Pasquali Lab Journal Club - Pasquali-lab/LabEvents GitHub Wiki
- Send a copy of the article you'll be talking about (at least the Monday before) to all other members of the Journal Club.
- Prepare a simple presentation explaining the paper1. Highlight what you like and what you diseagree with.
- The scheduled day, you will present the paper and we'll have a discussion about it later. Mandatory to ask at least one question to stimulate the discussion!
| Date | Presenter | Paper | Links | Status |
|---|---|---|---|---|
| 26th January 2022 14:00 | Beatriz Pérez | CRISPR-based genome editing in primary human pancreatic islet cells | Paper | ✔️ |
| 9th February 2022 14:00 | Marc Subirana | Genome-wide profiling in colorectal cancer identifies PHF19 and TBC1D16 as oncogenic super enhancers | Paper | ✔️ |
| 23rd February 2022 14:00 | Mireia Ramos | Non-coding somatic mutations converge on the PAX8 pathway in ovarian cancer | Paper | ✔️ |
| 9th March 2022 14:00 | Georgina Fuentes | Interpreting type 1 diabetes risk with genetics and single-cell epigenomics | Paper | ✔️ |
| Date | Presenter | Paper | Links | Status |
|---|---|---|---|---|
| 20th October 2021 10AM | Beatriz Pérez | Immune-evasive human islet-like organoids ameliorate diabetes | Paper | ✔️ |
| 3rd November 2021 10AM | Marc Subirana | Large organized chromatin lysine domains help distinguish primitive from differentiated cell populations | Paper | ✔️ |
| 17th November 2021 10AM | Mireia Ramos | Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states | Paper | ✔️ |
| 1st December 2021 14:30 PM | Georgina Fuentes | Type 1 diabetes risk genes mediate pancreatic beta cell survival in response to proinflammatory cytokines | Paper | ✔️ |
| Date | Presenter | Paper | Links | Status |
|---|---|---|---|---|
| 26th May 2021 11AM | Marc Subirana | Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci | Paper | ✔️ |
| 9th June 2021 10AM | Beatriz Pérez | Modeling Type 1 Diabetes In Vitro Using Human Pluripotent Stem Cells | Paper | ✔️ |
| 22nd June 2021 10AM | Mireia Ramos | Enhancer release and retargeting activates disease-susceptibility genes | Paper | ✔️ |
Sungalee, S., Liu, Y., Lambuta, R.A. et al. Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci. Nat Genet 53, 650–662 (2021). https://doi.org/10.1038/s41588-021-00842-x- Lee, C.A., Abd-Rabbo, D. & Reimand, J. Functional and genetic determinants of mutation rate variability in regulatory elements of cancer genomes. Genome Biol 22, 133 (2021). https://doi.org/10.1186/s13059-021-02318-x
- Emanuele Bosi, Piero Marchetti, Guy A. Rutter, Decio L. Eizirik. The gene signatures of human alpha cells in types 1 and 2 diabetes indicate disease-specific pathways of alpha cell dysfunction. bioRxiv 2022.02.22.481528; doi: https://doi.org/10.1101/2022.02.22.481528
- Fasolino, M., Schwartz, G.W., Patil, A.R. et al. Single-cell multi-omics analysis of human pancreatic islets reveals novel cellular states in type 1 diabetes. Nat Metab 4, 284–299 (2022). https://doi.org/10.1038/s42255-022-00531-x
Chiou, J., Geusz, R.J., Okino, ML. et al. Interpreting type 1 diabetes risk with genetics and single-cell epigenomics. Nature (2021). https://doi.org/10.1038/s41586-021-03552-w
- Wigger, L., Barovic, M., Brunner, AD. et al. Multi-omics profiling of living human pancreatic islet donors reveals heterogeneous beta cell trajectories towards type 2 diabetes. Nat Metab (2021). https://doi.org/10.1038/s42255-021-00420-9
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Oh, S., Shao, J., Mitra, J. et al. Enhancer release and retargeting activates disease-susceptibility genes. Nature (2021). https://doi.org/10.1038/s41586-021-03577-1 -
Pachano, T., Sánchez-Gaya, V., Ealo, T. et al. Orphan CpG islands amplify poised enhancer regulatory activity and determine target gene responsiveness. Nat Genet (2021). https://doi.org/10.1038/s41588-021-00888-x
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Crispatzu, G., Rehimi, R., Pachano, T. et al. The chromatin, topological and regulatory properties of pluripotency-associated poised enhancers are conserved in vivo. Nat Commun 12, 4344 (2021). https://doi.org/10.1038/s41467-021-24641-4
- Hua, P., Badat, M., Hanssen, L.L.P. et al. Defining genome architecture at base-pair resolution. Nature (2021). https://doi.org/10.1038/s41586-021-03639-4
- Wang, X., Xu, J., Zhang, B. et al. Genome-wide detection of enhancer-hijacking events from chromatin interaction data in rearranged genomes. Nat Methods 18, 661–668 (2021). https://doi.org/10.1038/s41592-021-01164-w
[1]: Yes Marc, the whole paper.