publications

2026

2025

1. arXiv

   Pearl: A Foundation Model for Placing Every Atom in the Right Location

   Genesis Research Team

   2025

   arXiv
2. arXiv

   Triangle Multiplication Is All You Need For Biomolecular Structure Representations

   Jeffrey Ouyang-Zhang, Pranav Murugan, Daniel J. Diaz, and 7 more authors

   2025

   arXiv

2024

1. PhysRevE

   Minimal framework for optimizing vaccination protocols targeting highly mutable pathogens

   Saeed Mahdisoltani, Pranav Murugan, Arup K. Chakraborty, and 1 more author

   Physical Review E Dec 2024

   HTML
2. eLife

   Coordinated head direction representations in mouse anterodorsal thalamic nucleus and retrosplenial cortex

   Marie-Sophie H Goes, Jakob Voigts, Jonathan P Newman, and 4 more authors

   eLife Mar 2024

   Abs HTML

   The sense of direction is critical for survival in changing environments and relies on flexibly integrating self-motion signals with external sensory cues. While the anatomical substrates involved in head direction (HD) coding are well known, the mechanisms by which visual information updates HD representations remain poorly understood. Retrosplenial cortex (RSC) plays a key role in forming coherent representations of space in mammals and it encodes a variety of navigational variables, including HD. Here, we use simultaneous two-area tetrode recording to show that RSC HD representation is nearly synchronous with that of the anterodorsal nucleus of thalamus (ADn), the obligatory thalamic relay of HD to cortex, during rotation of a prominent visual cue. Moreover, coordination of HD representations in the two regions is maintained during darkness. We further show that anatomical and functional connectivity are consistent with a strong feedforward drive of HD information from ADn to RSC, with anatomically restricted corticothalamic feedback. Together, our results indicate a concerted global HD reference update across cortex and thalamus.

2020

1. PNAS

   Optimizing immunization protocols to elicit broadly neutralizing antibodies

   Kayla G. Sprenger, Joy E. Louveau, Pranav M. Murugan, and 1 more author

   Proceedings of the National Academy of Sciences Mar 2020

   Abs HTML

   Natural infections and vaccination with a pathogen typically stimulate the production of potent antibodies specific for the pathogen through a Darwinian evolutionary process known as affinity maturation. Such antibodies provide protection against reinfection by the same strain of a pathogen. A highly mutable virus, like HIV or influenza, evades recognition by these strain-specific antibodies via the emergence of new mutant strains. A vaccine that elicits antibodies that can bind to many diverse strains of the virus—known as broadly neutralizing antibodies (bnAbs)—could protect against highly mutable pathogens. Despite much work, the mechanisms by which bnAbs emerge remain uncertain. Using a computational model of affinity maturation, we studied a wide variety of vaccination strategies. Our results suggest that an effective strategy to maximize bnAb evolution is through a sequential immunization protocol, wherein each new immunization optimally increases the pressure on the immune system to target conserved antigenic sites, thus conferring breadth. We describe the mechanisms underlying why sequentially driving the immune system increasingly further from steady state, in an optimal fashion, is effective. The optimal protocol allows many evolving B cells to become bnAbs via diverse evolutionary paths.