Kevin Drew
@ksdrew.bsky.social
Assistant Professor at University of Illinois at Chicago (UIC) in Biological Sciences focused on macromolecular assemblies.
Pinned
Kevin Drew
@ksdrew.bsky.social
· Jul 29
DirectContacts2: A network of direct physical protein interactions derived from high-throughput mass spectrometry experiments
Cellular function is driven by the activity proteins in stable complexes. Protein complex assembly depends on the direct physical association of component proteins. Advances in macromolecular structur...
www.biorxiv.org
We are excited to share our preprint describing DirectContacts2! Here we develop a machine learning model to discriminate between direct and indirect protein interactions. We use our model to construct a highly accurate wiring diagram of the human cell.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Kevin Drew
Modern biology research is biased towards investigating genes that are widely conserved and present in humans. What about genes that ARE widely conserved but NOT present in humans? Can genes missing from humans tell us something about what makes our biology different from that of other animals? 1/8
December 31, 2025 at 7:29 PM
Modern biology research is biased towards investigating genes that are widely conserved and present in humans. What about genes that ARE widely conserved but NOT present in humans? Can genes missing from humans tell us something about what makes our biology different from that of other animals? 1/8
Reposted by Kevin Drew
I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests.
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Know when to co-fold'em
This is the official web page for the James Fraser Lab at UCSF.
fraserlab.com
December 29, 2025 at 10:25 PM
I'm really excited to break up the holiday relaxation time with a new preprint that benchmarks AlphaFold3 (AF3)/“co-folding” methods with 2 new stringent performance tests.
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Thread below - but first some links:
A longer take:
fraserlab.com/2025/12/29/k...
Preprint:
www.biorxiv.org/content/10.6...
Reposted by Kevin Drew
RFpeptides made it to the cover of Nature Chemical Biology December issue!
Credit to Stephen Rettie for leading the work and making this very cool graphic!
Credit to Stephen Rettie for leading the work and making this very cool graphic!
Our December issue is live!
www.nature.com/nchembio/vol...
The cover depicts a diffusion-based generative deep learning pipeline for de novo design of a macrocyclic peptide targeting the protein, myeloid cell leukemia 1
www.nature.com/nchembio/vol...
The cover depicts a diffusion-based generative deep learning pipeline for de novo design of a macrocyclic peptide targeting the protein, myeloid cell leukemia 1
December 3, 2025 at 10:58 PM
RFpeptides made it to the cover of Nature Chemical Biology December issue!
Credit to Stephen Rettie for leading the work and making this very cool graphic!
Credit to Stephen Rettie for leading the work and making this very cool graphic!
Reposted by Kevin Drew
Very happy to share our latest led by the relentless @shawnfayer.bsky.social! We developed multiplexed assays to measure variant effects across diverse genetic and cell contexts in stem cell and differentiated cells. 🧵 👇
The effects of genetic variants primarily occur in differentiated cells meaning we need to access these cell types to measure variant effects for most disease genes. We developed saturation genome editing in stem cells (iPSC-SGE) to enable phenotyping in diverse genetic and cell contexts at scale!
Editing stem cell genomes at scale to measure variant effects in diverse cell and genetic contexts
Multiplexed assays of variant effect (MAVEs) systematically measure variant function but have been limited to cancer cell lines rather than disease-relevant cell types. We developed saturation genome ...
www.medrxiv.org
November 22, 2025 at 5:08 PM
Very happy to share our latest led by the relentless @shawnfayer.bsky.social! We developed multiplexed assays to measure variant effects across diverse genetic and cell contexts in stem cell and differentiated cells. 🧵 👇
Reposted by Kevin Drew
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
November 19, 2025 at 9:16 PM
New preprint! We measured temperature- and pH-induced aggregation for over 18,000 natural and de novo designed protein domains!
Reposted by Kevin Drew
Congratulations to the newly minted Dr. Brittney Voigt! After defending a fantastic thesis spanning work in my lab and the @edwardmarcotte.bsky.social lab.
November 19, 2025 at 2:03 AM
Congratulations to the newly minted Dr. Brittney Voigt! After defending a fantastic thesis spanning work in my lab and the @edwardmarcotte.bsky.social lab.
Reposted by Kevin Drew
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Proteome-wide in silico screening for human protein-protein interactions
Protein-protein interactions (PPIs) drive virtually all biological processes, yet most PPIs have not been identified and even more remain structurally unresolved. We developed a two-step computational...
biorxiv.org
November 12, 2025 at 9:26 PM
Thrilled to share that the final piece of my PhD work is now on bioRxiv! biorxiv.org/content/10.1... With support from @nvidia and the @NSF, we used AlphaFold to screen 1.6M+ protein pairs, revealing thousands of potential novel PPIs. All data can be viewed at predictomes.org/hp
Reposted by Kevin Drew
Last week, the research of Rui Gao and lab was published by
@Science.org and featured on the issue's cover! Dr. Rui Gao is an Assistant Professor in Biological Sciences and Chemistry.
science.org/doi/10.1126/...
@Science.org and featured on the issue's cover! Dr. Rui Gao is an Assistant Professor in Biological Sciences and Chemistry.
science.org/doi/10.1126/...
A new method called VIPS enables organ-wide nanoscale reconstruction for quantitative mapping of connectivity and molecular landscape in intact tissue.
Learn more this week in Science: https://scim.ag/4n4GKPm
Learn more this week in Science: https://scim.ag/4n4GKPm
October 23, 2025 at 4:14 PM
Last week, the research of Rui Gao and lab was published by
@Science.org and featured on the issue's cover! Dr. Rui Gao is an Assistant Professor in Biological Sciences and Chemistry.
science.org/doi/10.1126/...
@Science.org and featured on the issue's cover! Dr. Rui Gao is an Assistant Professor in Biological Sciences and Chemistry.
science.org/doi/10.1126/...
Reposted by Kevin Drew
The Gao lab at #UIC reports a breakthrough in volumetric fluorescence imaging, featured on the cover of Science Magazine!
Their new technique, VIPS (Volumetric Imaging via Photochemical Sectioning), enables reconstruction of 3D images of whole tissues with unprecedented detail.
Their new technique, VIPS (Volumetric Imaging via Photochemical Sectioning), enables reconstruction of 3D images of whole tissues with unprecedented detail.
October 16, 2025 at 10:27 PM
The Gao lab at #UIC reports a breakthrough in volumetric fluorescence imaging, featured on the cover of Science Magazine!
Their new technique, VIPS (Volumetric Imaging via Photochemical Sectioning), enables reconstruction of 3D images of whole tissues with unprecedented detail.
Their new technique, VIPS (Volumetric Imaging via Photochemical Sectioning), enables reconstruction of 3D images of whole tissues with unprecedented detail.
Reposted by Kevin Drew
#Wolbachia has puzzled scientists with its power to rewire insect reproduction. What if I tell you that we found one of the keys Wolbachia use to rewire its host AND a small molecule inhibitor uses this key to mimic what this microbe has mastered for millions of years.
www.cell.com/cell-reports...
www.cell.com/cell-reports...
Beyond Wolbachia—Can a small molecule control insect reproduction?
Kaur et al. demonstrate reduced histone acetylation as a key mechanism underpinning
Wolbachia’s paternal-effect embryonic lethality trait in Drosophila melanogaster.
Recapitulation of this trait by in...
www.cell.com
October 3, 2025 at 12:58 PM
#Wolbachia has puzzled scientists with its power to rewire insect reproduction. What if I tell you that we found one of the keys Wolbachia use to rewire its host AND a small molecule inhibitor uses this key to mimic what this microbe has mastered for millions of years.
www.cell.com/cell-reports...
www.cell.com/cell-reports...
Reposted by Kevin Drew
Congrats Qian www.science.org/doi/full/10....
www.science.org
September 29, 2025 at 1:19 PM
Congrats Qian www.science.org/doi/full/10....
Reposted by Kevin Drew
I am excited to share our new preprint on the CAGE complex, a mysterious hollow protein complex that I first saw years ago while surveying Tetrahymena ciliary lysate www.biorxiv.org/content/10.1... #cilia #protistsonsky 🧬🧪
September 23, 2025 at 5:08 PM
I am excited to share our new preprint on the CAGE complex, a mysterious hollow protein complex that I first saw years ago while surveying Tetrahymena ciliary lysate www.biorxiv.org/content/10.1... #cilia #protistsonsky 🧬🧪
Reposted by Kevin Drew
Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...
10 Rules for a Structural Bioinformatic Analysis
The Protein Data Bank (PDB) is one of the richest open‑source repositories in biology, housing over 277,000 macromolecular structural models alongside much of the experimental data that underpins thes...
chemrxiv.org
September 11, 2025 at 2:28 PM
Structural bioinformatics is incredibly powerful on its own or when paired with theory or experiment. One of the PDB's superpowers isn’t from one structure, but comparing many to uncover folds, binding sites, and subtle conformational shifts. chemrxiv.org/engage/chemr...
Excited for you to join us!
Excited to share that I’ll be joining @uicbios.bsky.social as an Asst. Prof. in Jan 2026! My lab will explore the epi/genetic principles of host–microbe interactions, symbiosis, and vector biology. We’ll be hiring postdocs and techs—details and lab website coming soon!
bios.uic.edu/news-stories...
bios.uic.edu/news-stories...
Meet the Faculty | Biological Sciences | University of Illinois Chicago
bios.uic.edu
September 10, 2025 at 1:37 AM
Excited for you to join us!
Reposted by Kevin Drew
🚨The Bits to Binders Competition has concluded!🧬
One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors
Spoiler: They work!
One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors
Spoiler: They work!
September 2, 2025 at 2:45 PM
🚨The Bits to Binders Competition has concluded!🧬
One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors
Spoiler: They work!
One year ago we gathered scientists from around the world to design and submit protein binders that cause immune cells to target and eliminate CD20+ tumors
Spoiler: They work!
Reposted by Kevin Drew
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
August 27, 2025 at 4:14 PM
Exciting to see our protein binder design pipeline BindCraft published in its final form in @Nature ! This has been an amazing collaborative effort with Lennart, Christian, @sokrypton.org, Bruno and many other amazing lab members and collaborators.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Kevin Drew
Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Scaling down protein language modeling with MSA Pairformer
Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...
biorxiv.org
August 5, 2025 at 6:31 AM
Excited to share work with
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org
biorxiv.org/content/10.1...
TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵
We are excited to share our preprint describing DirectContacts2! Here we develop a machine learning model to discriminate between direct and indirect protein interactions. We use our model to construct a highly accurate wiring diagram of the human cell.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
DirectContacts2: A network of direct physical protein interactions derived from high-throughput mass spectrometry experiments
Cellular function is driven by the activity proteins in stable complexes. Protein complex assembly depends on the direct physical association of component proteins. Advances in macromolecular structur...
www.biorxiv.org
July 29, 2025 at 8:58 PM
We are excited to share our preprint describing DirectContacts2! Here we develop a machine learning model to discriminate between direct and indirect protein interactions. We use our model to construct a highly accurate wiring diagram of the human cell.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Kevin Drew
‼️🚨Preprint alert! 🚨‼️
Excited to have some of my first works as a postdoc, and first corresponding author (!!), on biorxiv! This was a fun side quest of a project marrying a few things I deeply love, development, cilia, and hormones in the pituitary! Happy reading!
www.biorxiv.org/content/10.1...
Excited to have some of my first works as a postdoc, and first corresponding author (!!), on biorxiv! This was a fun side quest of a project marrying a few things I deeply love, development, cilia, and hormones in the pituitary! Happy reading!
www.biorxiv.org/content/10.1...
Primary cilia and BBS4 are required for postnatal pituitary development
Primary cilia orchestrate several signaling pathways, and their disruption results in pleiotropic disorders called ciliopathies. Bardet Beidl syndrome (BBS), one such ciliopathy, provides insights int...
www.biorxiv.org
July 19, 2025 at 5:58 PM
‼️🚨Preprint alert! 🚨‼️
Excited to have some of my first works as a postdoc, and first corresponding author (!!), on biorxiv! This was a fun side quest of a project marrying a few things I deeply love, development, cilia, and hormones in the pituitary! Happy reading!
www.biorxiv.org/content/10.1...
Excited to have some of my first works as a postdoc, and first corresponding author (!!), on biorxiv! This was a fun side quest of a project marrying a few things I deeply love, development, cilia, and hormones in the pituitary! Happy reading!
www.biorxiv.org/content/10.1...
Reposted by Kevin Drew
1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬
www.science.org/doi/full/10....
www.science.org/doi/full/10....
June 24, 2025 at 4:52 PM
1/27 We have a new paper out! Turns out that snowflake yeast have been hiding a secret from us - they've evolved a (very!) crude circulatory system. Not with blood vessels or a heart, but through spontaneous fluid flows powered by their metabolism. 🧪🔬
www.science.org/doi/full/10....
www.science.org/doi/full/10....
Reposted by Kevin Drew
BioEmu now published in @science.org !!
What is BioEmu? Check out this video:
youtu.be/LStKhWcL0VE?...
What is BioEmu? Check out this video:
youtu.be/LStKhWcL0VE?...
July 10, 2025 at 6:57 PM
BioEmu now published in @science.org !!
What is BioEmu? Check out this video:
youtu.be/LStKhWcL0VE?...
What is BioEmu? Check out this video:
youtu.be/LStKhWcL0VE?...
Reposted by Kevin Drew
Cilia Alert! So excited to finally have this paper on the CPLANE complex out in @natcomms.nature.com! We show that RSG1 is a human ciliopathy protein and links CPLANE to the transition zone. 1/n
www.nature.com/articles/s41...
www.nature.com/articles/s41...
The human ciliopathy protein RSG1 links the CPLANE complex to transition zone architecture - Nature Communications
The CPLANE complex is essential for ciliogenesis, and mutations to all but one subunit have been associated with ciliopathies. Here they identify three familial mutations in the final subunit, RSG1, t...
www.nature.com
July 1, 2025 at 5:22 PM
Cilia Alert! So excited to finally have this paper on the CPLANE complex out in @natcomms.nature.com! We show that RSG1 is a human ciliopathy protein and links CPLANE to the transition zone. 1/n
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Kevin Drew
Reposted by Kevin Drew
@bmoore-beth.bsky.social We are delighted to announce that Dr. Teresa O'Meara was awarded the Henry Russel award at U-M. Our highest honor for an early-mid career faculty member for her outstanding research and teaching! @teresaomeara.bsky.social @umichmicroimmuno.bsky.social
June 16, 2025 at 8:03 PM
@bmoore-beth.bsky.social We are delighted to announce that Dr. Teresa O'Meara was awarded the Henry Russel award at U-M. Our highest honor for an early-mid career faculty member for her outstanding research and teaching! @teresaomeara.bsky.social @umichmicroimmuno.bsky.social
Reposted by Kevin Drew
New lab preprint - Delora Baptista tested AlphaFold 2 and 3 for the prediction of structures of host-pathogen interactions and then applied these to study convergence of binding and molecular mimicry in host-pathogen vs. host-host interactions.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
AlphaFold models of host-pathogen interactions elucidate the prevalence and structural modes of molecular mimicry
Pathogens exploit host cellular machinery through protein-protein interactions (PPIs), often using molecular mimicry to hijack host cellular processes. While there have been thousands of host-pathogen...
www.biorxiv.org
June 9, 2025 at 6:58 AM
New lab preprint - Delora Baptista tested AlphaFold 2 and 3 for the prediction of structures of host-pathogen interactions and then applied these to study convergence of binding and molecular mimicry in host-pathogen vs. host-host interactions.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...