Omar Kamileen

Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.

Multimodal learning enables chat-based exploration of single-cell data - @bocklab.bsky.social @cemm.oeaw.ac.at @meduniwien.ac.at go.nature.com/3WPGJnW

How to write your paper like a page turner Working my way through scientific articles I often lose my focus.

Tension, suspense, or narrative arc in a story is the stuff that keeps the reader going. But how do you introduce suspense in a scientific article? That is what my latest post is all about.
aboutacademicwritingandzo.substack.com/p/how-to-wri...

#AcademicWriting #WritingTips #NarrativeArc #Suspense

Growth-coupled microbial biosynthesis of the animal pigment xanthommatin - Nature Biotechnology A growth-coupled biosynthetic pathway enables xathommatin synthesis in the soil bacterium Pseudomonas putida.

www.nature.com/articles/s41... Really fabulous work! Animal pigments engineered in bacteria.

Binary vector copy number engineering improves Agrobacterium-mediated transformation - Nature Biotechnology Agrobacterium-mediated transformation of plants and fungi is enhanced by plasmid copy number variants.

Agrobacterium-mediated transformation of plants and fungi is enhanced by plasmid copy number variants go.nature.com/3CdewQS
rdcu.be/eNaje

Excited to see our paper online! We combined scMS and scRNA-seq from the same plant cells 🌱 — a step toward true single-cell multi-omics in plants.
Overview 👇

Discovery and engineering of the biosynthesis of rotenoids - Nature Synthesis Rotenoids are natural insecticides from Fabaceae plants. Here the complete biosynthetic pathway to make rotenoids is elucidated in Amorpha fruticosa and Tephrosia vogelii, revealing a unique Fe(II)-de...

Discovery and engineering of the biosynthesis of rotenoids www.nature.com/articles/s44... @natsynth.nature.com

Discovery of iridoid cyclase completes the iridoid pathway in asterids - Nature Plants Iridoids are terpenoid metabolites found in thousands of plants. Using single-cell transcriptomics, the authors discovered an unexpected enzyme that has been neofunctionalized to catalyse the cyclization required to form the iridoid scaffold.

Very exciting to finally see our iridoid cyclase ICYC online @natplants.nature.com!
A joined effort with Robin Buell’s lab with Josh Wood generating snRNA-seq, and my student Chloée Tymen performing the initial experiment.
#natprod
#PlantScience
@mpi-ce.bsky.social
www.nature.com/articles/s41...

Mapping multi-substrate specificity of Arabidopsis aminotransferases Nature Plants - Systematic characterization of Arabidopsis aminotransferase family enzymes uncovered many previously unrecognized activities and revealed their multi-substrate specificity, aspects...

Our new study in Nature Plants maps how "multi-tasking" enzymes in plants transfer nitrogen, a key step toward improving crop N use efficiency. 🌱

Big thanks to our collaborators from Max Planck, Hokkaido Univ, & MSU, and for support from @NSF and @DOE.

Learn more: rdcu.be/eFOFN

#PlantMetabolism

Discovery of homoharringtonine pathway enzymes reveals a whole plant model for coordinated biosynthesis Plants have evolved to produce diverse molecules that inhibit protein translation. A lead example is homoharringtonine (HHT), both a key tool for ribosomal profiling and an FDA-approved treatment for ...

Beautiful work by Yaereen and former lab member Kevin! Learn more about the anti-cancer compound homoharringtonine and its'biosynthesis in plants here 🌿https://www.biorxiv.org/content/10.1101/2025.08.26.672243v1

The multilayered regulation of aromatic amino acid biosynthesis in plants The shikimate and aromatic amino acid (AAA) biosynthetic pathways are crucial for the production of L-phenylalanine (Phe), L-tyrosine (Tyr), and L-tryptophan (Trp), as well as vitamins, hormones, and ...

The multilayered regulation of aromatic amino acid biosynthesis in plants: Trends in Biochemical Sciences www.cell.com/trends/bioch...

Discovery happens less when you're trying to be the expert and more when you're trying to be the learner.

Protein Structural Phylogenetics Abstract. Protein structural phylogenetics is an interdisciplinary branch of molecular evolution that (i) uses 3D structural data to trace evolutionary his

Protein Structural Phylogenetics academic.oup.com/gbe/article/...

Into natural product biosynthesis & tailoring enzymes? Frustrated by the lack of a dedicated resource to explore their functions? Tired of endless literature searches for reaction info? Meet the MITE database, freely available at mite.bioinformatics.nl. Preprint: doi.org/10.26434/che... (1/8)

Natural molecular glues spur next-gen small molecules for ‘undruggable’ targets - Nature Biotechnology Inspired by natural molecular glues, drug hunters are chasing protein–protein interactions with next-gen small molecules tuned for enhanced tissue specificity and reduced toxicity.

Inspired by natural molecular glues, drug hunters are chasing protein–protein interactions with next-gen small molecules tuned for enhanced tissue specificity and reduced toxicity www.nature.com/articles/s41...
rdcu.be/eAC91

Couldn't have said it better! Great job @taralowensohn.bsky.social, Will, and Chun! Special thanks to the Gao lab at @stanford.edu #singlecell #plantbiology

A truly enabling new approach by @taralowensohn.bsky.social Will Cody and @sattelylab.bsky.social to probe plant genetics at scale.

Single-gene-per-cell delivery coupled to an effective transcriptional selection system

www.biorxiv.org/content/10.1...

Identification of BAHD‐acyltransferase enzymes involved in ingenane diterpenoid biosynthesis The plant family Euphorbiaceae is an abundant source of structurally complex diterpenoids, many of which have reported anticancer, anti-HIV, and anti-inflammatory activities. Among these, ingenol-3-...

Ingenane biosynthesis enzymes in @newphyt.bsky.social by @matildeflorean.bsky.social, @carstenschotte.bsky.social from @oconnorlab.bsky.social @mpi-ce.bsky.social in collaboration with Ian Graham lab members.
#natprod
#PlantScience

doi.org/10.1111/nph....

Enzymatic epimerization of monoterpene indole alkaloids in kratom - Nature Chemical Biology Monoterpene indole alkaloids are formed via a 3S stereoselective condensation between secologanin and tryptamine. Here the authors uncover the mechanism of epimerization behind uncommon 3R-containing ...

Here, the authors @oconnorlab.bsky.social @mpi-ce.bsky.social uncover the mechanism of epimerization behind uncommon 3R-containing alkaloids in Mitragyna speciosa (Kratom) and study their inclusion in downstream biosynthesis #PlantScience #natprod

www.nature.com/articles/s41...

A SynBio explosion: a whole new world for Rubisco engineering This article comments on:Archer J, Kathpalia M, Lee B, Li S, Wang T. 2025. Effects of chaperone selectivity on the assembly of plant Rubisco orthologs in E

SynBio: it’s what plants crave
doi.org/10.1093/jxb/...
J Exp Bot Insights article from *Dan Hong Loh* - she discusses the impacts of Rubisco SynBio tool expansions from Archer et al. 2025 (doi.org/10.1093/jxb/...).

Streamlining experimental setups A new software tool called Heron helps researchers to design and run complex experimental systems without needing in-depth technical expertise.

Heron is a new intuitive software tool that helps researchers design complex experiments even if they don’t have in-depth technical expertise.
🔗

July Issue. Read FREE: Sequencing historical RNA: unrealized potential to increase understanding of the plant tree of life (see cover); Decoding the evolution of C4 photosynthesis; Transcellular regulation of ETI-induced cell death; & much more
www.cell.com/trends/plant...
#plantscience

Psilocybin delays aging, extends lifespan, new Emory study suggests | Emory University | Atlanta GA Emory University researchers identified that psilocin, a byproduct of consuming psilocybin, the active ingredient in psychedelic mushrooms, actively delays aging in cells and organisms.

Researchers @emoryuniversity.bsky.social observe #longevity benefit of #psilocybin #psychedelic mushroom

news.emory.edu/stories/2025...

— extended human skin & lung cell lifespan by 50%
— increase aged mice survival by 30%
— reduces oxidative stress
— improves DNA repair

🧪 #health #science #aging

blog.addgene.org Tips and Tricks for Using Golden Gate Modular Cloning (MoClo)

Want to become a cloning wizard? 🪄
Our latest blog post is packed with hands-on tips for mastering Modular Cloning — advice on how to prepare for the process, handle reagents, high-throughput methods, and more.
Start your MoClo quest here:
https://twp.ai/4io9Rn

Yes when I was on the board of @cornelluniversity.bsky.social the women profs told us exactly this..and even moreso for the minority profs: minority students flocked to them as role models to ask for mentoring and advice, taking time away from the Prof's own research #womeninscience #womeninstem

This is figure 2 showing how SNAP-tag engineering is aiming for faster and brighter fluorescence labeling

SNAP-tag is a widespread tool for labelling protein for bioimaging. An article published in Nature Chemical Biology presents SNAP-tag2 with increased labelling kinetics and brightness, which translates into a better performance in live-cell super-resolution imaging. go.nature.com/46fMIZd 🧪

'Night science' is what you do when you're not sure what's the question.

Defining and benchmarking open problems in single-cell analysis - Nature Biotechnology Nature Biotechnology - Defining and benchmarking open problems in single-cell analysis

Defining and benchmarking open problems in single-cell analysis - @krishnaswamylab.bsky.social @fabiantheis.bsky.social bit.ly/4l8dsiF

Broad application of the ALFA tagging technology for in planta nanobody-based imaging and biochemical characterization of plant proteins #resource #PlantCommunications cell.com/plant-commun...

In situ foliar augmentation of multiple species for optical phenotyping and bioengineering using soft robotics A soft robotic gripper enables nondestructive delivery of nanosensors and genes into leaves of diverse plant species.

www.science.org/doi/10.1126/...

Robots for precision agroinfiltration. Really cool engineering effort with the biology in mind 👍🏾

A composite universal DNA signature for the tree of life. #DNAbarcoes #DNAsignatures #GenomeSequencing @natecoevo.nature.com
www.nature.com/articles/s41...