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- research-articleSeptember 2014
RImmPort: enabling ready-for-analysis immunology research data
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Page 751https://doi.org/10.1145/2649387.2666619Broad open access to entire clinical research studies data is on the rise. Public access to raw clinical research data has created tremendous opportunity to evaluate new research hypotheses that were not originally formulated in the studies; by ...
- research-articleSeptember 2014
Towards the characterization of normal peripheral immune cells with data from ImmPort
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 749–750https://doi.org/10.1145/2649387.2666618To date, our understanding of a normal immune system is far behind that of other healthy organ systems. One reason for this is the lack of standardization in the lab techniques, especially flow cytometry.
To take a step towards the characterization of a ...
- posterSeptember 2014
Detecting privacy-sensitive events in medical text
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 617–620https://doi.org/10.1145/2649387.2662451In this paper, we present a novel semi-supervised technique for finding privacy-sensitive events in clinical text. Unlike traditional semi-supervised methods, we do not require large amounts of unannotated data. Instead, our approach relies on ...
- posterSeptember 2014
Comparing and optimizing transcriptome assembly pipeline for diploid wheat
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 603–604https://doi.org/10.1145/2649387.2662450Gene expression and transcriptome analysis are currently one of the main focuses of research for a great number of scientists. However, the assembly of raw sequence data to obtain a draft transcriptome of an organism is a complex multi-stage process ...
- research-articleSeptember 2014
A system for ubiquitous distributed acquisition of voice alteration samples through a mobile application
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 813–818https://doi.org/10.1145/2649387.2660853Dysphonia, caused by irregular vocal folds vibration, is one of the major symptoms of benign laryngeal diseases and other organic and functional pathologies. The paper presents a cloud-based system for remote analysis of vocal samples submitted by ...
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- research-articleSeptember 2014
Pheno2GRN: a workflow for phenotype to gene network study and reverse engineering comparison
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 797–804https://doi.org/10.1145/2649387.2660851While efforts have been made to both retrieve genes associated with a phenotype, and model gene regulatory networks (GRNs), no such progress has been made regarding the creation of GRNs from phenotype keywords and reverse engineered large-scale gene ...
- research-articleSeptember 2014
Automatic biosystems comparison using semantic and name similarity
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 790–796https://doi.org/10.1145/2649387.2660850With the growth of bio-systems model development, automatic approaches are needed to support systems biologists in model similarity evaluation. Several algorithms have been proposed, but they lack efficiency. We have developed an efficient, intuitive ...
- research-articleSeptember 2014
Heuristic parallelizable algorithm for similarity based biosystems comparison
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 782–789https://doi.org/10.1145/2649387.2660849Biosystem comparison plays a major role in system biology. Similar biosystems are identified based on the similarity of species naming. Since the species naming does not follow a standard nomenclature, similarity is not easy to formalize. A single ...
- research-articleSeptember 2014
Evidence of post translational modification bias extracted from the tRNA and corresponding amino acid interplay across a set of diverse organisms
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 774–781https://doi.org/10.1145/2649387.2660848A post-translational modification (PTM) describes a form of biosynthesis for the task of initializing proteins for specific functions. PTMs are complexes which are involved in developing or customizing proteins to increase their functional diversity. In ...
- research-articleSeptember 2014
An R-based tool for miRNA data analysis and correlation with clinical ontologies
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 768–773https://doi.org/10.1145/2649387.2660847miRNAs are small fragments of RNA composed by 22 nucleotides. Many researchers are involved in studying these molecules that are considered as potential biomarkers and therapeutic targets for many diseases. The interests of computer scientists is ...
- research-articleSeptember 2014
Incremental network querying in biological networks
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 752–759https://doi.org/10.1145/2649387.2660845Comparative network analysis finds similarities between a query and a target network by aligning them. Biological network evolves over time; and so does the topology of the query network extracted from it. We denote a sequence of query networks where ...
- research-articleSeptember 2014
The interplay of sequence conservation and T cell immune recognition
- Anne Bresciani,
- Jason Greenbaum,
- Cecilia S. Lindestam Arlehamn,
- Alessandro Sette,
- Morten Nielsen,
- Bjoern Peters
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 739–743https://doi.org/10.1145/2649387.2660843Predicting which peptides can elicit a T cell response (i.e. are immunogenic) is of great importance for many immunological studies. While it is clear that MHC binding is a necessary requirement for peptide immunogenicity, other variables exist that are ...
- research-articleSeptember 2014
Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 733–738https://doi.org/10.1145/2649387.2660842Computational prediction of HLA class II restricted T cell epitopes has great significance in many immunological studies including vaccine discovery. With the development of novel bioinformatics approaches, prediction of HLA class II binding has ...
- research-articleSeptember 2014
An integrative framework for structure-based prediction of biological effects mediated by antipeptide antibodies
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 725–732https://doi.org/10.1145/2649387.2660841B-cell epitope prediction remains relatively underdeveloped as compared with T-cell epitope prediction. To address this deficiency, a generic framework is presented herein for quantitative prediction of biological effects mediated by antipeptide ...
- research-articleSeptember 2014
Improving decoy databases for protein folding algorithms
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 717–724https://doi.org/10.1145/2649387.2660839Predicting protein structures and simulating protein folding are two of the most important problems in computational biology today. Simulation methods rely on a scoring function to distinguish the native structure (the most energetically stable) from ...
- research-articleSeptember 2014
Construction of protein backbone pieces using segment-based FBCCD and Cryo-EM skeleton
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 711–716https://doi.org/10.1145/2649387.2660838Cryo-Electron Microscopy is a biophysical technique that generates volumetric images of macromolecules. Although it is hard to distinguish the backbone from the density map at medium resolutions such as 5-10Å, the location of major secondary structure ...
- research-articleSeptember 2014
Variational Bayesian clustering on protein cavity conformations for detecting influential amino acids
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 703–710https://doi.org/10.1145/2649387.2660837Proteins are large flexible biological molecules and conformational flexibility is a shared challenge in comparisons of protein structure. Many tools have been developed to identify remote homologs in cases where backbone flexibilities are considered. ...
- research-articleSeptember 2014
Network-regularized bi-clique finding for tumor stratification
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 686–687https://doi.org/10.1145/2649387.2660832Complex diseases such as cancer are known to be highly heterogeneous which results in tumor subtypes that show varying behavior, including different survival time, treatment responses, and recurrence rates. One important problem in biomedical research ...
- research-articleSeptember 2014
Computational identification of functional network modules associated with the pathogenicity of Fusarium verticillioides
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Page 685https://doi.org/10.1145/2649387.2660831Biological functions are executed through elaborate collaboration of various biomolecules, and there has been increasing interest in the computational identification of functional modules from large-scale experimental data. In this study, we performed a ...
- research-articleSeptember 2014
A novel context-sensitive random walk model for estimating node correspondence between two biological networks
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Page 684https://doi.org/10.1145/2649387.2660830In this work, we propose a novel context-sensitive random walk model to accurately estimate the node correspondence between two biological networks. We adopt a Markov random walk model that performs a simultaneous walk on two networks. At each step, the ...