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Hi, I am Jackie

Jackie Valeri

Data Scientist at Moderna

I am currently a Data Scientist at Moderna in the Data Science and Artificial Intelligence team. I recently received my PhD in Biological Engineering from the lab of Jim Collins at MIT. In 2018, I graduated with my undergraduate and masters degree in BE from the University of Pennsylvania. I am energized by opportunities to mentor, promote inclusive environments, and do science outreach.

ML / AI
Syn Bio
Antibiotics
AutoML
Systems Bio
Mentoring

Skills

Experiences

Data Science and Artificial Intelligence Team

August 2023 - Present

Moderna, Cambridge, MA

Data Scientist

August 2023 - Present

Responsibilities:
  • Working on making science faster, easier, and more rigorous for a diverse range of biological questions. The ultimate goal is to get medicines to patients faster.
  • Involved in protein engineering campaigns to optimize protein function in novel sequence space.
  • Using machine learning models and algorithms to predict and design molecules involved in lipid nanoparticles.
Lab of Jim Collins

September 2018 - August 2023

MIT, Cambridge, MA

PhD Student

September 2018 - August 2023

Responsibilities:
  • Developed machine learning tools for synthetic biology components such as toehold switches. Built on this work to improve accessibility of machine learning by constructing ‘automated’ tools for synthetic and systems biologists with limited programming experience.
  • Used computational tools to assist the discovery and design of new antibiotics. Specifically, worked on antibiotics relevant for metabolically dormant bacteria and serious pathogens for which we urgently need new drugs.
  • MIT-Takeda Fellow in Artificial Intelligence and Health 2021 - 2022.
  • Siebel Scholar, Class of 2023.
Lab of Jennifer Phillips-Cremins

January 2016 - July 2018

University of Pennsylvania, Philadelphia, PA

Research Assistant

January 2016 - July 2018

Responsibilities:
  • Developed a tool to modulate gene expression in embryonic stem cells using blue light.
  • Co-planned and executed a labwide “Molecular Biology Bootcamp” as a 1 week intensive course.
  • Class of 1971 Robert J. Holtz Award Summer 2017 from Center for Undergraduate Research & Fellowships.
  • Abraham Noordegraaf Undergraduate Research Fellow Summer 2017.
  • Silver Medal for Rachleff Scholar Poster Presentation Summer 2016.

Education

MIT
2018 - 2023
Ph.D in Biological Engineering
GPA: 5.00 out of 5.00
Taken Courses:
  • Principles of Molecular Bioengineering
  • Biological Networks
  • Deep Learning for Biological Life Sciences
  • Methods & Problems in Microbiology
  • The Hallmarks of Cancer
Extracurricular Activities:
  • 2020 - 2023 BE Data Lab Fellow.
  • 2020 - 2022 Co-President of MITxHarvard Women in Artificial Intelligence.
  • 2018 - 2023 Student Liaison for the Institute Discriminiation and Harassment Response (IDHR) Office; Previously, Chair of Messaging and Partnerships Subcommittee of IDHR-Student Advisory Committee.
  • 2020 - 2023 Representative for Committe on Sexual Misconduct Prevention and Response.
  • Spring 2021 Teaching Assistant for Deep Learning in the Life Sciences.
  • 2018 - 2023 BE Admissions Assistance Program (BEAAP) Mentor.
University of Pennsylvania
2016 - 2018
M.S.E. in Biological Engineering
GPA: 4.00 out of 4.00
Taken Courses:
  • Molecular Basis of Disease
  • Multiscale Modeling of Biological Systems
  • Epigenomics
  • Ethical Aspects of Health & Technology
  • Intro to Computational Biology & Biological Modeling
  • Intro to Bioinformatics
Extracurricular Activities:
  • Honorable Mention for Penn Engineering Master’s Academic Award Spring 2018.
University of Pennsylvania
2014 - 2018
B.S.E. in Biological Engineering
GPA: 3.99 out of 4.00
Taken Courses:
  • Engineering Principles of Human Physiology
  • Molecular Physiology & Cellular Engineering
  • Advanced Physical Chemistry of Bioengineering
  • Molecular Biology & Genetics
  • Biomedical Ethics
  • Computer Science Minor
Extracurricular Activities:
  • Penn Band Clarinet Section Leader.
  • Tau Beta Pi Engineering Honor Society Secretary.
  • Co-Director of Penn Innoworks Science Camp.
  • Co-recipient of 2018 Wolf-Hallac Award for top female senior in Penn Engineering School.
  • Selected for Penn 10 2018, the “30 Under 30” equivalent for 10 graduating seniors.

Projects

Deep learning–enabled discovery of antibiotics effective against Neisseria gonorrhoeae
Science Translational Medicine, 2026

Using deep learning to screen antibacterials effective against Neisseria gonorrhoeae.

abx phd
Star
A generative deep learning approach to de novo antibiotic design
Cell 2025

Using genetic algorithms and autoencoders to generate novel antibacterials.

abx phd
Star
A high-throughput synthetic biology approach for studying combinatorial chromatin-based transcriptional regulation
Molecular Cell, 2024

Evaluate the effect of chromatin regulator combinations on gene expression in yeast.

seqfunc phd
Details
Discovery of antibiotics active against stationary-phase bacteria
Cell Chemical Biology, 2023

Experimental and computational screening techniques to discover and characterize small molecules active against “metabolically dormant” bacteria.

abx phd
Star
Explainable ML for antibiotic class discovery
Nature, 2023

Using explainable machine learning techniques to discover a structural class of antibiotics active against S. aureus.

abx phd
Details
Automated machine learning for biological sequences
Cell Systems, 2023

Easing barriers for biologists to use machine learning to analyze, intepret, and design nucleic acid, peptide, and glycan sequences.

seqfunc phd
Star
Machine learning for toehold switches
Nature Communications, 2020

Sequence-to-function deep learning frameworks for engineered riboregulators.

seqfunc phd
Star
Android app for lateral flow assay image analysis
Nature Biomedical Engineering, 2020

A CRISPR-based assay for the detection of opportunistic infections post-transplantation and for the monitoring of transplant rejection.

phd
Star
Blue light-induced genome folding
Nature Methods, 2019

LADL, light-activated dynamic looping for endogenous gene expression control. Highlighted in Nature’s technologies to watch in 2020.

undergrad
Details
Communication interface for Deaf patients and hearing physicians
Senior Design, 2018

Created neural machine translation and video capture algorithm. Honorable mention in Engineering senior design competition.

undergrad
Details

Recent Posts

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PyCon US 2024

I really enjoyed attending PyCon US in Pittsburgh a few weeks ago. PyCon was a great opportunity to meet other people who use Python, from data scientists to software engineers to hobbyists. Many of the talks and tutorials were focused on learning new skills and Python programming paradigms, which was different than my previous experiences attending academic-centered conferences. While this shift from “sharing scientific updates” to “teaching the audience something new” took some time to get used to, PyCon was a great learning environment and I really feel like I leveled up my programming.

Tuesday, June 18, 2024 Read
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Introduction: Hello World!

Hello and welcome to my blog! I’m Jackie Valeri (she/her), and I’m thrilled to share a bit about myself and my interests with you. Who Am I? 👋 Brief Introduction I currently work as a Data Scientist at Moderna, where I am part of a data science team within research and early development. I hold a PhD in Biological Engineering from the Massachusetts Institute of Technology (MIT), where I was a Siebel Scholar (Class of 2023) and a Takeda Fellow (2021-2022) in the lab of Jim Collins. My research in the Collins Lab centered around machine learning for small molecule drug discovery, specifically antibiotics, as well as training sequence-to-function models for synthetic biology applications. I hold Master’s and Bachelor’s degrees in Bioengineering from the University of Pennsylvania where I also obtained a minor in computer science.

Tuesday, June 11, 2024 Read

Outside of Work

Skiing

Baking

Hiking and Climbing

Hanging with Friends