Konstantin Okonechnikov

PostDoc at Hopp Children’s Cancer Center (KiTZ) and German Cancer Research Center (DKFZ)
Scientist in pediatric neuorooncology, bioinformatics enthusiast

[Konstantin Okonechnikov @mad_kook]

Super happy to share our new paper in Nature, a multi-omic single-cell study demonstrating how #medulloblastoma brain tumor evolves and uncovering its subclonal structure https://t.co/ES5qfHamTT

[Konstantin Okonechnikov @mad_kook]

Example demonstarting that science still remains honest: https://t.co/LpwDJnUaW6 Nature manuscript with false result was retracted after external post-publication review. Full respect to this review authors.

[Konstantin Okonechnikov @mad_kook]

Huge thanks to all involved in the project , especially to Piyush and @VeKoerber for awesome work and to @Lena_Kutscher and Stefan Pfister for leading it. This work wouldn’t have been possible without efforts from #KiTZ , #DKFZ and multiple other hospitals,
& institutions 🙌

[Konstantin Okonechnikov @mad_kook]

Super happy to share our new paper in Nature, a multi-omic single-cell study demonstrating how #medulloblastoma brain tumor evolves and uncovering its subclonal structure https://t.co/ES5qfHamTT

[Konstantin Okonechnikov @mad_kook]

We hope this study pushes forward the understanding of pediatric brain tumor evolution and inspires new diagnostic and therapeutic strategies. All data and code are publicly available, check the results using interactive resource: https://t.co/JtaRUITr0w

[Konstantin Okonechnikov @mad_kook]

https://t.co/W8sRcGrvb8 Glioma myeolid cells are charactarized from single cell multi-omics data analysis, impressive study. NMF method might be most optimal strategy to combine mulitple datasets and avoid batch effects that have such strong impact on single cell data.

[Konstantin Okonechnikov @mad_kook]

Good start of 2025: our manuscript about the search of novel critical genes for ZFTA ependymoma tumors is out! BGN could be a perspective marker in diagnostics. Check the paper for more details: https://t.co/v8ARWYF2vw Thanks to all involved in this project and happy NY :)

[Konstantin Okonechnikov @mad_kook]

Probably main blocking step in the usage of neural network resources for scientific research. Small hint: there is also SciHub.

[Mushtaq Bilal, PhD @MushtaqBilalPhD]

Limitation of Gemini Deep Research:

Gemini can't access full texts of paywalled research papers yet. This may be one of the major limitations holding AI back.

And it's not a limitation in terms of capability but legality and access.

[Konstantin Okonechnikov @mad_kook]

It's only on halloween like this, right? 😅

[Alejo Rodriguez-Fraticelli @AlejoFraticelli]

Ready for halloween!!!! I’m your worst nightmare!!!!

[Konstantin Okonechnikov @mad_kook]

Wow, that's cool news - Nobel prize in chemistry for computational modelling of the proteins ! Glad to see that people from computational biology are also considered as cruicial for sceince. And yes, AlfphaFold2 is super useful, fully deserved prize IMHO https://t.co/XQUtfixXVq

[Konstantin Okonechnikov @mad_kook]

So true, I still have 10 year old linux laptop for some tasks 😂

[🧬Jacob L Steenwyk @jlsteenwyk]

hey, who made this to make fun of me?!
😂🤣😂🤣

[Konstantin Okonechnikov @mad_kook]

@sepp_mari @SimonsFdn @SFARIorg @ZmbhH @kaessmannlab Congratulations!!! 🥳

[Konstantin Okonechnikov @mad_kook]

Was super glad to present at #SpatialOmics24! Conference was awesome, many cool talks. The next main direction in this area seems to be spatial proteomics. Btw, benefit of CNV calling from snATAC as we demonstrated in our study was confirmed in several other presented projects :)

[Konstantin Okonechnikov @mad_kook]

Our study about the deconvolution anlaysis of medulloblastoma Group 3/4 tumors is published, thanks to all authors! Uncovering single cell composition from bulk RNA-seq profiles potentially could be useful for diagnostics, check manuscript for details: https://t.co/qevOgzrUEc

[Konstantin Okonechnikov @mad_kook]

Very perspective project IMHO , crucial for pediatric brain tumors, but of course will require a lot of computational resources, thus I think development of optimal novel algorithms is another imporant part of it https://t.co/dQ4oY2EjCN

[Karsten Rippe @KarstenRippe]

Which of the different spatial transcriptomics (ST) technologies should you use for your research? The lessons we have learnt from comparing RNAscope, Molecular Cartography (MC), Merscope, Xenium and Visium are now on bioRxiv https://t.co/gP2BlT5Fzs 🧵

[Konstantin Okonechnikov @mad_kook]

Tiny boost of study #2: we found that in medulloblastomas the initiating somatic events are large scale chromosomal aberrations, while single oncogene aberrations such as MYC/N amplifcations arise late and typically subclonal! Check both manuscripts for more exciting novelties

[Lena Kutscher @Lena_Kutscher]

I’m excited to share our latest work investigating the underlying biology and tumor mechanisms of Group 3/4 medulloblastoma. Our collaborative team @KiTZ includes Stefan Pfister, @mad_kook, Piyush Joshi, Tamina Stelzer, @VeKoerber

https://t.co/Uku2c28ODg
https://t.co/N6hPrC5ArR

[Konstantin Okonechnikov @mad_kook]

Glad to note that our study focusing on MBENs is out! Would like to high-light identification of unique tumor astroctyes based on CNV profiling and mutation calling from single cell profiles, showing benefits of this data type. Maybe similar exist patterns in other CNS tumors?

[Hopp-Kindertumorzentrum Heidelberg (KiTZ) @KiTZ_HD]

Original publication: Ghasemi D.R., Okonechnikov K. et al. Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage. In: Nature Communications. https://t.co/1UojTcEspL

[Konstantin Okonechnikov @mad_kook]

@sepp_mari Congratulations!!!! 🥳🥳🥳