https://www.romerolab.org/news-1 daily 0.75 2024-08-23 https://www.romerolab.org/news-1/nishit-banka-successfully-defends-his-thesis monthly 0.5 2024-08-23 https://www.romerolab.org/news-1/juan-diaz-successfully-defends-thesis monthly 0.5 2024-08-23 https://www.romerolab.org/news-1/chase-sarah-and-petes-manuscript-published-in-nature-communications monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/a36155c7-3bbf-4f02-bd1b-74fc77915792/Extra_NN.png News - Chase, Sarah, and Pete’s Manuscript Published in Nature Communications - Make it stand out Abstract Machine learning (ML) has transformed protein engineering by constructing models of the underlying sequence-function landscape to accelerate the discovery of new biomolecules. ML-guided protein design requires models, trained on local sequence-function information, to accurately predict distant fitness peaks. In this work, we evaluate neural networks’ capacity to extrapolate beyond their training data. We perform model-guided design using a panel of neural network architectures trained on protein G (GB1)-Immunoglobulin G (IgG) binding data and experimentally test thousands of GB1 designs to systematically evaluate the models’ extrapolation. We find each model architecture infers markedly different landscapes from the same data, which give rise to unique design preferences. We find simpler models excel in local extrapolation to design high fitness proteins, while more sophisticated convolutional models can venture deep into sequence space to design proteins that fold but are no longer functional. We also find that implementing a simple ensemble of convolutional neural networks enables robust design of high-performing variants in the local landscape. Our findings highlight how each architecture’s inductive biases prime them to learn different aspects of the protein fitness landscape and how a simple ensembling approach makes protein engineering more robust. DOI: https://doi.org/10.1038/s41467-024-50712-3 https://www.romerolab.org/news-1/lab-moving-to-duke-university-in-august monthly 0.5 2024-08-23 https://www.romerolab.org/news-1/blog-post-title-one-6pepl monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/17886914-7bb6-41fe-9387-e6db80496f86/Jacob_SDL.png News - Jacob's work on self-driving labs is published in inaugural issue of Nature Chemical Engineering! - Make it stand out https://www.natsure.com/articles/s44286-023-00002-4 https://www.romerolab.org/news-1/blog-post-title-one-6pepl-rmwdx monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/1724350597216-1L6ME5ZYS731Z4RX05GV/WSF4.jpg News - Romero Lab participates in the Wisconsin Science Festival! https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/1724350597405-XE65OQU96U1TXENCUITH/WSF3.jpg News - Romero Lab participates in the Wisconsin Science Festival! https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/1724350599310-6WAW4FO304HRCD766JKH/WSF2.jpeg News - Romero Lab participates in the Wisconsin Science Festival! https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/1724350600410-SX0JQXQEHCHOFS8QIRME/WSF1.jpeg News - Romero Lab participates in the Wisconsin Science Festival! https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3 monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/8428843d-c7fe-4669-b9b4-4940ae58f77f/journal.pcbi.1010956.g003.jpg News - Sameer and Emily's paper on ML from directed evolution data is published in PLoS Comp Biology! - Make it stand out https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010956 https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6 monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/0eff81c4-d5cf-4c12-ac6e-a644ec5c79ad/ACE2.png News - Pete's paper engineering ACE2 as a protein therapeutic is published Protein Science - Make it stand out https://onlinelibrary.wiley.com/doi/10.1002/pro.4597 https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be monthly 0.5 2024-08-23 https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be-fxx9a monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/8aabc8b5-7e86-4053-8e23-8f89dce80833/Graphical%2BAbstract%2Bv1_blue-01.jpg News - Leland's paper developing molecular SNP detection methods is published in Cell Reports Methods! - Make it stand out https://www.sciencedirect.com/science/article/pii/S2667237522001114?via%3Dihub https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be-fxx9a-j9dnk monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/59140eb3-6f01-421f-bc44-1fab4145fe59/ML4PE.png News - Chase and Sarah's review on ML-guided protein engineering is published in Curr Opin Biotech! - Make it stand out https://www.sciencedirect.com/science/article/pii/S0958166922000465?via%3Dihub https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be-fxx9a-j9dnk-w5ysl monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/cfb578fe-fa14-45f9-b86c-5dd7f556a587/IMG_1679.jpeg News - Farewell to Leland, Hridindu, and Jonathan! - Make it stand out The first wave of Romero Lab PhD students. It’s been a fun ride and best of luck with the new positions! https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be-fxx9a-j9dnk-w5ysl-7x2yj monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/d3fc9166-48f7-466f-97c0-05207a549c7a/Jonathan.jpg News - Congrats to Jonathan for an awesome PhD defense! - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be-fxx9a-j9dnk-w5ysl-7x2yj-far4x monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/1f5dfa6d-55ee-4509-b7aa-ebe4d9b6d4f4/Defense_Jonathan_maybe.jpg News - Congrats to Hridindu for successfully defending his PhD thesis! - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be-fxx9a-j9dnk-w5ysl-7x2yj-far4x-lyj9j monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/10b8a102-e8a9-4845-9c61-3e73876b42d3/CDD.png News - Congrats to Hridindu for publishing his caspase deep mutational scanning work in Cell Death Discovery - Make it stand out https://www.nature.com/articles/s41420-021-00799-0 https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be-fxx9a-j9dnk-w5ysl-7x2yj-far4x-lyj9j-zt28t monthly 0.5 2024-08-23 https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be-fxx9a-j9dnk-w5ysl-7x2yj-far4x-lyj9j-zt28t-gemhc monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/612cc876-d10a-4572-a111-38adefe26d59/pnas.202104878fig01.jpg News - Our deep learning collaboration with Tony Gitter is published in PNAS! - Make it stand out https://www.pnas.org/doi/full/10.1073/pnas.2104878118 https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be-fxx9a-j9dnk-w5ysl-7x2yj-far4x-lyj9j-zt28t-gemhc-4tkd4 monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/564c4455-7d82-4590-b942-55db3671827f/Jonathen_Metabolic.png News - Jonathan's work engineering acyl-ACP reductases is published in Nature Communications! - Make it stand out https://www.pnas.org/doi/full/10.1073/pnas.2104878118 https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be-fxx9a-j9dnk-w5ysl-7x2yj-far4x-lyj9j-zt28t-gemhc-4tkd4-dbpt8 monthly 0.5 2024-08-22 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/88f1896f-ff2e-4379-9d81-c2089f66fcce/WARF.jpg News - We've received funding through the WARF Accelerator program to commercialize Leland's microfluidic single-cell analysis methods - Make it stand out https://biochem.wisc.edu/news/2021/news-phil-romero-warf-accelerator-award-2021-08-03 https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be-fxx9a-j9dnk-w5ysl-7x2yj-far4x-lyj9j-zt28t-gemhc-4tkd4-dbpt8-flya3 monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/efe956f4-e51c-41b1-a326-48cfed63d653/website_fig-01.png News - Leland's work on single-cell gene expression profiling is published in Nucleic Acids Research! - Make it stand out https://academic.oup.com/nar/article/49/18/e103/6316829?login=true https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be-fxx9a-j9dnk-w5ysl-7x2yj-far4x-lyj9j-zt28t-gemhc-4tkd4-dbpt8-flya3-673lg monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/3387e693-7f78-4ffd-9b6d-75b58558729d/Symbol.jpg News - Our collaborative project to produce carbon-negative fuels and chemicals led by Brian Pfleger was funded by ARPA-E! - Make it stand out Press release: https://arpa-e.energy.gov/news-and-media/press-releases/us-department-energy-invests-35-million-dramatically-reduce-carbon https://www.romerolab.org/news-1/blog-post-title-one-6pepl-9h5p3-863e6-sh9be-fxx9a-j9dnk-w5ysl-7x2yj-far4x-lyj9j-zt28t-gemhc-4tkd4-dbpt8-flya3-673lg-kc6ky monthly 0.5 2024-08-23 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/fae7e014-f075-4c1b-a092-d33b5b317d46/ACE2-spike.gif News - Pete's paper mapping ACE2 interactions with SARS-CoV-2 is published in PLoS One! - Make it stand out https://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0251585 https://images.squarespace-cdn.com/content/v1/66989691b854426c895ce7ca/5202cdac-b05e-4066-8e0f-f33fc2c1c060/Progress.png News - Pete's paper mapping ACE2 interactions with SARS-CoV-2 is published in PLoS One! - Make it stand out Whatever it is, the way you tell your story online can make all the difference. 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