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| Ines Thiele; Ronan M. T. Fleming; Richard Que; Aarash Bordbar; Bernhard O. Palsson. |
| The genetic code is redundant as amino acids are encoded by synonymous codons that are unequally used.This codon usage bias (CUB) affects gene expression and cellular functions yet the underlying mechanisms have not been elucidated. We used a sequence-specific, stoichiometric model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655 to test the effect of randomly changed CUB on growth maximization under various environmental conditions. Amongst CUB mutant strains, we identified reduced growth phenotypes, which were caused by tRNA supply shortage. We propose, supported by computations and bibliomic data, that expansion of tRNA gene content or tRNA reading is a mechanism to respond to changes in CUB. Our systems biology modelling... |
| Tipo: Manuscript |
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6312/version/1 |
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| Kameshwar R. Ayasolla; Ravi K. R. Kalathur; Matthias E. Futschik. |
| Although the disease causing gene huntingtin has been known for some time, the exact cause of neuronal cell death during _Huntington's disease_ (HD) remains unknown. One potential mechanism contributing to the massive loss of neurons in HD brains might be the _Unfolded Protein Response_ (UPR) which is activated by accumulation of misfolded proteins in the endoplasmic reticulum (ER). As an adaptive response, UPR upregulates transcription of chaperones, temporarily attenuating new translation and activates protein degradation via the proteasome. However, at high levels of ER stress, UPR signalling can contribute to neuronal apoptosis.

Our primary aims include (a) construction of the UPR signalling network, (b)... |
| Tipo: Poster |
Palavras-chave: Neuroscience; Bioinformatics. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7078/version/1 |
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| Yuguang P. Xiong; Padmini Rangamani; Benjamin Dubin-Thaler; Michael Sheetz; Ravi Iyengar. |
| Cell motility is important for many physiological processes and the underlying
biochemical reactions motility have been well-characterized. Mathematical models, using
the biochemical reactions and focused on different types of spreading behavior have been
constructed and analyzed. In this study, we build on these previous models to develop a
three-dimensional stochastic model of isotropic spreading of mammalian fibroblasts. The model is composed of three actin remodeling reactions that occur stochastically in space and time and are regulated by membrane resistance forces. Numerical simulations indicate that the model qualitatively captures the experimentally observed isotropic cell... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/62/version/1 |
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| Yuguang P. Xiong; Padmini Rangamani; Benjamin Dubin-Thaler; Michael Sheetz; Ravi Iyengar. |
| Cell motility is important for many physiological processes and the underlying
biochemical reactions motility have been well characterized. Mathematical models, using
the biochemical reactions and focused on different types of spreading behavior have been
constructed and analyzed. In this study, we build on these previous models to develop a
three-dimensional stochastic model of isotropic spreading of mammalian fibroblasts. The model is composed of three actin remodeling reactions that occur stochastically in space and time and are regulated by membrane resistance forces. Numerical simulations indicate that the model qualitatively captures the experimentally observed isotropic cell... |
| Tipo: Manuscript |
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/62/version/2 |
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| Robert Muetzelfeldt. |
| The aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3 Core specification. The approach is illustrated with reference to Simile, a modelling environment which appears to have most of the capabilities of the various SBML Level 3 package proposals which deal with model structure. Simile (http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships between them.

The note is organised around the 6 packages listed on the SBML Level 3 Proposals web page... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4372/version/1 |
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| Lev V. Kalmykov; Vyacheslav L. Kalmykov. |
| The origin of species richness is one of the most widely discussed questions in ecology. The absence of unified mechanistic model of competition makes difficult our deep understanding of this subject. Here we show such a two-species competition model that unifies (i) a mechanistic niche model, (ii) a mechanistic neutral (null) model and (iii) a mechanistic violation of the competitive exclusion principle. Our model is an individual-based cellular automaton. We demonstrate how two trophically identical and aggressively propagating species can stably coexist in one stable homogeneous habitat without any trade-offs in spite of their 10% difference in fitness. Competitive exclusion occurs if the fitness difference is significant (approximately more than 30%).... |
| Tipo: Manuscript |
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology. |
| Ano: 2012 |
URL: http://precedings.nature.com/documents/7089/version/1 |
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| Nascimento,Leandro Costa do; Costa,Gustavo Gilson Lacerda; Binneck,Eliseu; Pereira,Gonçalo Amarante Guimarães; Carazzolle,Marcelo Falsarella. |
| The Genosoja consortium is an initiative to integrate different omics research approaches carried out in Brazil. Basically, the aim of the project is to improve the plant by identifying genes involved in responses against stresses that affect domestic production, like drought stress and Asian Rust fungal disease. To do so, the project generated several types of sequence data using different methodologies, most of them sequenced by next generation sequencers. The initial stage of the project is highly dependent on bioinformatics analysis, providing suitable tools and integrated databases. In this work, we describe the main features of the Genosoja web database, including the pipelines to analyze some kinds of data (ESTs, SuperSAGE, microRNAs, subtractive... |
| Tipo: Info:eu-repo/semantics/article |
Palavras-chave: Bioinformatics; Database; Gene expression; Soybean; Genosoja. |
| Ano: 2012 |
URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000200002 |
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| Christian P. Robert. |
| Approximate Bayesian computation (ABC), also known as likelihood-free methods, have become a standard tool for the analysis of complex models, primarily in population genetics but also for complex financial models. The development of new ABC methodology is undergoing a rapid increase in the past years, as shown by multiple publications, conferences and even software. While one valid interpretation of ABC based estimation is connected with nonparametrics, the setting is quite different for model choice issues. We examined in Grelaud et al. (2009, Bayesian Analysis) the use of ABC for Bayesian model choice in the specific of Gaussian random fields (GRF), relying on a sufficient property only enjoyed by GRFs to show that the approach was legitimate. Despite... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Evolutionary Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5961/version/1 |
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| Tina Toni. |
| Approximate Bayesian Computation (ABC) methods can be used in situations where the evaluation of the likelihood is computationally prohibitive. They are thus ideally suited for analyzing the complex dynamical models encountered in systems biology, where knowledge of the full (approximate) posterior is often essential.

This talk gives an overview of an ABC algorithm based on Sequential Monte Carlo (ABC SMC). Different uses of the algorithm will be presented, depending on the application question of interest. The first is the general parameter estimation framework, where the interest lies in estimating the posterior parameter distribution from available experimental data. In the second context we ask whether the model can... |
| Tipo: Presentation |
Palavras-chave: Molecular Cell Biology; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5964/version/1 |
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| Silvia Vilasi; Raffaele Ragone. |
| The potent immunomodulatory, anti-inflammatory and procoagulant properties of the
protein no. 4 secreted from the rat seminal vesicle epithelium (SV-IV) have been
previously found to be modulated by a supramolecular monomer-trimer equilibrium.
More structural details that integrate experimental data into a predictive framework
have recently been reported. Unfortunately, homology modelling and fold-recognition
strategies were not successful in creating a theoretical model of the structural
organization of SV-IV. It was inferred that the global structure of SV-IV is not similar
to any protein of known three-dimensional structure. Reversing... |
| Tipo: Manuscript |
Palavras-chave: Bioinformatics. |
| Ano: 2007 |
URL: http://precedings.nature.com/documents/1394/version/1 |
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| Scott L. Carter; Matthew Meyerson; Gad Getz. |
| Interpretation of allelic copy measurements at polymorphic markers in cancer samples presents distinctive challenges and opportunities. Due to frequent gross chromosomal alterations occurring in cancer (aneuploidy), many genomic regions are present at homologous-allele imbalance. Within such regions, the unequal contribution of alleles at heterozygous markers allows for direct phasing of the haplotype derived from each individual parent. In addition, genome-wide estimates of homologue specific copy- ratios (HSCRs) are important for interpretation of the cancer genome in terms of fixed integral copy-numbers. We describe HAPSEG, a probabilistic method to interpret bi- allelic marker data in cancer samples. HAPSEG operates by partitioning the genome into... |
| Tipo: Manuscript |
Palavras-chave: Cancer; Genetics & Genomics; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6494/version/1 |
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| Nicolo Fusi; Oliver Stegle; Neil Lawrence. |
| Expression quantitative trait loci (eQTL) studies are an integral tool to investigate the genetic component of gene expression variation. A major challenge in the analysis of such studies are hidden confounding factors, such as unobserved covariates or unknown environmental influences. These factors can induce a pronounced artifactual correlation structure in the expression profiles, which may create spurious false associations or mask real genetic association signals. 

Here, we report PANAMA (Probabilistic ANAlysis of genoMic dAta), a novel probabilistic model to account for confounding factors within an
eQTL analysis. In contrast to previous methods, PANAMA learns hidden factors jointly with the... |
| Tipo: Manuscript |
Palavras-chave: Genetics & Genomics; Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/5995/version/1 |
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| Athanasios Tsanas; Max A. Little; Patrick E. McSharry; Lorraine O. Ramig. |
| Tracking Parkinson's disease (PD) symptom progression often uses the Unified Parkinson’s Disease Rating Scale (UPDRS), which requires the patient's presence in clinic, and time-consuming physical examinations by trained medical staff. Thus, symptom monitoring is costly and logistically inconvenient for patient and clinical staff alike, also hindering recruitment for future large-scale clinical trials. Here, for the first time, we demonstrate rapid, remote replication of UPDRS assessment with clinically useful accuracy (about 7.5 UPDRS points difference from the clinicians’ estimates), using only simple, self-administered, and non-invasive speech tests. We characterize speech with signal processing algorithms,... |
| Tipo: Manuscript |
Palavras-chave: Neuroscience; Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3920/version/1 |
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| Registros recuperados: 1.312 | |
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