Bioinformatics has evolved from providing basic solutions, such as sequence alignment, structure predictions, and phylogenetic analysis to an independent data-driven field. The unprecedented growth of genomic technologies and the enormous data have opened an avenue for bioinformaticians (Bioinformatics professionals) never been seen before in the history of mankind. The novel opportunity also requires creative solutions that need skills to deal with noisy, unstructured information to offer valuable biological insights. Currently, we are seeing only the tip of an iceberg and the future will revolve around big data sets in all forms of biological research. The emerging challenge is to unfold the hidden iceberg of data.
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http://dx.doi.org/10.6026/97320630016013 | DOI Listing |
Front Mol Biosci
January 2025
Department of Obstetrics and Gynecology, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China.
Background: Polycystic ovary syndrome (PCOS) is a common endocrine and metabolic condition impacting millions of women worldwide. This study sought to identify granulosa cell endoplasmic reticulum stress (GCERS)-related differentially expressed genes (DEGs) between women with PCOS and those without PCOS using bioinformatics and to investigate the related molecular mechanisms.
Methods: Two datasets were downloaded from GEO and analysed using the limma package to identify DEGs in two groups-PCOS and normal granulosa cells.
Hemasphere
January 2025
Université Paris Cité, Institut Cochin, INSERM U1016, CNRS UMR8104 Assistance Publique-Hôpitaux de Paris.Centre, Laboratory of Hematology, Hôpital Cochin Paris France.
Lower risk (LR) myelodysplastic syndromes (MDS) are heterogeneous hematopoietic stem and progenitor disorders caused by the accumulation of somatic mutations in various genes including epigenetic regulators that may produce convergent DNA methylation patterns driving specific gene expression profiles. The integration of genomic, epigenomic, and transcriptomic profiling has the potential to spotlight distinct LR-MDS categories on the basis of pathophysiological mechanisms. We performed a comprehensive study of somatic mutations and DNA methylation in a large and clinically well-annotated cohort of treatment-naive patients with LR-MDS at diagnosis from the EUMDS registry (ClinicalTrials.
View Article and Find Full Text PDFBiochemistry
January 2025
Department of Chemistry, Washington University in St. Louis, One Brookings Drive, St. Louis, Missouri 63130, United States.
Branch-point syntheses in nonribosomal peptide assembly are rare but useful strategies to generate tripodal peptides with advantageous hexadentate iron-chelating capabilities, as seen in siderophores. However, the chemical logic underlying the peptide branching by nonribosomal peptide synthetase (NRPS) often remains complex and elusive. Here, we review the common strategies for the biosynthesis of branched nonribosomal peptides (NRPs) and present our biochemical investigation on the NRPS-catalyzed assembly of fimsbactin A, a branched mixed-ligand siderophore produced by the human pathogenic strain .
View Article and Find Full Text PDFScience
January 2025
Electrical and Computer Engineering Department, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA.
Genomes contain mosaics of discordant evolutionary histories, challenging the accurate inference of the tree of life. While genome-wide data are routinely used for discordance-aware phylogenomic analyses, due to modeling and scalability limitations, the current practice leaves out large chunks of genomes. As more high-quality genomes become available, we urgently need discordance-aware methods to infer the tree directly from a multiple genome alignment.
View Article and Find Full Text PDFReproduction
January 2025
Y Yu, Reproductive medical center, Peking University Third Hospital, Beijing, China.
In recent decades, it has become increasingly clear that mammalian gametes and early embryos are highly sensitive to metabolic substrates. With advances in single-cell sequencing, metabolomics, and bioinformatics, we now recognize that metabolic pathways not only meet cellular energy demands but also play a critical role in cell proliferation, differentiation, and fate determination. Investigating metabolic processes during oocyte maturation and early embryonic development is thus essential to advancing reproductive medicine and embryology.
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