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Mathematical Aspects of Computational Biology and Bioinformatics

Submission Deadline: 15 October 2021 (closed)

Guest Editors

Prof. Dumitru Baleanu, Cankaya University, Turkey; Instiute of Space Sciences, Romania
Dr. Carla M. A. Pinto, Polytechnic of Porto, Portugal
Dr. Sunil Kumar, National Institute of Technology, India

Summary

Recent years have witnessed unprecedented progress in computational biology and biosciences. Our society is eager to see basic research quickly translated into longer and better quality of life through deeper understanding of disease mechanisms and better medical treatment. Accordingly, many topics from computational biology and bioscience have been given high priority in the research. This special issue (SI) highlights mathematical and computational approaches, to examine central problems of the computational biological sciences. The essential target of this special issue is to focus on computational biology - work that uses mathematical approaches to gain biological understanding or explain biological phenomena. Research papers should either provide biological insight as a result of mathematical analysis or identify and open up challenging new types of mathematical problems that derive from biological knowledge. New mathematical ideas, techniques, and results in a biological context are welcome in this proposed special issue. Research areas of mathematical biology covered include, but are not restricted to, cell biology, physiology, development, neurobiology, genetics and population genetics, population biology, ecology, behavioural biology, evolution, epidemiology, immunology, molecular biology, bio fluids, DNA and protein structure and function.


This special issue is mainly focused to address a wide range of the theory and applications of fractional-order derivatives and fractional-order integrals in different directions of mathematical biology. We invite authors to contribute original research articles for the special issue "Mathematical Aspects of Computational Biology and Bioinformatics" in the following potential topics that include, but are not limited to:


• Biomodelling

• Genomics

• Neuroscience

• Evolutionary biology

• Cancer computational biology

• Neuropsychiatry

• Image analysis

• Statistical network modelling

• Dynamic pathway modelling

• Protein structure

• Synthetic Biology and Molecular Programming

• Modelling on infectious disease models

• Fractional calculus and its applications on computational biology

• Biophysics, systems biology and computational biology


Published Papers

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  • Open Access

    EDITORIAL

    Introduction to the Special Issue on Mathematical Aspects of Computational Biology and Bioinformatics

    Dumitru Baleanu, Carla M. A. Pinto, Sunil Kumar
    CMES-Computer Modeling in Engineering & Sciences, Vol.136, No.1, pp. 1-3, 2023, DOI:10.32604/cmes.2023.026471
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract This article has no abstract. More >

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    498

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    ARTICLE

    Cherenkov Radiation: A Stochastic Differential Model Driven by Brownian Motions

    Qingqing Li, Zhiwen Duan, Dandan Yang
    CMES-Computer Modeling in Engineering & Sciences, Vol.135, No.1, pp. 155-168, 2023, DOI:10.32604/cmes.2022.019249
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract With the development of molecular imaging, Cherenkov optical imaging technology has been widely concerned. Most studies regard the partial boundary flux as a stochastic variable and reconstruct images based on the steadystate diffusion equation. In this paper, time-variable will be considered and the Cherenkov radiation emission process will be regarded as a stochastic process. Based on the original steady-state diffusion equation, we first propose a stochastic partial differential equation model. The numerical solution to the stochastic partial differential model is carried out by using the finite element method. When the time resolution is high enough, the numerical solution of the… More >

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    1401

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    727

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    ARTICLE

    Reducing the Range of Cancer Risk on BI-RADS 4 Subcategories via Mathematical Modelling

    Nezihal Gokbulut, Evren Hincal, Hasan Besim, Bilgen Kaymakamzade
    CMES-Computer Modeling in Engineering & Sciences, Vol.133, No.1, pp. 93-109, 2022, DOI:10.32604/cmes.2022.019782
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract Breast Imaging Reporting and Data System, also known as BI-RADS is a universal system used by radiologists and doctors. It constructs a comprehensive language for the diagnosis of breast cancer. BI-RADS 4 category has a wide range of cancer risk since it is divided into 3 categories. Mathematical models play an important role in the diagnosis and treatment of cancer. In this study, data of 42 BI-RADS 4 patients taken from the Center for Breast Health, Near East University Hospital is utilized. Regarding the analysis, a mathematical model is constructed by dividing the population into 4 compartments. Sensitivity analysis is… More >

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    934

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    ARTICLE

    Stability Analysis of Predator-Prey System with Consuming Resource and Disease in Predator Species

    Asad Ejaz, Yasir Nawaz, Muhammad Shoaib Arif, Daoud S. Mashat, Kamaleldin Abodayeh
    CMES-Computer Modeling in Engineering & Sciences, Vol.132, No.2, pp. 489-506, 2022, DOI:10.32604/cmes.2022.019440
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract The present study is concerned with formulating a predator-prey eco-epidemiological mathematical model assuming that an infection exists in the predator species. The two classes of predator species (susceptible and infected) compete for the same sources available in the environment with the predation option. It is assumed that the disease does not spread vertically. The proposed model is analyzed for the stability of the coexistence of the predators and prey. The fixed points are carried out, and the coexisting fixed point is studied in detail by constructing the Lyapunov function. The movement of species in search of food or protection in… More >

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    2127

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    989

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    ARTICLE

    Numerical Computational Heuristic Through Morlet Wavelet Neural Network for Solving the Dynamics of Nonlinear SITR COVID-19

    Zulqurnain Sabir, Abeer S. Alnahdi, Mdi Begum Jeelani, Mohamed A. Abdelkawy, Muhammad Asif Zahoor Raja, Dumitru Baleanu, Muhammad Mubashar Hussain
    CMES-Computer Modeling in Engineering & Sciences, Vol.131, No.2, pp. 763-785, 2022, DOI:10.32604/cmes.2022.018496
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract The present investigations are associated with designing Morlet wavelet neural network (MWNN) for solving a class of susceptible, infected, treatment and recovered (SITR) fractal systems of COVID-19 propagation and control. The structure of an error function is accessible using the SITR differential form and its initial conditions. The optimization is performed using the MWNN together with the global as well as local search heuristics of genetic algorithm (GA) and active-set algorithm (ASA), i.e., MWNN-GA-ASA. The detail of each class of the SITR nonlinear COVID-19 system is also discussed. The obtained outcomes of the SITR system are compared with the Runge-Kutta… More >

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    907

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    ARTICLE

    ResNet50-Based Effective Model for Breast Cancer Classification Using Histopathology Images

    Nishant Behar, Manish Shrivastava
    CMES-Computer Modeling in Engineering & Sciences, Vol.130, No.2, pp. 823-839, 2022, DOI:10.32604/cmes.2022.017030
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract Breast cancer is considered an immense threat and one of the leading causes of mortality in females. It is curable only when detected at an early stage. A standard cancer diagnosis approach involves detection of cancer-related anomalies in tumour histopathology images. Detection depends on the accurate identification of the landmarks in the visual artefacts present in the slide images. Researchers are continuously striving to develop automatic machine-learning algorithms for processing medical images to assist in tumour detection. Nowadays, computer-based automated systems play an important role in cancer image analysis and help healthcare experts make rapid and correct inferences about the… More >

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    2533

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    1984

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    ARTICLE

    Assess Medical Screening and Isolation Measures Based on Numerical Method for COVID-19 Epidemic Model in Japan

    Zhongxiang Chen, Huijuan Zha, Zhiquan Shu, Juyi Ye, Jiaji Pan
    CMES-Computer Modeling in Engineering & Sciences, Vol.130, No.2, pp. 841-854, 2022, DOI:10.32604/cmes.2022.017574
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract This study aims to improve control schemes for COVID-19 by a numerical model with estimation of parameters. We established a multi-level and multi-objective nonlinear SEIDR model to simulate the virus transmission. The early spread in Japan was adopted as a case study. The first 96 days since the infection were divided into five stages with parameters estimated. Then, we analyzed the trend of the parameter value, age structure ratio, and the defined PCR test index (standardization of the scale of PCR tests). It was discovered that the self-healing rate and confirmed rate were linear with the age structure ratio and… More >

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    1756

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    968

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    ARTICLE

    Sensitivity Analysis of COVID-19 in Mediterranean Island

    Ahmet Savasan, Bilgen Kaymakamzade, Nezihal Gokbulut, Evren Hincal, Elcin Yoldascan
    CMES-Computer Modeling in Engineering & Sciences, Vol.130, No.1, pp. 133-148, 2022, DOI:10.32604/cmes.2022.017815
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract The aim of this study is to examine the progress of the worldwide pandemic Covid-19. As authors, we have decided to analyze the situation of COVID-19 on Mediterranean island with accurate data. For this purpose, a mathematical model is constructed and proposed by dividing the whole population into sensible and suitable compartments. The study captures the dates February 01 till May 15, 2021. For the control of the spread of disease, vaccination and infection rates are compared and calculated. During calculations and comparison, MatLab software is used. All of the data that are used are taken from the Ministry of… More >

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    2905

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    1054

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    ARTICLE

    Near Future Perspective of ESBL-Producing Klebsiella pneumoniae Strains Using Mathematical Modeling

    Cemile Bagkur, Emrah Guler, Bilgen Kaymakamzade, Evren Hincal, Kaya Suer
    CMES-Computer Modeling in Engineering & Sciences, Vol.130, No.1, pp. 111-132, 2022, DOI:10.32604/cmes.2022.016957
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract While antibiotic resistance is becoming increasingly serious today, there is almost no doubt that more challenging times await us in the future. Resistant microorganisms have increased in the past decades leading to limited treatment options, along with higher morbidity and mortality. Klebsiella pneumoniae is one of the significant microorganisms causing major public health problems by acquiring resistance to antibiotics and acting as an opportunistic pathogen of healthcare-associated infections. The production of extended spectrum beta-lactamases (ESBL) is one of the resistance mechanisms of K. pneumoniae against antibiotics. In this study, the future clinical situation of ESBL-producing K. pneumoniae was investigated in… More >

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    1647

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    1079

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    ARTICLE

    Fractional Analysis of Dynamical Novel COVID-19 by Semi-Analytical Technique

    S. Iqbal, D. Baleanu, Javaid Ali, H. M. Younas, M. B. Riaz
    CMES-Computer Modeling in Engineering & Sciences, Vol.129, No.2, pp. 705-727, 2021, DOI:10.32604/cmes.2021.015375
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract This study employs a semi-analytical approach, called Optimal Homotopy Asymptotic Method (OHAM), to analyze a coronavirus (COVID-19) transmission model of fractional order. The proposed method employs Caputo's fractional derivatives and Reimann-Liouville fractional integral sense to solve the underlying model. To the best of our knowledge, this work presents the first application of an optimal homotopy asymptotic scheme for better estimation of the future dynamics of the COVID-19 pandemic. Our proposed fractional-order scheme for the parameterized model is based on the available number of infected cases from January 21 to January 28, 2020, in Wuhan City of China. For the considered… More >

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    1938

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    1160

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    ARTICLE

    Numerical Solutions of a Novel Designed Prevention Class in the HIV Nonlinear Model

    Zulqurnain Sabir, Muhammad Umar, Muhammad Asif Zahoor Raja, Dumitru Baleanu
    CMES-Computer Modeling in Engineering & Sciences, Vol.129, No.1, pp. 227-251, 2021, DOI:10.32604/cmes.2021.016611
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract The presented research aims to design a new prevention class (P) in the HIV nonlinear system, i.e., the HIPV model. Then numerical treatment of the newly formulated HIPV model is portrayed handled by using the strength of stochastic procedure based numerical computing schemes exploiting the artificial neural networks (ANNs) modeling legacy together with the optimization competence of the hybrid of global and local search schemes via genetic algorithms (GAs) and active-set approach (ASA), i.e., GA-ASA. The optimization performances through GA-ASA are accessed by presenting an error-based fitness function designed for all the classes of the HIPV model and its corresponding… More >

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    1796

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    1275

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    ARTICLE

    Solution of Modified Bergman Minimal Blood Glucose-Insulin Model Using Caputo-Fabrizio Fractional Derivative

    Ravi Shanker Dubey, Dumitru Baleanu, Manvendra Narayan Mishra, Pranay Goswami
    CMES-Computer Modeling in Engineering & Sciences, Vol.128, No.3, pp. 1247-1263, 2021, DOI:10.32604/cmes.2021.015224
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract Diabetes is a burning issue in the whole world. It is the imbalance between body glucose and insulin. The study of this imbalance is very much needed from a research point of view. For this reason, Bergman gave an important model named-Bergman minimal model. In the present work, using Caputo-Fabrizio (CF) fractional derivative, we generalize Bergman’s minimal blood glucose-insulin model. Further, we modify the old model by including one more component known as diet D(t), which is also essential for the blood glucose model. We solve the modified model with the help of Sumudu transform and fixed-point iteration procedures. Also,… More >

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    1655

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    1

  • Open Access

    ARTICLE

    A Binomial Model Approach: Comparing the R0 Values of SARS-CoV-2 rRT-PCR Data from Laboratories across Northern Cyprus

    Nazife Sultanoglu, Nezihal Gokbulut, Tamer Sanlidag, Evren Hincal, Bilgen Kaymakamzade, Murat Sayan
    CMES-Computer Modeling in Engineering & Sciences, Vol.128, No.2, pp. 717-729, 2021, DOI:10.32604/cmes.2021.016297
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract Northern Cyprus has implemented relatively strict measures in the battle against the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The measures were introduced at the beginning of the COVID-19 pandemic, in order to prevent the spread of the disease. One of these measures was the use of two separate real-time reverse transcription polymerase chain reaction (rRT-PCR) tests for SARS-CoV-2 referred to as the double screening procedure, which was adopted following the re-opening of the sea, air and land borders for passengers after the first lockdown. The rRT-PCR double screening procedure involved reporting a negative rRT-PCR test which was… More >

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    1811

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    1206

  • Open Access

    ARTICLE

    Modeling Dysentery Diarrhea Using Statistical Period Prevalence

    Fouad A. Abolaban
    CMES-Computer Modeling in Engineering & Sciences, Vol.128, No.1, pp. 183-201, 2021, DOI:10.32604/cmes.2021.015472
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract Various epidemics have occurred throughout history, which has led to the investigation and understanding of their transmission dynamics. As a result, non-local operators are used for mathematical modeling in this study. Therefore, this research focuses on developing a dysentery diarrhea model with the use of a fractional operator using a one-parameter Mittag–Leffler kernel. The model consists of three classes of the human population, whereas the fourth one belongs to the pathogen population. The model carefully deals with the dimensional homogeneity among the parameters and the fractional operator. In addition, the model was validated by fitting the actual number of dysentery… More >

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    2033

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    1337

  • Open Access

    ARTICLE

    Regarding on the Fractional Mathematical Model of Tumour Invasion and Metastasis

    P. Veeresha, Esin Ilhan, D. G. Prakasha, Haci Mehmet Baskonus, Wei Gao
    CMES-Computer Modeling in Engineering & Sciences, Vol.127, No.3, pp. 1013-1036, 2021, DOI:10.32604/cmes.2021.014988
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract In this paper, we analyze the behaviour of solution for the system exemplifying model of tumour invasion and metastasis by the help of q-homotopy analysis transform method (q-HATM) with the fractional operator. The analyzed model consists of a system of three nonlinear differential equations elucidating the activation and the migratory response of the degradation of the matrix, tumour cells and production of degradative enzymes by the tumour cells. The considered method is graceful amalgamations of q-homotopy analysis technique with Laplace transform (LT), and Caputo–Fabrizio (CF) fractional operator is hired in the present study. By using the fixed point theory, existence… More >

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    2656

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    1622

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    4

  • Open Access

    ARTICLE

    Dynamical Transmission of Coronavirus Model with Analysis and Simulation

    Muhammad Farman, Ali Akgül, Aqeel Ahmad, Dumitru Baleanu, Muhammad Umer Saleem
    CMES-Computer Modeling in Engineering & Sciences, Vol.127, No.2, pp. 753-769, 2021, DOI:10.32604/cmes.2021.014882
    （This article belongs to the Special Issue: Mathematical Aspects of Computational Biology and Bioinformatics)
    Abstract COVID-19 acts as a serious challenge to the whole world. Epidemiological data of COVID-19 is collected through media and web sources to analyze and investigate a system of nonlinear ordinary differential equation to understand the outbreaks of this epidemic disease. We analyze the diseases free and endemic equilibrium point including stability of the model. The certain threshold value of the basic reproduction number R0 is found to observe whether population is in disease free state or endemic state. Moreover, the epidemic peak has been obtained and we expect a considerable number of cases. Finally, some numerical results are presented which… More >

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    1586

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    5

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