Emerging studies underscore the promising capabilities of large language model-based chatbots in conducting fundamental bioinformatics data analyses. The recent feature of accepting image-inputs by ChatGPT motivated us to explore its efficacy in deciphering bioinformatics illustrations. Our evaluation with examples in cancer research, including sequencing data analysis, multimodal network-based drug repositioning, and tumor clonal evolution, revealed that ChatGPT can proficiently explain different plot types and apply biological knowledge to enrich interpretations. However, it struggled to provide accurate interpretations when quantitative analysis of visual elements was involved. Furthermore, while the chatbot can draft figure legends and summarize findings from the figures, stringent proofreading is imperative to ensure the accuracy and reliability of the content.
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http://dx.doi.org/10.1101/2023.10.15.562423 | DOI Listing |
Process-based models for range dynamics are urgently needed due to increasing intensity of human-induced biodiversity change. Despite a few existing models that focus on demographic processes, their use remains limited compared to the widespread application of correlative approaches. This slow adoption is largely due to the challenges in calibrating biological parameters and the high computational demands for large-scale applications.
View Article and Find Full Text PDFJ Cell Mol Med
January 2025
Department of Medical Biology, Faculty of Medicine, Kutahya Health Sciences University, Kutahya, Turkey.
Chemotherapy is a potent tool against cancer, but drug resistance remains a major obstacle. To combat this, understanding the molecular mechanisms behind resistance in cancer cells and the protein expression changes driving these mechanisms is crucial. Targeting the Ubiquitin-Proteasome System (UPS) has proven effective in treating multiple myeloma and shows promise for solid tumours.
View Article and Find Full Text PDFBMC Genomics
January 2025
Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre (Erasmus MC), Rotterdam, The Netherlands.
Background: The Joint Programming Initiative on Antimicrobial Resistance (JPIAMR) networks 'Seq4AMR' and 'B2B2B AMR Dx' were established to promote collaboration between microbial whole genome sequencing (WGS) and antimicrobial resistance (AMR) stakeholders. A key topic discussed was the frequent variability in results obtained between different microbial WGS-related AMR gene prediction workflows. Further, comparative benchmarking studies are difficult to perform due to differences in AMR gene prediction accuracy and a lack of agreement in the naming of AMR genes (semantic conformity) for the results obtained.
View Article and Find Full Text PDFBrief Bioinform
November 2024
Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No. 97 Buxin Road, Dapeng New District, Shenzhen 518124, China.
Identifying the regulatory effects of noncoding variants presents a significant challenge. Recently, the accumulation of epigenomic profiling data in wheat has provided an opportunity to model the functional impacts of these variants. In this study, we introduce Language of Genome for Wheat (LOGOWheat), a deep learning-based tool designed to predict the regulatory effects of noncoding variants in wheat.
View Article and Find Full Text PDFNPJ Syst Biol Appl
January 2025
Institute of Biomedical Engineering and Instrumentation, Hangzhou Dianzi University, Hangzhou, China.
Breast cancer prognosis is complicated by tumor heterogeneity. Traditional methods focus on cancer-specific gene signatures, but cross-cancer strategies that provide deeper insights into tumor homogeneity are rarely used. Immunotherapy, particularly immune checkpoint inhibitors, results from variable responses across cancers, offering valuable prognostic insights.
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