| 1. |
- Chatterjee, Saikat, et al.
(author)
-
SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition
- 2014
-
In: Bioinformatics. - : Oxford University Press. - 1460-2059 .- 1367-4803 .- 1367-4811. ; 30:17, s. 2423-2431
-
Journal article (peer-reviewed)abstract
- Motivation: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. As the sample sequence data typically harbors reads of variable lengths and different levels of biological and technical noise, accurate statistical analysis of such data is challenging. Currently popular estimation methods are typically time-consuming in a desktop computing environment.Results: Using sparsity enforcing methods from the general sparse signal processing field (such as compressed sensing), we derive a solution to the community composition estimation problem by a simultaneous assignment of all sample reads to a pre-processed reference database. A general statistical model based on kernel density estimation techniques is introduced for the assignment task, and the model solution is obtained using convex optimization tools. Further, we design a greedy algorithm solution for a fast solution. Our approach offers a reasonably fast community composition estimation method, which is shown to be more robust to input data variation than a recently introduced related method.Availability and implementation: A platform-independent Matlab implementation of the method is freely available at http://www.ee.kth.se/ctsoftware; source code that does not require access to Matlab is currently being tested and will be made available later through the above Web site.
|
|
| 2. |
- Davila Lopez, Marcela, et al.
(author)
-
eGOB: eukaryotic Gene Order Browser.
- 2011
-
In: Bioinformatics (Oxford, England). - : Oxford University Press (OUP). - 1367-4811 .- 1460-2059 .- 1367-4803. ; 27:8, s. 1150-1
-
Journal article (peer-reviewed)abstract
- A large number of genomes have been sequenced, allowing a range of comparative studies. Here, we present the eukaryotic Gene Order Browser with information on the order of protein and non-coding RNA (ncRNA) genes of 74 different eukaryotic species. The browser is able to display a gene of interest together with its genomic context in all species where that gene is present. Thereby, questions related to the evolution of gene organization and non-random gene order may be examined. The browser also provides access to data collected on pairs of adjacent genes that are evolutionarily conserved. AVAILABILITY: eGOB as well as underlying data are freely available at http://egob.biomedicine.gu.se SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. CONTACT: tore.samuelsson@medkem.gu.se.
|
|
| 3. |
- Fange, David, et al.
(author)
-
MesoRD 1.0 : Stochastic reaction-diffusion simulations in the microscopic limit
- 2012
-
In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 28:23, s. 3155-3157
-
Journal article (peer-reviewed)abstract
- MesoRD is a tool for simulating stochastic reaction-diffusion systems as modeled by the reaction diffusion master equation. The simulated systems are defined in the Systems Biology Markup Language with additions to define compartment geometries. MesoRD 1.0 supports scale-dependent reaction rate constants and reactions between reactants in neighbouring subvolumes. These new features make it possible to construct physically consistent models of diffusion-controlled reactions also at fine spatial discretization.
|
|
| 4. |
|
|
| 5. |
|
|
| 6. |
- Hayat, Sikander, et al.
(author)
-
BOCTOPUS : improved topology prediction of transmembrane β barrel proteins.
- 2012
-
In: Bioinformatics. - : Oxford University Press. - 1460-2059 .- 1367-4811 .- 1367-4803. ; 28:4, s. 516-522
-
Journal article (peer-reviewed)abstract
- MOTIVATION: Transmembrane β barrel proteins (TMBs) are found in the outer membrane of Gram-negative bacteria, chloroplast and mitochondria. They play a major role in the translocation machinery, pore formation, membrane anchoring and ion exchange. TMBs are also promising targets for antimicrobial drugs and vaccines. Given the difficulty in membrane protein structure determination, computational methods to identify TMBs and predict the topology of TMBs are important.RESULTS: Here, we present BOCTOPUS; an improved method for the topology prediction of TMBs by employing a combination of support vector machines (SVMs) and Hidden Markov Models (HMMs). The SVMs and HMMs account for local and global residue preferences, respectively. Based on a 10-fold cross-validation test, BOCTOPUS performs better than all existing methods, reaching a Q3 accuracy of 87%. Further, BOCTOPUS predicted the correct number of strands for 83% proteins in the dataset. BOCTOPUS might also help in reliable identification of TMBs by using it as an additional filter to methods specialized in this task.AVAILABILITY: BOCTOPUS is freely available as a web server at: http://boctopus.cbr.su.se/. The datasets used for training and evaluations are also available from this site.
|
|
| 7. |
- Höhna, Sebastian, 1983-
(author)
-
Fast simulation of reconstructed phylogenies under global time-dependent birth-death processes
- 2013
-
In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 29:11, s. 1367-1374
-
Journal article (peer-reviewed)abstract
- Motivation: Diversification rates and patterns may be inferred from reconstructed phylogenies. Both the time-dependent and the diversity-dependent birth–death process can produce the same observed patterns of diversity over time. To develop and test new models describing the macro-evolutionary process of diversification, generic and fast algorithms to simulate under these models are necessary. Simulations are not only important for testing and developing models but play an influential role in the assessment of model fit.Results: In the present article, I consider as the model a global time-dependent birth–death process where each species has the same rates but rates may vary over time. For this model, I derive the likelihood of the speciation times from a reconstructed phylogenetic tree and show that each speciation event is independent and identically distributed. This fact can be used to simulate efficiently reconstructed phylogenetic trees when conditioning on the number of species, the time of the process or both. I show the usability of the simulation by approximating the posterior predictive distribution of a birth–death process with decreasing diversification rates applied on a published bird phylogeny (family Cettiidae).Availability: The methods described in this manuscript are implemented in the R package TESS, available from the repository CRAN (http://cran.r-project.org/web/packages/TESS/).
|
|
| 8. |
- Liakata, Maria, et al.
(author)
-
Automatic recognition of conceptualisation zones in scientific articles and two life science applications
- 2012
-
In: Bioinformatics. - : Oxford University Press (OUP). - 1460-2059 .- 1367-4811 .- 1367-4803. ; 28:7, s. 991-1000
-
Journal article (peer-reviewed)abstract
- Motivation: Scholarly biomedical publications report on the findings of a research investigation. Scientists use a well-established discourse structure to relate their work to the state of the art, express their own motivation and hypotheses and report on their methods, results and conclusions. In previous work we have proposed ways to explicitly annotate the structure of scientific investigations in scholarly publications. Here we present the means to facilitate automatic access to the scientific discourse of articles by automating the recognition of eleven categories at the sentence level, which we call Core Scientific Concepts (CoreSCs). These include: Hypothesis, Motivation, Goal, Object, Background, Method, Experiment, Model, Observation, Result and Conclusion. CoreSCs provide the structure and context to all statements and relations within a paper and their automatic recognition can greatly facilitate biomedical information extraction by characterising the different types of facts, hypotheses and evidence available in a scientific publication. Results: We have trained and compared machine learning classifiers (SVM and CRF) on a corpus of 265 full articles in biochemistry and chemistry to automatically recognise CoreSCs. We have evaluated our automatic classifications against a manually annotated gold standard, and have achieved promising accuracies with `Experiment', `Background' and `Model' being the categories with the highest F1-scores (76%, 62% and 53% respectively). We have analysed the task of CoreSC annotation both from a sentence classification as well as sequence labelling perspective and we present a detailed feature evaluation. The most discriminative features are local sentence features such as unigrams, bigrams and grammatical dependencies while features encoding the document structure, such as section headings, also play an important role for some of the categories. We also discuss the usefulness of automatically generated CoreSCs in two biomedical applications as well as work in progress. Availability: A web-based tool for the automatic annotation of papers with CoreSCs and corresponding documentation is available on-line at http://www.sapientaproject.com/software http://www.sapientaproject.com also contains detailed information pertaining to CoreSC annotation and links to annotation guidelines as well as a corpus of manually annotated papers, which served as our training data. Contact: liakata@ebi.ac.uk
|
|
| 9. |
- Raue, Andreas, et al.
(author)
-
Comparison of approaches for parameter identifiability analysis of biological systems.
- 2014
-
In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 30:10, s. 1440-8
-
Journal article (peer-reviewed)abstract
- Modeling of dynamical systems using ordinary differential equations is a popular approach in the field of Systems Biology. The amount of experimental data that are used to build and calibrate these models is often limited. In this setting, the model parameters may not be uniquely determinable. Structural or a priori identifiability is a property of the system equations that indicates whether, in principle, the unknown model parameters can be determined from the available data.
|
|
| 10. |
- Schaal, Wesley, et al.
(author)
-
Automated QuantMap for rapid quantitative molecular network topology analysis
- 2013
-
In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811 .- 1460-2059. ; 29:18, s. 2369-2370
-
Journal article (peer-reviewed)abstract
- SUMMARY:The previously disclosed QuantMap method for grouping chemicals by biological activity used online services for much of the data gathering and some of the numerical analysis. The present work attempts to streamline this process by using local copies of the databases and in-house analysis. Using computational methods similar or identical to those used in the previous work, a qualitatively equivalent result was found in just a few seconds on the same dataset (collection of 18 drugs). We use the user-friendly Galaxy framework to enable users to analyze their own datasets. Hopefully, this will make the QuantMap method more practical and accessible and help achieve its goals to provide substantial assistance to drug repositioning, pharmacology evaluation and toxicology risk assessment.AVAILABILITY:http://galaxy.predpharmtox.orgCONTACT: mats.gustafsson@medsci.uu.se or ola.spjuth@farmbio.uu.seSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
|
|
