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| Registros recuperados: 612 | |
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| Francesca Diella; Allegra Via; Claudia Chica; Katja Luck; Catherin M. Gould; Toby J. Gibson. |
| Linear motifs are short and evolutionarily variable sequence patterns associated with particular functions often involving post-translational modifications, such as phosphorylation, acetylation, glycosylation, targeting signals for cellular compartments, protein cleavage sites and protein–protein interaction.

Experimentally they are often neglected because their short length (4-10 residues long), and the fact that they often reside in disordered regions in proteins makes them difficult to detect. For a similar reason, using the sole regular expression to detect linear motifs matches in sequences has almost no predictive power because they are both statistically insignificant and prone to massive... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3152/version/1 |
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| Heather A. Piwowar; Douglas B. Fridsma. |
| Background
 Many initiatives and repositories exist to encourage the sharing of research data, and thousands of microarray gene expression datasets are publicly available. Many studies reuse this data, but it is not well understood which datasets are reused and for what purpose.

 Materials and Methods
 We trained a machine-learning algorithm to automatically classify full-text gene expression microarray studies into two classes: those that generated original microarray data (n=900) and those which only reused data (n=250). We then compared the Medical Subject Heading (MeSH) terms of two classes to identify MeSH topics which were over- or under-represented by publications with... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/425/version/1 |
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| Laurent Gatto; Kathryn S. Lilley. |
| The development of MSnbase aims at providing researchers dealing with labelled quantitative proteomics data with a transparent, portable, extensible and open-source collaborative framework to easily manipulate and analyse MS2-level raw tandem mass spectrometry data. The implementation in R gives users and developers a great variety of powerful tools to be used in a controlled and reproducible way. Furthermore, MSnbase has been developed following an object-oriented programming paradigm: all information that is manipulated by the user is encapsulated in ad hoc data containers to hide it's underlying complexity. We illustrate the usage and achievements of our software using a published spiked-in data set in which varying quantities of test proteins... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5010/version/1 |
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| Matthias Lange; Christian Colmsee; Steffen Flemming; Jinbo Chen; Matthias Klapperstück; Uwe Scholz. |
| Retrieval and citation of primary data is the important factor in the approaching age of “data science”. Digital data are easily shared, and just as easily wiped or lost. The problem of keeping on-line data accessible and
retrievable is especially difficult for SME like plant breeders plant biotech companies as well as research projects in this domain.
Intension of eDAL is the provisioning of an information retrieval and data citation infrastructure that meets the requirements of the “data science” age and implements a re-usable platform for data retrieval, data
citation, and data publication. Like a shopping cart, the idea is to combine a search engine and a... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4935/version/1 |
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| Alexandra Chittka; Ursula Grazini. |
| During cortical development, neural stem cells (NSCs) switch from proliferative to neuron-generating asymmetric divisions. Here we investigated the role of Schwann cell factor 1 (SC1/PRDM4), a transcriptional repressor highly expressed in the developing nervous system, during NSCs development. We found that SC1 protein levels were down-regulated in newly differentiating neurons, while remaining high in undifferentiated NSCs, suggesting an asymmetric inheritance of SC1. Knockdown of SC1 in the NSCs led to precocious differentiation of neurons and its overexpression led to an increase in Nestin-expressing precursors. We found that SC1, through its amino-terminus, recruits the chromatin modifier PRMT5, a histone arginine methyltransferase that catalyses... |
| Tipo: Poster |
Palavras-chave: Molecular Cell Biology; Neuroscience. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4926/version/1 |
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| L K Dwivedi; Ankita Singh; Poonam Yadav. |
| Tuberculosis (TB), despite anti-mycobacterial therapies and vaccine, is a deadly infectious disease with about 12 million incident cases worldwide. Existing Bacillus Calmette-Guérin (BCG) vaccine is unquestionably inexpensive, safe and effective against severe forms of childhood TB but appears to be limited in effectiveness against adult pulmonary disease in endemic areas. Genetic variation in the population is the major obstruction inhibiting validation of biomarkers for protective human immunity against TB. Since current TB cases are presenting new challenges with threats of HIV co-infection therefore various attempts at a global platform are being made to develop a new modified vaccine against it. Consequently, Modified Vaccinia Ankara virus... |
| Tipo: Poster |
Palavras-chave: Immunology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5950/version/1 |
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| Ananya Gupta; Sergey Ustinov; Kaveh Mashayekhi; Anthony P. Moran. |
| Establishing a successful infection within the gastric environment and its varied and changing niches requires adaptation achieved through regulation of bacterial gene expression. In the gastric environment in addition to the low pH Helicobacter pylori is required to adapt to conditions of iron limitation. In this study, we used cDNA microarrays to identify genes whose expression was altered when the bacterium was grown under differing conditions of pH (5 versus 7) and iron limitation. cDNA microarray analyses following exposure to different growth conditions were carried out for three H. pylori strains 26695 (gastritis-associated), J99 (ulcer-associated) and AG-1 (atrophic gastritis-associated). Genes were identified whose expression was acid pH-dependent... |
| Tipo: Poster |
Palavras-chave: Microbiology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5842/version/1 |
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| Falko Krause; Timo Lubitz; Marvin Schulz; Edda Klipp. |
| semanticSBML 2.0 is a collection of online services for the processing of biochemical networks in the SBML (Systems Biology Markup Language) document format. It allows users to edit SBO (Systems Biology Ontology) and RDF based MIRIAM (Minimum Information Required in the Annotation of Models) annotations, check for semantic validity, compare and merge SBML documents, and to create submodels. Given an annotated SBML document similar SBML documents can be retrieved from the BioModels Database via a ranked similarity search. Further features of semanticSBML 2.0 include graph visualization of SBML documents, parameter balancing, creation of SBML documents using shorthand SBML, and an interface to the BioModels Database that allows the comparison of document... |
| Tipo: Poster |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5402/version/1 |
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| Lakshmanane P. Boominathan. |
| Identifying agents that inhibit the proliferation of cancer stem cells is of great importance in cancer biology. Curcumin has been shown to function as an anti-cancer agent. One of the tumor suppressors that appear to be induced in response to curcumin treatment is p53. A recent study suggests that curcumin increases the expression of miRNAs, such as miR-22, miR-181a, b, c, miR-34, miR-103, and miR-21. Intriguingly, miR-34, 181b, c, miR-103, miR-21, and miR-24 have been identified as transcriptional targets of the tumor suppressor p53. This data suggests a possibility that curcumin, by inducing the expression of p53, it could increase the expression of these microRNAs. A number of groups have shown that c-Myc, Sox-2, Klf-4, Oct-4, Sox-2, Nanog, and... |
| Tipo: Poster |
Palavras-chave: Cancer. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/4110/version/1 |
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| Om Prakash; Feroz Khan; R.S. Sangwan. |
| Withanolides are a group of natural C-28 steroids built on an ergostane skeleton and classified into two major groups according to their structural skeleton: (a) compounds with a beta-oriented side chain and (b) compounds with an alpha-oriented side chain. Withanolide E represents one of the members of the latter group. Classification of active compounds on the basis of pharmacophore against specific cancer cell line poses a serious concern at the primary stage of virtual screening. To overcome this problem we have developed an artificial neural network based virtual screening model for discriminating active and non-active Withanolide-E-like derivatives or analogs against human breast cancer cell line MCF-7. In the present work, a 2D chemical descriptors... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6616/version/1 |
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| Olga Lyashevska. |
| Biodiversity is a multi-dimensional concept that is represented by a large variety of measures. This complexity and lack of consistency limits the development of a coherent scientific understanding of biodiversity and how properties, such as ecosystem services, may depend on it. Here, I demonstrate that the formal discipline of creating a relational database (RDB) for information about biodiversity and its measures, is a useful tool in organising such knowledge into coherent sense. Following steps of the logical database design and data normalization to build a RDB, results in a formal definition of biodiversity within a well defined concept structure; mapping rules between the concepts of biodiversity and entities of RDB and a consistent information... |
| Tipo: Poster |
Palavras-chave: Ecology; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3327/version/1 |
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| Yuichi Kodama; Satoshi Saruhashi; Eli Kaminuma; Hideaki Sugawara; Toshihisa Takagi; Kousaku Okubo; Yasukazu Nakamura. |
| Massively parallel sequencers become widespread and produce unprecedented amounts of sequence reads in many biological fields. DNA Data Bank of Japan (DDBJ) has constructed the international sequence database collaboration (INSDC) together with EBI and NCBI. In 2008, DDBJ has established the DDBJ Read Archive (DRA) to archive raw output data from the new sequencing platforms. DRA archives and provides the raw data sets together with the other two INSDC partners the Sequence Read Archive (SRA) at NCBI and the European Sequence Read Archive (ERA) at EBI. These new sequencing platforms are also used to count DNA/RNA molecules instead of microarray experiment because of their higher accuracy. Since 2004, DDBJ has operated CIBEX as a repository database for... |
| Tipo: Poster |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5085/version/1 |
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| Lawrence J. Herskowitz; Anthony L. Salvagno; Brian P. Josey; Andy Maloney; Steven J. Koch. |
| Kinesin-1 (conventional kinesin) is a homodimeric motor protein important for axonal transport. It has been well studied through ensemble and single-molecule assays. However, the enzymatic stepping cycle is complex, with many rate constants that are modulated by interaction of the two motor domains. This makes it difficult to predict how changes in a given rate constant may affect observable properties such as processivity, velocity, or stall force. We have written a simulation of kinesin walking using a Stochastic Simulation Algorithm. The model allows for interactions between the heads, and includes states that are not considered part of the normal cycle. This adds to the complexity of the model but also allows for probing rare events, such as those that... |
| Tipo: Poster |
Palavras-chave: Molecular Cell Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4468/version/1 |
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| Saeid Hadi; Hamid Mobasheri. |
| OmpF an outer-membrane porin channel of _E. Coli_ posses beta-barrel structure, whose conductivity and gating phenomena are affected by changes in pH, salt concentration and so on. The distribution of amino acids in OmpF induces a non homologous electric potential in channel lumen. The intrinsic charge distribution caused be amino acid may be affected by lipid bilayer, extra and intra cellular ion concentration, and other physico-chemical condition of environment including, pH, temperature, polyelectrolytes etc. Nucleotides are considered as one of most important metabolite in the cell that have pass through membrane whenever necessary. The experimental study of translocation of such a molecules through channels have provided invaluable information... |
| Tipo: Poster |
Palavras-chave: Molecular Cell Biology. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5101/version/1 |
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| Roxana Moslehi; Caroline Signore; James Troendle; Amiran Dzutsev; James L. Mills. |
| The effects of DNA repair and transcription genes in human prenatal life have never been studied. Trichothiodystrophy (TTD) is a rare (affected frequency of 10^-6^) recessive disorder caused by mutations in genes involved in the nucleotide excision repair (NER) pathway and in transcription. Based on our clinical observations, we conducted a genetic epidemiologic study to investigate gestational outcomes associated with TTD. We compared pregnancies resulting in TTD-affected offspring (N=24) with respect to abnormalities in their antenatal and neonatal periods to pregnancies resulting in their unaffected siblings (N=18), accounting for correlation, and to population reference values. Significantly higher incidence of several severe gestational complications... |
| Tipo: Poster |
Palavras-chave: Developmental Biology; Genetics & Genomics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3582/version/1 |
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| Ruben E. Valas; Philip E. Bourne. |
| Determining which branches of the tree of life have derived features narrows down the possible location of the root. Currently the polarization of indels done by Lake _et al_.^1-5^ and the polarizing transitions of Cavalier-Smith^6^ arrive at contradictory positions for the root of the tree. We have analyzed the sequence based indel arguments using protein structure wherever possible. Structure strongly supports some of the polarizations, but in other indels it argues for a different conclusion. We conclude that there is no contradiction between Lake _et al_. and Cavalier-Smith; the root of the tree of life must be near the Chloroflexi.
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| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Bioinformatics; Evolutionary Biology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3290/version/1 |
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| Abhishek Kumar; S Krishnaswamy. |
| 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 that 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 lesser possibilities of errors... |
| Tipo: Poster |
Palavras-chave: Biotechnology. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/2803/version/1 |
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| Jared J. Gerschler-Zia; James F. Dunne; Aaron D. Sadow. |
| Titanium complexes possessing sterically encumbered ligands have allowed for the preparation of reactive moieties (imido, alkylidene and alkylidyne species) relevant to reactions such as olefin polymerization and alkyne hydroamination. For this reason, we have targeted robust scorpionate ancillary ligands to support reactive titanium centers. Thus, a series of titanium complexes were synthesized using an achiral oxazoline-based scorpionate ligand, tris(4,4-dimethyl-2-oxazolinyl)phenyl borate [To^M^]^-^ as well as the related chiral ligand, tris(4-isopropyl-2-oxazolinyl)phenyl borate [To^P^]^-^. The complex [Ti(κ^3^- To^M^)Cl~3~] was prepared in moderate yield (43%) by the rapid (<1 min at room temperature) reaction of Li[To^M^] and... |
| Tipo: Poster |
Palavras-chave: Chemistry. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4763/version/1 |
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| Registros recuperados: 612 | |
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