We have developed a new freely available web app for analyzing CRISPR screen data based on the script we published in Henkel et al., and datasets from DepMap.
More info and tutorials will follow, but in the meanwhile test it out here: https://correlate.cmm.se/
Videos are found here
This series covers analysis of CRISPR screen data using different free online tools – no coding required. From processing MAGeCK and DepMap data to exploring STRING-db, g:Profiler, Enrichr, geneMANIA, ImmGen, Human Protein Atlas (HPA), cBioPortal, ChatGPT, and vibe-coding GSEA, the series shows how to turn gene lists into biological insights. Although focused on CRISPR screens, all tutorials are equally applicable to other omics datasets such as RNA-seq or proteomics.
See https://greenlisted.cmm.se/ as well as the linked publication:
CRISPR J. 2025 Jun;8(3):216-223. doi: 10.1089/crispr.2025.0023. Epub 2025 May 7.
Esbjörn Henkel 1, Zhaojun Li 1, Daniel Uvehag 1, Bernhard Schmierer 2, Martin Henkel 3, Fredrik Wermeling 1
Custom CRISPR screens are powerful tools for rapid, hypothesis-driven discovery, but their design is often complex and time-consuming. Green Listed v2.0 simplifies this process with an intuitive workflow for designing custom CRISPR spacer libraries and supports downstream analysis for all users, irrespective of their computational experience. The web application features a user-friendly graphical interface freely accessible at https://greenlisted.cmm.se. Version 2.0 includes significant upgrades to the original 2016 version that were implemented based on user feedback. This includes a new gene synonym tool, expanded library options, optimized output lists, performance improvements, and linked scripts for the rational design of custom CRISPR screen gene sets.
Thanks everyone involved for making the CRISPR symposium organized by Bernhard Schmierer and I such a success!
151 participants and fantastic presentations from:
Tuuli Lappalainen, NY Genome Center and KTH Stockholm
John Doench, Broad MIT, US
Randall Platt, ETH Zürich, CH
Douglas Ross-Thriepland, AZ and CRUK Functional Genomics Centre, Cambridge, UK
Jacob Corn, ETH Zürich, CH
Neville Sanjana, New York Genome Center, US
Eric Shifrut, University of Tel Aviv, IL
Yumeng Mao, Uppsala University
Magdalena Strauss, EBI, Cambridge, UK
Pia Johansson, Lund University
Jennifer Stott, IDT
Zofia Świątczak, Synthego
Alexander Espinosa, Karolinska Institutet
Verónica Rendo, Uppsala University
Jenna Persson, MOMA Tx, Boston, US
Linnea Kristenson, University of Gothenburg
Guido Alessandro Baselli, SciLifeLab and Karolinska Institutet
Generous support provided by SciLifeLab, Cancerfonden, PhenoTarget, Synthego, IDT, Countage, Parse Biosciences, BioNordika, and Singleron Biotech.
The plasmid modified by Dr. Sudeepta Panda has recived a Blue Flame Award (https://www.addgene.org/blue-flame-award/)
The plasmid can be found here: http://addgene.org/137729/)
https://bioicons.com/ with extensions for e.g. Incscape.
Another resource of free science illustrations: https://smart.servier.com/
A great achievement and milestone!
Super proud of the work by Vaishnavi Iyer developing antisense oligonucleotides to modulate T-cell activation. Great collaboration with labs at Karolinska Institutet and NTU, Singapore.
As always, the linked soundtrack: https://tinyurl.com/mr2avjs6
Paper: https://www.sciencedirect.com/science/article/pii/S0896841122000658
This award will allow us to continue and intensify our CRISPR-based studies to identify novel drug targets to overcome cancer drug resistance.
https://www.cancerfonden.se/forskning/for-forskare/samtliga-anslagsbeslut
The Wermeling lab 