@structbioinf

Educator and Researcher in Artificial Intelligence - Biological Intelligence Tweets are my own. RTs are not endorsements.

 Cambridge MA
Joined November 2022
  • Tweets26
  • Following67
  • Followers36
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ST-PARM: Pareto-Complete Inference-Time Alignment for Multi-Objective Protein Design biorxiv.org/content/10.64898… #biorxiv_bioinfo
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Congratulations to Yihong for his first conference presentation, just three months into his Ph.D. program! 🎉 Thank you CAGI7 @CAGInews and @NIH for sponsoring the travel fellowship and nurturing the next generation of scientific trainees. #CAGI #NIH #Genomics #VariantEffect #AI
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Yang Shen retweeted
Alex Rives
@alexrives6 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-…

Launching the first large-scale scientific initiative combining frontier AI with frontier biology...

The large-scale scientific effort combines frontier AI with frontier biology to accelerate discovery and solve disease.

biohub.org
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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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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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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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.@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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Taking a Deep Dive into Chemical Space, a symposium at #ACSfall2023 biosolveit.de/2023/06/23/acs…

ACS Fall Symposium "Taking a Deep Dive into Chemical Space" • BioSolveIT

We are pleased to announce an upcoming ACS symposium that will delve into the exploration of chemical spaces. This symposium is set to take place during

biosolveit.de
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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 – at Kansas, USA
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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!

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

Nature - The determination in 1953 of the structure of deoxyribonucleic acid (DNA), with its two entwined helices and paired organic bases, was a tour de force in X-ray crystallography. But more...

nature.com
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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.

The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of...

Genome Biology - A promising alternative to comprehensively performing genomics experiments is to, instead, perform a subset of experiments and use computational methods to impute the remainder....

link.springer.com
Jacob Schreiber@jmschreiber913 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 🧵 1/
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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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@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/…

Multimodal learning of noncoding variant effects using genome sequence and chromatin structure

Motivation A growing amount of noncoding genetic variants, including single-nucleotide polymorphisms (SNPs), are found to be associated with complex human traits and diseases. Their mechanistic...

biorxiv.org
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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
Santiago
@svpino6 Jan 2023
11 ways ChatGPT saves me hours of work every day, and why you'll never outcompete those who use AI effectively. A list for those who write code: 1 of 16
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Multimodal learning of noncoding variant effects using genome sequence and chromatin structure biorxiv.org/cgi/content/shor… #biorxiv_bioinfo
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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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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
Nature Computational Science@NatComputSci19 Dec 2022
Replying to @NatComputSci
News & Views by Yang Shen nature.com/articles/s43588-0… 👉rdcu.be/c1UbO

Predicting protein structure from single sequences

Nature Computational Science - As artificial intelligence begins to profoundly impact structural biology, one of the next challenges is to predict protein structures from individual sequences...

nature.com
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Great perspective on the field of protein structure prediction since #AlphaFold 2 and the winning solutions at #CASP15.
Arne Elofsson @arneelof.bsky.social@arneelof16 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

Protein Structure Prediction until CASP15

In Dec 2020, the results of AlphaFold2 were presented at CASP14, sparking a revolution in the field of protein structure predictions. For the first time, a purely computational method could...

arxiv.org
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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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more replies
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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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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