@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
3Media
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
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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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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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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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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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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