Sigve Nakken

Computational scientist at Oslo University Hospital, Norway. General interest in computational cancer genomics and cancer precision medicine.

[Sigve Nakken @sigven]

Happy to release v1.0.0 of the Personal Cancer Genome Reporter (PCGR). Easier installation, updated data bundle. See more at https://t.co/l6lxJ2rYwt Great collab with Peter Diakumis @UMCCR

[Paul Gordon @YYCist]

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. https://t.co/WMXj1gb0xK

[Sigve Nakken @sigven]

@adbeggs Happy to see the fresh release of https://t.co/fKTGRHrw3m in action! Open-source, installable through Conda/Docker/Apptainer. Interactive genomic interpretation report for precision cancer medicine powered by #rstats #Python @quarto_pub

[Andrew Beggs @adbeggs]

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):

[ELIXIRFinland @ELIXIRFinland]

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

https://t.co/4Hqz48PNvl

[Sigve Nakken @sigven]

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

[Centre for Cancer Cell Reprogramming @CanCell_UiO]

@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
https://t.co/0gHLmgCw1n

[Paul Gordon @YYCist]

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. https://t.co/SJXMb7ymRj

[Sigve Nakken @sigven]

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

[Josh Weinstock @josh_weinstock]

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 https://t.co/hTXXaNwedr

[James Black @jrm_black]

📢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: https://t.co/L8ZuY3u6t2 (1/8)

[GlobalBiodata @globalbiodata]

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 https://t.co/JeWPpPEV1S #opendata

[Kjetil Tasken @KjetilTasken]

Our latest paper with #mutationalanalysis, #signalingproteinprofiling and #cancerdrugsensitivityscreening in #multiplemyeloma cell lines is now out in @FrontOncology! @Mariase55115145 @SigridSkanland @TorilHol @KristineMisund @sigven @MezaZepeda https://t.co/ngxs0bhoNB

[Sigve Nakken @sigven]

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

[Khrono @AvisenKhrono]

— 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. https://t.co/mj0DGzPJV3

[Elli Papaemmanuil, PhD @PapaemmanuilLab]

Feasibility of clinical whole genome and transcriptome sequencing (WGTS) in oncology. A 🧵 on our latest study published in Nature Communications today:https://t.co/6007GkYDAc

[Sigve Nakken @sigven]

@jomcinerney If you are working with cancer check out oncoEnrichR (https://t.co/fsjVdECZ22). Provides a comprehensive output for your gene list (html report + Excel workbook). R package and web-based access (https://t.co/GNa4iyN76Q)

[Sigve Nakken @sigven]

Accompanying release of the Cancer Predisposition Sequencing Reporter (CPSR), v1.0.0. https://t.co/LgKqgTgoJN. CPSR provides a detailed and flexible report of cancer-predisposing germline variants on a per-patient basis.

[Sigve Nakken @sigven]

Happy to release v1.0.0 of the Personal Cancer Genome Reporter (PCGR). Easier installation, updated data bundle. See more at https://t.co/l6lxJ2rYwt Great collab with Peter Diakumis @UMCCR

[Filippo Valsorda @filippo.abyssdomain.expert @FiloSottile]

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.

https://t.co/RK26lKGg3h

[Muhammad Ali @muhammadali_uio]

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 https://t.co/jiUr4Auk6X