Amy Weeks
@amyweeks.bsky.social
Asst Prof @ UW-Madison Biochemistry. Protein Engineering, Chemical Biology, Proteomics, Proteases, Enzymology.
A bit late but…Tenured! Immense gratitude for those who got us here. Firstly the students/postdocs (too many to list!) who took a chance on an unproven lab and were unafraid to pursue some strange new ideas. I couldn't have predicted our path, and I couldn’t be more excited for what's next.
Had a lot of fun writing this dispatch article for @currentbiology.bsky.social with PhD student Caitlin Doyle www.sciencedirect.com/science/arti..., highlighting cell morphogenesis and recent work on suctorian growth control principles. 1/3
sciencedirect.com
Had a blast putting this video abstract together with colleagues for @zjmaggiexu.bsky.social story in @currentbiology.bsky.social on how the "vampire cell" P. collini builds the perfect feeding trap 👀. Be sure to check out the full paper: www.cell.com/current-biol... www.youtube.com/watch?v=Ikzm...
A cellular vampire builds the perfect feeding trap / Curr. Biol., June 24, 2026 (Vol. 36, Issue 14)
YouTube video by Cell Press
youtube.com
@zjmaggiexu.bsky.social's story on suctorian trap structure adaptation is now online in @currentbiology.bsky.social , with new evolutionary analyses and modeling! This fall, Maggie will keep exploring predatory protists as a PD in @nbellono.bsky.social group; keep an eye out for her she's amazing!
sciencedirect.com
Scott Coyle@cellraiser.bsky.social · 9mo agoHow do cells adapt morphology to function? In a 🔥 preprint by @zjmaggiexu.bsky.social , with @dudinlab.bsky.social and @amyweeks.bsky.social , we identify a self-organizing single-cell morphology circuit that optimizes the feeding trap structure of the suctorian P. collini. 🧵 tinyurl.com/4k8nv926
Excited to share our new bioRxiv preprint! We introduce RIPPLE, a synthetic platform that couples reaction–diffusion signaling with protein condensation to generate tunable intracellular architectures. Grateful to @zjmaggiexu.bsky.social and @cellraiser.bsky.social. It’s been a rewarding journey.
Scott Coyle@cellraiser.bsky.social · 2mo agoSub-cellular architectures arise through integrating signaling and structure. @edenchang.bsky.social and @zjmaggiexu.bsky.social show how coupling reaction-diffusion signaling to protein condensation provides a tunable, regulatable landscape for sub-cellular structure www.biorxiv.org/content/10.6...
Sub-cellular architectures arise through integrating signaling and structure. @edenchang.bsky.social and @zjmaggiexu.bsky.social show how coupling reaction-diffusion signaling to protein condensation provides a tunable, regulatable landscape for sub-cellular structure www.biorxiv.org/content/10.6...
Now online @pnas.org: We developed a simple, scalable, and accessible platform for deep profiling of phosphoeraser specificity using human phosphoproteome-derived peptide libraries (PhosPropels!) 🧪👩🔬https://www.pnas.org/doi/10.1073/pnas.2523183123
Phosphoproteome-derived peptide libraries for deep specificity profiling of phosphatases and phospholyases | PNAS
Protein phosphorylation is dynamically regulated by the opposing activities of phosphowriter enzymes (kinases) and phosphoeraser enzymes (phosphata...
pnas.org
Thanks to the Ono Pharma Foundation and The University of Chicago for supporting this amazing symposium! And congratulations to the Weeks lab's own Sopo Jalalishvili for winning a poster prize for her work on phospholyases! 👩🔬🧪@uwbiochem.bsky.social
ONO PHARMA FOUNDATION@onoinitiative.bsky.social · 2mo agoGreat momentum at 2026 Chicago Chemical Biology and Therapeutics Symposium, hosted by CCBT at The University of Chicago and Ono Pharma Foundation. Insightful presentations and meaningful interactions drove the success of the meeting. Grateful to all attendees! ccbt.bsd.uchicago.edu/events/
Only 102 public comments so far on the biggest threat to publicly funded science in my lifetime. Please comment if you can. I know this sounds like "vote harder" but we have to keep fighting www.regulations.gov/document/OMB...
Regulations.gov
regulations.gov
Excited to share our lab's latest preprint, led by graduate student Minhee Lee, with contributions from former undergrad Zijing Wang and grad student Andrew Johns! We show that substrate specificity information coupled with AF3 models can be used to design selective tyrosine kinase inhibitors.
bioRxiv Biochemistry@biorxiv-biochem.bsky.social · 3mo agoSubstrate-derived peptides for selective covalent inhibition of protein tyrosine kinases https://www.biorxiv.org/content/10.64898/2026.05.11.724146v1
Excited that our paper on enzymatic bromination of peptides is now online at ACS Chemical Biology! Led by Haley Bridge, we showed that the flavin-dependent halogenase RebH and its variants can be used for late-stage chemoenzymatic diversification of bioactive peptides: pubs.acs.org/doi/10.1021/...
Enzymatic Bromination of Native Peptides for Late-Stage Structural Diversification via Suzuki–Miyaura Coupling
Flavin-dependent halogenases (FDHs) provide a biocatalytic approach for the site-selective halogenation of aromatic compounds, but their use in late-stage functionalization of peptides has remained li...
pubs.acs.org
Super excited that our SEE-CITE photoaffinity labeling method is now out in @natchem.nature.com rdcu.be/ffBSC. Here we introduce a custom silyl ether cleavable linker between a diazirine photocrosslinker handle and molecules of interest to streamline site-of-labeling analysis for PAL chemoproteomics
🚨 excited to share our latest preprint on bioRxiv, led by the soon-to-be Dr. Guy Kunzmann! We tackle a striking case of conditional dependence on UFMylation, a UBL modification pathway whose contributions to cell fitness have been a bit of a "black box." 🧵
bioRxiv Cell Biology@biorxiv-cellbio.bsky.social · 4mo agoDynamic UFMylation governs cellular fitness by coordinating multi-organelle proteostasis https://www.biorxiv.org/content/10.64898/2026.03.27.714830v1
Congratulations to my student Dennis Bolshakov and his coauthors @weix.us, Tommy, and @born2raisecell.bsky.social on making the cover of ACS Synthetic Biology! A great paper and an awesome cover 🥳 pubs.acs.org/doi/10.1021/...
Huge congratulations to my student Rohith Rajasekaran @born2raisecell.bsky.social (now a postdoc in Kole Roybal's lab at UCSF) on being selected for a Weintraub award! Super proud of you and all the work you've done!
Fred Hutch Basic Sciences Division@basicsci.fredhutch.org · 5mo agoHuge congratulations to the recipients of the 2026 Harold M. Weintraub Graduate Student Award! These twelve exceptional graduate students exemplify the bold, creative, and pioneering spirit embodied by Dr. Hal Weintraub. www.fredhutch.org/en/news/rele...
Some excellent preLights to end 2025 🎆 The latest was written by Zhang-He Goh @goh-zhanghe.bsky.social, discussing an enzymatic method for tryptophan-specific bromination described in a recent #preprint from the lab of @amyweeks.bsky.social. #preLight ⬇️ prelights.biologists.com/highlights/e...
Enzymatic bromination of native peptides for late-stage structural diversification via Suzuki-Miyaura coupling - preLights
Ready, set, brominate: RebH and engineered variant for bromination of peptidyl-Trp residues
prelights.biologists.com
New preprint! We found that the flavin-dependent halogenase RebH catalyzes sequence-tolerant Trp bromination in peptides 🧪https://www.biorxiv.org/content/10.64898/2025.12.17.694899v1
New in ACS SynBio: led by Dennis Bolshakov, we used the awesome power of yeast to define how expression levels, noise, and sequence program the dynamics of synthetic protein waves, allowing us to genetically encode new cellular timescales stable over generations! pubs.acs.org/doi/full/10....
Thrilled to share our work on the 🔥 single-celled predator Podophrya collini, which rewires its cell morphology to hunt more efficiently. Huge thanks to our amazing team—Amy, Lauren, Omaya, Marine, Mari, and especially Scott—for making this shine! ✨
Scott Coyle@cellraiser.bsky.social · 9mo agoHow do cells adapt morphology to function? In a 🔥 preprint by @zjmaggiexu.bsky.social , with @dudinlab.bsky.social and @amyweeks.bsky.social , we identify a self-organizing single-cell morphology circuit that optimizes the feeding trap structure of the suctorian P. collini. 🧵 tinyurl.com/4k8nv926
How do cells adapt morphology to function? In a 🔥 preprint by @zjmaggiexu.bsky.social , with @dudinlab.bsky.social and @amyweeks.bsky.social , we identify a self-organizing single-cell morphology circuit that optimizes the feeding trap structure of the suctorian P. collini. 🧵 tinyurl.com/4k8nv926
A beautiful example of how spatiotemporal dynamics can enable multiplexed measurements.
Excited to share our new preprint, which was years in the making! chemrxiv.org/engage/chemr... New reactions are typically developed by trial and error. How can we speed up this process? Read on to learn how we used DNA scaffolding to perform >500,000 parallel reactions on attomole scale. 1/n
DNA-Scaffolded Ultrahigh-Throughput Reaction Screening
Discovering and optimizing reactions is central to synthetic chemistry. However, chemical reactions are traditionally screened using relatively low-throughput methods, prohibiting exploration of diver...
chemrxiv.org
New preprint: we developed a method that uses phosphoproteome-derived peptide libraries (PhosPropels) for deep specificity profiling of phosphatases and phospholyases www.biorxiv.org/content/10.1...
Check out our new manuscript on parallel LC separations! Super cool how the very high scan rates of modern MS systems coupled with DIA can allow us to run several samples at the same time with little loss in depth. Congrats to Noah and the team. #JASMS pubs.acs.org/doi/10.1021/...
SynchroSep-MS: Parallel LC Separations for Multiplexed Proteomics
Achieving high throughput remains a challenge in MS-based proteomics for large-scale applications. We introduce SynchroSep-MS, a novel method for parallelized, label-free proteome analysis that leverages the rapid acquisition speed of modern mass spectrometers. This approach employs multiple liquid chromatography columns, each with an independent sample, simultaneously introduced into a single mass spectrometer inlet. A precisely controlled retention time offset between sample injections creates distinct elution profiles, facilitating unambiguous analyte assignment. We modified the DIA-NN workflow to effectively process these unique parallelized data, accounting for retention time offsets. Using a dual-column setup with mouse brain peptides, SynchroSep-MS detected approximately 16,700 unique protein groups, nearly doubling the peptide information obtained from a conventional single proteome analysis. The method demonstrated excellent precision and reproducibility (median protein %RSDs less than 4%) and high quantitative linearity (median R2 greater than 0.96) with minimal matrix interference. SynchroSep-MS represents a new paradigm for data collection and the first example of label-free multiplexed proteome analysis via parallel LC separations, offering a direct strategy to accelerate throughput for demanding applications such as large-scale clinical cohorts and single-cell analyses without compromising peak capacity or causing ionization suppression.
pubs.acs.org
Excited to share our latest: we engineered the reactivity of a bacterial E1-like enzyme for ATP-driven modification of C termini. Our tool mimics the logic of peptide bond formation in biology for precision modification of proteins in vitro. 🧪https://rdcu.be/ewN7C
Engineered reactivity of a bacterial E1-like enzyme enables ATP-driven modification of protein and peptide C termini
Nature Chemistry - In living systems, ATP provides an energetic driving force for protein synthesis and modification. Now, an engineered enzymatic tool has been developed for high-yield, ATP-driven...
rdcu.be
Great success at the Ono Pharma Foundation Symposium in Boston! Highlights include inspiring talks by Xiao Wang @amyweeks.bsky.social Robert Spitale @stevenbanik.bsky.social @michael-erb.bsky.social Matthew Shoulders Michelle Arkin and a keynote from Chuan He. Posters fueled inspired exchange.
Congrats to Weeks lab graduate student Debashrito Deb @thepeptidetailor.bsky.social, who won a poster prize at the Bioorganic GRC last week! Thanks to conference chairs @doc-jlmeier.bsky.social and Denise Field who knocked it out of the park with a memorable and inspiring meeting this year!
Despite ~20 years in/around #chembio research, I went to my first Bioorganic GRC this week. This community is amazing and so supportive. I feel energized (and tired, lol) and find myself rooting for the next generation of chemical biologists. Sooooo much awesome science - We can’t/won’t be stopped!
The 13th General Meeting of the International Proteolysis Society will be held in Búsios, Brazil Oct 26-30, 2025. Training workshops will be held at the Instituto Oswaldo Cruz Oct 23-23. Register now! Links below. 1/3
excited to share our latest work now online @natmetabolism.nature.com, led by @kyle-flickinger.bsky.social, where we unravel a mechanistic basis for the conditional essentiality of NADK, one of the many interesting hits from our previously reported CRISPR screening with HPLM rdcu.be/ekpu6
