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| Mark Moll; Lydia E. Kavraki. |
| There is an increasing number of proteins with known structure but unknown function. Determining their function would have a significant impact on understanding diseases and designing new therapeutics. Computational methods can facilitate function determination by identifying proteins that have high structural and chemical similarity. Below, we will briefly describe LabelHash, a new method for partial structure comparison. In partial structure comparison, the goal is to find the best geometric and chemical similarity between a set of 3D points called a _motif_ and a subset of a set of 3D points called the _target_. Both the motif and targets are represented as sets of labeled 3D points. A motif is ideally composed of the functionally most-relevant residues... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2199/version/1 |
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| Chris T. Evelo. |
| Until recently nutrigenomics was mainly about transcriptomics related data. That already confronted us with overwhelming analytical problems. We learned to mathematically and statistically treat genome wide expression studies and studies directed to gene expression regulation. Nutrigenomics researchers had to become bilingual speaking: English and R1 and learned to think about co-expression, clusters and false discovery rates. The latter in fact proofed to be a trap. Removing all the false positives made us loose the information we were really interested in. To understand the results of our genomics experiments we often had to confront what we were measuring with what we already knew. After all false positives are not likely to all be related to the same... |
| Tipo: Presentation |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5689/version/1 |
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| Roderic Page. |
| Taxonomy is in many ways still predigital. Most taxonomic databases are little more than digitized index cards linking names to often-cryptic bibliographic citations, oblivious to the growing volume of scientific literature that is now online. A growing fraction of taxonomic literature is becoming freely available, either through adoption of Open Access publishing models, or through digitizing efforts such as the Biodiversity Heritage Library. Yet much of the most basic information about biodiversity, namely taxonomic description, remains either behind a pay wall, or only available in paper form. This talk sketches the goal of an "Open Taxonomy." The first step towards this goal is digitally linking scientific names to the primary... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6560/version/1 |
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| Yupeng Wang; Xinyu Liu; Romdhane Rekaya. |
| Genome-wide association studies (GWAS) have become a standard method for finding genetic variations that contribute to common, complex diseases. Recently, it is suggested that these diseases may be caused by epistatic interactions of multiple genetic variations. Although tens of software tools have been developed for epistasis detection, few are able to infer pathway importance from the identified epistatic interactions. AntEpiSeeker is originally an algorithm for detecting epistatic interactions in case-control studies, using a two-stage ant colony optimization (ACO) algorithm. We have developed AntEpiSeeker2.0, which extends the AntEpiSeeker algorithm to inference of epistasis-associated pathways, based on a natural use of the ACO pheromones. By looking... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/6994/version/1 |
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| Amos Bairoch. |
| We are entering a new era in the exploration of the human proteome.
Advances in technologies are allowing researchers to map with a much
better resolution and improved accuracy this very complex universe. Such
an exploration also requires a compendium of adequate bioinformatics
tools, data repositories and knowledge resources. We are going to describe
what are the state of the art in term of data and knowledge resources for
human proteins: from repositories of proteomics data such as PRIDE,
PeptideAtlas or Peptidome, databases such as SRMAtlas and HPA and
knowledgebase such as UniProtKB/Swiss-Prot.... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5050/version/1 |
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| M. Balakrishnan; R.C. Srivastava; M. Ramachandran. |
| Structure function relation of glucose kinese in Streptococcus pneumoniae. However, a solved structure for _Streptococcus pneumoniae_ glucose kinese is not available at the protein data bank. Glucose kinase is a regulatory enzyme capable of adding phosphate group to glucose in the first step of streptomycin biosynthesis. The activity of glucose kinase was regulated by the Carbon Catabolite Repression system. So, we created a model of glucose kinese from _Streptococcus pnemoniae_ using the X-ray crystallography structure of glucose kinese enzymes from _Enterobacteria faecalis_ as template with Molsoft ICM v3.5 software. The model was validated using protein structure checking tools such as PROCHECK, WHAT IF: for reliability. The active site amino acid... |
| Tipo: Manuscript |
Palavras-chave: Molecular Cell Biology; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3207/version/1 |
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| Francisco Buitrago; Silvia Restrepo; Diego Riaño-Pachón. |
| In this study we identify, and classify into families, transcription factors (TFs) and other transcriptional regulators (TRs) in genome sequences available from the Stramenopile group. For this we exploit the presence of protein domains and their combinations to build rules in the form of boolean rules, that are specific for each family of TFs and TRs. We found a correlation between the family size and some traits that has been described to be involved in the complexity of organisms. Furthermore, we found specific gains, losses and families that shows higher abundance in different lineages, which may be involved in the regulation of specific traits for some Stramenopile species. |
| Tipo: Poster |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7002/version/1 |
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| Huiying Li. |
| The human microbiota contributes to our normal postnatal development and plays a significant role in defining our physiology. To understand the role of microbiota in human health and disease, we study the skin microbiome in pilosebaceous units (hair follicles) and its association with acne.

Acne is one of the most common skin diseases. Although its etiology still needs to be defined, a bacterial factor has been suggested in the development of the disease. In fact, antibiotic therapy targeting _Propionibacterium acnes_ has been a mainstay treatment for more than 30 years.

Our preliminary study shows that the microcomedone, a specialized skin compartment where acne arises, has a tractable... |
| Tipo: Marker Paper / Data Plan |
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5305/version/1 |
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| Simon Anders; Wolfgang Huber. |
| Motivation: High throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq), cell counting. Statistical inference of differential signal in these data needs to take into account their natural variability throughout the dynamic range. When the number of replicates is small, error modeling is needed to achieve statistical power. 

Results: We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power.

Availability: A free open-source... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Microbiology; Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4282/version/1 |
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| Matúš Kalaš; Jon Ison. |
| Life-scientific Web services are increasingly available and diverse. Their semantic interoperability is crucial to enable automated workflow construction and efficient searching for the right service. At the same time, smooth programmatic access must be possible with all the main programming, scripting, or workflow languages.

This tutorial gave an introduction to the "SAWSDL":http://www.w3.org/standards/techs/sawsdl#w3c_all standard for semantic annotation of Web services and XML Schemas; the "EDAM":http://edamontology.sourceforge.net ontology for describing bioinformatics tools; and "BioXSD":http://bioxsd.org as a canonical data model for bioinformatics Web services.... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5565/version/1 |
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| Delphine Dauga; Olivier Tassy; Fabrice Daian; Daniel Sobral; Patrick Lemaire. |
| NISEED (Network for In situ Expression and Embryological Data) is a generic infrastructure for the creation, maintenance and integration of molecular and anatomical information on model organisms. We applied it to ascidians which are marine invertebrate chordates. These animals constitute model organisms of choice for developmental biology because their embryos develop with a small number of cells and an invariant lineage, allowing their study with a cellular level of resolution. In ANISEED (Ascidian NISEED), embryogenesis of ascidian is represented at the level of the genome via functional gene annotations, cis-regulatory elements or gene expression data, at the level of the cell by representing its morphology, fates, lineage, and relations with its... |
| Tipo: Poster |
Palavras-chave: Developmental Biology; Genetics & Genomics; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3168/version/1 |
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| Ravi K. Kalathur; Matthias E. Futschik. |
| The use of high-throughput technologies has provided us with large amounts of data for _Huntington's disease_ (HD), especially at the gene and protein levels. As phenotypic changes in HD may not just be due to the activity of individual genes but interrelated alterations of whole molecular networks, it is important to systematically analyse and represent accumulated data in a network-based approach.

Methods: To analyse and visualise protein interaction networks through a dedicated database to HD, we have established "HDNetDB": http://hdnetdb.sysbiolab.eu. This platform will not only help to understand molecular mechanisms better, but also assist in identifying potential molecular markers... |
| Tipo: Poster |
Palavras-chave: Neuroscience; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7090/version/1 |
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| Gábor Zsurka; Attila Csordás. |
| So far researchers, web users were restricted to non-intuitive and visually poor text based databases every time they wanted to take a look on the mitochondrial DNA and find a region of interest. But with MitoWheel the situation is about to change. MitoWheel is a graphical representation of the circular human mitochondrial genome available on the web at "http://mitowheel.org":http://mitowheel.org.

The human mitochondrial DNA is a 16569 basepair long, circular molecule and this very circularity is the basic idea behind MitoWheel. The mitochondrial genome can be represented with a wheel and by spinning this wheel users can quickly scan through, browse and identify the particular regions. The spinning is... |
| Tipo: Poster |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3167/version/1 |
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| Registros recuperados: 1.312 | |
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