CV

Education

Massachusetts Institute of Technology, PhD in Biological Engineering (Jan 2019)
Mining the human microbiome for clinical insight; thesis, defense

Columbia University, B.S. in Biomedical Engineering (2013)

James Bowie High School, Austin, TX (2009)

Professional Experience

Science for America (2023-present)
Scientist, STEM

Analyze US education data (IPEDS completions) to develop novel metrics and data visualization approaches for understanding underrepresentation in STEM fields across higher education and within individual institutions.
Develop Python package to facilitate working with IPEDS data.
Investigate opportunities and approaches to reduce calculus’ role as a barrier to STEM in US higher education.
Launch communication coaching program for early-stage founders leading non-profit initiatives in STEM Equity and Education (in collaboration with Founder to Leader).
Work with Chief Scientific Officer and Strategic Advisors to set Science for America’s direction in STEM Equity and Education.
Define internal team strategy, manage Science for America fellows, and establish positive and collaborative culture within Science for America.

Freelance consulting (2023-present) Computational biology consultant & technical advisor, Skkellie LLC

Develop pipeline and interactive visualizations to support design and evaluation of siRNA candidates for provided gene targets. (Python, make, Dash, Plotly). Robigo
Identify hundreds of putative retrotransposons by searching for matches to a known retrotransposon across a large variety of taxonomies. (Python, ElasticBLAST, blast WGS, Nextflow, AWS Batch). Diamond Age Data Science, subcontractor
Audit current practices and provide strategic recommendations for code versioning, environment management, and knowledge sharing within early-stage computational team. Plonts
Download thousands of bacterial genomes and perform gene annotations with DRAM to develop a database supporting product development R&D. (Python & Biopython; AWS EC2, S3, and Athena). Plonts
Serve as strategic advisor to the Director of Engineering, with a specific focus on developing the company’s data science function. Concerto Biosciences

Biobot Analytics (2019-2023)
Founding Staff Data Scientist (Nov 2022 - present)
Founding Technical Lead, Data Science (Dec 2021 - Nov 2022)
Senior Data Scientist (Mar 2021 - Dec 2021)
Data scientist (Jul 2019 - Mar 2021)

As an early employee of Biobot Analytics, I wore many hats and did many things:

Data science: Analyze SARS-CoV-2 and opioid data from thousands of wastewater samples to gain public health insight (pandas, geopandas, scikit learn, scipy). Build data visualizations to communicate data concisely (matplotlib, seaborn, geopandas, altair). Work with other data scientists to build and launch data science features that make wastewater data more interpretable and actionable.
Technical leadership: Define data science priorities and lead a team of internal data scientists, consultants, and academic collaborators to build statistical models to interpret SARS-CoV-2 and opioid metabolite concentrations in sewage. Work with company leadership to develop Biobot’s data science strategy and roadmap.
Science communication & customer success: Communicate Biobot’s science through customer webinars, blog posts, and academic publications. Support customer success team to answer customers’ technical questions.
People management & team building: manage teams of 1-2 junior data engineers, 3-4 senior data scientists, and 2-3 junior data analysts. Establish consistent and successful hiring processes, and build the data science organization from 1 person to over 15 across three subteams. Establish & foster a positive and collaborative working culture.
Data engineering: Design and build data processing pipelines (Python, snakemake, bash, Jenkins) to convert lab results into customer pdf reports. Collaborate with senior software engineers to migrate legacy pipelines to cloud-hosted infrastructure (AWS, lambda).
Technical architecture and design: Design, build, and manage Biobot’s database and processes (Airtable, zapier) supporting all company needs related to ordering, customer metadata, laboratory, and data management. Work with software engineering, product, and project management teams to migrate legacy systems to scalable and cloud-based technologies (AWS, postgres, APIs). Write technical specifications and requirements documents for a variety of data science and software projects.
Project and program management: Coordinate high-visibility, high-impact projects that touch many departments within Biobot. Lead internal technical workstreams and serve as an external technical point person for large federal contracts.

Research experience

Alm lab, Massachusetts Institute of Technology (2014-2019)
Under the direction of Eric Alm

I did my PhD in Eric Alm’s lab at MIT. You can learn more about my research interests on our lab website and on my publications and research pages. You can download my thesis and defense slides, and also view them on my github.

Molecular and Microscale Bioengineering Laboratory, Columbia University (2011-2013) Under the direction of Samuel K. Sia

I was an undergraduate research assistant in Sam Sia’s lab for two years at Columbia. There, I worked on developing a point-of-care microfluidic device to diagnose multi-drug resistant tuberculosis. I primarily focused on the DNA amplification and detection modules, optimizing primers and reaction conditions off-chip.

Laboratoire de Biochimie, Ecole Polytechnique (Summer 2012)
Under the direction of Cedric Norais

I was an international undergraduate research intern at Ecole Polytechnique the summer before my senior year. There, I worked with Cedric Norais to study the acquired-immunity CRISPR system in E. coli.

Publications

See publications page.

Presentations

Oral presentations

March 2023 - HSPH Center for Communicable Disease Dynamics ID Epi Seminar Series Spring 2023. Watch the recording.

Oct. 2022 - MIT Microbiome Club Industry Seminar.

Mar. 2022 - “Supporting a nationwide Covid-19 wastewater monitoring program.” WEF Public Health and Water Conference, Wastewater Disease Surveillance Summit.

June 2021 - Boston Society of Civil Engineers 2021 Freeman Lecture.

May 2021 - “Wastewater analysis to understand community consumption of opioids.” EAPCCT 2021: Toxicology 2.0.

Aug. 2019 - “24-hour multi-omics analysis of residential sewage reflects human activity and informs public health.” American Chemical Society National Meeting. Wastewater-Based Epidemiology: Opportunities, Challenges & Applications to Public Health & Safety.

Apr. 2019 - “Intro to microbiome data visualization.” Cornell University 2019 Microbiome Hackathon: Microbiome Hack. Slides: cduvallet.github.io/mbiome-data-viz/

Feb. 2019 - “Tips, tricks, and philosophies on computational work.” Alm lab summit. Slides: cduvallet.github.io/phdchat-philosophies/

Nov. 2018 - “Framework for rational donor selection in fecal microbiota transplant clinical trials.” International Conference on Microbiome Engineering.

May 2018 - “Distribution-based methods to increase power and reduce redundancy in microbiome data.” Teaching and Developing QIIME 2 Workshop. (abstract)

Mar. 2018 - “Meta-analysis to identify consistent disease-associated microbiome shifts.” MIT-Harvard Microbiome Symposium.

Feb. 2018 - “Aspiration changes relationships in the aerodigestive microbiome.” Bioengineering and Toxicology Seminar

Oct. 2017 - “Meta-analysis to identify consistent disease-associated microbiome shifts.” MIT Department of Biological Engineering Retreat.

Oct. 2016 - “The human gut microbiome in health and disease.” Bioengineering and Toxicology Seminar

Poster presentations

Mar. 2018 - “Meta-analysis to identify consistent disease-specific and shared responses.” MIT-Harvard Microbiome Symposium. pdf

Mar. 2018 - “Meta-analysis of gut microbiome studies identifies disease-specific and shared responses.” Women in Data Science Cambridge. pdf

Jan. 2018 - “Meta-analysis of gut microbiome studies identifies disease-specific and shared responses.” Pacific Symposium on Biocomputing. pdf

Leadership and service

Read more about my leadership and service activities during my PhD.

Academic and Professional

MIT Microbiome Club, co-Founder, President (2015-2016), Executive board member (2016-2018)

MIT-Harvard Microbiome Symposium, co-founder and Organizing committee (2016 and 2017)

MIT Biotech Group, Beyond the Bench Initiative board member (2017-2018)

Departmental and MIT

Graduate Student Council Diversity and Inclusion Subcommittee, Vice Chair and Department and Classroom Inclusion co-coordinator (2017-2019)

In this role, I coordinated and oversaw semesterly conduit assemblies, which bring together diversity representatives from all MIT departments.

BE Graduate Student Board, Diversity Chair (2015-2018)

As Diversity Chair, I co-started the BE Application Assistance Program, co-wrote the BE Departmental Values Statement, and spearheaded the 2016 BE Diversity Climate Survey, which has informed diversity-related efforts since.

BE Resources for Easing Friction and Stress, BE Ref (2016-2019)

Biological Engineering Department Visiting Committee, Graduate student representative (2018)

Graduate Student Advisory Group for Engineering (GradSAGE), Advisory group to the Dean of the School of Engineering, Advisor/advisee relations subcommittee (2017-2019)

Mentorship

Insight Health Data Science Fellows, Supervised two data science fellows (Sep-Oct 2019).

MIT SuperUROP Program, Microbiome superUROP mentor (2016-2017). Supervised one undergraduate researcher.

Outreach

Science Club for Girls Young leaders in STEM program (Summer 2016 and 2017). Developed and taught three-day course on microbiology and the human microbiome.

Mr. John Bartucz’s computer science class (2017). Introduction to my career path and research.

MIT SPLASH (2015). “Microbiome 101: What’s in your poop?”

E3: Empowering, Encouraging, and Eliminating Barriers for Women in STEM (2015). Mentor and guest presenter.