Systematic Oversimplification

Science may be described as the art of systematic oversimplification — the art of discerning what we may with advantage omit.

~ Karl Popper

Swagatam Mukhopadhyay (Swɑːg), PhD

Cross-Disciplinary serial entrepreneur: Applied Mathematics, AI/ML, Quantitative & Molecular Biology, Genomics, Drug Development, Polymer & Soft-Condensed Matter Physics

Google Scholar

Welcome to my homepage. I am a polymath who has worn many hats— 

  • Worked on theoretical models of Vulcanization Transition, Random Solids and Polymer Systems for my PhD at University of Illinois at Urbana-Champaign — PhD Advisor was Paul Goldbart. I was enormously influenced by another polymath, Nigel Goldenfeld and a Novel Laureate Tony Leggett who taught us Renormalization Group Theory and Quantum Field Theory, respectively
  • Worked on Glassy Physics, Jamming Transition, Complexity and Disorder for my post-doc at University of California Santa Barbara— PI was Jim Langer
  • Switched to understanding complexity and systems-level design in Molecular and Quantitative Biology—working very closely with experimentalists at Rutgers University with another polymath physicist, Anirvan Sengupta
  • Spent a few years at Cold Spring Harbor Lab—worked with Greg Hannon on RNAi, with Partha Mitra on large-scale Mouse-Brain Connectome project, got terribly interested and ended up working on Autism Genomics (Simons Simplex Collection) with Mike Wigler
  • Worked at a large scale genotype-phenotype mapping company, Human Longevity, during the early days when it was led by Craig Venter
  • Build and led the creation of the first set of ML models to predict pharmacology (efficacy, tolerability, IC50) of ASOs from in vitro and in vivo (rodent) screening data at Ionis Pharmaceuticals across all critical pharmacology endpoints
  • Cofounded and lead (as Chief Scientific & Innovation Officer, Board Member) Creyon Bio — a nucleic acid engineering company — our team went from bed-to-bedside in creating and dosing a novel N-of-1 medicine in a record time of under 13 months
  • Honed my professional management skills by completing the Executive Program for Senior Life Sciences Leaders (Mini-MBA)—an eight months long program focused on educating senior industry professionals evidence-based management principles

My mission with founding Creyon was to make gene-centric medicine immediate accessible and affordable globally. The crazy What if?

What if we could build a drug printer that would sit next to a sequencer to print clinic-ready medicine immediately, targeting the specific genetic cause (mutation, pathway) of a diseases? What if we could predict human pharmacology for nucleic acid polymers with such high accuracy that Phase I/II becomes just a validation step, and not a trial-and-error human experiment?

I am big believer of informational drug. I chose oligonucleotides and nucleic acids as the ideal gene-expression modulators. Over the years, I have worked on gene-editing and other related nucleic acid modalities.

I have built labs. At Creyon, I lead the lab build-up and hiring the team, especially in India—my team built an elaborate CRO network spanning chemistry, biology and processes—novel nucleic acid chemistry R&D, oligo synthesis, animal pharmacology GMP/ GLP. etc.

I love interdisciplinary science and communicating science—at CSHL I co-led a Demystifying Science series of lectures for non-scientific staff.

I really enjoy building parsimonious computational, physical, statistical, ML/AI models of complex systems rooted in the data generation process and in a lab-in-a-loop settings.

Recent work

Over last 2 year, I have been researching protein Language Models and RNA language models. With an amazing collaborator, Mausum, I have been investigating outlier features in LLMs.

I have been plotting mischief (ahem, stealth-mode startup) with the amazing Todd Martinez, David Pekker and Stefano Ermon!

I have strong experience in working as a consultant with small and large biotechs on Business Strategies, Nucleic Acid Medicine R&D and nurturing high-performance teams. I have co-lead major business deals.

On the technical side of modern AI I love working on Diffusion Models, Latent Space Methods, Attention mechanism, Transformers & Protein- RNA- Foundation Models.

Selected Press

  • TNPO2 story, AI-Guided ASO Development for an Ultra-Rare Diseases
  • Long Island Boy, 2, Gets ‘Life-Changing Dose Of His Own Medicine’
  • Bio Builders Interview, June 2023, Builders Episode 16
  • C&EN: March 2022, Creyon debuts to disrupt oligonucleotide research
  • Fierce Biotech, March 2022, Creyon joins wave of AI biotechs with $40M to create ’on demand’ RNA-based medicines
  • Fierce Biotech, April 2025, Eli Lilly pens Creyon Bio AI oligonucleotide pact with $1B in biobucks on the table
  • Axios, April 2025, Creyon Bio inks $1B licensing partnership as it eyes more funding

Patents

What’s with the name—Vislesy? Well, the word viśleṣaṇa means analysis and synthesis in Sanskrit. And swagatam means “welcome” in Sanskrit and is obviously not available as a domain name!