Feature Papers in Computational Biology

A special issue of Computation (ISSN 2079-3197). This special issue belongs to the section "Computational Biology".

Deadline for manuscript submissions: 31 October 2025 | Viewed by 402

Special Issue Editors


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Guest Editor
Marchuk Institute of Numerical Mathematics of the Russian Academy of Sciences, Sechenov Medical University, Moscow, Russia
Interests: system immunology; virus infections; mathematical modelling
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Guest Editor
Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
Interests: machine learning; data integration; bioinformatics; systems biology

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Guest Editor
1. Senior Principal Investigator, Head of Division Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
2. Visiting Professor of Systems Biology, Faculty of Science and Engineering, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
Interests: computational systems biology; bioinformatics; metabolomics; dynamic modelling; synthetic biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue, entitled “Feature Papers in Computational Biology", aims to present cutting-edge research that utilizes computational methods to address critical questions in biology. We welcome contributions that encompass a broad range of topics, including but not limited to, systems biology, bioinformatics, computational genomics, structural bioinformatics, and machine learning applications in biological data analysis.

Advances in computational biology heavily rely on the development of powerful methods and software for the numerical treatment of a broad range of models that implement multiscale, multiphysics and hybrid approaches to describe various aspects of biological complexity. The mathematical exploration of biological systems requires the integration of various mathematical techniques, such as graph theory, network analysis, representation theory, identification methods and information-theoretic inference.

We encourage the submission of papers that explore innovative methodologies for the analysis of high-throughput sequencing data, the modeling of protein interactions, the dynamics and control of chronic diseases, and understanding complex biological systems. Both empirical studies and theoretical contributions are welcome, provided that they advance the field and offer new insights into biological phenomena.

This Special Issue seeks to foster interdisciplinary collaboration and serve as a comprehensive resource for researchers and practitioners in the field of computational biology, promoting the integration of computational techniques in biological research. Finally yet importantly is the need to present modelling studies, which could be categorized as biologically-relevant, question-driven, and data-validated examples from various branches of biomedicine.

Prof. Dr. Gennady Bocharov
Prof. Dr. Dick De Ridder
Prof. Dr. Rainer Breitling
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Computation is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • computational biology
  • bioinformatics
  • systems biology
  • computational genomics
  • machine learning
  • high-throughput sequencing
  • protein interaction modeling
  • data analysis
  • structural bioinformatics
  • evolutionary dynamics
  • biological networks
  • biomechanics
  • population dynamics
  • multiscale modelling
  • biological complexity
  • multiphysics models
  • hierarchical regulation
  • biological control and optimization

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Published Papers (1 paper)

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Research

22 pages, 1039 KiB  
Article
A Machine Learning-Based Computational Methodology for Predicting Acute Respiratory Infections Using Social Media Data
by Jose Manuel Ramos-Varela, Juan C. Cuevas-Tello and Daniel E. Noyola
Computation 2025, 13(4), 86; https://doi.org/10.3390/computation13040086 - 25 Mar 2025
Viewed by 313
Abstract
We study the relationship between tweets referencing Acute Respiratory Infections (ARI) or COVID-19 symptoms and confirmed cases of these diseases. Additionally, we propose a computational methodology for selecting and applying Machine Learning (ML) algorithms to predict public health indicators using social media data. [...] Read more.
We study the relationship between tweets referencing Acute Respiratory Infections (ARI) or COVID-19 symptoms and confirmed cases of these diseases. Additionally, we propose a computational methodology for selecting and applying Machine Learning (ML) algorithms to predict public health indicators using social media data. To achieve this, a novel pipeline was developed, integrating three distinct models to predict confirmed cases of ARI and COVID-19. The dataset contains tweets related to respiratory diseases, published between 2020 and 2022 in the state of San Luis Potosí, Mexico, obtained via the Twitter API (now X). The methodology is composed of three stages, and it involves tools such as Dataiku and Python with ML libraries. The first two stages focuses on identifying the best-performing predictive models, while the third stage includes Natural Language Processing (NLP) algorithms for tweet selection. One of our key findings is that tweets contributed to improved predictions of ARI confirmed cases but did not enhance COVID-19 time series predictions. The best-performing NLP approach is the combination of Word2Vec algorithm with the KMeans model for tweet selection. Furthermore, predictions for both time series improved by 3% in the second half of 2020 when tweets were included as a feature, where the best prediction algorithm is DeepAR. Full article
(This article belongs to the Special Issue Feature Papers in Computational Biology)
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