Joined November 2022
- Tweets 26
- Following 67
- Followers 37
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3 Photos and videos
Yang Shen retweeted
ST-PARM: Pareto-Complete Inference-Time Alignment for Multi-Objective Protein Design biorxiv.org/content/10.64898… #biorxiv_bioinfo
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Yang Shen retweeted
6 Nov 2025
Today CZI is announcing an unprecedented new scientific initiative to build the future of AI-powered biology. I am joining CZI to lead this initiative as Head of Science, and the EvolutionaryScale team is joining forces with Biohub.
This is the first large scale scientific effort to combine frontier AI and frontier biology.
I feel an incredible sense of optimism in this moment. There is a path to build predictive models of life that can fundamentally accelerate science, and unlock a new understanding of disease.
biohub.org/blog/frontier-ai-…
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11 Dec 2024
We are #hiring for Postdoctoral Associate in AI4Science at Texas A&M University. Message me if you're interested in joining our team. We are attending Conference on Neural Information Processing Systems (NeurIPS 2024) if you would like to meet! #NeurIPS2024
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Yang Shen retweeted
14 Aug 2024
This paper was a collaborative effort from @marinkazitnik @_michellemli @aydin_wells @GysiDeisy @compbiologist @t_m_murali @pedjagogue @sroyyors @BaudotAnais @bozdags @kapil_devkota_ @anthonygitter @sargoshoe @piehiram @Meng_CS @ziynet_ @koyuturkm @jmuiuc @xanderpico @NatasaPrzulj @benjraphael @anna_m_ritz @StructBioinf @profmonasingh @dkslonim @haiyuanyu @ProfMilenkovic
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Yang Shen retweeted
14 Aug 2024
Just published: "Current and future directions in network biology", a comprehensive review by leading experts in the field! Read it here: doi.org/10.1093/bioadv/vbae0… #NetworkBiology #ISCB
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Yang Shen retweeted
19 Sep 2023
.@bozdags, Byung-Jun Yoon, @structbioinf, & I led the section on Machine Learning on Networks w/ contributions from Ziynet Nesibe Kesimoglu & @haiyuanyu. Thanks to @marinkazitnik for tons of input.
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1 Aug 2023
Taking a Deep Dive into Chemical Space, a symposium at #ACSfall2023 biosolveit.de/2023/06/23/acs…
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25 May 2023
It’s great to be back at MPI after almost five years, see many familiar faces again, and hearing great science progress in modeling of protein interactions! #MPI2023
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25 Apr 2023
70 years ago on the day of Apr. 25, a short but revolutionary paper was published. nature.com/articles/171737a0 Let's keep in mind the historic contributions from Watson, Crick, Rosalind Franklin and others. Happy National DNA Day!
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Yang Shen retweeted
19 Apr 2023
Finally, after ~6 years of work, this is published! genomebiology.biomedcentral.…
Thanks to all my co-authors and the participants of the challenge for seeing this through.
3 Aug 2022
At the beginning of 2018 at an @ENCODE_NIH meeting, the idea for the ENCODE Imputation Challenge was born: an open contest to predict genome-wide genomics experiments given fixed train/test sets and encourage development of large-scale imputation methods.
warning: drama 🧵
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15 Feb 2023
Look forward to attending #bps2023 in just a few days! My students will present their works on predicting the effects of protein and noncoding variants. We hope to connect with more experimental researchers on #ProteinDesign!
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16 Feb 2023
@Stephen05485935
- Structure-informed Protein Language Models
Wuwei Tan - Multimodal learning of noncoding variant effects using genome sequence and chromatin structure biorxiv.org/content/10.1101/…
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Yang Shen retweeted
13 Feb 2023
It's frustrating reading comp bio articles these days because many keep falling into the same pitfalls. Hard to know if the method actually works, or whether they messed up the evaluation. Here are some issues I've seen recently (w/o names):
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Yang Shen retweeted
21 Dec 2022
Multimodal learning of noncoding variant effects using genome sequence and chromatin structure biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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Yang Shen retweeted
23 Dec 2022
In two new papers we have found that the ESM2 language model generalizes beyond natural proteins, and enables programmable generation of complex and modular protein structures.
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19 Dec 2022
Great pleasure to introduce a new study on single sequence protein structure prediction rdcu.be/c1Ubu and share my views rdcu.be/c1UbO ! @SpringerNature @NatComputSci
19 Dec 2022
News & Views by Yang Shen nature.com/articles/s43588-0…
👉rdcu.be/c1UbO
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18 Dec 2022
Great perspective on the field of protein structure prediction since #AlphaFold 2 and the winning solutions at #CASP15.
16 Dec 2022
My take on the last year of Protein structure prediction up and including #CASP15 comments are welcome.
[2212.07702] Protein Structure Prediction until CASP15 arxiv.org/abs/2212.07702
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16 Dec 2022
It is interesting to see how the community of protein structure prediction has responded to AlphaFold2 (AF2) (2020-21) while participating in the next competition of #CASP15. The short answer is: "if you can't beat them, join them". But there is more.
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16 Dec 2022
3. Retrain/refine/customize the model. This was done by few groups for now and will be done by more in future. It needs clear rational / loss function, big and clean data, and BIG computing resources.
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16 Dec 2022
4. Embrace the model as part of the protocol. Most are using AF2 as a sampling tool now. One would think that scoring would be a coupled challenge. Yes and no.
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