Josh Derrick

Josh Derrick

MIT grad and JHU CMDB Ph.D. candidate in the Ludington/Farber labs. Interested in the microbiome, nutrition, and running.

Publications

Science

  1. Asialoglycoprotein receptor subunit Asgr1a loss results in attenuated cholesterol absorption in zebrafish fed a Western diet (2026) This is my second first-author paper. In this paper, Dr. Tabea Moll (a former Farber lab PhD) and I created two zebrafish knockouts of the liver glycoprotein receptor ASGR1. This receptor was of interest because mutations that drive a loss of function in humans have been shown via GWAS to dramatically reduce cardiovascular disease risk. Although we didn’t see any of the lipoprotein phenotypes described in humans, these mutations did dramatically protect against hepatic steatosis and lead to accumulation of extra cholesterol in the stool of fish, which we determined was due to attenuated absorption by the intestine. While we didn’t quite figure out the atheroprotective mechanism of ASGR1, we did highlight the complex, inter-organ importance of this liver receptor.
  2. PeakClimber: A software tool for the accurate quantification of complex HPLC chromatograms (2025) This was my first first-author paper ever! This manuscript describes a software tool, which we called PeakClimber, that more accurately fits HPLC data using a sum of exponential Gaussian functions. This improved the quantitative accuracy of HPLC data analysis, which we showed by analyzing the differences between lipid profiles of colonized and germ-free flies. Aside from the mass-spec analysis and some helpful conceptual advice from my advisors, I was responsible for the entirety of this project.
  3. Structure, function, and quantitative biology of the Drosophila gut microbiome (2025) What it says on the tin. My mentor (Will Ludington) wrote most of this, but I contributed a small section on lipid absorption.
  4. First-passage-time statistics of growing microbial populations carry an imprint of initial conditions (2023) This paper was a collaboration between myself and Simon Fraser Research Fellow Eric Jones. We grew E. coli and S. aureus from various very small inoculation sizes and measured the variance in the amount of time it took these inocula to reach a certain density. We found that these two variables were related via a power-law. The encoding of the population history in the variation allows inferences about population growth at low-densities to be studied, which was previously most commonly done with expensive microscopy “mother” machines.

  5. From worms to humans: Understanding intestinal lipid metabolism via model organisms (2023) Darby Kozan, a colleague and friend from Steve Farber’s lab, and I did a literature review on the various systems involved in lipid metabolism (absorption, trafficking, storage), and how these systems differ between common laboratory animals including C. elegans, Drosophila, zebrafish, chickens, and rodents. The overall goal of this review was to highlight the advantages of model organisms for this kind of research, with a special emphasis on non-mammalian systems which are often a better choice financially and ethically.

  6. Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies (2022) I was a rotation student in Dr. Bob Johnston’s lab for this project. Normally when we think of cells differentiating into different cell types, we think of this change being primarily driven by differential protein or RNA expression. However, the question remains as to where these expression changes come from. In this paper, my rotation mentor, Dr. Luke Voortman, showed that expression of the gene spineless (ss), which determines photoreceptor fate choice in the fly eye, is controlled by the accessibility of the region containing the spineless gene to transcription factors. This is in turn controlled by a non-protein-forming burst of transcription early in development. My role in this project was to perform long-read sequencing on some of the mutants used to test this model.

Creative Writing

  1. Ser Ghostwriter This was my creative writing thesis from college. It combines the plot of George R. R. Martin’s the Hedge Knight with characters based on Romantic Poets and a magic system based on the quality of verse. I hope to get to work on a sequel soon (ish).

  2. Dreams from Yesterday A collection of haikus of haikus (mega-haikus) that I wrote for poetry class in 2018 and 2020.

Software

  1. ScrambleSentences Anki add-on Ever memorize the content of a sentence mining card rather than the word you’re trying to memorize? Look no further. ScrambleSentences generates random sentences for a user-given vocabulary word, and then randomly cycles through them every time you review the card. That way you’re memorizing the word rather than the context of the sentence. GitHub for alternate download site.

  2. Lexical Coverage Anki add-on This add-on will analyze your lexical and corpus coverage based on your sentence mining Anki cards and estimate the CEFR coverage of your cards. Right now this only works for Spanish, but I also want to expand this to work for Italian, although I’m hesitant to expand to other languages because I don’t feel qualified to rate the quality of the corpus coverage or test if it works.