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Next Tuesday, 11/14 @ 4 pm EST we'll have Samuel Stanton and Nate Gruver present: Protein Design with Guided Discrete Diffusion Read the paper: arxiv.org/abs/2305.20009 Zoom links will be sent out via email as per usual, sign up on our website to receive them in your inbox!

Happening tomorrow 11/14 @ 4 pm ET! Sign up on our website to get the zoom link via email or DM us if you want to attend!

We're back for the spring semester! Next Tuesday (Feb 6 @ 4 pm ET), nabil_ibtehaz will present Domain-PFP Read the paper here: nature.com/articles/s4200…… See the full schedule below, and sign up on our website to get Zoom links. DM with any questions! ml4proteinengineering.com/schedule

Exciting new work from our lab describing a novel platform for MHC-II recognition, called TRACeR, that uses just a single loop! Congratulation to Haotian Du, Jingjia Liu, and the team biorxiv.org/content/10.110…

Very excited to share my first paper on TRACeR platform! (and I registered a twitter account for it🫣)

Next Tuesday -- 2/20 @ 4 pm ET -- we'll have Tianhao Yu present enzyme function prediction using contrastive learning! Huimin Zhao Read the paper: science.org/doi/10.1126/sc… Sign up on our website to receive Zoom links via email / DM to join!

Our sequel review paper titled “Sparks of function by de novo protein design” is now out in Nature Biotechnology! Alex Chu Tianyu Lu Full-access link here: rdcu.be/dyJue

Sparks of function by de novo protein design go.nature.com/48jXz1z

Short summary thread of our recent review on de novo protein design: (Poster-sized figure (36 x 48 inches) for printing: drive.google.com/file/d/1sG3OlE…)

Next Tuesday, March 19 @ 4 pm ET, Alexander Kroll will present Enzyme Substrate Prediction, a transformer based model! Read the paper: nature.com/articles/s4146… Sign up on our website to receive Zoom links via email!

Next Tuesday, April 16th @ 4 pm ET we're very excited to have Brian Hie Eric Nguyen present Evo: sequence modeling and design from molecular to genome scale Read the preprint here: biorxiv.org/content/10.110… Sign up on our website to be added to the mailing list to receive Zoom links!

Next Tuesday, 5/07 @ 4 pm EST, we're very excited to have Jeff Ruffolo @stephennaybach from Profluent present OpenCRISPR! Read the paper here: biorxiv.org/content/10.110… Sign up on our website to get the Zoom link via email next week!

Next Tuesday, 5/28 @ 4 pm ET, we'll have Zaixiang Zheng present 'Diffusion Language Models Are Versatile Protein Learners' Read the paper: arxiv.org/pdf/2402.18567 Sign up on our website to receive Zoom details! ml4proteinengineering.com/signup

This week (6/18 @ 4 pm ET) we'll have a trio of speakers Kieran Didi @ICLR Simon Mathis Francisco Vargas present DEFT, finetuning conditional diffusion models, with exciting updates to the previous version Read the new paper: arxiv.org/abs/2406.01781 Sign up/DM to receive Zoom info!

This week's seminar -- tomorrow, 7/02 @ 4 pm ET -- will be on Genie 2 with Yeqing Lin: Designing and Scaffolding Proteins at the Scale of the Structural Universe with Genie 2 Read the paper here: arxiv.org/abs/2405.15489 Sign up to receive Zoom links via email or DM us!

We're looking for 2-3 enthusiastic co-organizers, ideally PhD students. This initiative is a great way to meet other researchers and stay on top of recent work! Please fill out this form if you are interested by July 26 forms.gle/8kuPEDLVsBhPJ9… Email/DM with questions!

This week — tomorrow, 7/15 @ 4 pm ET — we'll have Francesca-Zhoufan Li @ ICLR'25 present a comprehensive evaluation to understand transfer learning for protein language models (PLMs)! Read the paper here: biorxiv.org/content/10.110… Sign up to receive the Zoom link via email or DM us!

Next week, 7/23 @ 4 pm ET, we'll have Roshan Rao EvolutionaryScale present ESM3: Simulating 500 million years of evolution with a language model! Read the paper here: biorxiv.org/content/10.110… Sign up on our website to receive Zoom info via email!

A framework for evaluating how well generative models of protein structure match the distribution of natural structures. Possu Huang Lab

Super excited to be closing out this semester’s Berkeley BioML Seminar on Monday 4/28 with a talk from Tianyu Lu on SHAPES, a framework that addresses key limitations in computational protein design evals, helping us generate more viable structures! lu.ma/j1aby8wq