Hi, my name is Arsenij

I am an aspiring bioinformatics and data scientist with a solid background in biology. My skills in the analysis of high throughput and NGS data allow me to apply common methods in the fields of genomics, transcriptomics, and metabolomics. My professional interest is aimed at circRNA, sphingolipids, network analysis, and the broad field of oncology.

Smart automation and creative solutions are my guidelines for successful data analysis.

Working experience

09.2020 - today

Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), Mainz
University Medical Center of the Johannes Gutenberg University Mainz
- Working in oncological german consortia: MIRACUM, DNPM, PM4Onco;
- IT-support of the Molecular Tumorboard (UCT) and Data Integration Center Mainz;
- PhD student: field of oncology & bioinformatics;

04.2019 - 08.2020

Max Planck Institute for Heart and Lung Research, Bad Nauheim
Software developement:
- R Shiny application i2dash (https://loosolab.github.io/i2dash/)
- single-cell RNA-Seq analysis

Education

10.2021 - today

Johannes-Gutenberg University Mainz
Doctorate in Biology
Preliminary thesis title: "Prediction of ganglioside GD2 using transcriptome data and machine learning across tumor entities."

10.2017 - 10.2020

Justus-Liebig-Universität Gießen (JLU) & University of Applied Science Central Hesse (THM, Giessen campus), Gießen, MA in Bioinformatics and Systems Biology
Thesis title: "i2dash - Programmatic creation of interactive and web-based dashboards with the focus on single-cell RNA sequencing analysis"
Specializations: High throughput data analysis, Innovative algorithms in bioinformatics

09.2014 - 09.2017

Justus-Liebig-Universität Gießen (JLU), Gießen, BA in Biology
Thesis title: "Identification of circular RNA with function as microRNA-sponge"
Specializations: Bioinformatics, Genetics, and Biochemistry
Acquisition of the Bachelor of Science

2006 - 2014

Gymnasium: Liebigschule Gießen (G8)
Acquisition of the general entitlement to study at universities

Social commitment

  • Board member of the chess club 1858 Gießen e.V. (2014)
  • Voluntary youth trainer in the chess club 1858 Gießen e.V. (2014)
  • Voluntary work as course instructor in the DRZ Gießen e.V. (2014 - 2017)
  • Voluntary work in the youth club JunOst-Gießen (2018 - now)

Skills

Summary

Through my Bachelor thesis, the Master program and two internships at the University Department for Microbiology and Molecular Biology and in the field of pathophytology, I was able to gain practical experience in the analysis of various omics data and workflow systems. During my work in the bioinformatics service group at the Max Planck Institute for Heart and Lung Research in Bad Nauheim, I got experience in the field of single-cell RNA-seq analysis. The development of an R-package enabled me to enhance my skills in software development, data analysis and visualization.

Languages

- German

- English

- Russian

Programming languages

- Python

- R

- Shell scripting

- SQL

- Java

- Groovy

Workflow Managment Systems

- Snakemake
- Nextflow

Systems and Environments

- Windows
- Linus

- Docker
- Conda

Web development

- HTML
- CSS
- R Shiny
- JavaScript

Graphic design

- Photoshop
- InDesign
- Corel Draw
- Clip studio PAINT

EDV

- MS Word, Excel, PowerPoint
- Latex

Methodical skills

- Target orientation
- Reliability
- Good organization

Individual skills

- Quick comprehension & curiosity
- Self-reflection
- Responsibility & discipline

Social skills

- Team spirit
- Communication skills
- Empathy

Publications

Google Scholar profile: link

Nicole Ziegler, Mariela Cortés-López, Francesca Alt, Maximilian Sprang, Arsenij Ustjanzew, Nadine Lehmann, Khalifa El Malki, Arthur Wingerter, Alexandra Russo, Olaf Beck, Sebastian Attig, Lea Roth, Julian König, Claudia Paret & Jörg Faber, Analysis of RBP expression and binding sites identifies PTBP1 as a regulator of CD19 expression in B-ALL, OncoImmunology, 12:1, 2023, https://doi.org/10.1080/2162402X.2023.2184143.
Khalifa El Malki, Pia Wehling, Francesca Alt, Roger Sandhoff, Sebastian Zahnreich, Arsenij Ustjanzew, Carolin Wilzius, Marc A Brockmann, Arthur Wingerter, Alexandra Russo, Olaf Beck, Clemens Sommer, Malte Ottenhausen, Katrin BM Frauenknecht, Claudia Paret, Jörg Faber, Glucosylceramide Synthase Inhibitors Induce Ceramide Accumulation and Sensitize H3K27 Mutant Diffuse Midline Glioma to Irradiation, Journal of Molecular Sciences 24 (12), 9905, 2023 https://doi.org/10.3390/ijms24129905.
Caroline Stellmach, Julian Sass, Bernd Auber, Martin Boeker, Thomas Wienker, Andrew J Heidel, Manuela Benary, Simon Schumacher, Stephan Ossowski, Frederick Klauschen, Yvonne Möller, Rita Schmutzler, Arsenij Ustjanzew, Patrick Werner, Aurelie Tomczak, Thimo Hölter, Sylvia Thun, Creation of a structured molecular genomics report for Germany as a local adaption of HL7’s Genomic Reporting Implementation Guide, Journal of the American Medical Informatics Association, Volume 30, Issue 6, June 2023, Pages 1179–1189, https://doi.org/10.1093/jamia/ocad061.
Claudia Paret, Arsenij Ustjanzew, Sara Ersali, Larissa Seidmann, Richard Jennemann, Nicole Ziegler, Khalifa El Malki, Alexandra Russo, Arthur Wingerter, Franziska Ortmüller, Angelina Bornas, Pia Charlotte Wehling, Adina Lepădatu, Malte Ottenhausen, Wilfried Roth, Clemens Sommer, Barbara Fliss, Katrin BM Frauenknecht, Roger Sandhoff, Jörg Faber, GD2 Expression in Medulloblastoma and Neuroblastoma for Personalized Immunotherapy: A Matter of Subtype, Cancers 2022, 14(24), 6051, https://doi.org/10.3390/cancers14246051.
Ustjanzew, Arsenij, Valentin Sencio, François Trottein, Jörg Faber, Roger Sandhoff, and Claudia Paret, Interaction between Bacteria and the Immune System for Cancer Immunotherapy: The α-GalCer Alliance, International Journal of Molecular Sciences 23, no. 11: 5896, 2022, https://doi.org/10.3390/ijms23115896.
Annekathrin Ludt,Arsenij Ustjanzew,Harald Binder,Konstantin Strauch,Federico Marini, Interactive and Reproducible Workflows for Exploring and Modeling RNA-seq Data with pcaExplorer, Ideal, and GeneTonic, Current Protocols, 2, 2022, https://doi.org/10.1002/cpz1.411.
Arsenij Ustjanzew, Alexander Desuki, Christoph Ritzel, Alina Corinna Dolezilek, Daniel-Christoph Wagner, Jan Christoph, Philipp Unberath, Thomas Kindler, Jörg Faber, Federico Marini, Torsten Panholzer & Claudia Paret, cbpManager: a web application to streamline the integration of clinical and genomic data in cBioPortal to support the Molecular Tumor Board, BMC Med Inform Decis Mak 21, 358, 2021, https://doi.org/10.1186/s12911-021-01719-z.
Niklas Reimer, Philipp Unberath, Hauke Busch, Melanie Börries, Patrick Metzger, Arsenij Ustjanzew, Christopher Renner, Hans-Ulrich Prokosch, Jan Christoph, Challenges and Experiences Extending the cBioPortal for Cancer Genomics to a Molecular Tumor Board Platform, Studies in Health Technology and Informatics, IOS Prss Ebooks, 2021, https://doi.org/10.3233/shti210833.
Arsenij Ustjanzew, Jens Preussner, Mette Bentsen, Carsten Kuenne, Mario Looso, i2dash: Creation of Flexible, Interactive and Web-based Dashboards for Visualization of Omics Data, Genomics, Proteomics & Bioinformatics, 2021, , ISSN 1672-0229, https://doi.org/10.1016/j.gpb.2021.01.007.

Projects

Flussdiagramm

Pipeline for the identification of circular RNA

In the course of the Bachelor thesis, a complex pipeline was developed, that can automatically identify and analyze circRNAs from HITS-CLIP data sets. For the evaluation and visualization of the results several Pythonscripts were developed and integrated into the pipeline. For this
purpose, the Snakemake workflow management system was used to program and coordinate command chains in an effective and reproducible manner. Based on the results of the data sets that were used to test the pipeline, hypotheses about the function of the identified circRNAs could be established.

i2dash

i2dash

Scientific communication and data visualization are important aspects to illustrate complex concepts and results from data analyses. The R package i2dash provides functionality to create customized, web-based dashboards for data presentation, exploration and sharing. i2dash integrates easily into existing data analysis pipelines and can organize scientific findings thematically across different pages and layouts.

i2dash.scRNAseq

i2dash.scRNAseq

Recent development of single-cell technologies enables the molcular investigation of thousands of individual cells in a single experiment. Single-cell applications are available for e.g. transcriptomes or chromatin accessibility of individual cells. Respective analysis workflows allow for the identification of cellular sub-populations, gene regulatory networks and dynamic cellular trajectories. In order to improve reporting on SC applications, we extended i2dash to enable users to create dashboards with a focus on visualization and exploration of data from single-cell RNA-seq.

Contact me:

Address:

55130 Mainz, DE

E-mail:

Arsenij.Ustjanzew@uni-mainz.de

© Copyright 2023 Arsenij Ustjanzew - All Rights Reserved