Profile Details

Create Project

★★★★★

☆☆☆☆☆

USD 50 /hr

★★★★★

☆☆☆☆☆

Hire Dr. Bora U.

Germany

USD 50 /hr

Senior Bioinformatics Scientist with a focus on (multi)-omics data science in the context of human diseases.

Profile Summary

I am a Senior Staff Scientist at the Bioinformatics & Omics Data Science platform of the Max-Delbruck-Center for Molecular Medicine. My roles in the platform include research in human diseases with a systems biology approach, research collaborations with other labs in the institute, and supporting other researchers in the form of consultations, mentorships, workshops, and user-friendly software development for wet-lab researchers. My current research is focused on development of deep learning-based multi-modal data integration tools for precision oncology. My work in the last 15 years spanned various categories such as comparative genomics, protein sequence analysis in the context of molecular interactions and disease mechanisms, RNA bioinformatics, and omics data science with a focus on development of reproducible software for the bioinformatics community. I have developed various tools and pipelines for omics data processing, visualization, downstream analysis and marker discovery for applications both in basic and translational research.

Subject Matter Expertise

• ★ Bioinformatics
• ☆ Molecular Biology
• ☆ Omics
• ☆ Comparative Genomics
• ☆ Data Analysis
• ☆ Data Visualization
• ☆ Deep Learning
• ☆ Systems Biology
• ☆ Biomarker Discovery
• ☆ Python
• ☆ R
• ☆ Cancer Research
• ☆ Cancer Biology

Services

• Research
• Consulting
• Data & AI
• Product Development

Research Scientific and Technical Research, Systematic Literature Review

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling, Data Visualization, Data Processing, Data Insights

Product Development Quality Assurance & Control (QA/QC), Concept Development

Work Experience

Bioinformatics Scientist

Max Delbrück Centrum für Molekulare Medizin Berlin Buch

August 2015 - Present

Bioinformatics Scientist

Max Delbrück Centrum für Molekulare Medizin Berlin Buch

August 2015 - Present

Postdoc

European Molecular Biology Laboratory

November 2014 - July 2015

Education

PhD

European Molecular Biology Laboratory - Heidelberg/Germany

January 2011 - November 2014

MSc

Simon Fraser University - Vancouver/Canada

September 2008 - December 2010

BSc

Sabanci University - Istanbul/Turkiye

September 2003 - June 2008

Certifications

• Certification details not provided.

Publications

PREPRINT

Bora Uyar, Taras Savchyn, Ricardo Wurmus, Ahmet Sarigun, Mohammed Maqsood Shaik, Vedran Franke, Altuna Akalin (2024). Flexynesis: A deep learning framework for bulk multi-omics data integration for precision oncology and beyond .

Bora Uyar, Philipp Schmitt, Katrin Hönig, Ana Milojkovic, Kathleen Anders, Evelin Schröck, Sascha Sauer, Altuna Akalin, Inmaculada Martínez-Reyes, Thomas Blankenstein (2024). Oncogene inactivation-induced senescence facilitates tumor relapse .

Bora Uyar, Trendelina Rrustemi, Katrina Meyer, Yvette Roske, Altuna Akalin, Koshi Imami, Yasushi Ishihama, Oliver Daumke, Matthias Selbach (2023). Pathogenic mutations of human phosphorylation sites affect protein-protein interactions .

Bora Uyar, Artem Baranovskii, Irem B. Gunduz, Vedran Franke, Altuna Akalin(2022). Multi-omics alleviates the limitations of panel-sequencing for cancer drug response prediction . Cold Spring Harbor Laboratory

Bora Uyar, Artem Baranovskii, Irem B. Gunduz, Vedran Franke, Altuna Akalin(2022). Multi-omics alleviates the limitations of panel-sequencing for cancer drug response prediction . Cold Spring Harbor Laboratory

Bora Uyar, Jonathan Froehlich, Margareta Herzog, Kathrin Theil, Petar Glažar, Altuna Akalin, Nikolaus Rajewsky (2020). Parallel genetics of regulatory sequencesin vivo .

Bora Uyar, Marina Kolesnichenko, Nadine Mikuda, Uta E. Höpken, Maja Milanovic, A. Bugra Tufan, Wei Sun, Kolja Schleich, Linda von Hoff, Michael Willenbrock, et al. (2019). A novel IKK- and proteasome-independent mechanism of RelA activation triggers senescence associated secretome via transcriptional repression of NFKBIA .

JOURNAL ARTICLE

Bora Uyar, Trendelina Rrustemi, Katrina Meyer, Yvette Roske, Altuna Akalin, Koshi Imami, Yasushi Ishihama, Oliver Daumke, Matthias Selbach (2024). Pathogenic mutations of human phosphorylation sites affect protein–protein interactions . Nature Communications.

Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction <head> <META HTTP-EQUIV="Refresh" CONTENT="0;URL=/servlet/useragent"> </head> . Cancers.

Bora Uyar, Artem Baranovskii, Irem B. G&#252;nd&#252;z, Vedran Franke, ALTUNA AKALIN (2022). Multi-Omics Alleviates the Limitations of Panel Sequencing for Cancer Drug Response Prediction . Cancers.

(2021). Parallel genetics of regulatory sequences using scalable genome editing in vivo . Cell reports.

Bora Uyar, Marina Kolesnichenko, Nadine Mikuda, Uta E H&#246;pken, Eva K&#228;rgel, Ahmet Bugra Tufan, Maja Milanovic, Wei Sun, Inge Krahn, Kolja Schleich, et al. (2021). Transcriptional repression of NFKBIA triggers constitutive IKK‐ and proteasome‐independent p65/RelA activation in senescence . The EMBO Journal.

Bora Uyar, Daniel Palmer, Axel Kowald, Hugo Murua Escobar, Israel Barrantes, Steffen M&#246;ller, Altuna Akalin, Georg Fuellen(2020). Single-cell analyses of aging, inflammation and senescence . Ageing Research Reviews. 64. p. 101156. Elsevier {BV}

(2020). Single-cell analyses of aging, inflammation and senescence . Ageing Research Reviews.

(2019). The conserved histone chaperone LIN-53 is required for normal lifespan and maintenance of muscle integrity in Caenorhabditis elegans . Aging cell.

(2019). HOT or not: examining the basis of high-occupancy target regions . Nucleic Acids Research.

Bora Uyar, Nadine Mikuda, Marina Kolesnichenko, Patrick Beaudette, Oliver Popp, Wei Sun, Ahmet Bugra Tufan, Bj&#246;rn Perder, Altuna Akalin, Wei Chen, et al.(2018). The IκB kinase complex is a regulator of mRNA stability . The EMBO Journal. 37. (24). {EMBO}

Bora Uyar, Ricardo Wurmus, Brendan Osberg, Vedran Franke, Alexander Gosdschan, Katarzyna Wreczycka, Jonathan Ronen, Altuna Akalin(2018). PiGx: reproducible genomics analysis pipelines with GNU Guix . GigaScience. Oxford University Press ({OUP})

Meyer K, Kirchner M, Uyar B, Cheng JY, Russo G, Hernandez-Miranda LR, Szymborska A, Zauber H, Rudolph IM, Willnow TE, et al.(2018). Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs . Cell.

Kolundzic E, Ofenbauer A, Bulut SI, Uyar B, Baytek G, Sommermeier A, Seelk S, He M, Hirsekorn A, Vucicevic D, et al.(2018). FACT Sets a Barrier for Cell Fate Reprogramming in Caenorhabditis elegans and Human Cells . Developmental cell.

(2017). RCAS: an RNA centric annotation system for transcriptome-wide regions of interest . Nucleic acids research.

Bora Uyar, B&#225;lint M&#233;sz&#225;ros, Manjeet Kumar, Toby J. Gibson, Zsuzsanna Doszt&#225;nyi(2017). Degrons in cancer . Science Signaling. 10. (470). American Association for the Advancement of Science ({AAAS})

Uyar B, Yusuf D, Wurmus R, Rajewsky N, Ohler U, Akalin A, Nucleic acids research, 2017, 2017 .

Dinkel, H., Roey, K., Michael, S., Kumar, M., Uyar, B., Altenberg, B., Milchevskaya, V., Schneider, M., K&#252;hn, H., Behrendt, A., et al.(2016). ELM 2016 - Data update and new functionality of the eukaryotic linear motif resource . Nucleic Acids Research. 44. (D1). p. D294-D300.

Via, A., Uyar, B., Brun, C., Zanzoni, A.(2015). How pathogens use linear motifs to perturb host cell networks . Trends in Biochemical Sciences. 40. (1). p. 36-48.

Uyar, B., Weatheritt, R.J., Dinkel, H., Davey, N.E., Gibson, T.J.(2014). Proteome-wide analysis of human disease mutations in short linear motifs: Neglected players in cancer? . Molecular BioSystems. 10. (10). p. 2626-2642.

Van Roey, K., Uyar, B., Weatheritt, R.J., Dinkel, H., Seiler, M., Budd, A., Gibson, T.J., Davey, N.E.(2014). Short linear motifs: Ubiquitous and functionally diverse protein interaction modules directing cell regulation . Chemical Reviews. 114. (13). p. 6733-6778.

Dinkel, H., Van Roey, K., Michael, S., Davey, N.E., Weatheritt, R.J., Born, D., Speck, T., Kr&#252;ger, D., Grebnev, G., Kubań, M., et al.(2014). The eukaryotic linear motif resource ELM: 10 years and counting . Nucleic Acids Research. 42. (D1).

Davey, N.E., Van Roey, K., Weatheritt, R.J., Toedt, G., Uyar, B., Altenberg, B., Budd, A., Diella, F., Dinkel, H., Gibson, T.J.(2012). Attributes of short linear motifs . Molecular BioSystems. 8. (1). p. 268-281.

Dinkel, H., Michael, S., Weatheritt, R.J., Davey, N.E., Van Roey, K., Altenberg, B., Toedt, G., Uyar, B., Seiler, M., Budd, A., et al.(2012). ELM - The database of eukaryotic linear motifs . Nucleic Acids Research. 40. (D1).

Chu, J.S.C., Tarailo-Graovac, M., Zhang, D., Wang, J., Uyar, B., Tu, D., Trinh, J., Baillie, D.L., Chen, N.(2012). Fine tuning of RFX/DAF-19-regulated target gene expression through binding to multiple sites in Caenorhabditis elegans . Nucleic Acids Research. 40. (1). p. 53-64.

Uyar, B., Chu, J.S.C., Vergara, I.A., Chua, S.Y., Jones, M.R., Wong, T., Baillie, D.L., Chen, N.(2012). RNA-seq analysis of the C. briggsae transcriptome . Genome Research. 22. (8). p. 1567-1580.

She, R., Chu, J.S.-C., Uyar, B., Wang, J., Wang, K., Chen, N.(2011). genBlastG: Using BLAST searches to build homologous gene models . Bioinformatics. 27. (15). p. 2141-2143.

OTHER

Bora Uyar, Jan Dohmen, Artem Baranovskii, Jonathan Ronen, Vedran Franke, Altuna Akalin(2021). Identifying tumor cells at the single cell level . Cold Spring Harbor Laboratory

Bora Uyar, Jonathan Ronen, Vedran Franke, Gaetano Gargiulo, Altuna Akalin(2021). Multi-omics and deep learning provide a multifaceted view of cancer . Cold Spring Harbor Laboratory

Bora Uyar, Marina Kolesnichenko, Nadine Mikuda, Uta E. H&#246;pken, Maja Milanovic, A. Bugra Tufan, Wei Sun, Kolja Schleich, Linda von Hoff, Michael Willenbrock, et al.(2019). A novel IKK- and proteasome-independent mechanism of RelA activation triggers senescence associated secretome via transcriptional repression of NFKBIA . Cold Spring Harbor Laboratory