Gráfok és algoritmusok = Graphs and algorithms

A kutatás az elvárt eredménnyel zárult: tekintélyes nemzetközi konferenciákon és pubikációkban hoztuk nyilvánosságra az eredményéket, ideértve a STOC, SIAM és IEEE kiadványokat is, valamint egy könyvet is. A publikációk száma a matematikában elég magas (74). Ez nemzetközi összehasonlításban is kiemelkedő mutató a támogatás összegére vetítve. A projektben megmutattuk, hogy a gráfelmelet és a diszkrét matematika eszköztára számos helyen jól alkalmazható, ilyen terület a nagysebességű kommunikációs hálózatok tervezése, ezekben igen gyors routerek létrehozása. Egy másik terület a biológiai nagymolekulákon definiált gráfok és geometriai struktúrák. | The research concluded with the awaited results: in good international conferences and journals we published 74 works, including STOC conference, SIAM conferences and journals and one of the best IEEE journal. This number is high above average in mathematics research. We showed in the project that the tools of graph theory and discrete mathematics can be well applied in the high-speed communication network design, where we proposed fast and secure routing solutions. Additionally we also found applications in biological macromolecules

Finding all maximal perfect haplotype blocks in linear time

Recent large-scale community sequencing efforts allow at an unprecedented level of detail the identification of genomic regions that show signatures of natural selection. Traditional methods for identifying such regions from individuals' haplotype data, however, require excessive computing times and therefore are not applicable to current datasets. In 2019, Cunha et al. (Advances in bioinformatics and computational biology: 11th Brazilian symposium on bioinformatics, BSB 2018, Niteroi, Brazil, October 30 - November 1, 2018, Proceedings, 2018. 10.1007/978-3-030-01722-4_3) suggested the maximal perfect haplotype block as a very simple combinatorial pattern, forming the basis of a new method to perform rapid genome-wide selection scans. The algorithm they presented for identifying these blocks, however, had a worst-case running time quadratic in the genome length. It was posed as an open problem whether an optimal, linear-time algorithm exists. In this paper we give two algorithms that achieve this time bound, one conceptually very simple one using suffix trees and a second one using the positional Burrows-Wheeler Transform, that is very efficient also in practice.Peer reviewe

GPCRTree: online hierarchical classification of GPCR function

Background: G protein-coupled receptors (GPCRs) play important physiological roles transducing extracellular signals into intracellular responses. Approximately 50% of all marketed drugs target a GPCR. There remains considerable interest in effectively predicting the function of a GPCR from its primary sequence. Findings: Using techniques drawn from data mining and proteochemometrics, an alignment-free approach to GPCR classification has been devised. It uses a simple representation of a protein's physical properties. GPCRTree, a publicly-available internet server, implements an algorithm that classifies GPCRs at the class, sub-family and sub-subfamily level. Conclusion: A selective top-down classifier was developed which assigns sequences within a GPCR hierarchy. Compared to other publicly available GPCR prediction servers, GPCRTree is considerably more accurate at every level of classification. The server has been available online since March 2008 at URL: http://igrid-ext.cryst.bbk.ac.uk/gpcrtree

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Background The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly. These difficulties often delay the complete genome assembly projects. Results In order to overcome this, we developed SIMBA (SImple Manager for Bacterial Assemblies), a freely available web tool that integrates several component tools for assembling and finishing bacterial genomes. SIMBA provides a friendly and intuitive user interface so bioinformaticians, even with low computational expertise, can work under a centralized administrative control system of assemblies managed by the assembly center head. SIMBA guides the users to execute assembly process through simple and interactive pages. SIMBA workflow was divided in three modules: (i) projects: allows a general vision of genome sequencing projects, in addition to data quality analysis and data format conversions; (ii) assemblies: allows de novo assemblies with the software Mira, Minia, Newbler and SPAdes, also assembly quality validations using QUAST software; and (iii) curation: presents methods to finishing assemblies through tools for scaffolding contigs and close gaps. We also presented a case study that validated the efficacy of SIMBA to manage bacterial assemblies projects sequenced using Ion Torrent PGM. Conclusion Besides to be a web tool for genome assembly, SIMBA is a complete genome assemblies project management system, which can be useful for managing of several projects in laboratories. SIMBA source code is available to download and install in local webservers at http://ufmg-simba.sourceforge.net

On the hierarchical classification of G Protein-Coupled Receptors

Motivation: G protein-coupled receptors (GPCRs) play an important role in many physiological systems by transducing an extracellular signal into an intracellular response. Over 50% of all marketed drugs are targeted towards a GPCR. There is considerable interest in developing an algorithm that could effectively predict the function of a GPCR from its primary sequence. Such an algorithm is useful not only in identifying novel GPCR sequences but in characterizing the interrelationships between known GPCRs. Results: An alignment-free approach to GPCR classification has been developed using techniques drawn from data mining and proteochemometrics. A dataset of over 8000 sequences was constructed to train the algorithm. This represents one of the largest GPCR datasets currently available. A predictive algorithm was developed based upon the simplest reasonable numerical representation of the protein's physicochemical properties. A selective top-down approach was developed, which used a hierarchical classifier to assign sequences to subdivisions within the GPCR hierarchy. The predictive performance of the algorithm was assessed against several standard data mining classifiers and further validated against Support Vector Machine-based GPCR prediction servers. The selective top-down approach achieves significantly higher accuracy than standard data mining methods in almost all cases

Evolution of Genes Neighborhood Within Reconciled Phylogenies: An Ensemble Approach

Context The reconstruction of evolutionary scenarios for whole genomes in terms of genome rearrangements is a fundamental problem in evolutionary and comparative genomics. The DeCo algorithm, recently introduced by Bérard et al., computes parsimonious evolutionary scenarios for gene adjacencies, from pairs of reconciled gene trees. However, as for many combinatorial optimization algorithms, there can exist many co-optimal, or slightly sub-optimal, evolutionary scenarios that deserve to be considered. Contribution We extend the DeCo algorithm to sample evolutionary scenarios from the whole solution space under the Boltzmann distribution, and also to compute Boltzmann probabilities for specific ancestral adjacencies. Results We apply our algorithms to a dataset of mammalian gene trees and adjacencies, and observe a significant reduction of the number of syntenic conflicts observed in the resulting ancestral gene adjacencies

Hyperbolic Interaction Model For Hierarchical Multi-Label Classification

Different from the traditional classification tasks which assume mutual exclusion of labels, hierarchical multi-label classification (HMLC) aims to assign multiple labels to every instance with the labels organized under hierarchical relations. Besides the labels, since linguistic ontologies are intrinsic hierarchies, the conceptual relations between words can also form hierarchical structures. Thus it can be a challenge to learn mappings from word hierarchies to label hierarchies. We propose to model the word and label hierarchies by embedding them jointly in the hyperbolic space. The main reason is that the tree-likeness of the hyperbolic space matches the complexity of symbolic data with hierarchical structures. A new Hyperbolic Interaction Model (HyperIM) is designed to learn the label-aware document representations and make predictions for HMLC. Extensive experiments are conducted on three benchmark datasets. The results have demonstrated that the new model can realistically capture the complex data structures and further improve the performance for HMLC comparing with the state-of-the-art methods. To facilitate future research, our code is publicly available