Join us for our next Kipoi Seminar with with Pedro Tomaz da Silva @pedrotomazdasilva.bsky.social @gagneurlab.bsky.social @TU_Muenchen!
👉Nucleotide dependency analysis of DNA language models reveals genomic functional elements
📅Wed Feb 5, 5:30pm CET
🧬https://kipoi.org/seminar/
🦋kipoizoo.bsky
🚨🚨 MEGA JOB ALERT 🚨🚨
Independent Group Leader Positions in Computational Biology @humantechnopole.bsky.social!
Are you ready to start your own lab? Do you know someone who is? Repost this + share with everyone who might want to know about it. Thanks!!! 🙏
More details below... check it out! 🧵 1/3
If you’re at a European institution and are looking to poach American scientists, this would be a very good week to do it
American science and medicine has been thrown into chaos and uncertainty over the past week. Here are some stories to get up to speed. 1/12
🧵 A chilling compilation of news reports that reads almost like science fiction…
There is also this from our own pages. And there will be more (alas!)
www.nature.com/articles/d41...
Venn diagram illustrating microbial diversity of bacteria and archaea captured by isolates, metagenome-assembled genomes (MAGs) from NCBI and IMG, and metagenomes from IMG. A large portion of microbial diversity, labeled as 'Microbial Dark Matter,' represents species not captured by isolates or MAGs. Image modified from https://www.science.org/doi/10.1126/sciadv.adq2166
Genomes assembled from #metagenomes (a.k.a. MAGs) are awesome and have revolutionized our ability to study uncultivated microbes
...BUT: they still don't capture a lot of the 🦠 species that are out there
New @jgi.doe.gov paper led by Dongying Wu and Natalia Ivanova: www.science.org/doi/10.1126/...
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
Our ChromBPNet preprint out!
www.biorxiv.org/content/10.1...
Huge congrats to Anusri! This was quite a slog (for both of us) but we r very proud of this one! It is a long read but worth it IMHO. Methods r in the supp. materials. Bluetorial coming soon below 1/
Example alternative usage of ZF arrays
Example alternative usage of ZF arrays
Example alternative usage of ZF arrays
Summary of ZF alternative usage patterns
(12/n) When we applied RCADEEM to the GHT-SELEX data, we saw that not some, but in fact most of the TFs from the C2H2-ZF family use alternative sets of their ZF domains to bind to different DNA molecules.
Example GHT-SELEX peak
(6/n) Applying GHT-SELEX/MAGIX on 179 TFs, most of which were previously uncharacterized, we found that the majority do bind to the genome with high specificity, forming "peaks" that resemble those seen in vivo using ChIP-seq.
(1/n) What better way to start posting on Bluesky than to share our recent preprint, in collaboration with @timhughesto.bsky.social, on characterization of the intrinsic DNA binding specificities of 179 human transcription factors using a new assay, GHT-SELEX: www.biorxiv.org/content/10.1...
An 18 month old boy presents to your office for a well child visit.
Parents have no concerns but do mention that he eats a lot of paper.
You astutely decide to check a CBC and iron studies but wonder why iron deficiency causes this strange symptom?
#skeetorial #medsky 🧵
1/
Maybe so. Didn't look into it thoroughly tbh. Just noticed the intersection query which is one of the primary features of BEDOPS. Thanks for sharing it!
Thank you for being a advocate!
It always feels that bionformaticians are both a blessing and a curse when it comes to tool development. They come up with brilliant methods and implementations but tools lack all the support and robustness, often leading to giving up on the tools you love.
This post sums it up perfectly!
Illustration comparing the improvement process in software writing to rock climbing.
🧵 Bioinformatics faces a critical challenge: despite its importance, software quality often falls short due to the lack of proper development practices.
In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...
Ziga Avsec (Google DeepMind), Julien Gagneur (TU Munich), Tanja Kortemme (UCSF), David Kelley (Calico), Ben Lehner (Sanger), Franca Fraternali (UCL), Oliver Stegle (EMBL/DKFZ), and Amos Tanay (Weizmann)
Looking forward to the Inaugural Symposium of the Center for AI & Computational Biology vib.ai with a great line-up of speakers at the interface of AI & biology: D. Kelley, J. Gagneur, Z. Avsec, T. Kortemme, B. Lehner, F. Fraternali, A. Tanay & O. Stegle (20Nov) www.vibconferences.be/events/vibai...
Incredible resource for DNA binding protein specificity from the Codebook consortium.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Am reading these in detail & will have a lot to say. Stay tuned for thoughts.
