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Jonathan Nowacki

Jonathan Nowacki

Data Scientist

Roche

Technologies

My Portfolio Highlights

My New Course

ARIMA Models in Python

My New Course

Advanced Deep Learning with Keras

My New Course

Advanced NLP with spaCy

Python / R Guru | Loves Business & Science! | Adjunct Professor of Graduate Data Science & Artificial Intelligence | M.Sc. Bioinformatics | MBA | Data Analysis of Finance, Healthcare and Genetics | Hiking, Mixed Martial Arts & Acrobatics

My Work

Take a look at my latest work.

course

Introduction to Deep Learning in Python

course

Large Language Models (LLMs) Concepts

workspace

Course notes: Extreme Gradient Boosting with XGBoost

DataCamp Course Completion

Take a look at all the courses I’ve completed on DataCamp.

My Work Experience

Where I've interned and worked during my career.

Butler University | Jan 2023 - Present

Adjunct Professor of Data Science

- Professor of 600 level Data Science and Artificial Intelligence - Taught in Python and R - Keras, Tensorflow, scikit-learn, statsmodels, and more...
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Roche | Aug 2015 - Present

Senior Bioinformatician

In my present role, I develop bioinformatics software and pipelines. Projects include epigenetics, target enrichment, sequence capture, RNA analysis and viruses. During the pandemic, I developed multiple bioinformatics pipelines and software programs to analyze SARS-CoV-2 data coming off of a next generation high throughput sequencing platform. • In a production level environment, I developed a wide variety of pipelines to process DNA, RNA and raw instrument files to successfully enable Roche’s applications, marketing and automation teams to perform their jobs and process petabytes of genomic data. This includes, but is not limited to, whole genome shotgun, sequence capture, epigenetic, variant calling, transcriptome, umi, tumor, viral and metagenomics pipelines. • Worked with marketing to produce a competitor comparison to support the sales team. This resulted in convincing data that our products were significantly more cost effective than the competition in scanning for a wide range of medically relevant genes. This includes, but was not limited to, showing a 7 fold improvement compared to the competition when scanning for the famous breast cancer genes BRCA1 and BRCA2. • I used a competitor comparison analysis, that I developed with marketing, to give a 25 minute presentation at the largest international human genetics conference in the world. The video titled “Maximize Value with Target Enrichment”, was presented at the American Society of Human Genetics (ASHG) in 2020. This video is available at: https://youtu.be/kGicPOvh2iw • Placed in the top tier of a machine learning competition (RAAD challenge) which used machine learning to analyze biomarkers and medical records to predict mortality rate among 7 different types of cancer patient groups.

Roche | Sep 2008 - Aug 2016

Bioinformatics, Computational Biology Applications Consultant & IT

• Worked on marketing projects, created promotional posters, created brochures and made customer facing presentations at scientific conferences. Some of this material was used not only in scientific conferences, but also in the 2011 movie Contagion starring Matt Damon, Jude Law and Gwyneth Paltrow. • During the 2009 swine flu pandemic, I successfully supported Walter Reed Army Medical Center to enable them to successfully process H1N1 viral data they weren’t able to process without my help. Supported the 454 Sequencing Instrument, a next generation sequencing device that’s currently at the Smithsonian Institute and was used by the Department of Homeland Security (DHS) to scan for biological weapons. • Supported and managed High Performance Computing (HPC) Clusters at top institutions across the world. No matter what the problem, I made sure they were up and functioning with minimal downtime. Routinely coordinated the travel and dispatching of engineers and Ph.D. level field support across North America to ensure high value customers worth millions continued to function.

Indiana University School of Medicine | Nov 2006 - Sep 2008

Computational Biologist

Took lead in developing a bioinformatics knowledge base for the IU School of Medicine. A process that involved reviewing hundreds of abstracts and bioinformatics tools as well as programming in PHP, AJAX, jQuery, Javascript, MySQL and SQLite. Packaged and programmed bioinformatics software for distribution and cross- platform portability by utilizing PHP, MSSQL, MySQL, postgreSQL, SQLite and Nullsoft Scriptable Install System (NSIS). Aided in the development of laboratree.org by programming in CakePHP, PHP, Perl and MySQL. Structure prediction using Tripos, Sp3 and various other techniques. Aided in the construction of a database of receptor-ligand interactions with two and three-dimensional structures. Database also includes binding thermodynamics from isothermal titration calorimetry for aiding in virtual screening of drugs. Rendered the image on the cover of Chemical Biology & Drug Design, May 2007 - Vol. 69 Issue 5 Page 291-379.

Marine Biological Laboratory | Feb 2006 - Sep 2006

Bioinformatician

Worked on infectious diseases. Co-wrote genomics pipeline using Perl and MySQL in a Unix environment which performed close-to-real-time statistical analysis and visualization of genomic data from the high-throughput sequencing lab. Performed hardware analysis and documentation. Wrote ClusterFitch which used a portable batch system to run Fitch on a Beowulf cluster.

NASA - National Aeronautics and Space Administration | Feb 2006 - Sep 2006

Bioinformatician

NASA Astrobiology Institute. Worked for the Mitch Sogin lab in Woods Hole Massachusetts analyzing extremophiles which would give clues for extraterrestrial life. https://astrobiology.nasa.gov/nai/directory/sogin-mitchell/index.html

My Education

Take a look at my formal education

Master of Business Administration - MBA, Finance & EconomicsButler University | 2017
Masters of Science, Biomathematics, Bioinformatics, and ComputationalIndiana University Bloomington
Indiana University Bloomington

About Me

Jonathan Nowacki

Adjunct Professor of 600 Level Data Science & Artificial Intelligence | M.Sc. Bioinformatics | MBA | Data Analysis of Finance, Healthcare and Genetics | Hiking, Mixed Martial Arts & Acrobatics

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