Iulian Ichim

Bucharest, Romania • ichim.iulian12 [~at~] gmail.com

Bioinformatics Developer | Computational Biology · PK-PD/PBPK Modeling & QSP | Python, R, Flask

Bioinformatics developer and data analyst with a background in biomedical engineering, computational genomics, and pharmacokinetic modeling. I build tools that bridge R-based bioinformatics workflows with Python ecosystems — from Galaxy platform wrappers to genomic file format parsers to compartmental models for drug concentration estimation.

I have hands-on experience developing bioinformatics tooling at the Ziemann Lab (Deakin University / Burnet Institute), where I built a Python Galaxy wrapper and package for the DEE2 RNA-seq data repository, and at Oak Bioinformatics LLC, where I developed genomic file format parsers and annotation pipeline modules for the OakVar platform.

I have a strong interest in quantitative systems pharmacology (QSP) and PK-PD modeling — particularly ODE-based compartmental modeling of ADME dynamics — and independently develop PK-PD simulation tools in Python. My undergraduate background at Grigore T. Popa University spans wet-lab techniques, biosignal processing, and Bio-MEMS prototyping. Seeking opportunities in bioinformatics, computational biology, or QSP/PK-PD modeling.

Contact me

Experience

Ziemann Lab — Deakin University / Burnet Institute

Bioinformatics Intern • Feb. 2023 — Sep. 2023

  • Developed a Python Galaxy wrapper and standalone package for the getDEE2 R library, enabling Python-native access to the Digital Expression Explorer 2 (DEE2) - a repository of uniformly processed RNA-seq data across 9+ species.
  • Designed custom Python classes using rpy2 to bridge R SummarizedExperiment objects with pandas DataFrames for downstream statistical analysis and data export.
  • Implemented CLI and Galaxy-compatible interfaces, including XML tool definitions for local Galaxy instance integration.
  • Managed and deployed a production Galaxy instance on Nginx (VPS configuration, custom domain, server administration).
  • GitHub: github.com/IulianIV/dee2-galaxy

    • Oak Bioinformatics LLC

    Bioinformatician, Freelance • Jan. 2023 — Jan. 2024

  • Developed Python modules for the OakVar bioinformatics platform, focusing on genomic data processing and annotation pipeline testing.
  • Built test scripts for gene and variant-level annotator modules, improving quality assurance across the OakVar platform.
  • Designed and implemented MAF, GVF/GFF3 file reporter and converter modules for genomic data format interoperability.
  • Developed parsing algorithms for standard bioinformatics file formats, enabling conversion pipelines for annotation workflows.

    • PestControl Expert

    Marketing & Data Analytics Specialist • Sep. 2019 — Jun. 2023

  • Managed data-driven marketing operations across a multi-brand B2B/B2C portfolio.
  • Built ETL pipelines and automated reporting workflows using Google Apps Script and Python to support analytics and business decisions.
  • Applied statistical analysis and segmentation to campaign performance optimization across multiple channels.

    • Protectia Muncii SSM RSGE

    Data & Analytics Specialist • Jun. 2024 — Sep. 2024

  • Applied data analytics and statistical methods to B2B lead generation strategy, including segmentation models, risk assessment, and performance reporting.
  • Implemented automated reporting pipelines and tracking dashboards to support business decisions across client accounts.

    • Education

    University College Cork, Ireland

    Graduate Studies, Bioinformatics & Computational Biology • Sep. 2023 — May 2024

  • Completed graduate-level coursework in Computational Genomics, Biostatistics, Data Analysis with R, and Bioinformatics Programming.
  • Left the programme after completing coursework and research placements.

    • Grigore T. Popa University of Medicine & Pharmacy, Iași, Romania

    BSc, Bioengineering and Biomedical Engineering • 2015 — 2019

    Projects

    Developer • Feb. 2023 — Sep. 2023

    Python Galaxy wrapper and standalone package for the getDEE2 R library, enabling programmatic access to the DEE2 repository of uniformly processed RNA-seq data across 9+ species. Bridges R and Python via rpy2, converting SummarizedExperiment objects to pandas DataFrames. Supports CLI usage, Galaxy platform integration, and TSV export for downstream statistical analysis. Technologies: Python, R, rpy2, pandas, Galaxy Platform, XML, Nginx.

    PK-PD Concentration Modeling Tools

    Developer • 2024 — Present

    Pharmacokinetic modeling tools implementing one- and two-compartment models for estimating blood and tissue concentrations of bioactive compounds over time. Features ODE-based simulation of absorption, distribution, and elimination kinetics using SciPy, with support for multi-compound interaction modeling, dosing schedule optimization, and calibration against laboratory results. Technologies: Python, SciPy, NumPy, Flask, React.

    Research Experience

    Evaluation of the degree of degradation of Saccharomyces cerevisiae cells by fluorescence microscopy

    Degree Research • April — July 2019

  • Obtained experience with utilizing ultrasonication equipment while executing the degradation phase of cell membranes to further the study.
  • Applied fluorescence microscopy principles to determine the degree of destruction on cell membranes.

    • Device for the controlled administration of drugs in topical conditions

    National Bioengineering Conference for Students & Young Researchers • May 2019 • First place, poster section

  • Architected a prototype for a device that supports the treatment of topical ailments over extended periods of time by using knowledge acquired from Bio-MEMS (biomedical microelectromechanical systems) courses.
  • Used microcontrollers to enable the device to provide topical treatments on a regular basis according to a schedule appropriate for the selected drug.

    • Biosignal monitorization system using open-source platforms

    National Bioengineering Conference for Students & Young Researchers / International Balkan Workshop on Applied Physics and Materials Science • May 2017 / July 2018

  • Conducted an in-depth study into upper limb biomechanics using flex sensors connected to open-source microcontroller device libraries to facilitate rehabilitation and in silico biomechanical simulations.

    • Other research experience

    Faculty of Medical Bioengineering • 2015 through 2019

  • Completed a spectrometric determination of fluorine concentration in multiple local sources of water.
  • Performed a study of Streptomycin retention mechanism using fluidized layer ion exchangers in addition to the ion-exchange separation process of Vitamin B10.
  • Examined and analyzed the EMG & EKG biosignal processing using Arduino and open-source Python platforms.
  • Explored the applications and perspectives of Cold Electric Discharge Plasmas in Bio-Medicine.

    • Skills

    Bioinformatics & Computational Biology

    RNA-seq data analysis, genomic file formats (MAF, GVF/GFF3), Galaxy Platform, OakVar, rpy2, Bioconductor, variant annotation, biosignal processing (EEG, EKG, EMG).

    Pharmacokinetics & QSP Modeling

    One- and two-compartment PK-PD modeling, ODE-based simulation of ADME dynamics (SciPy), multi-compound interaction modeling, dosing schedule optimization, quantitative systems pharmacology (QSP), calibration against laboratory data.

    Programming

    Python (primary) — bioinformatics tooling, Flask web development, data pipelines, scripting. R — statistical analysis, Bioconductor, data analysis workflows. JavaScript / React — front-end development. C/C++ — microcontroller programming. SQL — SQLite, MySQL, PostgreSQL.

    Data Science & Analysis

    pandas, NumPy, SciPy, matplotlib, Plotly, statistical analysis, ETL pipelines, data visualization, Google Apps Script.

    Infrastructure & Tools

    Linux (Ubuntu), Nginx, VPS administration, cPanel, Git / GitHub, Arduino / microcontrollers, Capacitor (mobile).

    Languages

    English — C1, CAE Cambridge. Romanian — Native.

    Organizational Leadership

    Experience coordinating and leading teams through volunteer work — motivating people, identifying strengths, and organizing towards shared goals (Bioengineering Students Association, Coordinator → President, 2015–2018).

    Recognition

    First place, Poster Presentations

    National Bioengineering Conference for Students & Young Researchers • 2019

    Awarded for the development of a Device for the controlled administration of drugs in topical conditions.

    Volunteersim

    Bioengineering Students Association (Asociația Studenților Bioingineri)

    Coordinator, President • Oct. 2015 — May 2018

  • Served as Coordinator (Oct 2015 – Oct 2017) then President (Oct 2017 – May 2018).
  • Coordinated multiple local charitable events, sports events, and the National Bioengineering Conference for Students & Young Researchers, which grew into an international event.

    • IEEE International Conference EHB 2017

    Event Organizer • 2017

  • Provided support to the General Chair with the organization of the event by communicating with international participants.

    • Professional Affiliations

    Bioengineering Student Association

    Internal Affairs Vicepresident, Preisdent • Oct. 2015 — July 2019

  • Coordinated multiple local charitable events, local and national sports events, and the National Bioengineering Conference for Students & Young Researchers which became an international event

    • Outside Interests

    • Programing
    • Technology
    • Natural sciences
    • Boxing
    • Reading
    • Hiking
    • Music

    Social Links

    • Github: https://github.com/IulianIV
    • Facebook: https://www.facebook.com/IchimIuli/
    • LinkedIn: https://www.linkedin.com/in/iulianichim/
    • Website: https://iulianiv.github.io/