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CUBCO+: prediction of protein complexes based on min-cut network partitioning into biclique spanned subgraphs

Applied Network Science 2022年第1期7卷 1-12页

作者： Omranian, Sara Nikoloski, Zoran Technical University of Munich Petersgasse 18 Campus Straubing for Biotechnology and Sustainability Bioinformatics Straubing94315 Germany Weihenstephan-Triesdorf University of Applied Sciences Petersgasse 18 Straubing94315 Germany SynBiofoundry@TUM Technical University of Munich Schulgasse 22 Straubing94315 Germany Bioinformatics Institute of Biochemistry and Biology University of Potsdam Potsdam14476 Germany Systems Biology and Mathematical Modeling Max Planck Institute of Molecular Plant Physiology Potsdam14476 Germany

High-throughput proteomics approaches have resulted in large-scale protein–protein interaction (PPI) networks that have been employed for the prediction of protein complexes. However, PPI networks contain false-positive as well as false-negative PPIs that affect the protein complex prediction algorithms. To address this issue, here we propose an algorithm called CUBCO+ that: (1) employs GO semantic similarity to retain only biologically relevant interactions with a high similarity score, (2) based on link prediction approaches, scores the false-negative edges, and (3) incorporates the resulting scores to predict protein complexes. Through comprehensive analyses with PPIs from Escherichia coli, Saccharomyces cerevisiae, and Homo sapiens, we show that CUBCO+ performs as well as the approaches that predict protein complexes based on recently introduced graph partitions into biclique spanned subgraphs and outperforms the other state-of-the-art approaches. Moreover, we illustrate that in combination with GO semantic similarity, CUBCO+ enables us to predict more accurate protein complexes in 36% of the cases in comparison to CUBCO as its predecessor. © 2022, The Author(s).

关键词： Forecasting

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pasta: Pattern Analysis for Spatial Omics Data

arXiv

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arXiv 2024年

作者： Emons, Martin Gunz, Samuel Crowell, Helena L. Mallona, Izaskun Furrer, Reinhard Robinson, Mark D. Department of Molecular Life Sciences SIB Swiss Institute of Bioinformatics University of Zurich Zurich Switzerland Barcelona Spain Department of Mathematical Modeling and Machine Learning University of Zurich Zurich Switzerland

Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can give rise to very different data modalities. The characteristics of the two data types are well known in adjacent fields such as spatial statistics as point patterns and lattice data, and there is a wide range of tools available. This paper discusses the application of spatial statistics to spatially-resolved omics data and in particular, discusses various advantages, challenges, and nuances. This work is accompanied by a vignette, pasta, that showcases the usefulness of spatial statistics in biology using several R packages. © 2024, CC BY.

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Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits

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园艺研究（英文） 2022年第1期9卷 1524-1534页

作者： Hao Tong Amol N.Nankar Jintao Liu Velichka Todorova Daniela Ganeva Stanislava Grozeva Ivanka Tringovska Gancho Pasev Vesela Radeva-Ivanova Tsanko Gechev Dimitrina Kostova Zoran Nikoloski Center of Plant Systems Biology and Biotechnology Plovdiv4000Bulgaria Systems Biology and Mathematical Modeling Max Planck Institute of Molecular Plant PhysiologyPotsdam14476Germany Bioinformatics Institute of Biochemistry and BiologyUniversity of PotsdamPotsdam14476Germany Center of Plant Systems Biology and Biotechnology Plovdiv4000Bulgaria Systems Biology and Mathematical Modeling Max Planck Institute of Molecular Plant PhysiologyPotsdam14476Germany Maritsa Vegetable Crops Research Institute Plovdiv4003Bulgaria. Center of Plant Systems Biology and Biotechnology Plovdiv4000Bulgaria Maritsa Vegetable Crops Research Institute Plovdiv4003Bulgaria.

Selection of high-performance lines with respect to traits of interest is a key step in plant *** prediction allows to determine the genomic estimated breeding values of unseen lines for trait of interest using genetic markers,***-nucleotide polymorphisms(SNPs),and machine learning approaches,which can therefore shorten breeding cycles,referring to genomic selection(GS).Here,we applied GS approaches in two populations of Solanaceous crops,*** and pepper,to predict morphometric and colorimetric *** traits were measured by using scoring-based conventional descriptors(CDs)as well as by Tomato Analyzer(TA)tool using the longitudinally and latitudinally cut fruit *** GS performance was assessed in cross-validations of classification-based and regression-based machine learning models for CD and TA traits,*** results showed the usage of TA traits and tag SNPs provide a powerful combination to predict morphology and color-related traits of Solanaceous *** highest predictability of 0.89 was achieved for fruit width in pepper,with an average predictability of 0.69 over all *** multi-trait GS models are of slightly better predictability than single-trait models for some colorimetric traits in *** model validation performs poorly on wild tomato accessions,the usage as many as one accession per wild species in the training set can increase the transferability of models to unseen populations for some traits(*** shape for which predictability in unseen scenario increased from zero to 0.6).Overall,GS approaches can assist the selection of high-performance Solanaceous fruits in crop breeding.

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InterCriteria Analysis of the Financial System in the EU Countries 10

InterCriteria Analysis of the Financial System in the EU Cou...

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10th IEEE International Conference on Intelligent Systems, IS 2020

作者： Danailova-Veleva, Slaviiana Doukovska, Lyubka Atanassova, Vassia IICT-BAS Intelligent Systems Department Sofia Bulgaria IBBE-BAS Bioinformatics and Mathematical Modeling Department Sofia Bulgaria

ISBN: (纸本)9781728154565

The paper presents an analysis of the financial systems of the EU member states which is an actual problem. The paper showcases a new method of analyzing and grading of the connection between the criteria defining the state of the financial systems. The presented multicriteria decision making method is based on two fundamental concepts: Intuitionistic Fuzzy Sets (IFSs) and Index Matrices (IMs). We have named it 'InterCriteria' decision making approach. The data for the financial systems of the EU member states is sourced from the World Economic Forum's Global Competitiveness Reports for 2019. The assessment was made using 12 main drivers, so called Pillars. The main goal is to assess the competitiveness of each EU country. © 2020 IEEE.

关键词： Intelligent systems

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Tree edit distance with variables. Measuring the similarity between mathematical formulas

arXiv

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arXiv 2021年

作者： Akutsu, Tatsuya Mori, Tomoya Nakamura, Naotoshi Kozawa, Satoshi Ueno, Yuhei Sato, Thomas N. Bioinformatics Center Institute for Chemical Research Kyoto University Karydo TherapeutiX Inc. Center for Mathematical Modeling and Data Science Osaka University V-iCliniX Laboratory Nara Medical University

In this article, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas, especially, those appearing in mathematical models of biological systems. We analyze the computational complexities of several variants of this new model. In particular, we show that the problem is NP-complete for ordered trees. We also show for unordered trees that the problem of deciding whether or not the distance is 0 is graph isomorphism complete but can be solved in polynomial time if the maximum outdegree of input trees is bounded by a constant. This distance model is then extended for measuring the difference/similarity between two systems of differential equations, for which results of preliminary computational experiments using biological models are provided. © 2021, CC BY.

关键词： Polynomial approximation

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Kinetic modules are sources of concentration robustness in biochemical networks

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Science advances 2025年第22期11卷 eads7269页

作者： Damoun Langary Anika Küken Zoran Nikoloski Systems Biology and Mathematical Modeling Max Planck Institute of Molecular Plant Physiology 14476 Potsdam Germany. Bioinformatics Department Institute of Biochemistry and Biology University of Potsdam 14476 Potsdam Germany.

Modules represent fundamental building blocks of cellular networks and are thought to facilitate robustness of phenotypes against perturbations. While reaction kinetic shapes the concentration of components and reaction rates, its use in identification of modules entails knowledge of parameter values. Here, we demonstrate that kinetic modules can be efficiently identified on the basis of steady-state reaction rate couplings in large-scale biochemical networks endowed with mass action kinetics without knowledge of parameter values. We then link the kinetic modules of metabolic networks with robustness of metabolite concentrations to perturbations. Analyzing 34 metabolic network models of 26 organisms, we demonstrate that the ordered binding enzyme mechanism leads to increased concentration robustness compared to random binding. Our findings pave the way for usage of modules in synthetic biology and biotechnological applications.

关键词： Rate constants

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InterCriteria Analysis of the Financial System in the EU Countries

InterCriteria Analysis of the Financial System in the EU Cou...

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International IEEE Conference on Intelligent Systems, IS

作者： Slaviiana Danailova-Veleva Lyubka Doukovska Vassia Atanassova Intelligent Systems Department IICT-BAS Sofia Bulgaria Bioinformatics and Mathematical Modeling Department IBBE-BAS Sofia Bulgaria

ISBN: (数字)9781728154565

ISBN: (纸本)9781728154572

The paper presents an analysis of the financial systems of the EU member states which is an actual problem. The paper showcases a new method of analyzing and grading of the connection between the criteria defining the state of the financial systems. The presented multicriteria decision making method is based on two fundamental concepts: Intuitionistic Fuzzy Sets (IFSs) and Index Matrices (IMs). We have named it `InterCriteria' decision making approach. The data for the financial systems of the EU member states is sourced from the World Economic Forum's Global Competitiveness Reports for 2019. The assessment was made using 12 main drivers, so called Pillars. The main goal is to assess the competitiveness of each EU country.

关键词： Indexes Economic indicators Decision making Fuzzy sets Correlation Venture capital

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The theory of prioritized Muirhead mean operators under the presence of Complex Single-Valued Neutrosophic values

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Decision Analytics Journal 2023年 7卷

作者： Imran, Raiha Ullah, Kifayat Ali, Zeeshan Akram, Maria Senapati, Tapan Department of Mathematics Riphah Institute of Computing & Applied Sciences (RICAS) Riphah International University (Lahore Campus) Lahore 54000 Pakistan Department of Mathematics & Statistics International Islamic University Islamabad Islamabad 44000 Pakistan KERMIT Department of Mathematical Modeling Statistics and Bioinformatics Coupure Links 653 Ghent University Ghent Belgium School of Mathematics and Statistics Southwest University Chongqing Beibei 400715 China

The Muirhead mean (MM) operator is effective and feasible and is used for aggregating the finite collection of attributes into a singleton set, where the averaging and geometric aggregation operators are the special cases of the MM operator. Furthermore, the Complex Single-Valued Neutrosophic (CSVN) set theory is more reliable than the intuitionistic fuzzy set theory because it can easily handle awkward and unreliable information with the triplet, such as yes, abstinence, and no. In this manuscript, we present the theory of MM operators under the presence of CSVN values, such as the CSVN prioritized MM (CSVNPMM) operator and the CSVN prioritized dual MM (CSVNPDMM) operator. Some important and dominant properties are examined in the derived theory. Additionally, to verify the above information with the help of some appropriate examples, we demonstrate a Multi-Attribute Decision-Making (MADM) method for the proposed operators under the consideration of CSVN information. Finally, we compare the derived operators with some prevailing information to state the practicality and validity of the proposed method. © 2023 The Author(s)

关键词： Complex single-valued neutrosophic sets Decision support Dual Muirhead mean operators Multi-attribute decision-making Prioritized Muirhead

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Improvement of effluent quality and cost saving at a 750,000pe WRRF using an extensively validated CFD model 91

Improvement of effluent quality and cost saving at a 750,000...

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91st Annual Water Environment Federation Technical Exhibition and Conference, WEFTEC 2018

作者： Rehman, U. Audenaert, W. Bellandi, G. Flameling, T. Weijers, S. Nopens, I. BIOMATH Department of Mathematical Modeling Statistics and Bioinformatics Faculty of Bioscience Engineering Ghent University Coupure Links 653 Gent9000 Belgium AM-TEAM Advanced modelling for process optimisation Hulstbaan 63 Sint-Niklaas9112 Belgium Waterboard De Dommel PO Box 10.001 DA Boxtel5280 Netherlands Department of Civil and Environmental Engineering University of Florence via di S. Marta 3 Florence50139 Italy

ISBN: (纸本)9781510877474

Besides trial-and-error approaches, conventional flowsheet modelling (such as tanks-in-series (TIS)) is widely used to optimize the performance of Water Resource Recovery Facilities (WRRFs). However, this modelling approach lacks the ability to consider design parameters such as propellers and aerator configurations. Trial-and-error based optimisation of such parameters is in many cases highly risky or even impossible. By appropriate use of computational fluid dynamics (CFD), one can accurately and efficiently evaluate different design changes prior to actual implementation, while severely extending system understanding. The current study shows the practical application of CFD for full-scale bioreactor optimization in terms of performance (lower effluent nitrate) and cost. The CFD model was unprecedentedly validated using a construction crane for dissolved oxygen profiling. Also flow velocities were measured. Different new propeller settings and aerator configurations were tested. Unwanted oxygen near the inlet of the anoxic zone could be reduced up to 20%. One of the promising scenarios was implemented in practice and the impact on effluent quality is currently being evaluated. The operational change will have a potential operational cost saving of minimum 500,000 EUR/y. Copyright © 2018 Water Environment Federation

关键词： Bioreactors

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Generalized net model of surface emg data processing for control of active elbow orthosis device

Generalized net model of surface emg data processing for con...

引用

Advances in Neural Networks and Applications 2018, ANNA 2018

作者： Ribagin, Simeon Pencheva, Tania Shannon, Anthony Department of Bioinformatics and Mathematical Modelling Institute of Biophysics and Biomedical Engineering Bulgarian Academy of Sciences Sofia Bulgaria Department of Health and Social Care Medical College University "Prof. D-r Asen Zlatarov" Burgas Bulgaria Department of QSAR and Molecular Modeling Institute of Biophysics and Biomedical Engineering Bulgarian Academy of Sciences Sofia Bulgaria Warrane College University of New South Wales KensingtonNSW2033 Australia

ISBN: (纸本)9783800747566

Surface Electromyography (sEMG) signals have been increasingly used in many applications, including biomedical, neuroprosthetic limbs, orthotic or rehabilitation devices, human machine interactions etc. In order to use such signals for the control purposes, a certain processing algorithm has to be performed. This paper presents a novel approach for sEMG data processing with the usage of generalized nets theory. We propose an abstract model representing the sEMG data processing, which can be used in the control frameworks of active elbow orthosis devices. © 2018 VDE VERLAG GMBH Berlin Offenbach

关键词： Data handling

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