References

Prof. Lior Pachter (lpachter@caltech.edu)
California Institute of Technology (Caltech)
Bren Professor of Computational Biology, Departments of Biology and Computing & Mathematical Sciences
Prof. Pachter was my Ph.D. advisor at Caltech.

Prof. Saul Priceman (spriceman@coh.org)
City of Hope (soon: Founding Director of the KSOM/USC Norris Center for Cancer Cellular Immunotherapy Research at USC)
Associate Professor, Department of Hematology & Hematopoietic Cell Transplantation
Prof. Priceman and I have been closely collaborating since the beginning of 2022. I am responsible for analyzing the large transcriptomic datasets generated by his lab at City of Hope as part of the first clinical trials testing CAR T cell therapy for the treatment of solid tumors, including prostate and breast cancer.

Prof. Dennis Claessen (d.claessen@biology.leidenuniv.nl)
Leiden University
Professor of Molecular Microbiology and Director of Education
Prof. Claessen is the chair of the M.Sc. program I completed at Leiden University and was a co-mentor for my Bachelor’s and Master’s theses.

IT Skills

Python (expert, including machine learning methods and scRNAseq data analysis)

C++

Bash

R

LaTeX

Git and GitHub

Jupyter / Google Colab

Languages

German
Native bilingual

Catalan
Native bilingual

English
Full professional proficiency

Dutch
Full professional proficiency

Spanish
Limited professional proficiency

October 2021 – present

Efficient querying of genomic reference databases with gget

California Institute of Technology (Caltech), Pasadena (CA), USA
Department of Biology and Biological Engineering, Pachter lab

I developed gget, a free and open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of biocomputational analysis in a single line of code.

Since its first release in May 2022, gget has become a worldwide standard in transcriptomic and proteomic data analysis. It has been rapidly adopted, with over 800 stars on GitHub and 100,000 downloads.

Skills: Python, GitHub, SQL, UX, Project Management

Associated publications:
https://doi.org/10.1093/bioinformatics/btac836 (first author)
https://doi.org/10.1093/bioinformatics/btae095 (first author)
https://doi.org/10.1101/2023.07.20.549945

June 2022 - present
First clinical trials in humans: CAR T cell therapies for solid tumors
Pachter lab, California Institute of Technology (Caltech)

In collaboration with the Priceman lab at City of Hope National Medical Center, CA USA, we are developing and investigating the efficacy of CAR T cell therapy for solid tumors, including prostate and breast cancer. I analyzed the transcriptomic dataset, including single-cell gene expression and V(D)J immune repertoire sequencing, obtained from the blood, CAR T product, and solid tumor tissue of 12 prostate cancer patients at different time points of CAR T therapy, to reveal significant differences in the immune landscape dynamics. The transcriptomic data analysis identified relevant time points for clonotype expansion, and the existing dataset will be expanded accordingly, as well as to include data from breast cancer patients and cerebrospinal fluid samples.

Associated publications:
https://www.nature.com/articles/s41591-024-02979-8

April 2018 – December 2018

Development of an Optimized Fluorescent Probe for Subcellular Visualization of the Selective Serotonin Reuptake Inhibitor Fluoxetine.

California Institute of Technology (Caltech), Pasadena (CA), USA
Department of Biology and Biological Engineering, Lester lab

Resulted in 1st master’s thesis (Grade: A+), which was awarded Best Master’s Thesis by the Leiden University International Studies Fund.

Skills: Evolution of biosensor proteins by site-saturation mutagenesis (SSM); Protein purification using Ni-NTA affinity chromatography; Confocal imaging and electrophysiological recordings of live brain slices; HELA cell culture handling and transfection; Laboratory mouse husbandry and surgery (intracranial AAV injections)

Associated publications:
https://doi.org/10.7554/eLife.74648 (co-first author)
https://doi.org/10.1523/JNEUROSCI.1519-22.2022

Work experience & volunteering

December 2023
Documentary short film about gget, Berlin, Germany
YouTube
I produced and starred in a short documentary about my software gget and the importance of open-source software in collaboration with the Prototype Fund and VAYM Productions, with funding from the Open Knowledge Foundation Germany, the German Aerospace Center (DLR), and the Federal Ministry of Education and Research.

July 2023
Recorded a podcast episode for the Prototype Fund Public Interest Podcast about the importance of open-source software and its role in academic research (in German).

February 2020 – February 2021
Teacher at Family Coding Nights at the Altadena Library, Altadena, CA USA
Teaching interested parents and children basic JavaScript coding using p5.js

January 2021
Caltech Biology Recruitment Organizer, Caltech
Developed a virtual environment to facilitate graduate student recruitment at Caltech and allow candidates to “visit” Caltech during the coronavirus pandemic, even from the other side of the globe. I originally built the virtual Caltech for the Biology option. Due to its enormous popularity, I later created and hosted several versions of the virtual Caltech for recruitment to other options, including Geological and Planetary Sciences (GPS), Chemistry and Chemical Engineering (CCE), Neurobiology (NB), and Bioengineering (BE).

January 2020 – June 2021
Volunteer and fundraiser for Girls on the Run Orange County, Santa Ana School District, CA USA
Raised $600 for the charity Girls on the Run Orange County to run the SDCCU OC Half Marathon. Girls on the Run focuses on the empowerment of young girls (3rd-8th grade) through research-based curricula, service projects, and training for a 5 km race event.

November 2017 – April 2018  
Intern at the IT-company Moddix, Leiden, The Netherlands
As part of the Leiden Leadership Program, I designed a virtual toolkit to promote effective communication between company and clients, assisting fruitful collaborations with several prominent clients such as Events Travel and the Dutch State Lottery.

July 2017 – August 2017 (summer job)
Clinical Research Associate in the analytical chemistry laboratory at Biofrontera Bioscience GmbH, Leverkusen, Germany
I was directly involved in the formulation development of a cosmetic product for sensitive skin and validated formulations using high-pressure liquid chromatography.

May 2016 - April 2018
Beta and Life Science Representative at the Honors Academy, Leiden University, The Netherlands
The Honors Academy encompasses all seven Honors Colleges at Leiden University. I organized joint events to bring students and teachers from all fields of study together and to improve the Honors experience.

November 2015 -April 2018
Student Ambassador Honors College Beta and Life Sciences, Leiden University, The Netherlands
My role as ambassador of the Honors College for STEM students included the recruitment of new Honors students, as well as mentoring of existing students. To increase inter-division bonding, I organized a student-versus-teacher pub quiz and excursions to scientific companies and exhibitions, such as Rijk Zwaan and Micropia.

TEACHING & mentorship

June – August 2023
Summer Undergraduate Research Fellowships (SURF) Mentor, Caltech
I mentored an aspiring Caltech computer science sophomore over a 10-week period during the summer, which resulted in the development and publication of the gget elm project.

December 2021
Visiting Lecturer at Proof School, San Francisco, CA USA
Guest lecture to high school students about Drosophila as a model organism and an introduction to Drosophila genetics.

September – December 2021
Sole Teaching Assistant for Bi/CNS 216 - Behavior of Mammals, Caltech
I generated and maintained the online course material (using Canvas) and general course management. I was the main point of contact for students and lecturers, and graded student presentations

June – August 2021
WAVE Fellows Program Mentor, Caltech
This program supports Caltech’s diversity, equity, and inclusion mission by increasing visibility and accessibility to graduate school options. I mentored a UW-Madison undergraduate over a 10-week period during the summer, teaching her how to work with Drosophila as a transgenic model organism, perform immunohistochemistry and confocal microscopy, and develop imaging data analysis pipelines using Fiji and Python.

March – June 2021
Head Teaching Assistant for NB/Bi/CNS 150 - Introduction to Neuroscience, Caltech
In addition to the tasks listed below for NB/Bi/CNS 150 in 2020, I designed and taught the lecture on vision and visual processing.
I was awarded Caltech Best Teaching Assistant 2021 for my efforts.

March – June 2020
Head Teaching Assistant for NB/Bi/CNS 150 - Introduction to Neuroscience, Caltech
I generated and maintained the online course material (using Canvas and Piazza) and general course management, including workload distribution among the teaching assistants. Moreover, I designed and graded weekly problem sets, quizzes for each lecture (3 lectures per week), and exams (midterm and final). Lastly, I gave weekly office hours and was the main point of contact for students, lecturers, and the other teaching assistants.

Extracurricular activities

September 2017 – June 2018
Leiden Leadership Program, Leiden University, The Netherlands
In addition to my M.Sc. degree program, I participated in and completed the Leiden Leadership Program (LLP). The LLP is a competitive program focused on leadership skills, teamwork, and business development.

January 2015 – July 2017
Honors College, Leiden University, The Netherlands
Specialization: Beta & Life Science
I completed additional coursework and activities in the field of education and research, including a two-month internship at the Max Planck Florida Institute for Neuroscience, Jupiter, FL, USA.

Certificates & Relevant Coursework

July 2022
Caltech Data Science and Artificial Intelligence (DataSAI) Bootcamp

March 2022
IBM Professional Data Science

September – December 2021
Caltech Mathematics in Biology
(probability and stochastic processes, linear algebra and transforms, dynamical systems, scientific programming)

January - March 2020
Caltech Statistical Inference in the Biological Sciences
(generative modeling, parameter estimation, model comparison, hierarchical modeling, Markov chain Monte Carlo, graphical display of inference results, and principled workflows)

August 2019
Master of Science in Molecular Genetics and Biotechnology (GPA: 4.0/4, cum laude)

December 2018
TOEFL iBT (118/120)

June 2018
Leiden Leadership Program (cum laude)

August 2017
Bachelor of Science in Biology with Honors College certificate (GPA: 3.8/4)

July 2014
GCE Advanced Level Physics (cum laude)

November 2013
GCE Advanced Level Chemistry (cum laude)

HONORS & Awards

2024
Finalist at the Bill Gross Prize for Entrepreneurship

2022
Open Knowledge Foundation Prototype Fund Award for innovative open-source software
Caltech Best Teaching Assistant 2021 (awarded by the Graduate Student Council)

2021
Tianqiao and Chrissy Chen Graduate Innovator Award

2019
Best Master’s Thesis funded by the Leiden University International Studies Fund
Additional media coverage here and here

2016
Best Oral Presentation at the LACDR 3rd Annual Symposium

fellowships & Grants

2024
Tianqiao and Chrissy Chen Travel Grant to attend the Winter Q-Bio conference
Merkin Translational Research Grant (TRG) (I initiated and wrote a collaborative TRG, which was awarded to the Pachter, Chen, and Gradinaru labs.)

2023
James P. Taylor Foundation for Open Science (CSHL Biology of Genomes Scholarship)

2019
Caltech Biology and Biological Engineering Graduate Research Fellowship

2018
Leiden University International Studies Fund (LISF L18020-1-45)

Leiden University Master of Science Biology Award for exceptional research abroad

LUSTRA+ Scholarship for outstanding academic research outside of Europe

Posters & presentations

The University of Sydney Statistical Bioinformatics Seminar (September 2024) (invited speaker)
“How to catch a virus (and write software that biologists can actually use)”

7th International Conference of Quantitative Genetics (ICQG7) (July 2024) (speaker)
“How to catch a virus.”

Three-Minute Thesis (May 2024)
“The Secret World of Viruses” YouTube

Ph.D. thesis defense (March 2024)
“Complexity of Transcriptomic Data Analysis and Implications for Biological Discovery” YouTube

11th annual Winter q-bio meeting 2024 (1st author poster)
“Efficient and accurate detection of viral sequences at single-cell resolution reveals putative novel viruses perturbing host gene expression”

Prototype Fund Demo Day 2023 (keynote speaker)
“Auf der Suche nach NUDEL im Datenbankspaghetti.” YouTube
(“Looking for the gene NUDEL in the genomic database spaghetti.”)

Cold Spring Harbor Laboratory (CSHL) Biology of Genomes conference 2023 (speaker)
“How to catch a virus.” YouTube

Caltech Biolunch 2023 (speaker)
“Efficient querying of genomic reference databases with gget.”

American Society of Human Genetics (ASHG) in Los Angeles 2022 (1st author poster)
”Efficient querying of genomic reference databases with gget”

Caltech Biolunch 2022 (speaker)
“Biological consequences of electromechanical effects in neurons.”

Cleveringa conference in New York 2019 (keynote speaker)
”The Secret Life of Antidepressants - A Story About Biosensors”

Society for Neuroscience Annual Meeting in Chicago 2019 (1st author poster)
”An Optimized Biosensor Visualizes the Selective Serotonin Reuptake Inhibitor Fluoxetine in the Endoplasmic Reticulum of Live Cells”

Society for Neuroscience Annual Meeting in San Diego 2018 (2nd author poster)
“Imaging Escitalopram in the Endoplasmic Reticulum of Live Cells and Extensions to Other Antidepressants“