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Selected Papers from the International Conference on Intelligent Biology and...
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Selected Papers from the International Conference on Intelligent Biology and Medicine (ICIBM 2023)

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Technologies and Resources for Genetics".

Deadline for manuscript submissions: closed (20 August 2023) | Viewed by 1628

Special Issue Editor

Dr. Fuhai Li

E-Mail Website
Guest Editor
Institute for Informatics, Department of Pediatrics, Washington University in St Louis, St Louis, MO 63108, USA
Interests: artificial intelligence and deep learning; graph neural network; multi-omics data analysis; network inference; disease-immune cell–cell signaling interactions; drug repurposing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The 2023 International Conference on Intelligent Biology and Medicine (ICIBM 2023) will be held on July 16–19, 2023 in Tampa, FL, USA. The webpage for this event is https://icibm2023.iaibm.org/.

The ICIBM conference series has two main aims: 1) to foster interdisciplinary and multidisciplinary research in bioinformatics-related fields, and 2) to provide an educational program for trainees and young investigators across a range of scientific disciplines to learn about frontier research in these areas and to build a network among both established and junior investigators.

The current Special Issue invites submissions on unpublished original work describing recent advances in all aspects of bioinformatics, systems biology, intelligent computing, and medical informatics, including but not restricted to the following topics:

  • Genomics and genetics, including integrative and functional genomics, and genome evolution.
  • Next-generation sequencing data analysis, applications, and software and tools.
  • Big data science including storage, analysis, modeling, visualization, and cloud.
  • Precision medicine, translational bioinformatics, and medical informatics.
  • Drug discovery, design, and repurposing.
  • Single-cell sequencing data analysis.
  • Microbiome and metagenomics.

A full list of topics is available on the conference website.

Dr. Fuhai Li
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. Genes 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 2600 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
  • systems biology
  • integrative and functional genomics
  • genome evolution
  • NGS
  • analysis
  • precision medicine
  • translational research
  • drug discovery
  • single cell sequencing data analysis
  • microbiome and metagenomics
  • synthetic biological systems
  • biological processes pathways and networks
  • EHR-based phenotyping

Published Papers (1 paper)

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Research

12 pages, 3943 KiB  
Article
Osteogenic Differentiation Potential of Mesenchymal Stem Cells Using Single Cell Multiomic Analysis
by Duojiao Chen, Sheng Liu, Xiaona Chu, Jill Reiter, Hongyu Gao, Patrick McGuire, Xuhong Yu, Xiaoling Xuei, Yichen Liu, Jun Wan, Fang Fang, Yunlong Liu and Yue Wang
Genes 2023, 14(10), 1871; https://doi.org/10.3390/genes14101871 - 26 Sep 2023
Cited by 2 | Viewed by 1269
Abstract
Mesenchymal stem cells (MSC) are multipotent stem cells that can differentiate into multiple cell types, including osteoblasts, chondrocytes, and adipocytes. Osteoblast differentiation is reduced during osteoporosis development, resulting in reduced bone formation. Further, MSC isolated from different donors possess distinct osteogenic capacity. In [...] Read more.
Mesenchymal stem cells (MSC) are multipotent stem cells that can differentiate into multiple cell types, including osteoblasts, chondrocytes, and adipocytes. Osteoblast differentiation is reduced during osteoporosis development, resulting in reduced bone formation. Further, MSC isolated from different donors possess distinct osteogenic capacity. In this study, we used single-cell multiomic analysis to profile the transcriptome and epigenome of MSC from four healthy donors. Data were obtained from ~1300 to 1600 cells for each donor. These cells were clustered into four groups, indicating that MSC from different donors have distinct chromatin accessible regulatory elements for regulating gene expression. To investigate the mechanism by which MSC undergo osteogenic differentiation, we used the chromatin accessibility data from the single-cell multiome data to identify individual-specific enhancer–promoter pairs and evaluated the expression levels and activities of the transcriptional regulators. The MSC from four donors showed distinct differentiation potential into osteoblasts. MSC of donor 1 showed the largest average motif activities, indicating that MSC from donor 1 was most likely to differentiate into osteoblasts. The results of our validation experiments were consistent with the bioinformatics prediction. We also tested the enrichment of genome-wide association study (GWAS) signals of several musculoskeletal disease traits in the patient-specific chromatin accessible regions identified in the single-cell multiome data, including osteoporosis, osteopenia, and osteoarthritis. We found that osteoarthritis-associated variants were only enriched in the regions identified from donor 4. In contrast, osteoporosis and osteopenia variants were enriched in regions from donor 1 and least enriched in donor 4. Since osteoporosis and osteopenia are related to the density of bone cells, the enrichment of variants from these traits should be correlated with the osteogenic potential of MSC. In summary, this study provides large-scale data to link regulatory elements with their target genes to study the regulatory relationships during the differentiation of mesenchymal stem cells and provide a deeper insight into the gene regulatory mechanism. Full article
(This article belongs to the Special Issue Selected Papers from the International Conference on Intelligent Biology and Medicine (ICIBM 2023))
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