Final-Year Student · MOLECULAR BIOLOGY & GENETICS
WET-LAB // DRUG DESIGN // BIOINFO
Personal Academic & Research Portfolio

Uğur Cem Yıldız

MOLECULAR BIOLOGY & GENETICS

Final-year Molecular Biology and Genetics student with hands-on wet-lab experience from an international research internship at LMU Klinikum, Munich, where I carried out protein- and RNA-level analyses within a cardiovascular research group. Comfortable across core molecular biology techniques (protein extraction, Western blot, RNA extraction, qPCR, immunofluorescence), complemented by computational research experience in structure-based drug design and cancer bioinformatics through two completed bachelor's theses. Seeking a laboratory internship or research assistant position to deepen experimental skills in a molecular biology or biomedical research setting.

Focus & Core Competencies01 / SCHEMA
01Molecular & Wet Lab

Core laboratory techniques including Western blot, qPCR, IF staining, and cellular assays.

02Computational Drug Design

Molecular docking (AutoDock Vina), ADME/toxicity profiling, and receptor complementarity.

03Cancer Bioinformatics

TCGA/GTEx differential expression, survival outcomes, and immune-infiltration analysis.

Combining hands-on wet-lab molecular techniques with computational structural biology and cancer bioinformatics.

Final-year Molecular Biology and Genetics student with hands-on wet-lab experience from an international research internship at LMU Klinikum, Munich, where I carried out protein- and RNA-level analyses within a cardiovascular research group. Comfortable across core molecular biology techniques (protein extraction, Western blot, RNA extraction, qPCR, immunofluorescence), complemented by computational research experience in structure-based drug design and cancer bioinformatics through two completed bachelor's theses. Seeking a laboratory internship or research assistant position to deepen experimental skills in a molecular biology or biomedical research setting.

Academic Background
B.Sc. in Molecular Biology and GeneticsSep 2021 – 2027 (expected)

İnönü University, Faculty of Arts and Sciences, Malatya, Türkiye · GPA: 3.33 / 4.00

Completed two bachelor's graduation theses in computational structural biology and cancer bioinformatics.

Associate Degree in Computer Programming2025 – 2027 (expected)

Anadolu University, Open Education Faculty, Eskişehir, Türkiye · GPA: 3.26 / 4.00

Pursued concurrently with the B.Sc. to strengthen programming and computational foundations; first year completed.

LanguagesTurkish (Native) · English (Professional working proficiency, B2)
LocationÇekmeköy / İstanbul, Türkiye
InterestsCoding, reading, cooking, cycling, music, travel

Erasmus+ Research Intern

shRNA-mediated knockdown of CXCR4:

  • Performed protein extraction, BCA protein assays, and Western blotting for protein-level analyses.
  • Carried out RNA extraction, reverse transcription, and quantitative PCR (qPCR), alongside immunofluorescence (IF) staining.
  • Analyzed gene expression data, including next-generation sequencing (NGS) datasets.

Completed bachelor's graduation research projects in computational structural biology and cancer bioinformatics.

THESIS-01İnönü University · Supervisor: Dr. Seçil Demiral

Structure-Based Design and Computational Evaluation of Amentoflavone Derivatives as Novel CXCR4 Antagonists

  • Rationally designed five novel amentoflavone derivatives as CXCR4 antagonists using a structure-based drug design workflow against the CXCR4 crystal structure (PDB ID: 3ODU).
  • Performed molecular docking with AutoDock Vina and identified Fluoro-Deoxy-Amentoflavone as the lead candidate (−11.9 kcal/mol), outperforming the FDA-approved antagonist Plerixafor (−9.4 kcal/mol).
  • Predicted ADME / drug-likeness (SwissADME) and computational toxicity (ProTox-II), and analyzed protein–ligand interactions with BIOVIA Discovery Studio.
  • Established selective deoxygenation as the key driver of receptor complementarity via a directed hydrogen bond with the pharmacophore-critical residue Tyr55.
Bachelor's ThesisRead Full Thesis
THESIS-02İnönü University · Supervisor: Dr. Samet Kocabay

A Bioinformatic Investigation into the Role of the CXCR4 Chemokine Receptor in Cancer Progression and Metastasis: Expression, Prognosis, and Immune Infiltration

  • Investigated CXCR4 expression, genomic alterations, prognosis, and immune infiltration across breast (BRCA), lung (LUAD), and colorectal (COAD/READ) cancers using TCGA data.
  • Analyzed differential expression (GEPIA2), genomic alterations (cBioPortal), survival outcomes (Kaplan–Meier Plotter), immune infiltration (TIMER2.0), and protein–protein interaction networks (STRING).
  • Demonstrated a context-dependent prognostic role: high CXCR4 expression correlated with improved survival in LUAD (p = 0.007), associated with increased CD8+ T-cell infiltration.
Bachelor's ThesisRead Full Thesis
01

Molecular & Wet Lab

Experimental and laboratory protocols

  • DNA/RNA isolation (manual and kit-based)
  • PCR
  • qPCR / Real-Time PCR
  • cDNA synthesis
  • Western blot
  • BCA assay
  • immunofluorescence
  • agarose gel electrophoresis
  • spectrophotometry and standard curves
  • cell counting (hemocytometer)
  • culture media preparation
  • mitochondria isolation
02

Computational Drug Design

Structure-based modeling & predictive workflows

  • AutoDock Vina
  • AutoDock Tools
  • BIOVIA Discovery Studio
  • SwissADME
  • ProTox-II
  • OpenBabel
  • molecular docking
  • structure-based drug design
  • ADME and toxicity prediction
03

Cancer Bioinformatics

Transcriptomic, clinical & immune analysis

  • GEPIA2
  • cBioPortal
  • Kaplan–Meier Plotter
  • TIMER2.0
  • STRING
  • TCGA/GTEx data analysis
  • differential expression
  • survival and immune-infiltration analysis
04

Programming & Data

Computational foundations for bio-data analysis

  • Python
  • R
  • Linux (foundational, for bioinformatics data analysis)
  • Java (foundational)
Get in Touch

Inquiries & Research Dialogue

Seeking a laboratory internship or research assistant position to deepen experimental skills in a molecular biology or biomedical research setting.