Dr. Ulf Schmitz

Research interest

As long-time member of the Department of Systems Biology and Bioinformatics I benefitted from more than 10 years experience in interdisciplinary collaborations. My personal interest and goals lie on the integration of bioinformatics and systems biology methods to challenge biomedical problems.

In particular I am designing integrative workflows combining various computational disciplines with experimentation to approach molecular biological and medical problems (see exemplary workflow here). These workflows are implemented and applied to identify and study molecular interactions, functional mechanisms of gene-regulation, cell signaling pathways and gene regulatory networks for the goal of getting deeper insights into disease emergence and progression with a focus on different cancer entities. In this context the ultimate goal is to identify possible avenues for therapeutic interventions and optimized treatment schedules.

Collaborations

I enjoy collaborating and discussing with colleagues in the department which profits from engaged people with heterogeneous backgrounds. Furthermore, I am involved in several collaborations with biomedical research institutes in the University and beyond.

More specifically in a project with the Institute of Experimental Gene Therapy and Cancer Research (Rostock), led by Prof. Brigitte P

Academic background

See my resume here:
CV

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Selected publications

MiR-205-5p and miR-342-3p cooperate in the repression of the E2F1 transcription factor in the context of anticancer chemotherapy resistance.

Lai X, Gupta SK, Schmitz U, Marquardt S, Knoll S, Spitschak A, Wolkenhauer O, Pützer BM, Vera J

Theranostics. 2018 Jan 1;8(4):1106-1120.

Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures

Khan FM, Marquardt S, Gupta SK,Knoll S, Schmitz U,Spitschak A, Engelmann D, Vera J, Wolkenhauer O & Pützer BM

Nature Communications

MicroRNA and Transcription Factor Gene Regulatory Network Analysis Reveals Key Regulatory Elements Associated with Prostate Cancer Progression

Sadeghi M, Ranjbar B, Ganjalikhany MR, Khan FM, Schmitz U, Wolkenhauer O, Gupta SK

PLoS One. 2016 Dec 22;11(12):e0168760.

TRAPLINE: A standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation

Markus Wolfien, Christian Rimmbach, Ulf Schmitz, Julia Jeannine Jung, Stephan Krebs, Gustav Steinhoff, Robert David, Olaf Wolkenhauer (2016)

BMC Bioinformatics

Personalized cancer immunotherapy using systems medicine approaches.

Gupta SK, Jaitly T, Schmitz U, Schuler G, Wolkenhauer O, Vera J

Briefings in Bioinformatics 2015.

The RNA world in the 21st century – a systems approach to finding non-coding keys to clinical questions

Schmitz U, NAderi-Meshkin H, Gupta SK, Wolkenhauer O, Vera J

Briefings in Bioinformatics 2015.

Naïve Bayes classifier predicts functional microRNA target interactions in colorectal cancer

Raheleh A, Schmitz U, Farazmand A, Gupta SK, Ahmadi H, Wolkenhauer O

Molecular BioSystems 2015; 11(8): 2126-34.

A mutation in the NADH-dehydrogenase subunit 2 suppresses fibroblast aging

Schauer M, Kottek T, Schönherr M, Bhattacharya A, Ibrahim SM, Hirose M, Köhling R, Fuellen G, Schmitz U, Kunz M

Oncogene, in press.

miR-638 promotes melanoma metastasis and protects melanoma cells from apoptosis and autophagy

Bhattacharya A, Schmitz U, Raatz Y, Schönherr M, Kottek T, Schauer M, Franz S, Saalbach A, Anderegg U, Wolkenhauer O, Schadendorf D, Simon JC, Magin T, Vera J, Kunz M

Accepted in Oncotarget.

MicroRNA-mRNA interactions in colorectal cancer and their role in tumor progression

Amirkhah R, Schmitz U, Linnebacher M, Wolkenhauer O, Farazmand A

Genes, Chromosomes and Cancer, 54:129–141,

E2F1 induces miR-224/452 expression to drive EMT through TXNIP downregulation

Knoll S, Fürst K, Kowtharapu B, Schmitz U, Marquardt S, Wolkenhauer O, Martin H, Pützer BM

EMBO reports, 15 (12), pp.1315-1329.

Cooperative gene regulation by microRNA pairs and their identification using a computational workflow

Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta S

Nucleic Acids Research 2014, 42 (12): 7539-7552,

A systems biology approach to study microRNA-mediated gene regulatory networks (2013)

Lai X, Bhattacharya A, Schmitz U, Kunz M, Vera J, Wolkenhauer O

BioMed Research International, vol. 2013,

Hybrid modeling of the crosstalk between signaling and transcriptional networks using ordinary differential equations and multi-valued logic

Khan FM, Schmitz U, Nikolov S, Engelmann D, Pützer BM,Wolkenhauer O, Vera J

Biochim Biophys Acta; 1844 (1 Pt B): 289-98.

Kinetic modeling-based detection of genetic signatures that provide chemoresistance via the E2F1-p73/DNp73-miR-205 network

Vera J, Schmitz U, Lai X, Engelmann D, Khan FM, Wolkenhauer O, Pützer BM (2013)

Cancer Research,

Regulation of cell cycle checkpoint kinase WEE1 by miR-195 in malignant melanoma

Bhattacharya A, Schmitz U, Wolkenhauer O, Schönherr M, Raatz Y, Kunz M (2012)

Oncogene,

Systems Biology and Bioinformatics in Aging Research: A Workshop Report

Fuellen G, Dengjel J, Hoeflich A, Hoeijmakers J, Kestler H, Kowald A, Priebe S, Rebholz-Schuhmann D, Schmeck B, Schmitz U, Stolzing A, Sühnel J, Wuttke D, Vera J (2012)

Rejuvenation Research, Vol 15, No 6,

E2F1 confers anticancer drug resistance by targeting ABC transporter family members and Bcl-2 via the p73/DNp73-miR-205 circuitry

Alla V, Kowtharapu BS, Engelmann D, Emmrich S, Schmitz U, Steder M, Pützer BM (2012)

Cell Cycle, 11:1

Computational analysis of target hub gene repression regulated by multiple and cooperative miRNAs

Lai X, Schmitz U, Gupta S, Bhattacharya A, Kunz M, Wolkenhauer O, Vera J (2012)

Nucleic Acids Research, 40: 8818-8834.

Analysis of cell adhesion during early stages of colon cancer based on an extended multi-valued logic approach

Guebel DV, Schmitz U, Wolkenhauer O, Vera J (2012)

Molecular Biosystems 8(4):1230-1242

Computational analysis and modeling the effectiveness of "Zanamivir" targeting neuraminidase protein in pandemic H1N1 strains

Gupta SK, Gupta SK, Smita S, Srivastava M, Lai X, Schmitz U, Rahman Q, Wolkenhauer O, Vera J (2011)

Infection, Genetics and Evolution 11: 1072 - 1082

Identification of immunogenic consensus T-cell epitopes in globally distributed influenza-A H1N1 neuraminidase

Gupta SK, Srivastava M, Akhoon BA, Smita S, Schmitz U, Wolkenhauer O, Vera J, Gupta SK (2011)

Infection, Genetics and Evolution 11: 308 - 319

A model-based strategy to investigate the role of microRNA regulation in cancer signalling networks

Nikolov S, Vera J, Schmitz U, Wolkenhauer O (2011)

Theory in Biosciences 130: 55-69

Non-coding RNA detection methods combined to improve usability, reproducibility and precision

Raasch P, Schmitz U, Patenge N, Vera J, Kreikemeyer B, Wolkenhauer O (2010)

BMC Bioinformatics 11: 491

Tumor-promoting role of signal transducer and activator of transcription (Stat)1 in late-stage melanoma growth

Schultz J, Koczan D, Schmitz U, Ibrahim SM, Pilch D, Landsberg J, Kunz M (2010)

Clinical & Experimental Metastasis 27: 133-140

Effective ncRNA detection

Raasch P, Schmitz U, Kreikemeyer B, Wolkenhauer O (2010)

Rostocker Informatik-Berichte 32: 158-166

ISBN 13 (print): 9783832540050

Exploration of homodimer receptor - homodimer protein interactions

Vera J, Kwon T, Schmitz U, Kolch W, Wolkenhauer O (2009)

International Journal of Bioinformatics Research and Applications 4: 447-457

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2-DE profiling of GDNF overexpression-related proteome changes in differentiating ST14A rat progenitor cells

Hoffrogge R, Beyer S, Hübner R, Mikkat S, Mix E, Scharf C, Schmitz U, Pauleweit S, Berth M, Zbrzycki IZ, Christoph H, Pahnke J, Wolkenhauer O, Uhrmacher A, Völker U, Rolfs R (2007)

Proteomics 7: 33-46

Bioinformatics analysis of interactions of receptor homodimers with intracellular protein homodimers

Vera J, Kwon T, Schmitz U, Millat T, Wolkenhauer O

Rostocker Informatik-Berichte, 31, 2007

Systems Medicine

Schmitz U, Wolkenhauer O, (eds.)

Springer (2016), Series Title Methods in Molecular Biology

ISBN 13 (print): 9781493932825

ISBN 13 (online): 9781493932832

URL: http://link.springer.com/book/10.1007/978-1-4939-3283-2

RNA Systems Biology for Cancer: From Diagnosis to Therapy

R. Amirkhah, A. Farazmand, O. Wolkenhauer, U. Schmitz

In Springer (2016), Systems Medicine, pp 305-330

ISBN 13 (print): 9781493932825

ISBN 13 (online): 9781493932832

URL: http://link.springer.com/protocol/10.1007/978-1-4939-3283-2_14

Cancer Systems Biology: Current Achievements in – Omics Data Analysis, Network Reconstruction and Mathematical Modelling

Vera J, Wolkenhauer O, Schmitz U (2014)

In: eLS. John Wiley & Sons Ltd, Chichester.

MicroRNA Cancer Regulation - Advanced Concepts, Bioinformatics and Systems Biology Tools

Schmitz U, Wolkenhauer O, Vera J (eds.)

Series: Advances in Experimental Medicine and Biology, Vol. 774
Springer 2012.

Computational microRNA biology

Schmitz U, Vera J

in: Encyclopedia of Systems Biology; Dubitzky W, Wolkenhauer O, Yokata H, Cho K-H (eds.); Springer 2012.

ISBN 13 (print): 9781441998620

Bioinformatics Analysis of High-Throughput Experiments

Gupta S, Schmitz U

in: Recent Trends in Biotechnology. Volume 2; Singh M P, Agrawal A, Sharma B (eds.); Nova Science Publishers 2011.

ISBN 13 (print): 9781617617973

Predicting targets of synergistic microRNA regulation

Schmitz U, Gupta S, Lai X, Vera J, Wolkenhauer O

German Conference on Bioinformatics 2013, Göttingen, Germany

Venue: Göttingen, Germany

New candidate oncomiRs for malignant melanoma

Bhattacharya A, Schmitz U, Raatz Y, Schönherr M, Kunz M

International Investigative Dermatology (IID) in Edinburgh, UK

Venue: Edinburgh, UK

The regulation of microRNA target hubs

Schmitz U, Lai X, Vera J, Wolkenhauer O

International Workshop on Small RNA in Cancer, Inflammation, and Aging, Copenhagen, Denmark, September 3 - 4 , 2012.

Venue: Copenhagen, Denmark

A systems biology approach to study the cellular function of microRNAs

Lai X, Schmitz U, Vera J, Wolkenhauer O

International Workshop on Small RNA in Cancer, Inflammation, and Aging, Copenhagen, Denmark, September 3 - 4, 2012.

Venue: Copenhagen, Denmark

Análisis de los fenómenos de adhesión celular en los estadios tempranos de cáncer de colon mediante un modelo de lógica multi-valuada extendida

Guebel DV, Schmitz U, Wolkenhauer O, Vera J

Facultad de Medicina, Universidad de Buenos Aires, Buenos Aires, Argentina, 13-16 September, 2011

Venue: Buenos Aires, Argentina

On the regulation of microRNA target hubs: a Systems Biology perspective

Lai X, Schmitz U, Gupta S, Kunz M, Wolkenhauer O, Vera J

12th International Conference on Systems Biology (ICSB), Heidelberg/Mannheim, Germany, 28 August - 1 September 2011

Venue: Heidelberg/Mannheim, Germany

Role of micro RNA 372 in melanoma progression

Bhattacharya A, Schmitz U, Schonherr M, Raatz Y, Kunz M

Experimental Dermatology (2011), Volume 20, Issue 2, 196.

An extensive Boolean network for analysing the signalling events in early stages of humen colon cancer

Guebel DV, Schmitz U, Wolkenhauer O, Vera J

11th International Conference on Systems Biology (ICSB), Edinburgh, UK, October 2010.

Venue: Edinburgh, UK

MicroRNAs in malignant melanoma progression

Schmitz U, Bhattacharya A, Gupta S, Schultz J, Kunz M, Wolkenhauer O

German Conference on Bioinformatics, Braunschweig, Germany, September 2010

Venue: Braunschweig, Germany

Local Genomic Properties as Indicators of Functional Elements

Raasch P, Schmitz U, Patenge N, Vera J, Kreikemeyer B, Wolkenhauer O

3. Gemeinsame Tagung der DGHM und der VAAM, Hannover, Germany, 28.03.-31.03.2010

Venue: Hannover, Germany

A JAVA framework to integrate ncRNA detection methods

Raasch P, Schmitz U, Kreikemeyer B, Wolkenhauer O

Systems Biology for Medical Applications Summer School, Costa Adeje, Spain, 30 October 2008

Venue: Costa Adeje, Spain

Modular education for interdisciplinary Systems Biology

Stalidzans E, Mozga I, Roos C, Fernandez E, Font J, Vanags J, Remm M, Schmitz U, Wolkenhauer O

9th International Conference on Systems Biology, Gothenburg, Sweden, 2008.

Venue: Gothenburg, Sweden

Exploring cell signalling homodimer receptor-homodimer protein interactions and their dynamical consequences

Vera J, Millat T, Kwon T, Schmitz U, Wolkenhauer O

German Conference on Bioinformatics, Potsdam, Germany, 26 September - 28 September 2007

Venue: Potsdam, Germany

An investigation of microRNA target regulation mechanisms using an integrative approach

Schmitz U

2015