@GenomeDataLab

Computational biology @UCPH_Research/@IRBBarcelona: genetics & evolution of tumors & human populations. #ERC, #HorizonEU, #NNF, #DCS, #DFF funded. PI @FranSupek

 Copenhagen & Barcelona
GenomeDataLab.org/
Joined June 2017
  • Tweets398
  • Following23
  • Followers951
Congrats to our CRISPy fresh doctor 👏👏 Marcel McCullough for successfully defending his PhD thesis: 🧬✂️Combinatorial Gene Editing in Human Cells to Model Deficiencies of DNA Repair in Cancer Thx to committee members @CeronLab @LValleResearch and @DSzuts for great discussion!
1
3
8
509
Double PhD defense day in the lab 🤩 Congrats to our dr. Guille Palou @gpaloumarquez, fresh from the oven 🎊🥳 and similarly so our newly-minted dr. Ignasi Toledano @IgnasiToledano! Amazing defense both, bravo 👏👏
1
4
1
10
1,700
The youngsters from lab are at @EMBLEvents DNA Replication symposium #EESreplication 🧬 Our alumna dr. Marina @msalvadoresf and PhD Marcell @MarcellVeiner gave talks on their recent work 👏-- identifying DNA replication origins by mutation patterns and neural nets🤖
4
11
1,586
📃"Joint inference of mutational signatures from indels and single-nucleotide substitutions reveals prognostic impact of homologous recombination deficiency in tumors" 🔗researchsquare.com/article/r… (3/3)
3
143
This "multimodal" approach extracts a cleaner SBS3, a tricky but important mut sig ➡️splits into SBS3a and SBS3b, based on indels ➡️cleaner link w/ BRCA2 variants ➡️strongly predicts survival in 4 cohorts of ovarian cancer (incl @deciderproject) (2/3) 👇Check out our preprint:
1
1
201
❓Want to learn an easy trick to improve your mutational signatures? ‼️Extract them from SNV and indel mutations jointly! A study by our Patricia F. @pferrert now online, focusing on HR deficiency signature SBS3🧬 Here is a TL;DR for you 👇 (1/3)
1
7
1
21
1,550
.@FranSupek presented Marina's @msalvadoresf study on large-scale mutation risk in cancer genomes ➡️nature.com/articles/s43018-0… at the Nobel Minisymposium No. 60 "Somatic mutation in aging" in Stockholm. Thanks to organizers for inviting! – at Stockholm, Sweden
1
1
9
1,392
First 3 doctoral theses #PhDone from our GenomeDataLab, and all 3 receiving the "cum laude" qualification! 🎊 👏👏👏 to David @davidmasp, Elizaveta B. and Marina @msalvadoresf, the 3 genomics musketeers! You rock! – at Barcelona, Spain
1
1
16
1,057
🔥🔥BRIC group leader positions (incl associate professorship or full professorship at @UCPH_Research, a leading 🇪🇺 uni) - broad search - interests: stem cell, neuro, cancer - core funded position - top-notch science - collaborative workplace Join us! ➡️tinyurl.com/BRICgroupleader
Fran Supek
@FranSupek10 Jan 2024
📢assoc prof & full professor positions! We at the BRIC @UCPH_BRIC -- a premier biomedical research centre in Denmark -- are recruiting new Group Leaders ✅vibrant environment ✅great colleagues ✅🔝 funding ecosystem ✅quality of life in Cph Join us!➡️ candidate.hr-manager.net/App…

160867 Professor or Associate Professor Research Group Leader(s) to the Biotech Research and...

candidate.hr-manager.net
1
3
1,823
📜4/4 The David @davidmasp preprint Mutation rate heterogeneity at the sub-gene scale due to local DNA hypomethylation. biorxiv.org/content/10.1101/… ~fin~
Watercolor painting of a DNA double helix unwinding and revealing segments of its structure. Brightly colored patches symbolize areas of hypomethylation, and hovering above are cloud-like structures representing mutation rate heterogeneity.

ALT Watercolor painting of a DNA double helix unwinding and revealing segments of its structure. Brightly colored patches symbolize areas of hypomethylation, and hovering above are cloud-like structures representing mutation rate heterogeneity.

1
180
📜3/4 The Marina @msalvadoresf preprint: Cell cycle alterations associate with a redistribution of mutation rates across chromosomal domains in human cancers. biorxiv.org/content/10.1101/…
Vector graphic of a circular cell cycle chart, with arrows indicating progression. Surrounding the chart are chromosomal segments with fluctuating graphs showing mutation rates. Icons for DNA damage and repair processes emphasize the association.

ALT Vector graphic of a circular cell cycle chart, with arrows indicating progression. Surrounding the chart are chromosomal segments with fluctuating graphs showing mutation rates. Icons for DNA damage and repair processes emphasize the association.

1
2
195
📜2/4 The Ignasi @IgnasiToledano preprint: Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules. biorxiv.org/content/10.1101/…
Photo of a scientist in a laboratory, intently studying a computer screen that displays the effects of various small molecules on pathogenic stop codon readthrough. There are 3D models of molecules, graphs of their effectiveness, and highlighted regions of the genome.

ALT Photo of a scientist in a laboratory, intently studying a computer screen that displays the effects of various small molecules on pathogenic stop codon readthrough. There are 3D models of molecules, graphs of their effectiveness, and highlighted regions of the genome.

1
112
Some cool hallucinations by the new 🤖DALL-E 3, inspired by biorxiv preprints from the lab: 📜1/4. The Liza preprint: Copy number losses of oncogenes and gains of tumor suppressor genes generate common driver events of human cancer. biorxiv.org/content/10.1101/…
Oil painting style visualization of a balance scale. On one side, oncogenes are represented by dimming light bulbs, indicating their loss. On the other side, shields symbolizing tumor suppressor genes are piling up, showcasing their gains.

ALT Oil painting style visualization of a balance scale. On one side, oncogenes are represented by dimming light bulbs, indicating their loss. On the other side, shields symbolizing tumor suppressor genes are piling up, showcasing their gains.

1
1
7
2,233
🍕GenomePizzaLab! Cheers Javi @jlanillos! – at Barcelona, Spain
Team members from the Genome Data Science laboratory at IRB Barcelona having pizza.

ALT Team members from the Genome Data Science laboratory at IRB Barcelona having pizza.

Team members from the Genome Data Science laboratory at IRB Barcelona having pizza.

ALT Team members from the Genome Data Science laboratory at IRB Barcelona having pizza.

16
2,079
👩‍🔬By focusing the analysis on somatic CNA two-hit events, we can identify more driver genes relevant to a specific tumor type. Similarly so by focussing on known 🔥hotspot mutations. This could lead to more targeted & effective treatments for patients. #PrecisionMedicine
1
265
😱Surprisingly, CNA gains in tumor suppressor genes also boost positive selection. (mutant allele gets amplifed⬆️⬆️) 🧬Thus two-hit events involving point mutations & CNA can universally "upgrade" #cancer driver genes, regardless of the type of copy number variant.
1
1
152
🤯We show increased positive selection on oncogene mutations with both CNA gains and however similarly so with CNA deletions! ✂️Removing the wild-type OG allele benefits the tumor. This extends conventional understanding of how 🧬CNAs influence cancer evolution. #Genomics
1
1
161
We have delved into the complex world of genetic #interactions, particularly what happens when point mutations & copy number alterations (CNAs) affect the same gene. Somatic CNAs are very common and so such 2⃣ "two-hit" events are important for understanding tumorigenesis.
1
2
331
✂️🧬Aleix @aleixbayona presents his (combinatorial!) gene editing study on DNA repair genes using CRISPR/Cas12 🧫 We model mutational processes (incl from chemotherapy💊) in ovarian+lung cancer cells #ismbeccb2023 – at Lyon, France
5
28
2,366
Load more