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#bioinformatics

12 posts11 participants1 post today
Public
SIB Swiss Bioinformatics

@bgeedb was used to design stem-cell based vaccines 💉against #cancer in mouse models, opening a door to a potential application with humans.

🔎 This is an example of the impact that #bioinformatics databases and tools developed by SIB groups have. Researchers use them to make sense of their data and tackle essential societal challenges.

👉 Learn more: sib.swiss/services/open-softwa

@marcrr @fbastian

#SIBResourceImpacts#OpenSoftwareAndDatabases
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Benjamin Carr, Ph.D. 👨🏻‍💻🧬

#Genetic data repo #OpenSNP to self-destruct before authoritarians weaponize it
The reason, according to #bioinformatics researcher Bastian Greshake Tzovaras, one of the founders of the project, is the dissolution of genetic testing biz #23andMe and the potential weaponization of genetic data by #farright #authoritarian regimes.
theregister.com/2025/04/01/ope

The Register · Genetic data repo OpenSNP to self-destruct before authoritarians weaponize itBy Thomas Claburn
Public
Cytology and Genetics

A Pan-Cancer Analysis of Ferroptosis-Related Gene Arachidonic Acid 15-Lipoxygenase-1 (ALOX15): Its Prognostic and Immunotherapeutic Values - #ferroptosis #bioinformatics #prognosis #pancancer #ALOX15 #biologicalfunctions #immune - link.springer.com/article/10.3

SpringerLinkA Pan-Cancer Analysis of Ferroptosis-Related Gene Arachidonic Acid 15-Lipoxygenase-1 (ALOX15): Its Prognostic and Immunotherapeutic Values - Cytology and GeneticsAbstract Background. Emerging research has identified ferroptosis as a novel form of programmed cell death, and Arachidonic acid 15-lipoxygenase-1 (ALOX15) stands out as a pivotal gene in mediating this process. Nonetheless, the role of ALOX15 in human tumors remains elusive. Methods. We utilized TIMER 2.0 to investigate the differential expression profiles of ALOX15 between pan-cancer and normal tissues. Further data from the TCGA, GEPIA, UALCAN, HPA, and CPTAC databases were analyzed to verify the levels of mRNA, protein expression, and promoter methylation across various cancer types. The survival prognosis, clinical features, and genetic alterations of ALOX15 were also evaluated. GO/KEGG enrichment analyses and single-cell transcriptome sequencing were employed for functional enrichment analysis. The gene mutation of ALOX15 and its prognostic value were analyzed using the cBioPortal platform. Finally, the relationship between ALOX15 and immune cell infiltration, Immune Checkpoints (ICKs), genomic instability, and drug sensitivity was further explored using GSCA. Results. Our findings revealed that the transcription and protein expression of ALOX15 were significantly reduced in HNSC, LUAD, LUSC, SKCM, KICH, and THCA, while they were up-regulated in ESCA, LIHC, PRAD, and UCEC. Notably, the expression of ALOX15 had prognostic value for certain cancers, including LUAD, LUSC, LIHC, KIRC, HNSC, THCA, and LGG. Additionally, ALOX15 expression was markedly correlated with clinical characteristics, immune cell infiltration, ICKs, genomic instability, and antitumor drug sensitivity in various tumors. Gene mutations of ALOX15 and their prognostic value were discovered in pan-cancers. Furthermore, GO/KEGG analysis and single-cell transcriptome sequencing indicated that ALOX15 was significantly associated with cancer-related pathways. Conclusion. Our comprehensive pan-cancer analysis shed light on the role and significance of ALOX15, suggesting its potential as a prognostic and immunotherapeutic marker for pan-cancer. These findings may provide new directions and evidence for cancer therapeutics.
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Thomas Sandmann

Big shoutout to the folks at NCBI GEO. They have been doing an incredible job managing enormous amounts of gene expression and related biomedical data for many, many years They do it efficiently and very, very well. I am so grateful: both when I download data published by others and when I submit my own data. You are true #bioinformatics heroes doing priceless and highly impactful work! 🦸 🧬 💻 #NCBI #nih

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Luke Pembleton

Does anyone have any posts or past toots they could reshare about how they have setup or are working within a team in #bioinformatics, #genomics, #research etc. things that how worked or haven’t worked, organising and sharing projects and code, notes and documentation, collaboration and communication, software, network and local or cloud compute arrangement. Always find reading others experiences insightful and beneficial.

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