About Me
Welcome to my website! My name is Nicholas Abad and I am currently a PhD Student in Heidelberg, Germany at the German Cancer Research Institute (DKFZ), which is the largest biomedical research center in Germany.
I recently submitted my PhD thesis called, "REMIND-Cancer: A Recurrence-Agnostic Workflow for Identifying and Prioritizing Functional Promoter Single Nucleotide Variants" and am planning on defending my thesis on 11 October 2024.
Briefly, my thesis is about the creation of a bioinformatics pipeline that identifies and prioritizes functional promoter SNVs, which are a class of mutations that are consistently missing from known oncogenic mutations.
Through the analysis of a public pan-cancer dataset as well as an internal precision oncology dataset, I used as input to my pipeline the genomic and transcriptomic information (if available) of roughly 3,000 samples and 30,000,000 mutations.
This analysis led to the positive in vitro validation of 10 promoter SNVs, some of which were highly-recurrent (i.e. occurring in many samples) and some of which were singletons (i.e. only in a single sample) and lowly-recurrent.
With my results, two papers are currently being written so I can't divulge too many details as of yet :)
In addition to being a PhD student, I'm also a part-time Machine Learning instructor at CodeOp, which is a company dedicated to providing tech-related bootcamps for women and/or people of the LGBTQ+ community, who are heavily misrepresented in the tech community, in a safe and inclusive fashion.
As one of the core members of the data science / machine learning educational team, I've designed, implemented, and taught a various amount of modules such as introduction to Python, Advanced Python, SQL, Exploratory Data Analysis, Machine Learning, and Advanced Machine Learning.
Also, to give a bit of a background on how I got to where I am, I'm originally from Silicon Valley where I received my Bachelor's Degree in Mathematics at the University of San Francisco (San Francisco, USA) with a minor in computer science. After graduating, I proceeded to move to the United Kingdom to earn my Masters Degree in Data Science with a Specialism in Statistcal Inference at Lancaster University (Lancaster, UK).
Soon after I completed my Masters, I then decided to again move to another country and decided to work as a Machine Learning Engineer in Cologne, Germany first for a start-up and then afterwards for a consultancy firm.
PhD Student at the German Cancer Research Center (DKFZ).
- Name: Nicholas Abad
- City: Heidelberg, Germany
- Hometown: San Francisco, USA
- Bachelor Degree: Mathematics
- Masters Degree: Data Science
- PhD Start Date: 1 December 2020
- PhD End Date: 11 October 2024
- Research Division: Division of Applied Bioinformatics
- Faculty: Heidelberg University Faculty of Engineering Sciences
- Working Experience: 6 Years (including PhD)
Skills
Years of Programming Experience in Python
Years of Programming Experience in R
Years of ML Experience and Education
Cups of Coffee Drank
Resume
Education
PhD Student
German Cancer Research Center (DKFZ)
Heidelberg, Germany
Dec 2020 - Oct 2024 (Expected)
Division of Applied Bioinformatics at the DKFZ
Faculty of Engineering at Heidelberg University
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Recently submitted my PhD thesis: “REMIND-Cancer: A Recurrence-Agnostic Workflow for Identifying and Prioritizing Functional Promoter Single Nucleotide Variants”
Designed and implemented a user-friendly and scalable pipeline (REMIND-Cancer Pipeline) to identify and prioritize functional promoter mutations using genomic and transcriptomic data.
Due to being in the process of submitting two manuscripts, further details of my project are not yet publicly available.
Masters Degree in Data Science
Lancaster University
Lancaster, United Kingdom
Specialization in Statistical Inference
Oct 2017 - Sep 2018
Graduated with Distinction (Highest Honors)
Courses Taken:
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Bayesian Inference
Likelihood Inference
Distributed Artificial Intelligence
Applied Data Mining (NLP)
Generalized Linear Models
Data Mining (Neural Networks)
Bachelors in Mathematics
University of San Francisco
San Francisco, CA
Minor in Computer Science
Aug 2012 - May 2016
Courses Taken:
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Data Mining
Statistics
Probability
Mathematical Modeling
Econometrics
Linear Algebra
Combinatorics
Programming in Python
Programming in R
Data Structures and Algorithms
Professional Experience
Data Science Instructor (Part Time)
CodeOp
Barcelona, Spain (fully remote)
April 2022 - Present
Teach Python and Data Science to women and/or people of the LGBTQ+ community, who are heavily misrepresented in the tech community, in a safe and inclusive fashion
Machine Learning Engineer
Alexander Thamm GmbH
Cologne, Germany
Jan 2020 - Dec 2020
By working for the best Data Science / AI consultancy firm in Germany, I worked directly with clients in various industries (i.e. Industrial, Marketing, Biomedical, etc.) to improve operational processes and create visionary, data-based products and solutions individually tailored to the needs of our clients.
Detailed Description of Tasks
Data Scientist
fedger.io
Cologne, Germany
Nov 2018 - Dec 2019
Using state-of-the-art Object Detection methods, I lead the AI Team in creating and continuously developing our neural network architecture in order to detect and extract structured information from documents.
Detailed Description of Tasks
Data Science Intern
Co-op Insurance
Manchester, United Kingdom
June 2018 - Sep 2018
As part of my Master's dissertation, I implemented both parametric and non-parametric modeling techniques and hyper-parameter optimization methods to improve the Co-op's Motor Insurance rates.
Detailed Description of Tasks
Consulting
Outisde of my PhD, I also offer individual and group consulting work in the following topics:Coding in Python/R
For basic or intermediate students.
Potential Topics:
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Python Fundamentals
Functions and Modules
Data Structures
Intermediate Topics
Coding Best Practices
Data Science
For basic or intermediate students.
Potential Topics:
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Introduction to Data Science
Data Manipulation
Statistical Theory
(Un)supervised ML Algorithms
Data Visualization
Story Telling via Data
DS/ML Interview Prep
For those trying to land their first Data Scientist or Data Analyst role.
Potential Topics:
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Building a Strong Foundation
Crafting Your Resume and Portfolio
Networking and Personal Branding
Interview Preparation
Are you eager to embark on a journey into the world of Python programming, data science, or kickstarting your career in this growing field? If so, I invite you to join me for a complimentary consultation session tailored just for you. Whether you're a beginner curious about Python's possibilities, an aspiring data scientist looking to master the fundamentals, or someone striving to land that elusive first data science job, I'm here to guide you every step of the way. During our free consultation, we'll discuss your goals, aspirations, and learning preferences. It's an opportunity for us to get to know each other, chart out a personalized learning path, and address any questions you may have.
As for pricing, I offer once-a-week video call sessions where we could discuss topics, your progress, and, most importantly, any questions that you may have for 100 euros a week (price negotiable). In addition to this, I'll be available for any/all questions via email and/or slack at your convenience and will also craft a peronsonalized learning plan. If this interests you, feel free to email me so we can get started :)
Outside of Work
Rather than trying to explain who I am outside of my education and profession, here are some of my favorite pictures to hopefully show you what I value the most and what I enjoy doing!
Dubrovnik, Croatia - 2019
Some of my best friends from San Francisco and I decided to rent jet-skis and go around the Adriatic Sea. Pictured in the background is the Fort Lovrijenac.
San Francisco, USA - 2016
Days before all of us graduated from the University of San Francisco, my best friends and I decided to have one last get together before each of us went our separate ways.
Zermatt, Switzerland - 2018
To cap off my three-week solo backpacking trip across Europe for the first time, my final destination was an acoustic music festival (Zermatt Unplugged) in the Swiss Alps.
Cerritos, USA - 2018
My crazy cousins and I taking a funny picture with the greatest grandpa in the world before our annual family Christmas party!
Cataract Falls, USA - 2017
Three of my good friends, including my roommate at the time (pictured in the back), and I decided to have a nice getaway in the nearby city of Stinson Beach to go hiking at this beautiful location!
Cologne, Germany - 2019
Me after completing one of my lifelong goals of running a full marathon! What you can't see (thankfully...) was the amount of pain and exhaustion that I was going through and how I could barely even walk afterwards... Either way, it was all worth it once I crossed that finish line! :)
Petaluma, California - 2017
To celebrate one of my best friends birthdays, my friend group and I went to a local brewery (Lagunitas) with amazing beer and even better people!
Edinburgh, Scotland - 2018
As you could probably tell by my big smile, I was super excited to be running in my first ever race, which happened to be the Edinburgh Half Marathon!
Cologne, Germany - 2019
To try something new, some of my friends and I actually completed an escape room - despite all the arguing and time pressure we were under :)
Lake Tahoe, California/Nevada - 2019
To celebrate the start of the New Year, some of my best friends and I spent a couple days in a cabin in Tahoe where we hung out, played board games, and played in the snow, which is something us Californians aren't all that used to
Contact
Location:
Division of Applied Bioinformatics at the DKFZ, Heidelberg, Germany
Email:
nicholas.a.abad@gmai.com
LinkedIn:
linkedin.com/in/nicholasabad
Twitter:
twitter.com/_nicholasabad_
GitHub:
github.com/nicholas-abad