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Egon Willighagen › Comments

Egon Willighagen
Rampant software errors undermine scientific results - http://www.citeulike.org/user...
F1000Research (11 December 2014), doi:10.12688/f1000research.5930.1 David Soergel - Egon Willighagen
Of course, the same must be said about rampant, unreproducible wetlab research! - Egon Willighagen
Egon Willighagen
A paper describing a R package that uses the CDK via +Rajarshi Guha's rcdk package but doesn't cite ... - https://plus.google.com/1041867...
A paper describing a R package that uses the CDK via +Rajarshi Guha's rcdk package but doesn't cite either paper while citing a bunch of others... :/ Abstract Summary: In chemoinformatics and bioinformatics fields, one of the main computational challenges in various predictive modeling is to find a suitable way to effectively represent the molecules under investigation, such as small molecules, proteins and even complex interactions. To solve this problem, we developed a freely available R/Bioconductor package, called Compound–Protein Interaction with R (Rcpi), for complex molecular representa... - Egon Willighagen
Egon Willighagen
Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions - http://www.citeulike.org/user...
Bioinformatics, Vol. 31, No. 2. (15 January 2015), pp. 279-281, doi:10.1093/bioinformatics/btu624 Summary: In chemoinformatics and bioinformatics fields, one of the main computational challenges in various predictive modeling is to find a suitable way to effectively represent the molecules under investigation, such as small molecules, proteins and even complex interactions. To solve this problem, we developed a freely available R/Bioconductor package, called Compound–Protein Interaction with R (Rcpi), for complex molecular representation from drugs, proteins and more complex interactions, including protein–protein and compound–protein interactions. Rcpi could calculate a large number of structural and physicochemical features of proteins and peptides from amino acid sequences, molecular descriptors of small molecules from their topology and protein–protein interaction and compound–protein interaction descriptors. In addition to main functionalities, Rcpi could also provide a number of... - Egon Willighagen
Egon Willighagen
Wikidata edits per day over a period of a bit more than two years. Willighagen, Egon; Hoch, Marius (2015): Wikidata edits per day (2012-2014). figshare. http://dx.doi.org/10...... - Egon Willighagen
Egon Willighagen
Introducing the new global community Ambassador scheme | Open Knowledge Foundation Blog - Egon Willighagen
Egon Willighagen
NRC Handelsblad (10 January 2015) Wat is de beste manier om wetenschappelijke artikelen voor iedereen gratis toegankelijk te maken? Uitgevers, overheden en academici hebben hun eigen belangen. M Aan de Brugh - Egon Willighagen
Egon Willighagen
Publiceren Wat is de beste manier om wetenschappelijke artikelen voor iedereen gratis toegankelijk te maken? Uitgevers, overheden en academici hebben hun eigen belangen. - Egon Willighagen
Egon Willighagen
I just was alerted that this 2009 PDF is now on the "Rising List". No idea what it means, but it sounds... - https://plus.google.com/1041867...
I just was alerted that this 2009 PDF is now on the "Rising List". No idea what it means, but it sounds positive. At least, it gives a nice short introduction to the CDK API :) CDK Workshop 2009 Intro Course Material - Egon Willighagen
Egon Willighagen
Quantification of cytosolic interactions identifies Ede1 oligomers as key organizers of endocytosis. - http://www.citeulike.org/user...
Molecular systems biology, Vol. 10 (2014) Clathrin-mediated endocytosis is a highly conserved intracellular trafficking pathway that depends on dynamic protein-protein interactions between up to 60 different proteins. However, little is known about the spatio-temporal regulation of these interactions. Using fluorescence (cross)-correlation spectroscopy in yeast, we tested 41 previously reported interactions in vivo and found 16 to exist in the cytoplasm. These detected cytoplasmic interactions included the self-interaction of Ede1, homolog of mammalian Eps15. Ede1 is the crucial scaffold for the organization of the early stages of endocytosis. We show that oligomerization of Ede1 through its central coiled coil domain is necessary for its localization to the endocytic site and we link the oligomerization of Ede1 to its function in locally concentrating endocytic adaptors and organizing the endocytic machinery. Our study sheds light on the importance of the regulation of... - Egon Willighagen
Egon Willighagen
What protein folding teaches us about biological function and molecular machines - http://www.citeulike.org/user...
Current Opinion in Structural Biology, Vol. 30 (February 2015), pp. 57-62, doi:10.1016/j.sbi.2014.12.003 Paul Whitford, José Onuchic - Egon Willighagen
Egon Willighagen
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping - http://www.citeulike.org/user...
Cell, Vol. 159, No. 7. (6 December 2014), pp. 1665-1680, doi:10.1016/j.cell.2014.11.021 We use in situ Hi-C to probe the 3D architecture of genomes, constructing haploid and diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 billion contacts, achieving 1 kb resolution. We find that genomes are partitioned into contact domains (median length, 185 kb), which are associated with distinct patterns of histone marks and segregate into six subcompartments. We identify ?10,000 loops. These loops frequently link promoters and enhancers, correlate with gene activation, and show conservation across cell types and species. Loop anchors typically occur at domain boundaries and bind CTCF. CTCF sites at loop anchors occur predominantly (>90%) in a convergent orientation, with the asymmetric motifs ?facing? one another. The inactive X chromosome splits into two massive domains and contains large loops anchored at CTCF-binding repeats. Suhas Rao, Miriam Huntley,... - Egon Willighagen
Egon Willighagen
Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes - http://www.citeulike.org/user...
Science, Vol. 347, No. 6217. (02 January 2015), 1258522, doi:10.1126/science.1258522 Control of mosquito vectors has historically proven to be an effective means of eliminating malaria. Human malaria is transmitted only by mosquitoes in the genus Anopheles, but not all species within the genus, or even all members of each vector species, are efficient malaria vectors. Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. Daniel Neafsey, Robert Waterhouse, Mohammad Abai, Sergey Aganezov, Max Alekseyev, James Allen, James Amon, Bruno Arcà, Peter Arensburger, Gleb Artemov, Lauren Assour, Hamidreza Basseri, Aaron Berlin, Bruce Birren, Stephanie Blandin, Andrew Brockman, Thomas Burkot, Austin Burt, Clara Chan, Cedric Chauve, Joanna Chiu, Mikkel Christensen, Carlo Costantini, Victoria Davidson, Elena Deligianni, Tania Dottorini, Vicky Dritsou, Stacey Gabriel, Wamdaogo Guelbeogo,... - Egon Willighagen
Egon Willighagen
The discovery of integrated gene networks for autism and related disorders - http://www.citeulike.org/user...
Genome Research, Vol. 25, No. 1. (01 January 2015), pp. 142-154, doi:10.1101/gr.178855.114 An international, peer-reviewed genome sciences journal featuring outstanding original research that offers novel insights into the biology of all organisms Fereydoun Hormozdiari, Osnat Penn, Elhanan Borenstein, Evan Eichler - Egon Willighagen
Egon Willighagen
COPS benchmark: interactive analysis of database search methods. - http://www.citeulike.org/user...
Bioinformatics (Oxford, England), Vol. 26, No. 4. (15 February 2010), pp. 574-575, doi:10.1093/bioinformatics/btp712 The performance of sequence database search methods is usually judged by receiver operating characteristic (ROC) analysis. The proper interpretation of the results obtained and a fair comparison across different methods critically depends on the properties of the data set used for such an analysis; in particular, each query must have the same number of true positives and true negatives. Here, we present a novel web service based on a dataset specifically designed for ROC analysis and the investigation of alignment quality. The data set is derived from a quantitative classification of protein structures (COPS), while analysis and results are presented through an intuitive web interface. The analysis provides details such as false positives per query, and visualization of the structural similarity between query and targets. Most importantly, results obtained for a... - Egon Willighagen
Egon Willighagen
The role of lipid transfer proteins in allergic diseases. - http://www.citeulike.org/user...
Current allergy and asthma reports, Vol. 10, No. 5. (September 2010), pp. 326-335 Nonspecific lipid transfer proteins (LTPs) are important allergens in fruits, vegetables, nuts, pollen, and latex. Despite their wide distribution throughout the plant kingdom, their clinical relevance is largely confined to the Mediterranean area. As they can sensitize via the gastrointestinal tract, LPTs are considered true food allergens, and IgE reactivity to LTPs is often associated with severe systemic symptoms. Although Pru p 3 represents the predominant LTP in terms of patients' IgE recognition, the contribution of pollen LTPs in primary sensitization cannot be ruled out. Due to structural homology, LTPs from different allergen sources are generally IgE cross-reactive. However, sensitization profiles among allergic patients are extremely heterogeneous, and individual cross-reactivity patterns can be restricted to a single LTP or encompass many different LTPs. Molecule-based approaches in allergy... - Egon Willighagen
Egon Willighagen
O-GlcNAcylation and Inflammation: A Vast Territory to Explore - http://www.citeulike.org/user...
Frontiers in Endocrinology, Vol. 5 (09 January 2015), doi:10.3389/fendo.2014.00235 L Baudoin, T Issad - Egon Willighagen
Egon Willighagen
A new antibiotic kills pathogens without detectable resistance - http://www.citeulike.org/user...
Nature, Vol. advance online publication (7 January 2015), doi:10.1038/nature14098 Losee Ling, Tanja Schneider, Aaron Peoples, Amy Spoering, Ina Engels, Brian Conlon, Anna Mueller, Till Schäberle, Dallas Hughes, Slava Epstein, Michael Jones, Linos Lazarides, Victoria Steadman, Douglas Cohen, Cintia Felix, Ashley Fetterman, William Millett, Anthony Nitti, Ashley Zullo, Chao Chen, Kim Lewis - Egon Willighagen
Egon Willighagen
Transcriptomic analysis of the late stages of grapevine (Vitis vinifera cv. Cabernet Sauvignon) berry ripening reveals significant induction of ethylene signaling and flavor pathways in the skin - http://www.citeulike.org/user...
BMC Plant Biology, Vol. 14, No. 1. (19 December 2014), 370, doi:10.1186/s12870-014-0370-8 Grapevine berry, a nonclimacteric fruit, goes through three developmental stages, the last one is the ripening stage, when the berry changes color and dramatically increases in sugar. Flavors derived from terpenoid and fatty acid metabolism develop at the very end of this ripening stage. Whole-genome microarray analysis was used to assess the transcriptomic response of pulp and skin of Cabernet Sauvignon berries in the late stages of ripening between 22 and 37 °Brix. Grant Cramer, Ryan Ghan, Karen Schlauch, Richard Tillett, Hildegarde Heymann, Alberto Ferrarini, Massimo Delledonne, Sara Zenoni, Marianna Fasoli, Mario Pezzotti - Egon Willighagen
Egon Willighagen
Gradient boosting machines, a tutorial - http://www.citeulike.org/user...
Frontiers in Neurorobotics, Vol. 7 (04 December 2013), 21, doi:10.3389/fnbot.2013.00021 Gradient boosting machines are a family of powerful machine-learning techniques that have shown considerable success in a wide range of practical applications. They are highly customizable to the particular needs of the application, like being learned with respect to different loss functions. This article gives a tutorial introduction into the methodology of gradient boosting methods. A theoretical information is complemented with many descriptive examples and illustrations which cover all the stages of the gradient boosting model design. Considerations on handling the model complexity are discussed. A set of practical examples of gradient boosting applications are presented and comprehensively analyzed. Alexey Natekin, Alois Knoll - Egon Willighagen
Egon Willighagen
Looking at microbial metabolism by high-resolution 2H-NMR spectroscopy - http://www.citeulike.org/user...
PeerJ, Vol. 1 (09 July 2013), e101, doi:10.7717/peerj.101 We analyzed the applicability of high-resolution 2H-HMR spectroscopy for the analysis of microbe metabolism in samples of mitochondrion isolated from rat liver and from aqueous extracts of homogenates of rat liver and other organs and tissues in the presence of high D2O contents. Such analysis is possible due to the fast microbe adaptation to life in the heavy water. It is also shown that some enzymatic processes typical for the intact cells are preserved in the homogenized tissue preparations. The microbial and cellular metabolic processes can be differentiated via the strategic use of cell poisons and antibiotics. Victor Kutyshenko, Petr Beskaravayny, Maxim Molchanov, Svetlana Paskevich, Dmitry Prokhorov, Vladimir Uversky - Egon Willighagen
Egon Willighagen
[duplicate] Accessing biological data in R with semantic web technologies - http://www.citeulike.org/user...
PeerJ PrePrints (16 March 2014), doi:10.7287/peerj.preprints.185v3 Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness shows advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows.Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be used in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library.Results. We here present three examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a BioMart... - Egon Willighagen
Egon Willighagen
Accessing biological data in R with semantic web technologies - http://www.citeulike.org/user...
PeerJ PrePrints (16 March 2014), doi:10.7287/peerj.preprints.185v3 Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness shows advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows.Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be used in the statistical environment R. The code is exposed as two R packages available from the Comprehensive R Archive Network (CRAN). The RJava library and a custom convenience class is used to bridge between R and the Jena library.Results. We here present three examples showing how the Resource Description Framework (RDF) and SPARQL query standards can be employed in R. The first example takes input on BRCA1 SNPs from a BioMart... - Egon Willighagen
Egon Willighagen
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
Attentional Filtering of Visual Information by Neuronal Ensembles in the Primate Lateral Prefrontal Cortex - http://www.citeulike.org/user...
Neuron, Vol. 85, No. 1. (8 January 2015), pp. 202-215, doi:10.1016/j.neuron.2014.11.021 The activity of neurons in the primate lateral prefrontal cortex (LPFC) is strongly modulated by visual attention. Such a modulation has mostly been documented by averaging the activity of independently recorded neurons over repeated experimental trials. However, in realistic settings, ensembles of simultaneously active LPFC neurons must generate attentional signals on a single-trial basis, despite the individual and correlated variability of neuronal responses. Whether, under these circumstances, the LPFC can reliably generate attentional signals is unclear. Here, we show that the simultaneous activity of neuronal ensembles in the primate LPFC can be reliably decoded to predict the allocation of attention on a single-trial basis. Decoding was sensitive to the noise correlation structure of the ensembles. Additionally, it was resilient to distractors, predictive of behavior, and stable over weeks.... - Egon Willighagen
Egon Willighagen
The original press release... - https://plus.google.com/1041867...
The original press release... The Royal Society of Chemistry has announced that it is donating 100 “RSC Gold” accounts – the complete portfolio of their journals and databases – to be used by Wikipedia editors who write about chemistry. The partnership is part of a wider collaboration between the Society's members and staff, ... - Egon Willighagen
Egon Willighagen
"Royal Society of Chemistry grants journals access to Wikipedia Editors" The Royal Society of Chemistry... - https://plus.google.com/1041867...
"Royal Society of Chemistry grants journals access to Wikipedia Editors" The Royal Society of Chemistry and Wikipedia just released an interesting press release : "The Royal Society of Chemistry has announced that it is donating 100 “RSC Gold” accounts – the complete portfolio of their journals and databases – to be used by Wiki... The Royal Society of Chemistry and Wikipedia just released an interesting press release: "The Royal Society of Chemistry has announced that it is donating 100 “RSC Gold” accounts – the complete portfolio of their journals and... - Egon Willighagen
Egon Willighagen
TL;DR. WE outline the tools and piepline which ContentMine will show on Sunday at Force2015. They are very general and accessible to everyone.... ContentMine technology and community is maturing quickly. We've just had a wonderful three days in Berlin with Johnny West a co-Shuttleowrth Fellow. - Egon Willighagen
Egon Willighagen
Finding Our Way through Phenotypes - http://www.citeulike.org/user...
PLoS Biol, Vol. 13, No. 1. (6 January 2015), e1002033, doi:10.1371/journal.pbio.1002033 Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to... - Egon Willighagen
Egon Willighagen
Simplified data access on human skeletal muscle transcriptome responses to differentiated exercise - http://www.citeulike.org/user...
Scientific Data, Vol. 1 (25 November 2014), doi:10.1038/sdata.2014.41 Few studies have investigated exercise-induced global gene expression responses in human skeletal muscle and these have typically focused at one specific mode of exercise and not implemented non-exercise control models. However, interpretation on effects of differentiated exercise necessitate direct comparison between essentially different modes of exercise and the ability to identify true exercise effect, necessitate implementation of independent non-exercise control subjects. Furthermore, muscle transcriptome data made available through previous exercise studies can be difficult to extract and interpret by individuals that are inexperienced with bioinformatics procedures. In a comparative study, we therefore; (1) investigated the human skeletal muscle transcriptome responses to differentiated exercise and non-exercise control intervention, and; (2) set out to develop a straightforward search tool to allow for easy... - Egon Willighagen
Egon Willighagen
Reshared post from Chris Mooney: - https://plus.google.com/1041867...
Can we now please stop burning oil and coal then? Original Post from Chris Mooney: The idea that global warming has "paused" was always dubious. Now, with 2014 on the verge of a new temperature record, it looks even worse  Putting to rest the myth that global warming is "slowing down." - Egon Willighagen
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