Sigve Nakken

Happy to release v1.0.0 of the Personal Cancer Genome Reporter (PCGR). Easier installation, updated data bundle. See more at sigven.github.io/pcgr Great collab with Peter Diakumis @UMCCR

GitHub update: Tamor, a Snakemake pipeline for Personal Cancer Genome Reports from FASTQ files + Dragen genome/transcriptome analysis, has been updated to work with @sigven’s 2.0 PCGR system! Now comes with working a public leukaemia data example. GitHub.com/nodrogluap/tam…

@adbeggs Happy to see the fresh release of github.com/sigven/pcgr in action! Open-source, installable through Conda/Docker/Apptainer. Interactive genomic interpretation report for precision cancer medicine powered by #rstats #Python @quarto_pub

Correction - should have tagged @sigven!

Excited to show our latest attempt at a clinically meaningful clinical cancer genome with rapid turn around (24 hours!) times using Oxford Nanopore sequencing technology for patients who need a rapid, whole genome assessment of their tumour and germline, offering them (1/n):

The iCAN-PEDI study & @viljmaria examine personalized childhood cancer treatment using genetics, drug responses, and AI. Read more about how this research aims to enhance personalized cancer treatment ⬇️🔬 @FIMM_UH @CSCfi @ELIXIREurope elixir-finland.org/en/artificial-…

@FIMM_UH @UniOslo @iCAN_Finland Thanks for your great hospitality and interesting discussions!

Yesterday we had the great pleasure of having Dr. Sigve Nakken from the Oslo University Hospital and @UniOslo visiting FIMM and @iCAN_Finland. Thank you for the visit and the inspiring talk on "Computational frameworks to support precision cancer medicine", @sigven!

@sigven and @Wesche_Lab have published a user-friendly reporting framework, oncoEnrichR, that allows for systematic interpretation of Genome-scale screening experiments and prioritizes long lists of candidate genes for in-depth follow-up experiments onlinelibrary.wiley.com/doi/10.1002/ij…

GitHub update: 'Tamor' is a 1st try at an easy-to-use workflow for rapid Personal Cancer Genome Report (amazing work from @sigven et al.) generation using @Illumina Dragen + Snakemake (@johanneskoester) + @condaproject. Instrument files ➡️ Web report. github.com/nodrogluap/tam…

@YYCist @illumina @johanneskoester @condaproject Awesome! Get in touch if you have qs etc

Little is known about non-coding somatic mutations in people without cancer. To learn a bit more about this class of mutations, we comprehensively profiled blood somatic mutations across ~43K individuals from the TOPMed consortium, now out @ScienceAdvances science.org/doi/10.1126/sc…

📢Our preprint ‘RNA allelic frequencies of somatic mutations encode substantial functional information in cancers’ is out today. Excited to tell you all about it, and our new tool, RVdriver: biorxiv.org/content/10.110… (1/8)

GBC today announces the first set of Global Core Biodata Resources (GCBRs) - a collection of 37 data resources whose long-term funding and sustainability is critical to the global research endeavour in life sciences and biomedicine. See globalbiodata.org/global-biodata… #opendata

Our latest paper with #mutationalanalysis, #signalingproteinprofiling and #cancerdrugsensitivityscreening in #multiplemyeloma cell lines is now out in @FrontOncology! @Mariase55115145 @SigridSkanland @TorilHol @KristineMisund @sigven @MezaZepeda frontiersin.org/articles/10.33…

@larsjuhljensen Thanks for very concise learning material :) These are very helpful resources!

100,000 views! I seem to be hitting one milestone after another with my YouTube channel lately. Thank you so much everyone, it wouldn't have happened without you. Yes, I know that I am stating the bleedin' obvious 😉

— Edvard og jeg er ikke kjent for å sutre, vi sutrer heller ikke nå, vi er sjokkerte og redde for framtida. Dette er et varsku, sier nobelprisvinner May-Britt Moser etter de varslede kuttene i Forskningsrådet. khrono.no/nobelprisvinne…

Feasibility of clinical whole genome and transcriptome sequencing (WGTS) in oncology. A 🧵 on our latest study published in Nature Communications today:rdcu.be/cNOyQ

@jomcinerney If you are working with cancer check out oncoEnrichR (github.com/sigven/oncoEnr…). Provides a comprehensive output for your gene list (html report + Excel workbook). R package and web-based access (oncotools.elixir.no)

Question: if you have a list of genes of interest and you want to get *information* (function, localisation etc) about these genes (on command line), what is your favourite way of doing this?

Accompanying release of the Cancer Predisposition Sequencing Reporter (CPSR), v1.0.0. sigven.github.io/cpsr. CPSR provides a detailed and flexible report of cancer-predisposing germline variants on a per-patient basis.

Happy to release v1.0.0 of the Personal Cancer Genome Reporter (PCGR). Easier installation, updated data bundle. See more at sigven.github.io/pcgr Great collab with Peter Diakumis @UMCCR

We all agree the status quo is unsustainable. Here are 1,000 words on how we could get the role of Open Source maintainer to graduate to a real, properly paid profession. The thing is, companies need it as much as maintainers do. blog.filippo.io/professional-m…

After a multi-year effort from so many brilliant people involved in this project, I am excited to share our work published today in @NatureBiotech. @JOlweus @Irenegr5 @Oslounivsykehus @UniOslo nature.com/articles/s4158…