Principal Investigator, Bioinformatics, NBACC https://xitter.cf/t.co/vIen8soRi2 PhDone @JohnsHopkins @JHUBME in the Salzberg Lab
Baltimore, MD
Joined December 2014
- Tweets93
- Following208
- Followers231
- Likes237
Markus Sommer retweeted
Check out our just-published AI-based (temporal convolutional network) system, PSAURON, for predicting eukaryotic proteins, from @markusjsommer. We used a similar method in BALROG, our bacterial gene finder. Note: the "P" is silent in PSAURON π€£ academic.oup.com/nargab/artiβ¦
βOne Model to rule them all, One Model to find them, One Model to score them all, and in the Paper cite them.β π§¬π§ββοΈThe eye of PSAURON seeks spurious proteins in your genome annotation! New paper with Aleksey Zimin and @StevenSalzberg1 biorxiv.org/content/10.1101/β¦
Closed source code? 10 free predictions per day? That seems a bit too evil, even for a dark lord. Unleash the power of PSAURON via βpip install psauronβ Code freely available at GitHub github.com/salzberg-lab/PSAUβ¦
Markus Sommer retweeted
Three @biorxivpreprint releases from my lab last week, and one more today! From postdoc @markusjsommer, his new eukaryotic gene recognizer, PSAURON (the "p" is silent), a successor to his bacterial gene finder Balrog #LOTR biorxiv.org/content/10.1101/β¦
Mystery disease decimating coral reefs off the coast of Florida? Sounds like a job for @JakobHeinz9 and novel metagenomics methods in the @StevenSalzberg1 lab, with guidance from Stephanie Rosales & Lindsay Huebner! Check out the paper! biorxiv.org/content/10.1101/β¦
Thank you to the @NatlAquarium Animal Care and Rescue Center for raising awareness of coral disease. This collaboration would not have happened without the tour I took in Oct. 2022 (shout-out to Duncan!)
Markus Sommer retweeted
How does alternative splicing regulate protein structure to enable cell-type-specific protein functions? With @momeara, we used AlphaFold2 + scRNA-seq to investigate this question in our latest preprint. biorxiv.org/content/10.1101/β¦π§΅
Markus Sommer retweeted
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 @elapertea @av_sparrow @thesteinegger @markusjsommer @ErdogduBeril @IliaMinkin and others: genomebiology.biomedcentral.β¦
Markus Sommer retweeted
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 @KuanHaoChao below.
π’π’Dear friends, our new software, Splam, a deep learning-based splice junction predictor, is now officially releasedπIf you do RNA-Seq data analysis or need a reliable tool to evaluate splice junctions/introns, Splam is the perfect fit for you
π github.com/Kuanhao-Chao/splaβ¦
(1/10)
Markus Sommer retweeted
ORFanage is new system by @av_sparrow @ErdogduBeril and @elapertea that finds protein-coding regions in RNA-seq assemblies, guided by annotation. Just published today in @NatComputSci:
rdcu.be/dibEl
Markus Sommer retweeted
Accurate DTU detection in complex diseases with SPIT by @ErdogduBeril,@stephaniehicks,@StevenSalzberg1,@elapertea! Findings include previously unreported DTU events in 6 genes associated with schizophrenia. Also available on Google Colab -> Learn more at biorxiv.org/content/10.1101/β¦
Markus Sommer retweeted
ORFanage is new system by @av_sparrow @ErdogduBeril and @elapertea 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/10.1101/β¦
Markus Sommer retweeted
I am thrilled to share our Han1 assembly in the @GeneticsGSA journal G3, with @StevenSalzberg1, @elapertea, and @AlekseyZimin5. Itβs a great way to start 2023!
doi.org/10.1093/g3journal/jkβ¦
first paper of 2023 for us: a gap-free, fully annotated genome of a southern Han Chinese individual, led by @KuanHaoChao, with @AlekseyZimin5 and @elapertea. We used the #T2T CHM13 genome to fill gaps academic.oup.com/g3journal/aβ¦
Markus Sommer retweeted
first paper of 2023 for us: a gap-free, fully annotated genome of a southern Han Chinese individual, led by @KuanHaoChao, with @AlekseyZimin5 and @elapertea. We used the #T2T CHM13 genome to fill gaps academic.oup.com/g3journal/aβ¦
Markus Sommer retweeted
The final version of our paper on using protein structure to determine functionality is out in @eLife: doi.org/10.7554/eLife.82556. Some of the prettiest figures we've had in any recent paper, like the one here. Led by @markusjsommer, plus @elapertea @thesteinegger et al.
Markus Sommer retweeted
Our paper describing our new, greatly improved human genome annotation is just out in preprint form, by @av_sparrow @elapertea @markusjsommer @ErdogduBeril @IliaMinkin @KuanHaoChao @JakobHeinz9 @alaina_shumate @thesteinegger @park_sukhwan et al. biorxiv.org/content/10.1101/β¦
Markus Sommer retweeted
Congrats! It was the most amazing talk on biodata2022! I hope it makes more people go for isoform specific transcriptomic analyses
Markus Sommer retweeted
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!
One of the most exciting papers I've been a part of for years, led by @markusjsommer, on how protein structure prediction yields dramatic insights into gene functions. With @thesteinegger @elapertea @av_sparrow @IliaMinkin et al. doi.org/10.7554/eLife.82556 @eLife
Markus Sommer retweeted
Protein structure prediction helps understand gene function
One of the most exciting papers I've been a part of for years, led by @markusjsommer, on how protein structure prediction yields dramatic insights into gene functions. With @thesteinegger @elapertea @av_sparrow @IliaMinkin et al. doi.org/10.7554/eLife.82556 @eLife