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Author

Annette M. Adler

Other affiliations: PARC, Xerox
Bio: Annette M. Adler is an academic researcher from Agilent Technologies. The author has contributed to research in topics: Biological data & The Internet. The author has an hindex of 24, co-authored 45 publications receiving 4374 citations. Previous affiliations of Annette M. Adler include PARC & Xerox.

Papers
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Journal ArticleDOI
TL;DR: This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest.
Abstract: Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.

2,313 citations

Proceedings ArticleDOI
Annette M. Adler1, Anuj Gujar1, Beverly L. Harrison1, Kenton O'Hara2, Abigail Sellen2 
01 Jan 1998
TL;DR: A diary study of how people read in the course of their daily working lives, using structured interviews to examine the range of reading activities that subjects carried out, and presents findings relating to both common characteristics and variation across the sample.
Abstract: In this paper we describe a diary study of how people read in the course of their daily working lives. Fifteen people from a wide variety of professions were asked to log their daily document activity for a period of 5 consecutive working days. Using structured interviews, we analysed their reading activities in detail. We examine the range of reading activities that our subjects carried out, and then present findings relating to both common characteristics and variation across the sample. From these findings, we discuss some implications for the design of digital readiig devices.

249 citations

Journal ArticleDOI
01 Sep 1996
TL;DR: A view of media spaces is argued for which, first, focuses on a wider interpretation of media space interaction than the traditional view of person-to-person connections, and, second, emphasises emergent communicative practices, rather than looking for the transfer of face- to-face behaviours.
Abstract: Workstations and personal computers are increasingly being delivered with the ability to handle multimedia data; more and more of us are linked by high-speed digital networks. With multimedia communication environments becoming more commonplace, what have we learned from earlier experiences with prototype media environments? This paper reports on some of our experiences as developers, researchers and users of flexible, networked, multimedia computer environments, or “media spaces”. It focusses on the lessons we can learn from extended, long-term use of media spaces, with connections that last not hours or days, but months or years. We take as our starting point a set of assumptions which differ from traditional analytical perspectives. In particular, we begin from the position that that real-world baseline is not always an appropriate point of comparison for new media technologies; that a set of complex and intricate communicative behaviours arise over time; and that media spaces connect not only individuals, but the wider social groups of which they form part. We outline a framework based on four perspectives — individual, interactional, communal and societal — from which to view the behaviour of individuals and groups linked by multimedia environments. On the basis of our long-term findings, we argue for a view of media spaces which, first, focuses on a wider interpretation of media space interaction than the traditional view of person-to-person connections, and, second, emphasises emergent communicative practices, rather than looking for the transfer of face-to-face behaviours.

248 citations

Proceedings ArticleDOI
27 Mar 1997
TL;DR: This paper considers several familiar systems and describes the shared characteristics these systems have developed to deal with critical concerns of collaboration, and extends this initial design space along three dimensions: the articulation of a persistent sense of location, the boundary tensions between real and virtual worlds, and the emergence and evolution of community.
Abstract: Collaboration has long been of considerable interest in the CHI community. This paper proposes and explores the concept of network communities as a crucial part of this discussion. Network communities are a form of technologymediated environment that foster a sense of community among users. We consider several familiar systems and describe the shared characteristics these systems have developed to deal with critical concerns of collaboration. Based on our own experience as designers and users of a variety of network communities. we extend this initial design space along three dimensions: the articulation of a persistent sense of location, the boundary tensions between real and virtual worlds, and the emergence and evolution of community.

178 citations

Journal ArticleDOI
TL;DR: The studies revealed that loss of differentiated smooth muscle cell gene expression is the primary expression signature of disease progression in atherosclerosis and provide insight into the severe form of coronary artery disease associated with diabetes, reporting an overabundance of immune and inflammatory signals in diabetics.
Abstract: Large-scale gene expression studies provide significant insight into genes differentially regulated in disease processes such as cancer. However, these investigations offer limited understanding of multisystem, multicellular diseases such as atherosclerosis. A systems biology approach that accounts for gene interactions, incorporates nontranscriptionally regulated genes, and integrates prior knowledge offers many advantages. We performed a comprehensive gene level assessment of coronary atherosclerosis using 51 coronary artery segments isolated from the explanted hearts of 22 cardiac transplant patients. After histological grading of vascular segments according to American Heart Association guidelines, isolated RNA was hybridized onto a customized 22-K oligonucleotide microarray, and significance analysis of microarrays and gene ontology analyses were performed to identify significant gene expression profiles. Our studies revealed that loss of differentiated smooth muscle cell gene expression is the primary expression signature of disease progression in atherosclerosis. Furthermore, we provide insight into the severe form of coronary artery disease associated with diabetes, reporting an overabundance of immune and inflammatory signals in diabetics. We present a novel approach to pathway development based on connectivity, determined by language parsing of the published literature, and ranking, determined by the significance of differentially regulated genes in the network. In doing this, we identify highly connected "nexus" genes that are attractive candidates for therapeutic targeting and followup studies. Our use of pathway techniques to study atherosclerosis as an integrated network of gene interactions expands on traditional microarray analysis methods and emphasizes the significant advantages of a systems-based approach to analyzing complex disease.

156 citations


Cited by
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Journal ArticleDOI
TL;DR: In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework.
Abstract: A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein-protein interactions, and importing known pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer of interaction knowledge between organisms based on gene orthology. In the latest version 10.5 of STRING, the biggest changes are concerned with data dissemination: the web frontend has been completely redesigned to reduce dependency on outdated browser technologies, and the database can now also be queried from inside the popular Cytoscape software framework. Further improvements include automated background analysis of user inputs for functional enrichments, and streamlined download options. The STRING resource is available online, at http://string-db.org/.

5,569 citations

Book
01 Jan 2003
TL;DR: In this paper, Sherry Turkle uses Internet MUDs (multi-user domains, or in older gaming parlance multi-user dungeons) as a launching pad for explorations of software design, user interfaces, simulation, artificial intelligence, artificial life, agents, virtual reality, and the on-line way of life.
Abstract: From the Publisher: A Question of Identity Life on the Screen is a fascinating and wide-ranging investigation of the impact of computers and networking on society, peoples' perceptions of themselves, and the individual's relationship to machines. Sherry Turkle, a Professor of the Sociology of Science at MIT and a licensed psychologist, uses Internet MUDs (multi-user domains, or in older gaming parlance multi-user dungeons) as a launching pad for explorations of software design, user interfaces, simulation, artificial intelligence, artificial life, agents, "bots," virtual reality, and "the on-line way of life." Turkle's discussion of postmodernism is particularly enlightening. She shows how postmodern concepts in art, architecture, and ethics are related to concrete topics much closer to home, for example AI research (Minsky's "Society of Mind") and even MUDs (exemplified by students with X-window terminals who are doing homework in one window and simultaneously playing out several different roles in the same MUD in other windows). Those of you who have (like me) been turned off by the shallow, pretentious, meaningless paintings and sculptures that litter our museums of modern art may have a different perspective after hearing what Turkle has to say. This is a psychoanalytical book, not a technical one. However, software developers and engineers will find it highly accessible because of the depth of the author's technical understanding and credibility. Unlike most other authors in this genre, Turkle does not constantly jar the technically-literate reader with blatant errors or bogus assertions about how things work. Although I personally don't have time or patience for MUDs,view most of AI as snake-oil, and abhor postmodern architecture, I thought the time spent reading this book was an extremely good investment.

4,965 citations

Journal ArticleDOI
18 Jul 2011-PLOS ONE
TL;DR: REVIGO is a Web server that summarizes long, unintelligible lists of GO terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures.
Abstract: Outcomes of high-throughput biological experiments are typically interpreted by statistical testing for enriched gene functional categories defined by the Gene Ontology (GO). The resulting lists of GO terms may be large and highly redundant, and thus difficult to interpret. REVIGO is a Web server that summarizes long, unintelligible lists of GO terms by finding a representative subset of the terms using a simple clustering algorithm that relies on semantic similarity measures. Furthermore, REVIGO visualizes this non-redundant GO term set in multiple ways to assist in interpretation: multidimensional scaling and graph-based visualizations accurately render the subdivisions and the semantic relationships in the data, while treemaps and tag clouds are also offered as alternative views. REVIGO is freely available at http://revigo.irb.hr/.

4,919 citations

Journal ArticleDOI
21 Jun 2012-Nature
TL;DR: The results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic CNAs on the transcriptome, and identify novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort.
Abstract: The elucidation of breast cancer subgroups and their molecular drivers requires integrated views of the genome and transcriptome from representative numbers of patients. We present an integrated analysis of copy number and gene expression in a discovery and validation set of 997 and 995 primary breast tumours, respectively, with long-term clinical follow-up. Inherited variants (copy number variants and single nucleotide polymorphisms) and acquired somatic copy number aberrations (CNAs) were associated with expression in 40% of genes, with the landscape dominated by cisand trans-acting CNAs. By delineating expression outlier genes driven in cis by CNAs, we identified putative cancer genes, including deletions in PPP2R2A, MTAP and MAP2K4. Unsupervised analysis of paired DNA–RNA profiles revealed novel subgroups with distinct clinical outcomes, which reproduced in the validation cohort. These include a high-risk, oestrogen-receptor-positive 11q13/14 cis-acting subgroup and a favourable prognosis subgroup devoid of CNAs. Trans-acting aberration hotspots were found to modulate subgroup-specific gene networks, including a TCR deletion-mediated adaptive immune response in the ‘CNA-devoid’ subgroup and a basal-specific chromosome 5 deletion-associated mitotic network. Our results provide a novel molecular stratification of the breast cancer population, derived from the impact of somatic CNAs on the transcriptome.

4,722 citations

Journal ArticleDOI
TL;DR: Version 2.8 introduces two powerful new features—Custom Node Graphics and Attribute Equations—which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities.
Abstract: Summary: Cytoscape is a popular bioinformatics package for biological network visualization and data integration. Version 2.8 introduces two powerful new features—Custom Node Graphics and Attribute Equations—which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities. Custom Node Graphics allow an image to be projected onto a node, including images generated dynamically or at remote locations. Attribute Equations provide Cytoscape with spreadsheet-like functionality in which the value of an attribute is computed dynamically as a function of other attributes and network properties. Availability and implementation: Cytoscape is a desktop Java application released under the Library Gnu Public License (LGPL). Binary install bundles and source code for Cytoscape 2.8 are available for download from http://cytoscape.org. Contact: [email protected]

4,186 citations