JMIR Bioinformatics and Biotechnology

Methods, web-based platforms, open data and open software tools for big data analytics, machine learning-based predictive models using genomic and imaging data, and information retrieval in biology and medicine.

Editor-in-Chief:

Ece D. Uzun, MS, Ph.D., FAMIA, Director of Clinical Bioinformatics, Lifespan Academic Medical Center; Associate Director, Center for Clinical Cancer Informatics and Data Science (CCIDS); and Assistant Professor of Pathology and Laboratory Medicine, Alpert Medical School, Brown University, USA


JMIR Bioinformatics and Biotechnology, (JBB, ISSN 2563-3570) (Editor-in-chief: Ece Uzun, MS, PhD, FAMIA) is a premier, open-access journal indexed in PubMed Central and PubMed, SCOPUS, Sherpa/Romeo, DOAJ and EBSCO/EBSCO Essentials. It focuses on bioinformatics, genomic variation detection algorithms and tools, AI applications in genomics and pathology informatics, mathematical modeling in biological systems including drug delivery and discovery, genomic data visualization, network biology and cancer genomic data analysis (See Focus and Scope). 

Recent Articles

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Viewpoint

Health care is at a turning point. We are shifting from protocolized medicine to precision medicine, and digital health systems are facilitating this shift. By providing clinicians with detailed information for each patient and analytic support for decision-making at the point of care, digital health technologies are enabling a new era of precision medicine. Genomic data also provide clinicians with information that can improve the accuracy and timeliness of diagnosis, optimize prescribing, and target risk reduction strategies, all of which are key elements for precision medicine. However, genomic data are predominantly seen as diagnostic information and are not routinely integrated into the clinical workflows of electronic medical records. The use of genomic data holds significant potential for precision medicine; however, as genomic data are fundamentally different from the information collected during routine practice, special considerations are needed to use this information in a digital health setting. This paper outlines the potential of genomic data integration with electronic records, and how these data can enable precision medicine.

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Bioinformatics, genomics, tools and databases

Genetic data are widely considered inherently identifiable. However, genetic data sets come in many shapes and sizes, and the feasibility of privacy attacks depends on their specific content. Assessing the reidentification risk of genetic data is complex, yet there is a lack of guidelines or recommendations that support data processors in performing such an evaluation.

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Editorial

The generative artificial intelligence (AI) model ChatGPT holds transformative prospects in medicine. The development of such models has signaled the beginning of a new era where complex biological data can be made more accessible and interpretable. ChatGPT is a natural language processing tool that can process, interpret, and summarize vast data sets. It can serve as a digital assistant for physicians and researchers, aiding in integrating medical imaging data with other multiomics data and facilitating the understanding of complex biological systems. The physician’s and AI’s viewpoints emphasize the value of such AI models in medicine, providing tangible examples of how this could enhance patient care. The editorial also discusses the rise of generative AI, highlighting its substantial impact in democratizing AI applications for modern medicine. While AI may not supersede health care professionals, practitioners incorporating AI into their practices could potentially have a competitive edge.

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Bioinformatics, genomics, tools and databases

The etiology of ischemic stroke is multifactorial. Several gene mutations have been identified as leading causes of cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL), a hereditary disease that causes stroke and other neurological symptoms.

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Bioinformatics, genomics, tools and databases

Current postpartum hemorrhage (PPH) risk stratification is based on traditional statistical models or expert opinion. Machine learning could optimize PPH prediction by allowing for more complex modeling.

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Bioinformatics Web Tools

Genetic testing is essential to identify research participants for clinical trials enrolling people with Parkinson disease (PD) carrying a variant in the glucocerebrosidase (GBA) or leucine-rich repeat kinase 2 (LRRK2) genes. The limited availability of professionals trained in neurogenetics or genetic counseling is a major barrier to increased testing. Telehealth solutions to increase access to genetics education can help address issues around counselor availability and offer options to patients and family members.

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Genome Analysis and Visualization

While genomic variations can provide valuable information for health care and ancestry, the privacy of individual genomic data must be protected. Thus, a secure environment is desirable for a human DNA database such that the total data are queryable but not directly accessible to involved parties (eg, data hosts and hospitals) and that the query results are learned only by the user or authorized party.

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Genomic and Evolutionary Analysis in COVID-19

COVID-19 and Middle East Respiratory Syndrome are two pandemic respiratory diseases caused by coronavirus species. The novel disease COVID-19 caused by SARS-CoV-2 was first reported in Wuhan, Hubei Province, China, in December 2019, and became a pandemic within 2-3 months, affecting social and economic platforms worldwide. Despite the rapid development of vaccines, there have been obstacles to their distribution, including a lack of fundamental resources, poor immunization, and manual vaccine replication. Several variants of the original Wuhan strain have emerged in the last 3 years, which can pose a further challenge for control and vaccine development.

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Editorial

JMIR Bioinformatics and Biotechnology supports interdisciplinary research and welcomes contributions that push the boundaries of bioinformatics, genomics, artificial intelligence, and pathology informatics.

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Genome Analysis and Visualization

A thorough understanding of the patterns of genetic subdivision in a pathogen can provide crucial information that is necessary to prevent disease spread. For SARS-CoV-2, the availability of millions of genomes makes this task analytically challenging, and traditional methods for understanding genetic subdivision often fail.

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Genome Analysis and Visualization

There is a great need to develop a computational approach to analyze and exploit the information contained in gene expression data. The recent utilization of nonnegative matrix factorization (NMF) in computational biology has demonstrated the capability to derive essential details from a high amount of data in particular gene expression microarrays. A common problem in NMF is finding the proper number rank (r) of factors of the degraded demonstration, but no agreement exists on which technique is most appropriate to utilize for this purpose. Thus, various techniques have been suggested to select the optimal value of rank factorization (r).

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Drug Repurposing and Off-Label Use

Dengue fever can progress to dengue hemorrhagic fever (DHF), a more serious and occasionally fatal form of the disease. Indicators of serious disease arise about the time the fever begins to reduce (typically 3 to 7 days following symptom onset). There are currently no effective antivirals available. Drug repurposing is an emerging drug discovery process for rapidly developing effective DHF therapies. Through network pharmacology modeling, several US Food and Drug Administration (FDA)-approved medications have already been researched for various viral outbreaks.

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