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- 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
On the impact of data integration and edge enrichment in mining significant signals from biological networks
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 760–767https://doi.org/10.1145/2649387.2660846The influx of high-throughput biotechnologies has resulted in considerable amounts of available and untapped data, useful for both interpretation and extrapolation. Due to the fact that the noise to signal ratio in most biological databases are non-...
- research-articleSeptember 2014
A computational model for data acquisition in SAXS
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 695–702https://doi.org/10.1145/2649387.2660836Small-angle x-ray scattering (SAXS) is an experimental biophysical method used for gaining insight into the structure of large biomolecular complexes. Under appropriate chemical conditions, the information obtained from a SAXS experiment can be equated ...
- research-articleSeptember 2014
Biological network clustering by robust NMF
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 688–689https://doi.org/10.1145/2649387.2660833We propose a Robust Non-negative Matrix Factorization (RNMF) formulation by introducing L1-norm regularization terms for decomposed factors to cluster noisy biological networks for identification of functional modules. To solve robust NMF, we develop an ...
- 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
Optimal cancer prognosis under network uncertainty
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 682–683https://doi.org/10.1145/2649387.2660827Typically, a vast amount of experience and data is needed to successfully determine cancer prognosis in the face of (1) the inherent stochasticity of cell dynamics, (2) incomplete knowledge of healthy cell regulation, and (3) the inherent uncertain and ...
- posterSeptember 2014
High-performance recursive dynamic programming for bioinformatics using MM-like flexible kernels
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 600–601https://doi.org/10.1145/2649387.2660796Dynamic Programming (DP) provides optimal solutions to a problem by combining optimal solutions to many overlapping subproblems. DP algorithms exploit this overlapping property to explore otherwise exponential-sized problem spaces in polynomial time, ...
- posterSeptember 2014
Validation and implementation of whole-exome sequencing bioinformatics processes for clinical applications
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 596–597https://doi.org/10.1145/2649387.2660794We established a bioinformatics procedure at our laboratory that processes sequencing data, identifies single nucleotide variants (SNVs) and small insertions/deletions (indels), annotates the variants based on the curated variant databases and ...
- posterSeptember 2014
The epitope landscape of CRC liver metastases analyzed by whole-exome sequencing and in silico epitope prediction
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Page 584https://doi.org/10.1145/2649387.2660777Many cancers appear to have an increased somatic mutation rate. Intriguingly, increased numbers of tumor-infiltrating T cells are often found in cancers with defective DNA repair, which especially accumulate high numbers of somatic mutations. These ...
- posterSeptember 2014
Global network alignment in the context of aging
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Page 580https://doi.org/10.1145/2649387.2660557Analogous to sequence alignment, network alignment (NA) can be used to transfer biological knowledge across species between conserved network regions. NA faces two algorithmic challenges: 1) Which cost function to use to capture "similarities" between ...
- posterSeptember 2014
Dynamic networks reveal key players in aging
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Page 579https://doi.org/10.1145/2649387.2660556Motivation: Because susceptibility to diseases increases with age, studying aging gains importance. Analyses of gene expression or sequence data, which have been indispensable for investigating aging, have been limited to studying genes and their ...
- research-articleSeptember 2014
Pathway analysis with signaling hypergraphs
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 249–258https://doi.org/10.1145/2649387.2649450Signaling pathways play an important role in the cell's response to its environment. Signaling pathways are often represented as directed graphs, which are not adequate for modeling reactions such as complex assembly and dissociation, combinatorial ...
- short-paperSeptember 2014
Discovering dysregulated phenotype-related gene patterns
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 524–532https://doi.org/10.1145/2649387.2649441With the abundance of vast amounts of "-omic" biological data from multiple sources that span diverse biological processes, approaches for answering critical questions become a vital mission. To grasp more comprehensive view of the biology of the ...
- research-articleSeptember 2014
Joint inference for end-to-end coreference resolution for clinical notes
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 192–201https://doi.org/10.1145/2649387.2649437Recent US government initiatives have led to wide adoption of Electronic Health Records (EHRs). More and more health care institutions are storing patients' data in an electronic format. These EHRs contain valuable information which can be used in ...
- research-articleSeptember 2014
Improving identification of key players in aging via network de-noising
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 164–173https://doi.org/10.1145/2649387.2649426Since human aging is hard to study experimentally due to long lifespan and ethical constraints, current "ground truth" knowledge about human aging has mostly been predicted computationally or statistically by transferring the knowledge from well-studied ...
- short-paperSeptember 2014
A comparison of combined p-value methods for gene differential expression using RNA-seq data
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 417–425https://doi.org/10.1145/2649387.2649421Detection of differentially expressed (DE) genes across conditions within RNA-Seq datasets yields insight into the differences in biological processes at work in these conditions. Most methods available for discovering DE genes use statistical methods ...
- short-paperSeptember 2014
AccuRMSD: a machine learning approach to predicting structure similarity of docked protein complexes
BCB '14: Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health InformaticsSeptember 2014, Pages 289–296https://doi.org/10.1145/2649387.2649392Protein-protein docking methods aim to compute the correct bound form of two or more proteins. One of the major challenges for docking methods is to accurately discriminate native-like structures. The protein docking community agrees on the existence of ...