Daniel Zhu
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Daniel Zhu

Molecular Biologist

Research

Spateo: Spatiotemporal modeling of molecular holograms

November 11th, 2024, Cell
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Related: Mapping cells through space and time with moscot

Introduces multi-omics single-cell optimal transport (moscot), a scalable framework for optimal transport in single-cell genomics. This can be used to align mouse cells across space and time.

Related: A single-cell time-lapse of mouse prenatal development from gastrula to birth

This study established a single-cell atlas spanning 12.4 million nuclei from 83 embryos, precisely staged at 2- to 6-hour intervals spanning late gastrulation, annotating hundreds of cell types.

Defining the determinants of protection against SARS-CoV-2 infection and viral control in a dose-down Ad26. CoV2. S vaccine study in nonhuman primates

May 2nd, 2022, PLoS Biology
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Related: Compromised Humoral Functional Evolution Tracks with SARS-CoV-2 Mortality

One of the first papers to deeply study the serological correlates of SARS-CoV-2 infection, finding IgG class switching timing to be very important.

Related: Selective functional antibody transfer into the breastmilk after SARS-CoV-2 infection

A study of the extent, assessed from serological measurements, to which anti-SARS-CoV-2 immunity is transferred via breastmilk.

Microtubule growth rates are sensitive to global and local changes in microtubule plus-end density

August 3rd, 2020, Current Biology
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Related: Changes in cytoplasmic volume are sufficient to drive spindle scaling

This study used a similar experimental setup to investigate the determinants of mitotic spindle sizing.

Related: Dynamic instability of microtubule growth

The seminal study by Mitchison & Kirschner that established microtubules as dynamic structures.

Reprogramming Factors Activate a Non-Canonical Oxidative Resilience Pathway that Can Rejuvenate RPEs and Restore Vision

September 1st, 2025, bioRxiv (preprint)
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Related: Reprogramming to recover youthful epigenetic information and restore vision

A landmark paper in the aging optics field from Yuancheng, the first to show that OSK expression in mouse retinal ganglion cells can reverse vision loss.

Related: Spatial transcriptomic clocks reveal cell proximity effects in brain ageing

A study that uses my favorite assays, spatial transcriptomics, to study neighborhood effects on neuronal aging.

Projects

Project Screenshot
🐍python
Spateo
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A bioinformatics platform. Spateo is a 3D spatiotemporal modeling framework that enables the creation of molecular holograms of whole embryos, allowing for the study of organ ecology at a molecular level in 3D space over time. Spateo enables scalable, partial, non-rigid alignment, multi-slice refinement, and mesh correction to construct 3D holograms from sequential 2D slices. It also introduces digitization methods to uncover multi-level biology from subcellular to whole organ, identifying expression gradients along arbitrary axes. It models intercellular communication to identify genes downstream of cell-cell interaction. Lastly, Spateo introduces "morphometric vector fields" of cell migration and integrates spatial differential geometry to unveil molecular programs underlying this movement.
Project Screenshot
🐍python
📐cad
MASLAB Competition Robot
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Our robot (affectionately named Nate), which placed 2nd in the 2026 MASLAB competition! MASLAB (Mobile Autonomous Systems Laboratory) is an MIT-run robotics competition where teams design and build autonomous robots to navigate and compete in dynamic environments. This year, the competition was a bracket-style tournament game where the goal was to collect colored Pringles cans and deposit them in the correct scoring zones, all while staying in bounds. We (our team of three) used computer vision, odometric position-finding and homographic mapping to navigate the field, find cans and score points. This was an unforgettable experience, and ended up being a really riveting blitz of CAD prototyping, 3D printing, laser cutting, and algorithm refinement in the last two weeks. We tried many more ambitious things and unfortunately didn't get the time to see them through- c'est la vie! It was really fun, highly recommend!
Project Screenshot
🐍python
Autonomous Indoor Drone
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My senior design project! We (my project partner and I) were interested in exploring the use of miniature drones to map the interiors of buildings, for possible applications in the construction and manufacturing industries. We retrofitted a small drone (with built-in inertial measurement unit (IMU)) with a stereo camera, 2D horizontal Light Detection and Ranging (LiDAR) sensor and downward-facing LiDAR distance sensor to provide forward and downward spatial awareness. We used the Dronekit Python API to send flight commands and MAVROS to receive information from the sensors for autonomous navigation. We tested the capabilities of this system with a Simultaneous Localization and Mapping (SLAM) task, managing to achieve a preliminary (but imperfect) mapping of the fifth floor of the University of Wyoming's Engineering Building. It would've been fun to continue this, but COVID-19 and then grad school had other plans; maybe one day I'll return to something like this on a larger scale.
Project Screenshot
💙typescript
GoFetch
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A chat-with-your-codebase application- think of it as "Perplexity for your own file storage"! This application helps users download local AI models and use them to answer questions using information from within folders they provide. When a folder is added, the application builds a folder tree, builds and persists a live index to handle file changes, and kicks off an initial embedding job. Source files are parsed into chunks and a vector search index is run against the user query to find the most relevant files/pieces of files. The chosen model is then used to format the retrieved files into a context block and output a response to the user query that cites the retrieved files. This started as a pet project to help me navigate my poorly-organized scientific paper repositories, and development is actively ongoing. We have a cute mascot because that's the most important part, naturally.

Hobbies

Baking Sweet Treats

Black Forest Cake
Black Forest Cake
A birthday cake for a friend. Chocolate sponge, cherry liqueur syrup, whipped cream, chocolate bark, pitted cherries and chocolate shavings.
Peppermint Pizzazz
Peppermint Pizzazz
Chocolate espresso sponge, peppermint buttercream, dark chocolate ganache, candy cane brittle and white chocolate peppermint bark.
Hazelnut Symphony
Hazelnut Symphony
No special occasion unless a love of Nutella counts as a special occasion. Chocolate sponge, hazelnut & almond streusel, hazelnut mousse, dark chocolate ganache, dark chocolate & Nutella shards, pecan shavings, Ferrero Rocher.
Oreo Domes
Oreo Domes
Cookies & cream mousse hemispheres, Oreos (whole cookies and crumble), brownie round, vanilla mirror glaze, caramel syrup, lemon shavings, decorative Pirouette chocolate fudge wafer.
Ode to Reese's
Ode to Reese's
Even though I stopped trick-or-treating over a decade ago, I still like to put out candy for everyone else. One year I had enough leftover peanut butter cups to make a cake- chocolate sponge, peanut buttercream, milk chocolate ganache, decorative Reese's cups.
Yuletide on the Forest Floor
Yuletide on the Forest Floor
Created for a holiday party! Chocolate genoise sponge, chocolate chestnut whipped cream, dark chocolate ganache, meringue mushrooms, cranberry, decorative rosemary, sugar and simple syrup.

Culinary Adventures

Xīnnián Kuàilè (Happy New Year)
Xīnnián Kuàilè (Happy New Year)
A celebration of the Lunar New Year. Egg fried rice, pork potstickers, sweet potato puree, radish, pea shoots, pork char siu, panda-styled red bean bun, fried sesame balls with ube jam.
Soil, Sea and Sky
Soil, Sea and Sky
A dish that represents each of the highest-level ecological zones: terrestrial, marine and aerial! Honey garlic salmon, orzo, sirloin steak, broccolini, pea puree, king oyster mushroom, duck, toasted sesame, tomato pearls and a teriyaki sauce & parsley tree.
Elevated Thanksgiving
Elevated Thanksgiving
Decided to have fun on Friendsgiving with this elevated take on Thanksgiving dinner. Turkey roulade, mashed potatoes, potato pave, cranberry gel, assorted vegetables.
Mediterranean Medley
Mediterranean Medley
A miscellaneous Mediterranean mashup! Falafel, pita crisps, tzatziki, yogurt, harissa tahini, pomegranate, mango chutney, cucumber slaw, and basmati rice.
KBBQ Plate
KBBQ Plate
Galbi (Korean BBQ short rib), nasi goreng w/ fried egg, Chinese cabbage slaw with sweet & sour homemade Asian dressing.
Deconstructed Big Mac Meal
Deconstructed Big Mac Meal
Had some fun injecting a little flair into a staple of my childhood. NY strip steak, toasted sesame buns, butter lettuce, pickle, onion, `special sauce`, pommes puree, ketchup, Sprite in a wine glass (not pictured).

Running

No better way to clear your head and relax than with constant searing lung pain! Just kidding, kind of. I love endurance running and it's also my preferred mode of transit. It's my favorite way of exploring new places!

Cambridge Half Marathon 2023

Thanksgiving 10k

5k PR