khushi singh.in

About

Hello, I’m Khushi

I’m a biologist who likes asking how living things sense their world, and how that sense becomes memory, from a single molecule to the next generation.

I study biology at IISER Pune (BS-MS, Biology major with a Chemistry minor), and I’m doing my master’s research at the Max Planck Institute of Immunobiology and Epigenetics in Freiburg, Germany.

My path has zig-zagged across scales. I started outdoors with insects and plants. Then came proteins that form droplets, the cell’s folding factory, RNA droplets that set aside the germline in fly embryos, and a glowing sensor that lets you watch a bacterial division protein burn its fuel. Today I work on a question that joins many of these threads: can metabolism, and the microbes a mother lives with, leave chemical notes on her children’s chromatin? Alongside it, I measure how metabolism shapes activity and sleep in flies.

I care about making science open and welcoming: explained in plain words (and soon in Hindi as well as English), with honest labels for what we know and what we don’t. This site is part of that.

How my research fits

I want to understand how gene expression is controlled in early development: at chromatin, and through RNA–protein condensates that place and time maternal mRNAs, with metabolism and behaviour as the links to the whole animal. Here is how my experience maps onto these fields, and the current research each one connects to.

  • Chromatin and gene regulation in early development

    My work

    Skills

    Fly genetics, embryo collection and staging, immunostaining, confocal imaging, quantitative image analysis

    Where the field is going

    How pioneer factors, co-activators and 3D genome folding prime genes before the genome switches on, and how marks inherited from the egg and metabolites set the timing (Zenk et al. 2017; Espinola et al. 2021; Li et al. 2024; Galouzis et al. 2025).

  • RNA–protein condensates and mRNA localisation

    My work

    Skills

    smFISH and probe design, single-molecule image analysis, protein biochemistry, turbidity assays

    Where the field is going

    How the composition, material state and RNA–RNA contacts of RNP granules decide where and when maternal mRNAs are translated (Trcek et al. 2015; Bose et al. 2022; Bose et al. 2024).

  • Metabolism, physiology and behaviour

    My work

    Skills

    Drosophila Activity Monitor assays, sleep and circadian analysis, fertility assays

    Where the field is going

    How diet, microbes and metabolic state shape sleep, feeding and reproduction, and whether the same metabolites act on chromatin (Keene et al. 2010; Krautkramer et al. 2016; Hudry et al. 2019).

  • Organelles and protein quality control

    My work

    Skills

    RNAi in flies, Western blotting, immunostaining of embryos and ovaries

    Where the field is going

    How ER shape and selective autophagy, including the turnover of the ER itself, keep proteins healthy in growing tissues (Voeltz et al. 2006; Khaminets et al. 2015).

  • Biochemistry, biosensors and enzyme kinetics

    My work

    Skills

    Mutagenesis, protein expression and purification, dye labelling, fluorescence spectroscopy, Michaelis–Menten analysis

    Where the field is going

    Real-time fluorescent reporters of enzyme activity, used to study and screen the bacterial division protein FtsZ as an antibiotic target (Brune et al. 1994; Haydon et al. 2008).

  • Quantitative imaging and code

    My work

    Skills

    Python, R and ImageJ macros, segmentation and quantification, reproducible figures

    Where the field is going

    Single-molecule and live imaging of gene expression, analysed with machine-learning segmentation (Raj et al. 2008; Garcia et al. 2013; Stringer et al. 2021).

Papers are cited by first author and year; full references are on the research interests and project pages.

What I value

Curiosity

Questions first. The best ones are simple to ask and hard to answer.

Care

Good science looks after people: the ones we study, the ones we teach, and the next generation.

Openness

Share methods, credit sources, admit uncertainty, and make knowledge free to reuse.

Science for everyone

  • Volunteer, Disha Club. Education outreach for children from underprivileged backgrounds.
  • Core member, Content and Communication in Science Club. Science communication at IISER Pune.
  • Women in Science committee, IISER Pune. Regular attendee of talks and seminars.

Off the bench

You’ll find me at a chessboard, on a badminton court, playing carrom, or on a trek somewhere green. Good thinking needs fresh air.

  • Chess
  • Badminton
  • Carrom
  • Trekking

What’s next

I’m open to PhD positions from 2027, especially in chromatin and gene regulation in development, RNA–protein condensates, and metabolism and behaviour.

Read my CVGet in touchPress & bios