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<!DOCTYPE html>
<html lang="en">
<head>
<meta name="generator" content="Hugo 0.74.3" />
<title>Jacqueline Valeri</title>
<meta name="description" content="Personal website of Jacqueline Valeri." />
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<a class="nav-link" href="#home">Home</a>
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<a class="nav-link" href="#about">About</a>
</li>
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<a class="nav-link" href="#outside-the-lab">Outside the Lab</a>
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<div class="container-fluid home" id="home">
<div
class="background container-fluid"
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<div class="container content text-center">
<img src="images/rectangular_profile.png"
class="rounded-circle mx-auto d-block img-fluid" />
<h1 class="greeting"> Hi, I'm Jackie</h1>
<div class="typing-carousel">
<span id="ityped" class="ityped"></span>
<span class="ityped-cursor"></span>
</div>
<ul id="typing-carousel-data">
<li>I am a biological engineer</li>
<li>I am a data scientist</li>
<li>I am a biologist</li>
<li>I am a machine learning engineer</li>
</ul>
<a href="#about"><i class="arrow bounce fa fa-chevron-down"></i></a>
</div>
</div>
<div class="container-fluid section-holder d-flex bg-white">
<div class="container anchor p-lg-5 about-section" id="about">
<div class="row pt-sm-2 pt-md-4 align-self-center">
<div class="col-sm-6">
<h3 class="p-1">Jacqueline Valeri</h3>
<h5 class="p-1">
Data Scientist
at <a href="https://www.modernatx.com/en-US">Moderna</a>
</h5>
<p class="p-1 text-justify">
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.
</p>
<div class="text-container ml-auto">
<ul class="social-link d-flex">
<li>
<a href="mailto:jackievaleri8@gmail.edu" target="/"><i
class="fas fa-envelope"></i></a>
</li>
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<a href="https://github.com/jackievaleri" target="/"><i
class="fab fa-github"></i></a>
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<a href="https://www.linkedin.com/in/jacquelinevaleri/"
target="/"><i class="fab fa-linkedin"></i></a>
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<a href="https://twitter.com/jackievalerisci" target="/"><i
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class="circular-progress-bar circular-progress-percentage-100"></span>
</span>
<span class="circular-progress-right">
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class="circular-progress-bar"></span>
</span>
<div class="circular-progress-value">ML / AI</div>
</div>
</div>
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<div class="circular-progress sky">
<span class="circular-progress-left">
<span
class="circular-progress-bar circular-progress-percentage-100"></span>
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<span class="circular-progress-right">
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class="circular-progress-bar"></span>
</span>
<div class="circular-progress-value">Syn Bio</div>
</div>
</div>
<div class="col-6 col-lg-4 p-2">
<div class="circular-progress blue">
<span class="circular-progress-left">
<span
class="circular-progress-bar circular-progress-percentage-100"></span>
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<span class="circular-progress-right">
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class="circular-progress-bar"></span>
</span>
<div class="circular-progress-value">Antibiotics</div>
</div>
</div>
<div class="col-6 col-lg-4 p-2">
<div class="circular-progress sky">
<span class="circular-progress-left">
<span
class="circular-progress-bar circular-progress-percentage-100"></span>
</span>
<span class="circular-progress-right">
<span
class="circular-progress-bar"></span>
</span>
<div class="circular-progress-value">AutoML</div>
</div>
</div>
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<div class="circular-progress blue">
<span class="circular-progress-left">
<span
class="circular-progress-bar circular-progress-percentage-100"></span>
</span>
<span class="circular-progress-right">
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class="circular-progress-bar"></span>
</span>
<div class="circular-progress-value">Systems Bio</div>
</div>
</div>
<div class="col-6 col-lg-4 p-2">
<div class="circular-progress sky">
<span class="circular-progress-left">
<span
class="circular-progress-bar circular-progress-percentage-100"></span>
</span>
<span class="circular-progress-right">
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class="circular-progress-bar"></span>
</span>
<div class="circular-progress-value">Mentoring</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="container-fluid section-holder d-flex bg-dimmed">
<div class="container-fluid anchor pb-5 experiences-section"
id="experiences">
<h1 class="text-center">Experiences</h1>
<div class="container timeline text-justify">
<div class="row align-items-center d-flex">
<div
class="col-1 col-lg-2 text-center vertical-line d-inline-flex justify-content-center">
<div class="circle font-weight-bold"></div>
</div>
<div class="col-10 col-lg-8">
<div class="experience-entry-heading">
<h5>Data Scientist</h5>
<h6>Data Science and Artificial Intelligence Team</h6>
<p class="text-muted">August 2023 - Present,
Moderna
</p>
</div>
<p></p>
<ul class="justify-content-around">
<li>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.</li>
</ul>
</div>
</div>
<div class="row horizontal-line">
<div class="col-1 col-lg-2 timeline-side-div">
<div class="corner"></div>
</div>
<div class="col-10 col-lg-8">
<hr />
</div>
<div class="col-1 col-lg-2 timeline-side-div">
<div class="corner"></div>
</div>
</div>
<div class="row align-items-center justify-content-end d-flex">
<div class="col-10 col-lg-8">
<div class="experience-entry-heading">
<h5>PhD Student</h5>
<h6><a href=https://collinslab.mit.edu>Lab of Jim
Collins</a></h6>
<p class="text-muted">September 2018 - August 2023,
MIT
</p>
</div>
<p></p>
<ul class="justify-content-around">
<li>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.</li>
<li>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.</li>
<li>MIT-Takeda Fellow in Artificial Intelligence and Health 2021
- 2022</li>
<li>Siebel Scholar, Class of 2023</li>
</ul>
</div>
<div
class="col-1 col-lg-2 text-center vertical-line d-inline-flex justify-content-center">
<div class="circle font-weight-bold"></div>
</div>
</div>
<div class="row horizontal-line">
<div class="col-1 col-lg-2 timeline-side-div">
<div class="corner"></div>
</div>
<div class="col-10 col-lg-8">
<hr />
</div>
<div class="col-1 col-lg-2 timeline-side-div">
<div class="corner"></div>
</div>
</div>
<div class="row align-items-center d-flex">
<div
class="col-1 col-lg-2 text-center vertical-line d-inline-flex justify-content-center">
<div class="circle font-weight-bold"></div>
</div>
<div class="col-10 col-lg-8">
<div class="experience-entry-heading">
<h5>PhD Student</h5>
<h6><a href=https://be.mit.edu>Biological Engineering
Dept.</a></h6>
<p class="text-muted">September 2018 - August 2023,
MIT
</p>
</div>
<p>GPA 5.00/5.00</p>
<ul class="justify-content-around">
<li>2020 - 2023 BE Data Lab Fellow</li>
<li>2020 - 2022 Co-President of MITxHarvard Women in Artificial
Intelligence</li>
<li>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</li>
<li>2020 - 2023 Representative for Committe on Sexual Misconduct
Prevention and Response</li>
<li>Spring 2021 Teaching Assistant for Deep Learning in the Life
Sciences</li>
<li>2018 - 2023 BE Admissions Assistance Program (BEAAP)
Mentor</li>
</ul>
</div>
</div>
<div class="row horizontal-line">
<div class="col-1 col-lg-2 timeline-side-div">
<div class="corner"></div>
</div>
<div class="col-10 col-lg-8">
<hr />
</div>
<div class="col-1 col-lg-2 timeline-side-div">
<div class="corner"></div>
</div>
</div>
<div class="row align-items-center justify-content-end d-flex">
<div class="col-10 col-lg-8">
<div class="experience-entry-heading">
<h5>Bachelor's and Master's Student</h5>
<h6><a href=https://be.seas.upenn.edu>Biological Engineering
Dept.</a></h6>
<p class="text-muted">September 2014 - May 2018,
University of Pennysylvania
</p>
</div>
<p>GPA 4.00/4.00 (M.S.E.) and 3.99/4.00 (B.S.E.)</p>
<ul class="justify-content-around">
<li>Penn Band Clarinet Section Leader</li>
<li>Tau Beta Pi Engineering Honor Society Secretary</li>
<li>Co-Director of Penn Innoworks Science Camp</li>
<li>Award, Honorable Mention for Penn Engineering Master’s
Academic Award Spring 2018</li>
<li>Award, Co-recipient of 2018 Wolf-Hallac Award for top female
senior in Penn Engineering School</li>
<li>Award, Selected for Penn 10 2018, the “30 Under
30” equivalent for 10 graduating seniors</li>
</ul>
</div>
<div
class="col-1 col-lg-2 text-center vertical-line d-inline-flex justify-content-center">
<div class="circle font-weight-bold"></div>
</div>
</div>
<div class="row horizontal-line">
<div class="col-1 col-lg-2 timeline-side-div">
<div class="corner"></div>
</div>
<div class="col-10 col-lg-8">
<hr />
</div>
<div class="col-1 col-lg-2 timeline-side-div">
<div class="corner"></div>
</div>
</div>
<div class="row align-items-center d-flex">
<div
class="col-1 col-lg-2 text-center vertical-line d-inline-flex justify-content-center">
<div class="circle font-weight-bold"></div>
</div>
<div class="col-10 col-lg-8">
<div class="experience-entry-heading">
<h5>Research Assistant</h5>
<h6><a href=http://creminslab.com>Lab of Jennifer
Phillips-Cremins</a></h6>
<p class="text-muted">January 2016 - July 2018,
University of Pennsylvania
</p>
</div>
<p></p>
<ul class="justify-content-around">
<li>Developed a tool to modulate gene expression in embryonic
stem cells using blue light</li>
<li>Co-planned and executed a labwide “Molecular Biology
Bootcamp” as a 1 week intensive course</li>
<li>Award, Class of 1971 Robert J. Holtz Award Summer 2017 from
Center for Undergraduate Research & Fellowships.</li>
<li>Award, Abraham Noordegraaf Undergraduate Research Fellow
Summer 2017</li>
<li>Award, Silver Medal for Rachleff Scholar Poster Presentation
Summer 2016</li>
</ul>
</div>
</div>
</div>
</div>
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<div class="container-fluid section-holder d-flex bg-white">
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<h1 class="text-center">Projects</h1>
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class="col-sm-12 col-md-6 col-lg-4 p-2 filtr-item"
data-category='all,past,phd'>
<div class="card mt-1">
<div class="card">
<a class="card-header"
href="https://www.cell.com/cell-chemical-biology/fulltext/S2451-9456(23)00387-2?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2451945623003872%3Fshowall%3Dtrue">
<div>
<div class="d-flex">
<h5 class="card-title mb-0">Discovery of antibiotics
active against stationary-phase bacteria</h5>
</div>
<div class="sub-title">
<span></span>
<span>Cell Chemical Biology, 2023</span>
</div>
</div>
</a>
<div class="card-body">
<p>Experimental and computational screening techniques to
discover and characterize small molecules active against
"metabolically dormant" bacteria.</p>
<span class="float-right">
<a
class="github-button-inactive"
href="https://github.com/jackievaleri/nontoxic_stat_phase_killing_abx"
data-icon="octicon-standard"
data-show-count="true"
aria-label="Star Non-toxic stationary-phase antibiotics discovery">Star</a>
</span>
</div>
</div>
</div>
</div>
<div
class="col-sm-12 col-md-6 col-lg-4 p-2 filtr-item"
data-category='all,past,phd'>
<div class="card mt-1">
<div class="card">
<a class="card-header"
href="https://www.nature.com/articles/s41586-023-06887-8">
<div>
<div class="d-flex">
<h5 class="card-title mb-0">Explainable ML for
antibiotic class discovery</h5>
</div>
<div class="sub-title">
<span></span>
<span>Nature, 2023</span>
</div>
</div>
</a>
<div class="card-body">
<p>Using explainable machine learning techniques to discover
a structural class of antibiotics active against S.
aureus.</p>
<span class="float-right">
</span>
</div>
</div>
</div>
</div>
<div
class="col-sm-12 col-md-6 col-lg-4 p-2 filtr-item"
data-category='all,past,phd'>
<div class="card mt-1">
<div class="card">
<a class="card-header"
href="https://www.cell.com/cell-systems/fulltext/S2405-4712(23)00151-5">
<div>
<div class="d-flex">
<h5 class="card-title mb-0">Automated machine learning
for biological sequences</h5>
</div>
<div class="sub-title">
<span></span>
<span>Cell Systems, 2023</span>
</div>
</div>
</a>
<div class="card-body">
<p>Easing barriers for biologists to use machine learning to
analyze, intepret, and design nucleic acid, peptide, and
glycan sequences.
<span class="float-right">
<a
class="github-button-inactive"
href="https://github.com/jackievaleri/BioAutoMATED"
data-icon="octicon-standard"
data-show-count="true"
aria-label="Star Automated machine learning for analyzing, interpreting, and designing biological sequences">Star</a>
</span>
</div>
</div>
</div>
</div>
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class="col-sm-12 col-md-6 col-lg-4 p-2 filtr-item"
data-category='all, past,phd'>
<div class="card mt-1">
<div class="card">
<a class="card-header"
href="https://www.nature.com/articles/s41467-020-18676-2">
<div>
<div class="d-flex">
<h5 class="card-title mb-0">Machine learning for
toehold switches</h5>
</div>
<div class="sub-title">
<span></span>
<span>Nature Communications, 2020</span>
</div>
</div>
</a>
<div class="card-body">
<p>Sequence-to-function deep learning frameworks for
engineered riboregulators.</p>
<span class="float-right">
<a
class="github-button-inactive"
href="https://github.com/midas-wyss/engineered-riboregulator-ML"
data-icon="octicon-standard"
data-show-count="true"
aria-label="Star Machine learning for toehold switches">Star</a>
</span>
</div>
</div>
</div>
</div>
<div
class="col-sm-12 col-md-6 col-lg-4 p-2 filtr-item"
data-category='all, past,phd'>
<div class="card mt-1">
<div class="card">
<a class="card-header"
href="https://doi.org/10.1038/s41551-020-0546-5">
<div>
<div class="d-flex">
<h5 class="card-title mb-0">Android app for lateral
flow assay image analysis</h5>
</div>
<div class="sub-title">
<span></span>
<span>Nature Biomedical Engineering, 2020</span>
</div>
</div>
</a>
<div class="card-body">
<p>A CRISPR-based assay for the detection of opportunistic
infections post-transplantation and for the monitoring
of transplant rejection.</p>
<span class="float-right">
<a
class="github-button-inactive"
href="https://github.com/jackievaleri/lateral_flow_quantification_app"
data-icon="octicon-standard"
data-show-count="true"
aria-label="Star Android app for lateral flow assay image analysis">Star</a>
</span>
</div>
</div>
</div>
</div>
<div
class="col-sm-12 col-md-6 col-lg-4 p-2 filtr-item"
data-category='all, past,undergrad'>
<div class="card mt-1">
<div class="card">
<a class="card-header"
href="https://www.nature.com/articles/s41592-019-0436-5">
<div>
<div class="d-flex">
<h5 class="card-title mb-0">Blue light-induced genome
folding</h5>
</div>
<div class="sub-title">
<span></span>
<span>Nature Methods, 2019</span>
</div>
</div>
</a>
<div class="card-body">
<p>LADL, light-activated dynamic looping for endogenous
gene expression control. Highlighted in Nature’s
technologies to watch in 2020.</p>
<span class="float-right">
<a
class="btn btn-outline-info btn-sm mb-2"
href="https://www.nature.com/articles/s41592-019-0436-5"
target="#">Details</a>
</span>
</div>
</div>
</div>
</div>
<div
class="col-sm-12 col-md-6 col-lg-4 p-2 filtr-item"
data-category='all, past,undergrad'>
<div class="card mt-1">
<div class="card">
<a class="card-header"
href="https://www.youtube.com/watch?v=3_n3bEUO4Lc&feature=youtu.be">
<div>
<div class="d-flex">
<h5 class="card-title mb-0">Communication interface
for Deaf patients and hearing physicians</h5>
</div>
<div class="sub-title">
<span></span>
<span>Senior Design, 2018</span>
</div>
</div>
</a>
<div class="card-body">
<p>Created neural machine translation and video capture
algorithm. Honorable mention in Engineering senior
design competition.</p>
<span class="float-right">
<a
class="btn btn-outline-info btn-sm mb-2"
href="https://www.youtube.com/watch?v=3_n3bEUO4Lc&feature=youtu.be"
target="#">Details</a>
</span>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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<div class="container-fluid anchor pb-5 skills-section" id="skills">
<h1 class="text-center">Skills</h1>
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<a class="skill-card-link">
<div class="card">
<div class="card-head d-flex">
<h5 class="card-title">Programming</h5>
</div>
<div class="card-body">
<p class="card-text">Proficient in Python, R, Java,
Matlab. Basic knowledge of HTML/CSS, OCaml, Linux</p>
</div>
</div>
</a>
</div>
<div class="col-xs-12 col-sm-6 col-lg-4 pt-2">
<a class="skill-card-link">
<div class="card">
<div class="card-head d-flex">
<h5 class="card-title">RNA-seq Analysis</h5>
</div>
<div class="card-body">
<p class="card-text">Bulk and single cell RNA-sequencing
analysis with DESeq2 and Seurat</p>
</div>
</div>
</a>
</div>
<div class="col-xs-12 col-sm-6 col-lg-4 pt-2">
<a class="skill-card-link">
<div class="card">
<div class="card-head d-flex">
<h5 class="card-title">Machine Learning</h5>
</div>
<div class="card-body">
<p class="card-text">Pytorch, Tensorflow/Keras, and
scikit-learn</p>
</div>
</div>
</a>
</div>
<div class="col-xs-12 col-sm-6 col-lg-4 pt-2">
<a class="skill-card-link">
<div class="card">
<div class="card-head d-flex">
<h5 class="card-title">App Development</h5>
</div>
<div class="card-body">
<p class="card-text">R Shiny and Android Studio</p>
</div>
</div>
</a>
</div>
<div class="col-xs-12 col-sm-6 col-lg-4 pt-2">
<a class="skill-card-link">
<div class="card">
<div class="card-head d-flex">
<h5 class="card-title">Cheminformatics and General Python
Packages</h5>
</div>
<div class="card-body">
<p class="card-text">RDKit, pandas, numpy, scipy</p>
</div>
</div>
</a>
</div>
<div class="col-xs-12 col-sm-6 col-lg-4 pt-2">
<a class="skill-card-link">
<div class="card">
<div class="card-head d-flex">
<h5 class="card-title">Molecular Biology</h5>
</div>
<div class="card-body">
<p class="card-text">PCR, Gibson cloning, Golden Gate
Assembly, Sanger and Illumina sequencing, IHC/IF</p>
</div>
</div>
</a>
</div>
<div class="col-xs-12 col-sm-6 col-lg-4 pt-2">
<a class="skill-card-link">
<div class="card">
<div class="card-head d-flex">
<h5 class="card-title">Rapid Prototyping and Electrical
Engineering</h5>
</div>
<div class="card-body">
<p class="card-text">Circuitry, Soldering, SolidWorks, 3D
printing</p>
</div>
</div>
</a>
</div>
</div>
</div>
</div>
</div>
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id="recent-posts">
<h1 class="text-center">Blog</h1>
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<div class="col-xs-12 col-sm-6 col-lg-4 pt-2 post-card">
<a class="markdown-container" href="categories/posts/post1.html">
<div class="card">
<div class="card-body">
<h5 class="card-title">Introduction: hello world!</h5>
<p class="post-summary">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.</p>
</div>
<div class="card-footer">
<span>Date: June 11, 2024</span>
</div>
</div>
</a>
</div>
<!-- Post Card 2 -->
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<a class="markdown-container" href="categories/posts/post2.html">
<div class="card">
<div class="card-body">
<h5 class="card-title">PyCon US 2024</h5>
<p class="post-summary">I really enjoyed attending PyCon US in Pittsburgh. Now that I have had some time to reflect on what I learned, I wanted to share my takeaways.</p>
</div>
<div class="card-footer">
<span>Date: June 18, 2024</span>
</div>
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</a>
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