Talmo Pereira, PhD

Talmo Pereira, PhD

Salk Fellow and Principal Investigator

Salk Institute for Biological Studies

Biography

Hi, I’m Talmo. I run a lab as a Salk Fellow at the Salk Institute for Biological Studies, where we use computer vision and deep learning to study animal behavior, neuroscience, and plants!

My work has been featured in Quanta Magazine, Nature Lab Animal, Nature Toolbox, The Scientist, Princeton Insights, and more.

I received my PhD in Neuroscience at the Princeton Neuroscience Institute, co-advised by Mala Murthy and Joshua Shaevitz.

Check out my lab website for updated information on our work.

Interests

  • Systems neuroscience
  • Ethology
  • Computer vision (pose estimation, action recognition)
  • Machine learning (deep learning, dimensionality reduction)
  • Plant phenotyping

Education

  • PhD in Neuroscience, 2021

    Princeton University

  • MS in Neuroscience, 2017

    Princeton University

  • BS in Bioinformatics and Computational Biology, 2015

    University of Maryland, Baltimore County

Research

 
 
 
 
 

Salk Fellow and Principal Investigator

Salk Institute for Biological Studies

Nov 2021 – Present La Jolla, CA
Running a lab (talmolab.org) focused on building deep learning-based tools for motion capture, biological phenotyping, and computational neuroscience.
 
 
 
 
 

Research Intern

Google AI

Jun 2020 – Dec 2020 Mountain View, CA

Research internship at Google AI in Machine Perception. Developed deep learning systems for network architecture search and human action recognition.

Supervisor: Shay Ohayon

 
 
 
 
 

PhD Student

Princeton Neuroscience Institute

Jun 2015 – Oct 2021 Princeton, NJ

Using fruit flies (Drosophila melanogaster) to study how the brain integrates sensory information to pattern behavioral sequences. Developed hardware and software for acquisition and processing of high resolution video, audio and realtime instrument control. Developed computational methods that leverage computer vision, deep learning, signal processing and unsupervised machine learning for quantifying behavior through few shot pose estimation and manifold embedding. Working on mapping the substrates and function of biological neural circuits involved in patterning the structure of complex motor behaviors.

Advisors: Mala Murthy, Joshua Shaevitz

 
 
 
 
 

Amgen Scholar

California Institute of Technology

Jun 2014 – Aug 2014 Pasadena, CA

Worked on computational analysis of aggressive behaviors in fruit flies using methods in computer vision for animal tracking and supervised machine learning for timeseries segmentation.

Advisor: David J. Anderson

 
 
 
 
 

Student Researcher

Massachusetts Institute of Technology

Jun 2013 – May 2014 Cambridge, MA

Worked on image processing algorithms for large scale (100-1000s GiB) electron microscopy image alignment/registration for connectomic reconstruction.

Advisor: Sebastian Seung

 
 
 
 
 

Student Researcher

University of Maryland, Baltimore County

Jan 2013 – May 2015 Baltimore, MD

Developed computational algorithm for GPU-accelerated transcription factor DNA binding site prediction in large scale (10-100s GiB) metagenomic sequencing data. to characterize transcriptional regulatory networks.

Advisor: Ivan Erill

 
 
 
 
 

Student Researcher

Broad Institute of MIT and Harvard

Jun 2012 – Aug 2012 Cambridge, MA

Worked on characterizing interactions between proteins associated with psychiatric disease in the axon initial segment via immunochemical assays.

Advisor: Jon Madison

 
 
 
 
 

HHMI Scholar

National Institutes of Health

Jun 2010 – Jun 2011 Bethesda, MD

Characterized the learning and memory impairment induced by knockout of a type-1 diabetes-associated neuroendocrine transport gene in mice.

Advisor: Abner L. Notkins

Awards

Harold M. Weintraub Graduate Student Award

Fred Hutch Cancer Center Mar 2022
See press release.

Porter Ogden Jacobus Fellowship

Princeton University Oct 2020

Awarded Princeton University’s top honor for graduate students.

See press release and award presentation video.

President’s Prize

Princeton University Jun 2015
Awarded honorific fellowship on admission to graduate program.

NSF Graduate Research Fellowship Program

National Science Foundation Apr 2015
One of 2,000 awardees selected from a pool of 16,500 applicants for the grant.

The Barry Goldwater Scholarship and Excellence in Education Program

Barry Goldwater Scholarship Feb 2014
Received an Honorable Mention from a pool of 1,166 nationwide nominees.

MARC Undergraduate Student Training in Academic Research

National Institutes of Health Aug 2013
The MARC U-STAR scholarship is an award funded by the NIH in an effort to support undergraduates in pursuing experiences and a career in research. Provides a research stipend, full academic scholarship, funding for lab expenses and travel.

UMBC Undergraduate Research Award (URA)

University of Maryland, Baltimore County Jan 2012
Research grant awarded to undergraduates pursuing research on campus.

Howard Hughes Medical Institute Scholar

Howard Hughes Medical Institute Jan 2012
Highly selective HHMI-sponsored program aiming to increase diversity in the biomedical sciences. Supports students with a research stipend, pre-professional advising and funding for summer research.

Meyerhoff Scholar

University of Maryland, Baltimore County Jun 2011
Selective scholarship program at UMBC supporting students pursuing a career in research in the STEM fields.

Broad Prize Scholar

University of Maryland, Baltimore County Jun 2011
Broad Prize scholarships are awarded to graduating seniors who have a demonstrated record of improving their grades over the course of their high school career and have a financial need by the Eli and Edythe Broad Foundation. One of thirteen awardees in Montgomery County, MD.

Publications

The list of publications below is out-of-date. Please see my lab website or Google Scholar for an updated list of publications.

Talmo D Pereira, Joshua W Shaevitz, Mala Murthy (2020). Quantifying behavior to understand the brain. Nature Neuroscience.

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Talmo D Pereira, Nathaniel Tabris, Junyu Li, Shruthi Ravindranath, Eleni S Papadoyannis, Z Yan Wang, David M Turner, Grace McKenzie-Smith, Sarah D Kocher, Annegret Lea Falkner, Joshua W Shaevitz, Mala Murthy (2020). SLEAP: Multi-animal pose tracking. bioRxiv.

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Jessica M Jones, William Foster, Colin R Twomey, Justin Burdge, Osama M Ahmed, Talmo D Pereira, Jessica A Wojick, Gregory Corder, Joshua B Plotkin, Ishmail Abdus-Saboor (2020). A machine-vision approach for automated pain measurement at millisecond timescales. Elife.

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Adam S Charles, Benjamin Falk, Nicholas Turner, Talmo D Pereira, Daniel Tward, Benjamin D Pedigo, Jaewon Chung, Randal Burns, Satrajit S Ghosh, Justus M Kebschull, William Silversmith, Joshua T Vogelstein (2020). Toward Community-Driven Big Open Brain Science: Open Big Data and Tools for Structure, Function, and Genetics. Annu. Rev. Neurosci..

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Princeton Open Ventilation Monitor Collaboration, Philippe Bourrianne, Stanley Chidzik, Daniel J Cohen, Peter Elmer, Thomas Hallowell, Todd J Kilbaugh, David Lange, Andrew M Leifer, Daniel R Marlow, Peter D Meyers, Edna Normand, Janine Nunes, Myungchul Oh, Lyman Page, Talmo Pereira, Jim Pivarski, Henry Schreiner, Howard A Stone, David W Tank, Stephan Thiberge, Christopher Tully (2020). Inexpensive multi-patient respiratory monitoring system for helmet ventilation during COVID-19 pandemic. medRxiv.

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David Deutsch, Diego A Pacheco, Lucas J Encarnacion-Rivera, Talmo Pereira, Ramie Fathy, Adam Calhoun, Elise C Ireland, Austin T Burke, Sven Dorkenwald, Claire McKellar, Thomas Macrina, Ran Lu, Kisuk Lee, Nico Kemnitz, Dodam Ih, Manuel Castro, Akhilesh Halageri, Chris Jordan, William Silversmith, Jingpeng Wu, H Sebastian Seung, Mala Murthy (2020). The Neural Basis for a Persistent Internal State in Drosophila Females. bioRxiv.

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Talmo D Pereira, Diego E Aldarondo, Lindsay Willmore, Mikhail Kislin, Samuel S-H Wang, Mala Murthy, Joshua W Shaevitz (2019). Fast animal pose estimation using deep neural networks. Nat. Methods.

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Aleksandra Badura, Jessica L Verpeut, Julia W Metzger, Talmo D Pereira, Thomas J Pisano, Ben Deverett, Dariya E Bakshinskaya, Samuel S-H Wang (2018). Normal cognitive and social development require posterior cerebellar activity. Elife.

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Jan Clemens, Philip Coen, Frederic A Roemschied, Talmo D Pereira, David Mazumder, Diego E Aldarondo, Diego A Pacheco, Mala Murthy (2018). Discovery of a New Song Mode in Drosophila Reveals Hidden Structure in the Sensory and Neural Drivers of Behavior. Curr. Biol..

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Gecia Bravo Hermsdorff, Talmo Pereira, Yael Niv (2018). Quantifying Humans' Priors Over Graphical Representations of Tasks. International Conference on Complex Systems.

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A Giovannucci, E A Pnevmatikakis, B Deverett, T Pereira, J Fondriest, M J Brady, S S-H Wang, W Abbas, P Parés, D Masip (2018). Automated gesture tracking in head-fixed mice. J. Neurosci. Methods.

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Talmo D Pereira, Mala Murthy (2017). To Fight or Not to Fight. Neuron.

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Andrea Giovannucci, Aleksandra Badura, Ben Deverett, Farzaneh Najafi, Talmo D Pereira, Zhenyu Gao, Ilker Ozden, Alexander D Kloth, Eftychios Pnevmatikakis, Liam Paninski, Chris I De Zeeuw, Javier F Medina, Samuel S-H Wang (2017). Cerebellar granule cells acquire a widespread predictive feedback signal during motor learning. Nat. Neurosci..

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Elizabeth T Hobbs, Talmo Pereira, Patrick K O'Neill, Ivan Erill (2016). A Bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data. Algorithms Mol. Biol..

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