Grigorios Georgolopoulos
@georgolog.bsky.social
#Bioinformatics team lead by day, dad of two by night, and in between, decoding gene regulation to engineer precision #genetherapy products. You may also see me post about #hematology.
Reposted by Grigorios Georgolopoulos
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
👉Nucleotide dependency analysis of DNA language models reveals genomic functional elements
📅Wed Feb 5, 5:30pm CET
🧬https://kipoi.org/seminar/
🦋kipoizoo.bsky
February 3, 2025 at 4:11 PM
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
👉Nucleotide dependency analysis of DNA language models reveals genomic functional elements
📅Wed Feb 5, 5:30pm CET
🧬https://kipoi.org/seminar/
🦋kipoizoo.bsky
Reposted by Grigorios Georgolopoulos
🚨🚨 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
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
January 29, 2025 at 10:40 AM
🚨🚨 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
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
Reposted by Grigorios Georgolopoulos
If you’re at a European institution and are looking to poach American scientists, this would be a very good week to do it
January 28, 2025 at 8:31 AM
If you’re at a European institution and are looking to poach American scientists, this would be a very good week to do it
Reposted by Grigorios Georgolopoulos
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
January 28, 2025 at 3:58 AM
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
Reposted by Grigorios Georgolopoulos
🧵 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...
There is also this from our own pages. And there will be more (alas!)
www.nature.com/articles/d41...
January 28, 2025 at 6:41 AM
🧵 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...
There is also this from our own pages. And there will be more (alas!)
www.nature.com/articles/d41...
Reposted by Grigorios Georgolopoulos
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/...
...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/...
January 17, 2025 at 9:53 PM
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/...
...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/...
Reposted by Grigorios Georgolopoulos
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/...
www.encodeproject.org/single-cell/...
Single cell – ENCODEHomo sapiens clickable body map
www.encodeproject.org
January 7, 2025 at 9:29 PM
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/...
www.encodeproject.org/single-cell/...
Reposted by Grigorios Georgolopoulos
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/
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/
December 25, 2024 at 11:48 PM
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/
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/
Reposted by Grigorios Georgolopoulos
(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.
November 21, 2024 at 3:24 AM
(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.
Reposted by Grigorios Georgolopoulos
(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.
November 21, 2024 at 3:24 AM
(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.
Reposted by Grigorios Georgolopoulos
(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...
GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors
A long-standing challenge in human regulatory genomics is that transcription factor (TF) DNA-binding motifs are short and degenerate, while the genome is large. Motif scans therefore produce many fals...
www.biorxiv.org
November 21, 2024 at 3:24 AM
(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...
Reposted by Grigorios Georgolopoulos
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/
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/
a little boy is eating a roll of toilet paper
ALT: a little boy is eating a roll of toilet paper
media.tenor.com
November 9, 2024 at 5:03 PM
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/
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/
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!
This post sums it up perfectly!
🧵 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...
In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...
November 18, 2024 at 3:08 PM
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!
This post sums it up perfectly!
Reposted by Grigorios Georgolopoulos
🧵 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...
In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...
November 18, 2024 at 2:48 PM
🧵 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...
In our latest paper, we advocate for improving software quality in bioinformatics through teamwork.
academic.oup.com/bioinformati...
Reposted by Grigorios Georgolopoulos
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...
November 12, 2024 at 11:26 AM
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...
Reposted by Grigorios Georgolopoulos
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.
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.
Extensive binding of uncharacterized human transcription factors to genomic dark matter
Most of the human genome is thought to be non-functional, and includes large segments often referred to as "dark matter" DNA. The genome also encodes hundreds of putative and poorly characterized tran...
www.biorxiv.org
November 13, 2024 at 6:35 PM
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.
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.