at the Impact Factor of the journal that you find it in. But as journals and scholars have moved online, and citation indexing has been automated, the wealth of information for citation discovery and analysis has vastly increased. Citation counts can tell a more accurate story about the scholarly impact that an individual article has made than the journal Imp... - Egon Willighagen
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