KRISTIAN ALIKAJ

Berlin, Germany | +49 176 42932104
alkajk27@gmail.com | My Portfolio Website

EDUCATION

Free University of Berlin
BSc. Bioinformatics
2020 – 2024

Charité Medical School Berlin
Medicine
2015 – 2020

Lower Saxony Preparatory College, Hanover, Germany
GPA: 1.0
2014 -2015

SKILLS

Programming Languages: Proficient in C++, Python, R, SQL & basic knowledge of Julia and Haskell, particularly in bioinformatics applications.
Bioinformatics & C++: Proficient in bioinformatics software development with expertise in global alignment (Needleman-Wunsch), string matching (Horspool), and data structures like suffix arrays, Burrows-Wheeler transformation, FM indices, and Q-Gram Index search. Web-App
Multi-Omics Data Integration: Hands-on experience in integrating and analyzing transcriptomics, (phospho-)proteomics, and metabolomics data. Project on GitHub
Machine Learning/ Deep Learning (PyTorch & Tensorflow): Developed models to predict silent heart attacks from ECG waveforms using convolutional and recurrent neural networks, as well as to predict the risk of diabetes by training models on patient data and implementing web app with best model. Diabetes | ECG Silent Heart attacks
SNP/Variant Calling Analysis: Experience with bash and other tools such as fastQC, bwa, samtools, bedtools, GATK, and workflow automation using PyVCF and Snakemake for SNP/variant analysis.
Single-cell RNA Sequencing Analysis (R, Python, Julia): Adept at analyzing single-cell RNA sequencing data using R (Seurat, edgeR, DESeq2), Python (Scanpy, scviTools, pyDeseo2), and Julia (SingleCellGenomics.jl) for differential expression and pathway analysis. Projects
Database Systems/SQL (PostgreSQL, Flask/Python): Capable of designing and developing web applications with expertise in creating interactive plots, filtering options, and databases, particularly with PostgreSQL.
Web App Development: Built bioinformatics web apps using Flask (Python), including tools for DNA-to-protein translation, phylogenetic tree construction, and diabetes risk prediction using Flask(Python) alongside HTML/CSS and JS.

Work Experience

German Heart Center of Charité (DHZC), Berlin
Intern: at AG Schiattarella
June 2024 – August 2024

Integrated and analyzed transcriptomics, (phospho-)proteomics, and metabolomics data using advanced bioinformatics tools in R and Python with the aim to identify key molecular pathways, networks, and interactions to uncover novel biomarkers and therapeutic targets for heart failure with preserved ejection fraction (HFpEF).
Built a web app that visualizes a 3D graph of gene regulatory networks, enabling users to select transcription factors and explore neighboring interactions.
View Web App

Berlin Institute of Health @ Charité – Center for Digital Health, Berlin
Internship: Artificial Intelligence Lab (aislab)
May 2023 - July 2023

Developed deep learning algorithms and models to mine electrocardiogram (ECG) waveforms for signals indicating prior heart attacks, aiming to diagnose future silent heart attacks using PyTorch for binary classification, achieving best results with convolutional and recurrent neural networks.
Created a web app to visualize predictions made by the best-performing model.
View Web App

CoviMedical Berlin GmbH, Berlin
COVID Testing Personnel (Werkstudent)
March 2020 – February 2022

Managed check-in, registration, and consultation for individuals undergoing COVID tests.
Conducted nasal swab testing and performed antigen rapid test evaluations.
Documented results of both antigen (rapid) tests and rapid-PCR tests digitally.

GESS Medical Berlin GmbH, Berlin
Nursing and Healthcare Assistant
December 2016 – March 2018

Assisted in the selection, implementation, and evaluation of nursing measures in hospitals and care facilities.
Supported and guided patients in health and care-related matters.
Aided in diagnostics and therapy, including the initiation of life-saving immediate measures.

Ritter Butzke (Guerilla Produktion Berlin GmbH)
Bartending
06/2018 – 07/2024

LANGUAGE SKILLS

German: Fluent / Business fluent
English: Fluent / Business fluent
Albanian: Native language
Italian: Very good knowledge
French: Good knowledge