My Start Page

(03 March 2005)

In this landmark work, NEW YORKER columnist James Surowiecki explores a seemingly counter-intuitive idea that has profound implications. Decisions taken by a large group, even if the individuals within the group aren't smart, are always better than decisions made by small numbers of 'experts'. This seemingly simply notion has endless and major ramifications for how businesses operate, how knowledge is advanced, how economies are (or should be) organised and how nation-states fare. With great erudition, Surowiecki ranges across the disciplines of psychology, economics, statistics and history to show just how this principle operates in the real world. Along the way Surowiecki asks a number of intriguing questions about a subject few of us actually understand - economics. What are prices? How does money work? Why do we have corporations? Does advertising work? His answers, rendered in a delightfully clear prose, demystify daunting prospects. As Surowiecki writes: 'The hero of this book is, in a curious sense, an idea, a hero whose story ends up shedding dramatic new light on the landscapes of business, politics and society'.
James Surowiecki

Nature protocols, Vol. 4, No. 3. (2009), pp. 356-362.

We have developed a novel approach called parallel analysis of RNA ends (PARE) for high-throughput identification of microRNA (miRNA) targets and diverse applications for the study of the RNA degradome. The method described here comprises a modified 5'-rapid amplification of cDNA ends, deep sequencing of 3' cleavage products of mRNA and bioinformatic analysis. Following RNA extraction and isolation of polyadenylated RNA, a 5'-RNA adapter that includes an MmeI recognition site is ligated to 5'-monophosphorylated products, which contain mRNA fragments generated through miRNA-induced cleavage. The ligated products are reverse-transcribed, slightly amplified and cleaved with MmeI. The 5' equally-sized fragments are gel-selected, ligated to a 3' double-stranded DNA adapter and PCR-amplified. Following gel purification, the products are subjected to deep sequencing. The data are then matched to cDNAs and analyzed through bioinformatics filters. We describe the high-throughput protocol in detail and indicate alternative uses for PARE. The procedure presented here can be accomplished in 6-7 d.
MA German, S Luo, G Schroth, BC Meyers, PJ Green

Interacting with Computers (30 June 2009)

This study extends the conventional and superficial notion of measuring digital skills by proposing definitions for operational, formal, information and strategic skills. The main purpose was to identify individual skill related problems that users experience when navigating the Internet. In particular, lower levels of education and aging seem to contribute to the amount of experienced operational and formal skill related problems. With respect to information skills, higher levels of education seem to perform best. Age did not seem to contribute to information skill related problems. Results did reveal that age had a negative effect on selecting irrelevant search results. Individual strategic Internet skill related problems occurred often, with the exception of subjects with higher levels of education. Younger subjects experienced far less operational and formal skill related problems, but there was no difference regarding information and strategic skill related problems.
Alexander van Deursen, Jan van Dijk

The British Journal of Occupational Therapy (June 2009), pp. 279-281.

Blogs are publicly accessible websites that are authored by one or several individuals (Boulos et al 2006). These individuals post regular entries and encourage comment on their work, thereby creating discussion and debate. Preliminary evidence suggests that blogging facilitates learning, assists personal and professional development, and provides an opportunity to reflect on issues raised by others from different cultural perspectives (Martin 2007). This opinion piece is based on the shared experiences of five occupational therapy bloggers from the United Kingdom, Aotearoa/New Zealand and the United States and suggests that blogging has a key role in demonstrating evidence of continuing professional development in a globalised community.
Sarah Bodell, Angela Hook, Merrolee Penman, Will Wade

The English Journal, Vol. 90, No. 2. (2000), pp. 38-41.
Geraldine Richards

The English Journal, Vol. 90, No. 2. (2000), pp. 22-26.
Lara, Kim Ford

College English, Vol. 61, No. 3. (1999), pp. 261-280.
Chris Anson

Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W356-362.

MicroRNAs (miRNAs) are small (19-24 nt), nonprotein-coding nucleic acids that regulate specific target' gene products via hybridization to mRNA transcripts, resulting in translational blockade or transcript degradation. Although miRNAs have been implicated in numerous developmental and adult diseases, their specific impact on biological pathways and cellular phenotypes, in addition to miRNA gene promoter regulation, remain largely unknown. To improve and facilitate research of miRNA functions and regulation, we have developed MMIA (microRNA and mRNA integrated analysis), a versatile and user-friendly web server. By incorporating three commonly used and accurate miRNA prediction algorithms, TargetScan, PITA and PicTar, MMIA integrates miRNA and mRNA expression data with predicted miRNA target information for analyzing miRNA-associated phenotypes and biological functions by gene set analysis, in addition to analysis of miRNA primary transcript gene promoters. To assign biological relevance to the integrated miRNA/mRNA profiles, MMIA uses exhaustive human genome coverage, including classification into various disease-associated genes as well as conventional canonical pathways and Gene Ontology. In summary, this novel web server (cancer.informatics.indiana.edu/mmia) will provide life science researchers with a valuable tool for the study of the biological (and pathological) causes and effects of the expression of this class of interesting protein regulators. 10.1093/nar/gkp294
Seungyoon Nam, Meng Li, Kwangmin Choi, Curtis Balch, Sun Kim, Kenneth Nephew

Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W323-328.

GeneSet2miRNA is the first web-based tool which is able to identify whether or not a gene list has a signature of miRNA-regulatory activity. As input, GeneSet2miRNA accepts a list of genes. As output, a list of miRNA-regulatory models is provided. A miRNA-regulatory model is a group of miRNAs (single, pair, triplet or quadruplet) that is predicted to regulate a significant subset of genes from the submitted list. GeneSet2miRNA provides a user friendly dialog-driven web page submission available for several model organisms. GeneSet2miRNA is freely available at http://mips.helmholtz-muenchen.de/proj/gene2mir/. 10.1093/nar/gkp313
Alexey Antonov, Sabine Dietmann, Philip Wong, Dominik Lutter, Hans Mewes

Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W273-276.

Computational microRNA (miRNA) target prediction is one of the key means for deciphering the role of miRNAs in development and disease. Here, we present the DIANA-microT web server as the user interface to the DIANA-microT 3.0 miRNA target prediction algorithm. The web server provides extensive information for predicted miRNA:target gene interactions with a user-friendly interface, providing extensive connectivity to online biological resources. Target gene and miRNA functions may be elucidated through automated bibliographic searches and functional information is accessible through Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The web server offers links to nomenclature, sequence and protein databases, and users are facilitated by being able to search for targeted genes using different nomenclatures or functional features, such as the genes possible involvement in biological pathways. The target prediction algorithm supports parameters calculated individually for each miRNA:target gene interaction and provides a signal-to-noise ratio and a precision score that helps in the evaluation of the significance of the predicted results. Using a set of miRNA targets recently identified through the pSILAC method, the performance of several computational target prediction programs was assessed. DIANA-microT 3.0 achieved there with 66% the highest ratio of correctly predicted targets over all predicted targets. The DIANA-microT web server is freely available at www.microrna.gr/microT. 10.1093/nar/gkp292
M Maragkakis, M Reczko, VA Simossis, P Alexiou, GL Papadopoulos, T Dalamagas, G Giannopoulos, G Goumas, E Koukis, K Kourtis, T Vergoulis, N Koziris, T Sellis, P Tsanakas, AG Hatzigeorgiou

Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W266-272.

MicroRNAs (miRNAs) are short RNAs that act as guides for the degradation and translational repression of protein-coding mRNAs. A large body of work showed that miRNAs are involved in the regulation of a broad range of biological functions, from development to cardiac and immune system function, to metabolism, to cancer. For most of the over 500 miRNAs that are encoded in the human genome the functions still remain to be uncovered. Identifying miRNAs whose expression changes between cell types or between normal and pathological conditions is an important step towards characterizing their function as is the prediction of mRNAs that could be targeted by these miRNAs. To provide the community the possibility of exploring interactively miRNA expression patterns and the candidate targets of miRNAs in an integrated environment, we developed the MirZ web server, which is accessible at www.mirz.unibas.ch. The server provides experimental and computational biologists with statistical analysis and data mining tools operating on up-to-date databases of sequencing-based miRNA expression profiles and of predicted miRNA target sites in species ranging from Caenorhabditis elegans to Homo sapiens. 10.1093/nar/gkp412
Jean Hausser, Philipp Berninger, Christoph Rodak, Yvonne Jantscher, Stefan Wirth, Mihaela Zavolan

Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W11-16.

DNA Data Bank of Japan (DDBJ) provides Web-based systems for biological analysis, called Web APIs for biology (WABI). So far, we have developed over 20 SOAP services and several workflows that consist of a series of method invocations. In this article, we present newly developed services of WABI, that is, REST-based Web services, additional workflows and a workflow navigation system. Each Web service and workflow can be used as a complete service or a building block for programmers to construct more complex information processing systems. The workflow navigation system aims to help non-programming biologists perform analysis tasks by providing next applicable services on Web browsers according to the output of a previously selected service. With this function, users can apply multiple services consecutively only by following links without any programming or manual copy-and-paste operations on Web browsers. The listed services are determined automatically by the system referring to the dictionaries of service categories, the input/output types of services and HTML tags. WABI and the workflow navigation system are freely accessible at http://www.xml.nig.ac.jp/index.html and http://cyclamen.ddbj.nig.ac.jp/, respectively. 10.1093/nar/gkp300
Yeondae Kwon, Yasumasa Shigemoto, Yoshikazu Kuwana, Hideaki Sugawara

Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W6-10.

The European Bioinformatics Institute (EMBL-EBI) has been providing access to mainstream databases and tools in bioinformatics since 1997. In addition to the traditional web form based interfaces, APIs exist for core data resources such as EMBL-Bank, Ensembl, UniProt, InterPro, PDB and ArrayExpress. These APIs are based on Web Services (SOAP/REST) interfaces that allow users to systematically access databases and analytical tools. From the user's point of view, these Web Services provide the same functionality as the browser-based forms. However, using the APIs frees the user from web page constraints and are ideal for the analysis of large batches of data, performing text-mining tasks and the casual or systematic evaluation of mathematical models in regulatory networks. Furthermore, these services are widespread and easy to use; require no prior knowledge of the technology and no more than basic experience in programming. In the following we wish to inform of new and updated services as well as briefly describe planned developments to be made available during the course of 2009-2010. 10.1093/nar/gkp302
Hamish Mcwilliam, Franck Valentin, Mickael Goujon, Weizhong Li, Menaka Narayanasamy, Jenny Martin, Teresa Miyar, Rodrigo Lopez

BMC Bioinformatics, Vol. 10, No. 1. (2009), 201.

BACKGROUND:Publicly available datasets of microarray gene expression signals represent an unprecedented opportunity for extracting genomic relevant information and validating biological hypotheses. However, the exploitation of this exceptionally rich mine of information is still hampered by the lack of appropriate computational tools, able to overcome the critical issues raised by meta-analysis. RESULTS:This work presents A-MADMAN, an open source web application which allows the retrieval, annotation, organization and meta-analysis of gene expression datasets obtained from Gene Expression Omnibus. A-MADMAN addresses and resolves several open issues in the meta-analysis of gene expression data. CONCLUSIONS:A-MADMAN allows i) the batch retrieval from Gene Expression Omnibus and the local organization of raw data files and of any related meta-information, ii) the re-annotation of samples to fix incomplete, or otherwise inadequate, metadata and to create user-defined batches of data, iii) the integrative analysis of data obtained from different Affymetrix platforms through custom chip definition files and meta-normalization. Software and documentation are available on-line at http://compgen.bio.unipd.it/bioinfo/amadman/.
Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, Davide Risso, Chiara Romualdi, Silvio Bicciato, Stefania Bortoluzzi

Journal of biomolecular techniques : JBT, Vol. 20, No. 2. (April 2009), pp. 135-151.

In the 2007 Association of Biomolecular Resource Facilities Microarray Research Group project, we analyzed HL-60 DNA with five platforms: Agilent, Affymetrix 500K, Affymetrix U133 Plus 2.0, Illumina, and RPCI 19K BAC arrays. Copy number variation was analyzed using circular binary segmentation (CBS) analysis of log ratio scores from four independently assessed hybridizations of each platform. Data obtained from these platforms were assessed for reproducibility and the ability to detect formerly reported copy number variations in HL-60. In HL-60, all of the tested platforms detected genomic DNA amplification of the 8q24 locus, trisomy 18, and monosomy X; and deletions at loci 5q11.2~q31, 9p21.3~p22, 10p12~p15, 14q22~q31, and 17p12~p13.3. In the HL-60 genome, at least two of the five platforms detected five novel losses and five novel gains. This report provides guidance in the selection of platforms based on this wide-ranging evaluation of available CGH platforms.
SD Hester, L Reid, N Nowak, WD Jones, JS Parker, K Knudtson, W Ward, J Tiesman, ND Denslow

Scientometrics, Vol. 72, No. 1. (July 2007), pp. 81-92.
Liwen Vaughan, Margaret Kipp, Yijun Gao

Scientometrics, Vol. 67, No. 2. (26 May 2006), pp. 291-300.

Summary

(14 March 2002)

David Weinberger's Small Pieces Loosely Joined does not merely celebrate the World Wide Web; it attempts to make a case that the institution has completely remodeled many of the world's self-perceptions. The book does so entertainingly, if not convincingly, and is a lively collection of epigrammatic phrases (the Web is "'place-ial' but not spatial"; "on the Web everyone will be famous to 15 people"), as well as illustrations of these changes. There are intriguing assertions: that the Web is "broken on purpose" and that its many pockets of erroneous information and its available forums for disputing, say, manufacturers' hyperbole, let people feel more comfortable with their own inherent imperfections. At other times the book seems stale: it declares that the Web has disrupted long-held axioms about time, space, and knowledge retrieval and that it has dramatically rearranged notions of community and individuality. Weinberger's analysis, though occasionally facile and too relentlessly optimistic and overstated, is surely destined to be the subject of furious debate in chat rooms the cyber-world over. --H. O'Billovich ...an ambitious look at how the web is transforming the concepts on which our society is built...Weinberger shows that the new medium of the web is not only altering social institutions such as business and govn't but reality itself
David Weinberger

Personal and Ubiquitous Computing
Lian Loke, Astrid Larssen, Toni Robertson, Jenny Edwards

(09 June 2008)

As modern organizations migrate from older information architectures to new Web-based systems, the discipline of software engineering is changing both in terms of technologies and methodologies. There is a need to examine this new frontier from both a theoretical and pragmatic perspective, and offer not only a survey of new technologies and methodologies but discussions of the applicability and pros/cons of each. **Software Engineering for Modern Web Applications: Methodologies and Technologies** presents current, effective software engineering methods for the design and development of modern Web-based applications, offering scholars, researchers, and practitioners innovative research on the theoretical frameworks, structures, management, and implications software engineering for modern Web applications.
Daniel Brandon