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| A. Patrice Seyed. |
| This paper examines the primitive relations (dependence, quality, and constitution) of the BFO and DOLCE upper ontologies, employed in developing domain ontologies of the biomedical sciences. The strengths in both upper ontologies are examined, which sets a framework for developing a common upper ontology that utilizes the assets of both. |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3481/version/1 |
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| Abhay Krishna. |
| Compared to other natural sciences ecological sciences has always been about seeing the bigger picture. The realization that local actions can have global impact has been the hallmark of ecological research. This integrative view is getting more and more accepted now with the recognition that whole is definitely more then sum of its parts. Advancement in computer sciences has now made it possible to comprehend the complexity arising from an integrative approach. This has given rise to a field interfacing computer science and ecological sciences called Ecoinformatics. The other popular parallel and more mature field is bioinformatics or computational biology. The presentation will take the audience on an Ecoinformatics tour touching on present status of... |
| Tipo: Presentation |
Palavras-chave: Ecology; Bioinformatics; Earth & Environment. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2018/version/1 |
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| Abhay Krishna. |
| In a fascinating tussle of perspectives in Volume 6 and issue no 3 of april 2008 Frontiers in Ecology and Evolution, Martin A Nuñez and Gregory M Crustinger enlist ways to brace up with the recent literature. They advocate that PhD students should choose a well studied system to have better chances of success. On the other side of this fascinating tussle Daniel Simberloff and Nathan J Sanders agree with there enthusiastic case and approaches for bracing up with the recent literature. However, they disagree with the play safe strategy of start-ups in ecology and evolution.

For me this tussle of perspectives is really fascinating. It underlines the story of our times. In the times of information explosion, should... |
| Tipo: Manuscript |
Palavras-chave: Ecology; Bioinformatics; Earth & Environment. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1959/version/1 |
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| Abhay Krishna; Ajit Narayanan. |
| Genome-scale molecular networks, including gene pathways, gene regulatory networks and protein interactions, are central to the investigation of the nascent disciplines of systems biology and bio-complexity. Dissecting these genome-scale molecular networks in its all-possible manifestations is paramount in our quest for a genotype-input phenotype-output application which will also take environment-genome interactions into account.

Machine learning approaches are now increasingly being used for reverse engineering such networks. Our work stresses the importance of a system approach in biological research and how artificial neural networks are at the forefront of Artificial Intelligence techniques that are increasingly... |
| Tipo: Presentation |
Palavras-chave: Ecology; Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2003/version/1 |
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| Abhay Sharma. |
| Pentylenetetrazole (PTZ) has recently been found to ameliorate cognitive impairment in rodent models of Down syndrome (DS). The mechanism underlying PTZ’s therapeutic effect is however not clear. Microarray profiling has previously reported differential expression of genes in DS. No mammalian transcriptomic data on PTZ treatment however exists. Nevertheless, a _Drosophila_ model inspired by rodent models of PTZ induced kindling plasticity has recently been described. Microarray profiling has shown PTZ’s downregulatory effect on gene expression in fly heads. In a comparative transcriptomics approach, I have analyzed the available microarray data in order to identify potential mechanism of PTZ action in DS. I find that transcriptomic... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Neuroscience; Pharmacology; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4330/version/1 |
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| Abhay Sharma; Farhan Mohammad; Priyanka Singh. |
| A male Drosophila model of locomotor deficit induced by chronic pentylenetetrazole (PTZ), a proconvulsant used to model epileptogenesis in rodents, has recently been described. Antiepileptic drugs (AEDs) ameliorate development of this behavioral abnormality. Time-series of microarray profiling of heads of male flies treated with PTZ has shown epileptogenesis-like transcriptomic perturbation in the fly model. Gender differences are known to exist in neurological and psychiatric conditions including epileptogenesis. We describe here the effects of chronic PTZ in Drosophila females, and compare the results with the male model. As in males, chronic PTZ was found found to cause a decreased climbing speed in females. In males, overrepresentation of Wnt, MAPK,... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Neuroscience; Pharmacology; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3460/version/1 |
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| Abhik Seal. |
| The treatment of acquired immunodeficiency syndrome (AIDS) is a challenging medical problem. TIBO is a nonnucleoside reverse transcriptase inhibitor, which binds non-competitively to the hydrophobic pocket on the p66 subunit of RT enzyme. We used a dataset consisting of physicochemical properties and reverse transcriptase inhibitor activities of 88 set of 4,5,6,7-tetrahydro-y-imidazo-[4,5,1-jk][1,4]-x-benzodiazepin-2-(1h)one derivatives that are variously substituted by halogens, alkyl groups. The dataset was taken from the BIOBYTE database at (www.davidhoekman.com). The concentration of the compound leading to 50% effect has been measured and expressed as IC50. The logarithm of the inverse of this parameter has been used as biological end points (log 1/C)... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5585/version/1 |
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| Abhishek Kumar. |
| Computational and statistical analysis has formed a large component of the biophysical efforts put forth to understand protein structure and function, due to the diversity and complexity of their structure. Outer membrane proteins form a diverse and complex set of proteins. Of these, porins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective. The objective of this study is to analyze the structural organization of porins using atomic temperature factor as a parameter. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. As good crystal structures have fewer possibilities of errors... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Microbiology; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7016/version/1 |
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| Abhishek Kumar; Hermann Ragg. |
| The superfamily of serine proteinase inhibitors (serpins) is involved in wide arrays of fundamental biological processes such as blood coagulation, complement activation, fibrinolysis, angiogenesis, inflammation and tumor suppression. The average protein size of a serpin family member is 350-400 amino acids, but gene structure varies in terms of number and position of exons and introns. All known serpins can be grouped into 16 clades and 10 orphan sequences. Vertebrate serpins can be conveniently classified into six sub-groups, based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels.
The objective of this study was to elucidate the phylogenetic kinships of serpins involved in... |
| Tipo: Poster |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2496/version/1 |
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| Adam A. Margolin; Teresa Palomero; Pavel Sumazin; Andrea Califano; Adolfo Ferrando; Gustavo A. Stolovitzky. |
| ChIP-on-chip has emerged as a powerful tool to dissect the complex network of regulatory interactions between transcription factors and their targets. However, most ChIP-on-chip analysis methods use conservative approaches aimed to minimize false-positive transcription factor targets. We present a model with improved sensitivity in detecting binding events from ChIP-on-chip data. Biochemically validated analysis in human T-cells reveals that three transcription factor oncogenes, NOTCH1, MYC, and HES1, bind one order of magnitude more promoters than previously thought. Gene expression profiling upon NOTCH1 inhibition shows broad-scale functional regulation across the entire range of predicted target genes, establishing a closer link between occupancy and... |
| Tipo: Manuscript |
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1364/version/1 |
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| Adam M. Goldstein. |
| Existing ontologies model components of evolution, but none synthesize them or describe the framework of ideas used to conceptualize evolution. The Evolution Ontology (EO) aims to do just this. EO models processes (e.g. natural selection); contexts (e.g. habitats); the entities that undergo evolution; and the theories, methods, and disciplines of evolutionary science. Uses include data curation, data mining, and literature curation, EO’s developers working on the latter two for works of Darwin and the Biodiversity Heritage Library. |
| Tipo: Poster |
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3557/version/1 |
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| Adeilton Brandao. |
| With the thousands of scientific papers being produced every month, picking an authors name, associate it to a research field and right evaluate his or her performance is in most of times a cumbersome task. I am proposing here that science indexes as h-index, g-index, total citations and published papers could be added to biomedical bibliographic citation in order to create a unique identifier for a given researcher. |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/794/version/1 |
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| Aditya Mittal. |
| Pattern generation and recognition in 3-D space have been of wide interest in fields varying from atomic and molecular structures to organization of celestial objects. Our thoughts towards investigating patterns (and elucidation of geometrical rules) followed by a known number of points with specific or specified coordinates are guided by the assumption/belief that there must be some thermodynamic and/or kinetic basis leading to the organization of coordinates of the known points. In terms of biomolecular structures, the DNA double helix is one of the strongest examples of such structures with coordinates of atoms in the phosphate backbone and the side-chains provide a helical geometrical configuration. It needs to be appreciated (and emphasized) that,... |
| Tipo: Presentation |
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Bioinformatics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6038/version/1 |
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| Adrian Mondry; Marie Loh; Alessandro Giuliani. |
| DNA microarray expression signatures are expected to provide new insights into patho- physiological pathways. Numerous variant statistical methods have been described for each step of the signal analysis. We employed five similar statistical tests on the same data set at the level of gene selection. Inter-test agreement for the identification of biological pathways in BioCarta, KEGG and Reactome was calculated using Cohen’s k- score. The identification of specific biological pathways showed only moderate agreement (0.30 < k < 0.79) between the analysis methods used. Pathways identified by microarrays must be treated cautiously as they vary according to the statistical method used. |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Genetics & Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1036/version/1 |
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| Adrian Paschke; Zhili Zhao. |
| Virtual e-Science infrastructures supporting Web-based scientific workflows are an example for knowledge-intensive collaborative and weakly-structured processes where the interaction with the human scientists during process execution plays a central role. In this paper we propose the lightweight dynamic user-friendly interaction with humans during execution of scientific workflows via the low-barrier approach of Semantic Wikis as an intuitive interface for non-technical scientists. Our Process Makna Semantic Wiki system is a novel combination of a business process management system adapted for scientific workflows with a Corporate Semantic Web Wiki user interface supporting knowledge intensive human interaction tasks during scientific workflow execution. |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5633/version/1 |
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| Adrian Paschke; Zhili Zhao. |
| To a large degree information and services for chemical e-Science have become accessible -anytime, anywhere -but not necessarily useful. The Rule Responder eScience middleware is about providing information consumers with rule-based agents to transform existing information into relevant information of practical consequences, hence providing control to the end-users to express in a declarative rule-based way how to turn existing information into personally relevant information and how to react or make automated decisions on top of it. |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5632/version/1 |
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| Aikkal Riju; Vadivel Arunachalam. |
| Expressed Sequence Tags or ESTs are small pieces of DNA sequence that are generated by sequencing either one or both ends of an expressed gene. ESTs provide researchers with a quick and inexpensive route for discovering new genes, for obtaining data on gene expression and regulation, and for constructing genome maps. Oil palm EST sequences as available in public domain are downloaded. They were grouped and made contigs using CAP3 and Phrap. Microsatellite repeats are located using 5 softwares (MISA, TRA, TROLL, SSRIT, SSR primer). Among the 5 methods MISA is found to be the best. It can elucidate the compound repeat also. Frequency and total number (202) of SSR were detected. Mononucleotide repeat is more abundant especially ‘A/T’... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3581/version/1 |
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| Registros recuperados: 1.312 | |
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