ENGIN YAPICI, PhD Portland, OR

312-***-****

Portfolio

ad2nmm@r.postjobfree.com

Data Scientist & Product Manager

Data scientist with expertise in scientific data analysis, engineering, and visualizations. Experienced product manager with a focus on cross-functional scientific product development. Scientist with experience in high-throughput data generation for AI/ML applications and validations. Core Competencies

Data mining and analysis

App architecture design

Server setup/maintenance

RESTful API design

End user research & support

Data visualizations

Customer interviews

Workflow optimizations

Database design

Kanban & scrum management

Mockup designs

UI/UX design & optimization

Web visualization

Timelines and roadmaps

Git version control

Tech Stack

Frontend: VueJS, jQuery, SCSS, Gulp, Adobe Illustrator, Affinity Designer Backend: Python, Django, Flask, PHP, Docker, SQL

Databases: MySQL, PostgreSQL, Django ORM

Data wrangling & visualization: Pandas, Numpy, Matplotlib, Plotly Dash, D3.js, Jupyter Experience

Associate Director, Drug Discovery Absci - Vancouver, WA 2021 - 2023 Built and led a team of scientists to characterize large sets of drug candidates and generate high-throughput data for AI/ML model development and validations. Achievements:

Led the team to generate over 60,000 high-precision data for AI model development for in silico antibody discovery, which resulted in two pre-print articles in bioRxiv (link 1, link 2).

Oversaw the analysis and organization of the wet-lab data for AI/ML team use.

Advised the software and UI/UX engineers on internal web application development for data visualizations and presentations for antibody drug discovery.

Co-hosted 2 company-wide seminars on racial bias and equity. Principal Scientist II / Manager – Data Science Schrödinger - Portland, OR 2018 - 2021 Built and led a team of data scientists and chemists to develop cheminformatics data analysis and visualization tools to aid and enable Schrödinger’s drug discovery efforts. Achievements:

Triaged and organized high-throughput screening biological assay datasets for the AI/ML team.

Worked directly with the Biology, Medicinal Chemistry, Computational Chemistry, and AI/ML teams to facilitate data ETL, organization, and visualization.

Planned and oversaw the development of 4+ comprehensive cheminformatics web applications:

Curator — Enabling data scientists to curate and verify SAR datasets. Uses RDKit & Indigo to process structures; structure & table recognition tools for automatic content extraction.

PubQuery — Target triage tool that brings ChEMBL, SureChEMBL, RCSB databases together to serve the available papers, assays, measurements, and crystal structures in one interface.

Pulse — Competitive landscape analysis with clinical trial summaries, therapeutic indication and target mutation views. Allows users set up email notifications for clinical updates.

Cell Line Catalog — A streamlined interface to load spreadsheets from CROs, map the cell lines to the ExPASy Cellosaurus DB, and allow users to search the unified database.

Co-authored a peer-reviewed journal article that was published in J. Med. Chem (link).

Co-hosted 2 company-wide seminars on racial bias and equity. Sr. Scientist Pfizer - Lake Forest, IL 2015 - 2018 Developed and launched various data organization and inventory management web applications. Achievements:

Designed, developed, and launched a web-based order management system for 60+ users using JavaScript, jQuery, HTML5, CSS in frontend; PHP, MySQL in backend. (Click here for screenshots).

Designed and developed a SharePoint-based inventory management system with an audit trail feature. Launched 2 instances for two separate teams.

Developed and launched several internal SharePoint sites for the biosimilars organization.

Organized and managed 1 project management training with 3 separate modules for 12 people. Scientist II/III Adello Biologics (Formerly TPI LLC) - Chicago, IL 2014 - 2015 Developed and launched various data organization and inventory management web applications. Achievements:

Developed, launched, and managed a web-based inventory management system for 30+ users.

Authored 11 technical documents including SOPs, test methods, method qualification protocols & reports, equipment IQ/OQ protocols & reports, similarity reports, forced degradation reports.

Identified a gap in an instrument software, and implemented a solution for CFR 21 Part 11 compliance.

Education

PhD - Biochemistry University of Illinois at Chicago - Chicago, IL 2014 Thesis: Time-Gated Luminescence Detection for High-Throughput Screening of Protein Interaction and Inhibitions (Download Link)

MSc - Chemistry University of Illinois at Chicago - Chicago, IL 2012 BSc - Biological Sciences Middle East Technical University - Ankara, Turkey 2009 Awards

Make a Difference Award Pfizer, Inc. 2017

Chancellor's Student Service & Leadership Award University of Illinois 2013, 2014 The Finn World Travel Award The Protein Society 2013 Protein Society Young Investigator Travel Grant The Protein Society 2013 Graduation with High Honors Middle East Technical University 2009 Publications

Shanehsazzadeh, A., et al., Unlocking de novo antibody design with generative artificial intelligence, bioRxiv, 2023.

Bachas, S., et al., Antibody optimization enabled by artificial intelligence predictions of binding affinity and naturalness, bioRxiv, 2022.

Sindhikara, D., et al. Automated Design of Macrocycles for Therapeutic Applications: from Small Molecules to Peptides and Proteins, Journal of Medicinal Chemistry, 63 (20), 121**-*****, 2020.

Rajendran, M., Yapici, E., Miller, L. W., Lanthanide-based imaging of protein-protein interactions in live cells. Inorganic Chemistry, 53 (4), 1839 – 1853, 2014.

Yapici E., Reddy D. R., Miller L. W., An adaptable luminescence resonance energy transfer assay for measuring and screening protein-protein interactions and their inhibition. ChemBioChem, 13 (4), 553

– 558, 2012 (Selected for cover picture).

Garip S., Yapici E., Ozek N. S., Severcan M., Severcan F., Evaluation and discrimination of simvastatin-induced structural alterations in proteins of different rat tissues by FTIR spectroscopy and neural network analysis. Analyst, 135 (12), 3233 – 3241, 2010.

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