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Bioengineering
Special Issues
Big Biological Data for Personalized Medicine
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Big Biological Data for Personalized Medicine

A special issue of Bioengineering (ISSN 2306-5354).

Deadline for manuscript submissions: closed (5 December 2024) | Viewed by 4581

Special Issue Editor

Dr. Wanwei Zhang

E-Mail Website
Guest Editor
Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
Interests: bioinformatics method development; multi-omics analysis; non-coding RNA; B cell development; genomic instability; retro-transposable elements; cancer
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Advances in high-throughput technologies and data-mining techniques have brought us into the “big biological data” era, a perfect time to develop personalized medicine for complex diseases, including cancer. With the help of multi-omics single-cell-level studies, more and more disease mechanisms and biomarkers are being revealed, which greatly improves the development of personalized medicine. To keep up with and contribute to this trend, we are collecting profound works in areas including, but not limited to, next- and third-generation sequencing data analysis, mass spectrometry analysis, single-cell data analysis, clinical (imaging) data analysis, data-driven biomarker discovery, systems/network biomarker discovery, biological/biomedical database development and bioinformatics tool development. With this collection, we hope to connect data scientists, biologists and clinicians to form a collaborative network and provide a platform where people can share resources and contribute most to personalized medicine in the big biological data era.

Dr. Wanwei Zhang
Guest Editor

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. Bioengineering 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 2700 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

  • bioinformatics tools
  • databases
  • multi-omics
  • single cell

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Published Papers (2 papers)

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Research

22 pages, 1825 KiB  
Article
Detecting Skin Reactions in Epicutaneous Patch Testing with Deep Learning: An Evaluation of Pre-Processing and Modality Performance
by Ioannis A. Vezakis, George I. Lambrou, Aikaterini Kyritsi, Anna Tagka, Argyro Chatziioannou and George K. Matsopoulos
Bioengineering 2023, 10(8), 924; https://doi.org/10.3390/bioengineering10080924 - 3 Aug 2023
Cited by 4 | Viewed by 1651
Abstract
Epicutaneous patch testing is a well-established diagnostic method for identifying substances that may cause Allergic Contact Dermatitis (ACD), a common skin condition caused by exposure to environmental allergens. While the patch test remains the gold standard for identifying allergens, it is prone to [...] Read more.
Epicutaneous patch testing is a well-established diagnostic method for identifying substances that may cause Allergic Contact Dermatitis (ACD), a common skin condition caused by exposure to environmental allergens. While the patch test remains the gold standard for identifying allergens, it is prone to observer bias and consumes valuable human resources. Deep learning models can be employed to address this challenge. In this study, we collected a dataset of 1579 multi-modal skin images from 200 patients using the Antera 3D® camera. We then investigated the feasibility of using a deep learning classifier for automating the identification of the allergens causing ACD. We propose a deep learning approach that utilizes a context-retaining pre-processing technique to improve the accuracy of the classifier. In addition, we find promise in the combination of the color image and false-color map of hemoglobin concentration to improve diagnostic accuracy. Our results showed that this approach can potentially achieve more than 86% recall and 94% specificity in identifying skin reactions, and contribute to faster and more accurate diagnosis while reducing clinician workload. Full article
(This article belongs to the Special Issue Big Biological Data for Personalized Medicine)
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16 pages, 3930 KiB  
Article
Assessment of the Influence of 5-Fluorouracil on SMAD4 and TGFB1 Gene Expression, Apoptosis Induction and DNA Damage in Human Cell Lines
by Agnieszka Wosiak, Dagmara Szmajda-Krygier, Jacek Pietrzak, Joanna Boncela and Ewa Balcerczak
Bioengineering 2023, 10(5), 570; https://doi.org/10.3390/bioengineering10050570 - 9 May 2023
Cited by 2 | Viewed by 2243
Abstract
Purpose: Suppressor of mothers against decapentaplegic homolog 4 (SMAD family member 4, SMAD4) is involved in the adenoma–carcinoma pathway, leading to the development of colon cancer. The encoded protein is a key downstream signaling mediator in the TGFβ pathway. This pathway has [...] Read more.
Purpose: Suppressor of mothers against decapentaplegic homolog 4 (SMAD family member 4, SMAD4) is involved in the adenoma–carcinoma pathway, leading to the development of colon cancer. The encoded protein is a key downstream signaling mediator in the TGFβ pathway. This pathway has tumor-suppressor functions, including cell-cycle arrest and apoptosis. Its activation in late-stage cancer can promote tumorigenesis, including metastasis and chemoresistance. Most colorectal cancer patients receive chemotherapy based on 5-FU as an adjuvant treatment. However, the success of therapy is hampered by multidrug resistance by neoplastic cells. In colorectal cancer, resistance to 5-FU-based therapy is influenced by SMAD4 gene expression, as patients with decreased SMAD4 gene expression probably have a higher risk of developing 5-FU-induced resistance. The mechanism leading to the development of this phenomenon is not fully understood. Therefore, the present study assesses the possible influence of 5-FU on changes in the expression of the SMAD4 and TGFB1 genes. Patients and methods: The effect of 5-FU on the expression of SMAD4 and TGFB1 in colorectal cancer cells derived from the CACO-2, SW480 and SW620 cell lines was evaluated using real-time PCR. The cytotoxicity of 5-FU on colon cancer cells was assessed by the MTT method, and its effect on the induction of cell apoptosis and the initiation of DNA damage using a flow cytometer. Results: Significant changes in the level of SMAD4 and TGFB1 gene expression were noted in the CACO-2, SW480 and SW620 cells treated with 5-FU at various concentrations during 24 h and 48 h exposure. The use of 5-FU at a concentration of 5 µmol/L resulted in a decrease in the expression of the SMAD4 gene in all cell lines at both exposure times, while the concentration of 100 µmol/L increased the expression of the SMAD4 gene in CACO-2 cells. The level of expression of the TGFB1 gene was higher for all cells treated with 5-FU at the highest concentrations, while the exposure time was extended to 48 h. Conclusion: The observed in vitro changes in CACO-2 cells caused by 5-FU may be of clinical relevance when choosing the drug concentration for treating patients with colorectal cancer. It is possible that 5-FU has a stronger effect on colorectal cancer cells at the higher concentrations. Low concentrations of 5-FU may not have a therapeutic effect and may also influence drug resistance in cancer cells. Higher concentrations and prolonged exposure time may affect SMAD4 gene expression, which may increase the effectiveness of therapy. Full article
(This article belongs to the Special Issue Big Biological Data for Personalized Medicine)
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