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Protein structure prediction helps understand gene function

Markus gave an excellent talk (the last of the meeting) at #biodata22 on this work. It's very exciting, and I'm glad to see it published now. I look forward to reading the paper!

Steven Salzberg 💙💛 Markus Sommer @thesteinegger Mihaela Pertea Ales Varabyou @IliaMinkin eLife - the journal Congrats! It was the most amazing talk on biodata2022! I hope it makes more people go for isoform specific transcriptomic analyses

Our paper describing our new, greatly improved human genome annotation is just out in preprint form, by Ales Varabyou Mihaela Pertea Markus Sommer Beril Erdogdu @IliaMinkin Kuan-Hao Chao Jakob Heinz Alaina Shumate, PhD @thesteinegger Sukhwan Park et al. biorxiv.org/content/10.110…

The final version of our paper on using protein structure to determine functionality is out in eLife - the journal: doi.org/10.7554/eLife.…. Some of the prettiest figures we've had in any recent paper, like the one here. Led by Markus Sommer, plus Mihaela Pertea @thesteinegger et al.

first paper of 2023 for us: a gap-free, fully annotated genome of a southern Han Chinese individual, led by Kuan-Hao Chao, with Aleksey Zimin and Mihaela Pertea. We used the #T2T CHM13 genome to fill gaps academic.oup.com/g3journal/adva…

I am thrilled to share our Han1 assembly in the Genetics Society of America journal G3, with Steven Salzberg 💙💛, Mihaela Pertea, and Aleksey Zimin. It’s a great way to start 2023! doi.org/10.1093/g3jour…

ORFanage is new system by Ales Varabyou Beril Erdogdu and Mihaela Pertea that finds protein-coding regions in gene annotation, esp. in RNA-seq assemblies. See what it can do in our new preprint biorxiv.org/content/10.110…

Accurate DTU detection in complex diseases with SPIT by Beril Erdogdu,Stephanie Hicks, PhD,Steven Salzberg 💙💛,Mihaela Pertea! Findings include previously unreported DTU events in 6 genes associated with schizophrenia. Also available on Google Colab -> Learn more at biorxiv.org/content/10.110…

watch out SpliceAI, there's a new kid on the block, Splam! More accurate at predicting splice sites and much faster too. Check out the code and the pre-print in the thread from Kuan-Hao Chao below.

ORFanage is new system by Ales Varabyou Beril Erdogdu and Mihaela Pertea that finds protein-coding regions in RNA-seq assemblies, guided by annotation. Just published today in Nature Computational Science: rdcu.be/dibEl

Our paper on the human gene annotation catalog CHESS, which now includes all of MANE and a more rigorous definition of genes of all types. With Mihaela Pertea Ales Varabyou @thesteinegger Markus Sommer Beril Erdogdu @IliaMinkin and others: genomebiology.biomedcentral.com/articles/10.11…

How does alternative splicing regulate protein structure to enable cell-type-specific protein functions? With Matthew O’Meara, we used AlphaFold2 + scRNA-seq to investigate this question in our latest preprint. biorxiv.org/content/10.110…🧵

Three bioRxiv releases from my lab last week, and one more today! From postdoc Markus Sommer, his new eukaryotic gene recognizer, PSAURON (the "p" is silent), a successor to his bacterial gene finder Balrog #LOTR biorxiv.org/content/10.110…

Check out our just-published AI-based (temporal convolutional network) system, PSAURON, for predicting eukaryotic proteins, from Markus Sommer. We used a similar method in BALROG, our bacterial gene finder. Note: the "P" is silent in PSAURON 🤣 academic.oup.com/nargab/article…