Shizuka Uchida, Ph.D. Associate Professor of Medicine

Shizuka Uchida, Ph.D. Associate Professor of Medicine Cardiovascular Innovation Institute University of Louisville 302 E Muhammad Ali Blvd Louisville, KY 40202, United States Phone: 502-854-0570 Fax: 502-852-7195 E-mail: [email protected]

EDUCATION

05/98 B.S. in Biology (cum laude), Creighton University, Omaha, Nebraska 09/03 M.S. in Bioinformatics, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan 03/07 Ph.D. in Molecular Biology, Japan Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan

ACADEMIC APPOINTMENTS

08/16 – pres. Associate Professor of Medicine Cardiovascular Innovative Institute University of Louisville Louisville, Kentucky U.S.A.

08/12 – 12/16 Independent Junior Group Leader (equivalent to Assistant Professor) Institute of Cardiovascular Regeneration Centre for Molecular Medicine Goethe University Frankfurt Frankfurt am Main Germany

OTHER POSITIONS AND EMPLOYMENT

08/96 – 05/97 Resident Advisor, Creighton University, Omaha, Nebraska 06/98 – 08/01 General Manager, Tsukasa, Inc., Hiroshima, Hiroshima, Japan 04/04 – 03/06 Bioinformatics Engineer, World Fusion Co., Ltd., Ningyo-cho, Tokyo, Japan 04/06 – 03/10 Post Doctoral Fellow, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany 04/10 – 07/12 Group Leader, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany

PROFESSIONAL MEMBERSHIPS AND ACTIVITIES

04/04 – 03/06 Member, Molecular Biology Society of Japan 04/04 – 03/06 Member, Japanese Society for Bioinformatics 10/15 – pres. Member, International Society for Computational Biology 08/16 – pres. Member, American Heart Association Editorial Boards 03/17 – pres. Review Editor for Frontiers in Cardiovascular Medicine

Shizuka Uchida, 04/17/2018 Page 2 of 18

Manuscript Peer Review Ad hoc Reviewer: 3Biotech, Aging, American Journal of Physiology-Cell Physiology, American Journal of Physiology-Heart and Circulatory Physiology, Antioxidants and Redox Signaling, Atherosclerosis, Bioinformatics, Biomedicine & Pharmacotherapy, BMC Developmental Biology, BMC Bioinformatics, Briefings in Bioinformatics, Cell Biology International, Cellular Physiology and Biochemistry, Cells, Circulation Research, Current Bioinformatics, Database, EMBO Molecular Medicine, European Heart Journal, FEBS Journal, FEBS Open Bio, Frontiers in Cardiovascular Medicine, Frontiers in Genetics, Frontiers in Neuroscience, Frontiers in Physiology, Gene, Gene Expression Patterns, Genes, Genome Biology, International Journal of Molecular Sciences, International Journal of Developmental Neuroscience, Journal of Clinical Investigation, JCI Insight, Journal of Clinical Medicine, Journal of Molecular and Cellular Cardiology, Journal of Cell Biology, Journal of Cellular Biochemistry, Mechanisms of Development, Mediators of Inflammation, Molecular Genetics and Genomics, Nucleic Acids Research, Nature Reviews Genetics, Non-Coding RNA, Oncotarget, Physiological Genomics, PLoS ONE, Scientific Journal of Musculoskeletal Disorders, Scientific Reports, Tumor Biology

Grant Peer Review 09/15 Research grant application from the German Research Foundation (DFG), Germany 02/16 Research grant application from the German Research Foundation (DFG), Germany 12/16 Research grant application from the German Research Foundation (DFG), Germany 10/17 Research grant application from the German Research Foundation (DFG), Germany 10/17 Research grant application from the Netherlands Organisation for Scientific Research (NWO), Netherlands 11/17 Research grant applications from the National Center of Science and Technology Evaluation (JSC), Kazakhstan 01/18 Fellowship program applications (GTOE Clinical committee) from the American Heart Association (AHA)

HONORS AND AWARDS

08/94 – 05/98 Lynn Scholarship, Creighton University, Omaha, Nebraska 08/03 – 12/03 Grosscurth Scholarship/University Fellowship, University of Louisville, Louisville, Kentucky 04/04 – 03/07 Tuition Fee Exemption Award for Excellent Students, Japan Advanced Institute of Science and Technology, Ishikawa, Japan 04/06 – 03/07 Foreign Study Grant, Mochida Memorial Foundation for Medical and Pharmaceutical Research, Tokyo, Japan 04/06 – 03/08 Research Fellowship for Young Scientists (DC2), Japan Society for the Promotion of Science, Tokyo, Japan (Declined for studying abroad at the Max Planck Institute for Heart and Lung Research) 03/06 – 03/08 Scholarship Program for College and Graduate Students Studying Abroad, Yoshida Scholarship Foundation, Tokyo, Japan 06/2011 Poster award, 2nd International Symposium of the Excellence Cluster Cardio Pulmonary System (ECCPS) (June 16- 18, 2011), Bad Nauheim, Germany 11/2015 Most downloaded review article from Circulation Research, AHA Scientific Sessions 2015 (November 10, 2015), Orlando, Florida

EDUCATIONAL ACTIVITIES

To Graduate Students 04/04 – 03/06 Teaching Assistant for molecular biology courses, Japan Advanced Institute of Science and Technology, Ishikawa, Japan 04/04 – 03/06 English Instructor, Japan Advanced Institute of Science and Technology, Ishikawa, Japan 04/08 – 07/12 Thesis/Dissertation Mentor for two diploma students in bioinformatics and six PhD students in developmental biology, cell biology, genetics and molecular biology, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany Shizuka Uchida, 04/17/2018 Page 3 of 18

08/12 – pres. Thesis/Dissertation Mentor for one bachelor student and one master student in bioinformatics and five PhD students in bioinformatics and cardiovascular biology, Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany 11/14 Instructor, Moderne Methoden (Vorlesung und Seminar—Next Generation Sequencing), Molecular Medicine Master of Science program, Goethe University Frankfurt, Frankfurt am Main, Germany 11/14 Instructor, Frankfurter Forschung (Vorlesung und Seminar), Molecular Medicine Master of Science program, Goethe University Frankfurt, Frankfurt am Main, Germany 10/15 Instructor, Moderne Methoden (Vorlesung und Seminar—Next Generation Sequencing), Molecular Medicine Master of Science program, Goethe University Frankfurt, Frankfurt am Main, Germany 11/15 Instructor, Frankfurter Forschung (Vorlesung und Seminar), Molecular Medicine Master of Science program, Goethe University Frankfurt, Frankfurt am Main, Germany

To Professionals 03/14 Instructor, SFB834 Workshop for Bioinformatics (bioinformatics analysis of microarrays and next generation sequencing data) 02/15 Instructor, SFB834 Workshop for Bioinformatics (bioinformatics analysis of microarrays and next generation sequencing data) 11/15 Instructor, SFB834 Workshop for Bioinformatics (Understanding the set of interesting genes that you identified via DAVID and NetworkAnalyst) 12/15 Instructor, SFB834 Workshop for Bioinformatics (Making a heatmap and performing clustering via MeV)

GRANTS AND CONTRACTS

Research Grants Current

1. 04/18 – 03/23 Co-Investigator, “The Role of Cariomyogenic Lineage Commitment in Cardiac Mesenchymal Cell- Mediated Extracellular Vesicle Signaling and Cardiac Repair, NIH-NHLBI, R01 HL141081 (PI: Moore) Direct Cost: $42,473

2. 09/17 – 08/22 Co-Investigator, “Protection of ischemic myocardium”, NIH-NHLBI, P01 HL078825 (PI: Bolli) Direct Cost: $33,469

3. 01/17 – 12/21 Co-PI, “Gibbs Lung Research Program”, GSG III Foundation, Louisville Direct Cost: $1,050,000 Past 1. 03/06 – 03/08 PI, “Elucidating the cardiomyocyte differentiation mechanisms of adult stem cells and their applications”, Yoshida Scholarship Foundation (Tokyo, Japan) Direct Cost: ¥2,500,000

2. 01/08 – 12/09 Co-PI with Dr. Tibor Ziegelhöffer (Kerckhoff-Klinik, Bad Nauheim, Germany), “Searching for Heart Failure Biomarkers: systems biology approach”, Kerckhoff Foundation (Bad Nauheim, Germany) Direct Cost: €21,000

3. 01/10 – 12/11 PI, “Characterization and induction of cardiac stem cells into functional cardiomyocytes”, Shizuka Uchida, 04/17/2018 Page 4 of 18

Excellence Cluster Cardio-Pulmonary System (Gießen, Germany) Direct Cost: €80,000

4. 01/11 – 12/12 PI, “Elucidation of stemness and differentiation of adult stem cells”, LOEWE Center for Cell and Gene Therapy (State of Hessen, Germany) Direct Cost: €40,000

5. 01/12 – 12/13 Project Scientist, “The fates of bronchioalveolar stem cells (BASCs) and other putative lung adult stem cells using cellular lineage tracing”, Universities of Giessen and Marburg Lung Center (UGMLC)(State of Hessen, Germany) Direct Cost: €100,000

6. 01/12 – 12/13 PI, “Uncovering the heterogeneity of Sca1-positive adult stem cells during the ageing process”, LOEWE Center for Cell and Gene Therapy (State of Hessen, Germany) Direct Cost: €80,000

7. 01/13 – 12/13 Co-PI with Prof. Stefanie Dimmeler (Goethe University Frankfurt, Frankfurt am Main, Germany) and Prof. Edgar Wingender (University of Göttingen, Göttingen, Germany), “Integration of comprehensive transcriptomes to decipher processes controlling cardiogenesis”, German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf- Forschung e. V. (DZHK))(Partner side Rhein-Main, Germany) Direct Cost: €35,700

8. 01/14 – 12/14 Co-PI with Prof. Edgar Wingender and Prof. Wolfram-Hubertus Zimmermann (University of Göttingen, Göttingen, Germany), “Elucidating the interactions among genes and noncoding RNAs controlling cardiogenesis”, German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf-Forschung e. V. (DZHK))(Partner side Rhein-Main, Germany), Direct Cost: €20,000

9. 01/13 – 12/13 Co-PI with Prof. Edgar Wingender and Prof. Wolfram-Hubertus Zimmermann (University of Göttingen, Göttingen, Germany), “LncRNA RIP-chip/-sequencing with data analysis”, German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf- Forschung e. V. (DZHK))(Partner side Rhein-Main, Germany) Direct Cost: €35,700

10. 01/14 – 12/15 Co-PI with Prof. Wolfram-Hubertus Zimmermann and Prof. Edgar Wingender (University of Göttingen, Göttingen,Germany), “Construction of a transcriptional network regulating in vitro cardiogenesis”, German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf-Forschung e. V. (DZHK))(Partner side Rhein-Main, Germany) Direct Cost: €10,000

11. 01/14 – 12/15 Co-PI with Prof. Stefanie Dimmeler (Goethe University Frankfurt, Frankfurt am Main Germany) and Prof. Nikolaus Rajewsky (Max Delbrück Center for Molecular Medicine, Berlin, Germany), “Building a knowledge database for endothelial coding and non-coding genes”, German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf- Forschung e. V. (DZHK)) (Partner side Rhein-Main, Germany), Direct Cost: €44,100

12. 01/14 – 12/15 Co-PI with Prof. Stefanie Dimmeler (Goethe University Frankfurt, Frankfurt am Main, Germany) Shizuka Uchida, 04/17/2018 Page 5 of 18

and Prof. Salim Seyfried (University of Potsdam, Potsdam, Germany), “Systematic screening for evolutionary-conserved, disease-relevant long noncoding RNAs”, German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf-Forschung e. V. (DZHK)) (Partner side Rhein-Main, Germany) Direct Cost: €39,000

13. 01/15 – 12/15 Co-PI with Prof. Stefanie Dimmeler (Goethe University Frankfurt, Frankfurt am Main, Germany) and Prof. Wolfram-Hubertus Zimmermann (University of Göttingen, Göttingen, Germany), “Comprehensive profiling of bioengineered heart muscle for translational application”, German Centre for Cardiovascular Research (Deutsches Zentrum für Herz- Kreislauf-Forschung e. V. (DZHK)) (Partner side Rhein-Main, Germany) Direct Cost: €20,000

14. 01/16 – 12/16 Co-PI with Prof. Wei Chen (Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany), “Elucidating the functions of evolutionary-conserved, cardiovascular-disease-related long non-coding RNA”, German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf-Forschung e. V. (DZHK)) (Partner side Rhein-Main, Germany) Direct Cost: €60,000

15. 08/12 – 12/16 PI, “Cardiovascular Bioinformatics”, LOEWE Center for Cell and Gene Therapy (State of Hessen, Germany), Direct Cost: €1,231,845

16. 10/16-12/16 PI, “LncRNA-dependent mechanism of DNA/RNA-binding proteins”, KBRIN-funded Next Generation Sequencing Project (University of Louisville) Direct Cost: $5,000

17. 03/17 – 12/17 PI, “Functional studies of lncRNAs regulated in cardiovascular disease”, V.V. Cooke Foundation, Louisville Direct Cost: $10,000

18. 01/17 – 12/17 PI, “Detection and analysis of RNA modifications for RNA epigenetics”, EVPRI Internal Grants Programs, University of Louisville Direct Cost: $10,000

19. 01/14 – 12/17 PI, “Z4: Next generation sequencing and bioinformatics platform”, German Research Foundation (Deutsche Forschungsgemeinschaft(DFG)), SFB834 Direct Cost: €249,600

20. 06/14 – 06/17 PI, “Molecular mechanism of long non-coding RNAs during cardiomyocyte differentiation”, German Research Foundation (Deutsche Forschungsgemeinschaft (DFG)) GZ: UC 67/2-1, Direct Cost: €196,550, Indirect Cost: €39,300

21. 04/17 – 03/18 PI, “Functional studies of lncRNAs regulated in cardiovascular disease”, School of Medicine Basic Research Grant, University of Louisville Direct Cost: $21,250

Shizuka Uchida, 04/17/2018 Page 6 of 18

ABSTRACTS AND PRESENTATIONS

ORAL PRESENTATIONS National/International Meetings 1. Uchida, S., Fushimi, K., Sabi, M. and Tsukahara, T.: Transcriptional profiling during cell commitment of teratocarcinoma cells: an oligo microarray study. Jaist International Symposium on Nano Technology 2004, Ishikawa, Japan, September 9-10, 2004. 2. Uchida, S., Gellert, P., Schneider, A., Jenniches, K., Zarjitskaya, P., and Braun, T.: A systematic identification and characterization of heart-specific genes with unknown functions. 18th Meeting of the Society for Developmental Biology, Hannover, Germany, March 25-27, 2009. 3. Uchida, S., Gellert, P., Jenniches, K., Teranishi, M,. John, D., De Gaspari, P., and Braun, T.: Annotating New Genes: From In Silico Screening to Validations by Experiments. Molecular Life Sciences 2011, Frankfurt, Germany, September 25, 2011. 4. Uchida, S., De Gaspari, P., Jenniches, K., Gellert, P., Teranishi, M., John, D., and Braun, T.: Lineage Tracing of Adult Stem Cells in Murine Heart. World Conference on Regenerative Medicine, Leipzig, Germany, November 3, 2011. 5. Uchida, S.*:Cardiac stem cells: lessons learned from lineage tracing. Ninth International Symposium on Stem Cell Therapy and Cardiovascular Innovation, Madrid, Spain, June 7, 2012. *Invited talk. 6. Uchida, S.*: Residente kardiale Stammzellen: Gibt es einen endogenen Reparaturmechanismus? (Resident Cardiac Stem Cells: Is there an endogenous repair mechanism?) 79th Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 3, 2013. *Invited talk. 7. Stellos, K., Amrhein, C., Boeckel, J. N., Gatsiou, K., Michalik, K., Kaluza, D., Wagner, J., John, D., You, X., Uchida, S., Chen, W., Boon, R., Zeiher, A., and Dimmeler, S.: A-to-I RNA Editing Regulates Gene Expression and Controls Angiogenesis in Human Endothelial Cells. American Heart Association (AHA) Scientific Sessions 2013, Dallas, Texas, November 16-20, 2013. The abstract published in Circulation. 128 (Suppl 22): A12268-A12268, 2013. 8. Michalik, K. M., You, X., Doddaballapur, A., Jaé, N., John, D., Chen, W., Uchida, S., Boon, R. A., and Dimmeler, S.: Identification of Laminar Flow Regulated Non-Coding RNAs in Endothelial Cells. American Heart Association (AHA) Scientific Sessions 2013, Dallas, Texas, November 16-20, 2013. The abstract published in Circulation. 128 (Suppl 22): A14568-A14568, 2013. 9. K. M. Michalik, K. M., You, X., Doddaballapur, A., Manavski, Y., John, D., Ponomareva, Y., Chen, W., Uchida, S., Boon, R. A., and Dimmeler, S.: The non-coding RNA MALAT1 inhibits endothelial cell proliferation and retina vascularization by interfering with cell cycle regulators. 80th Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 23-26, 2014. 10. Stellos, K., Gatsiou, A., Boon, R. A., John, D., Fürtig, B., Manavski, Y., Doddaballapur, A., Lunella, F. F., Amrhein, C., You, X., Uchida, S., Boeckel, J. N., Chen, W., Schwalbe, H., Zeiher, A., and Dimmeler, S.: Endothelial ADAR1-Mediated RNA Editing Controls Cathepsin S mRNA Stability and Angiogenesis. American Heart Association (AHA) Scientific Sessions, Chicago, Illinois, November 15-19, 2014. The abstract published in Circulation. 130(Suppl 2): A15691-A15691, 2014. 11. Boon, R., Hofmann, P., Michalik, K., Knau, A., Ponomareva, Y., Zeiher, A., Uchida, S., and Dimmeler, S.: Long Non-coding RNA Meg3 Regulates Senescence-associated Genes and Controls Endothelial Cell Function. American Heart Association (AHA) Scientific Sessions, Chicago, Illinois, November 15- 19, 2014. The abstract published in Circulation. 130(Suppl 2): A18412-A18412, 2014. 12. Michalik, K., John, D., Chen, W., Uchida, S., Schober, A., Weber, C., Boon, R. A., and Dimmeler, S.: Malat1 Regulates the Inflammatory Response of Endothelial Cells. American Heart Association (AHA) Scientific Sessions, Chicago, Illinois, November 15-19, 2014. The abstract published in Circulation. 130(Suppl 2): A18414-A18414, 2014. 13. Zehendner, C. M., Demolli, S., Michalik, K., Jaé, N., Wagner, J., John, D., Uchida, S., Zeiher, A., and Dimmeler, S.: Hypoxia Induces Phenotypic Switching of Human Pericytes Into Smooth Muscle Cells That is Associated With Changes in Pericyte-specific Non-coding RNA Expression. American Heart Shizuka Uchida, 04/17/2018 Page 7 of 18

Association (AHA) Scientific Sessions, Chicago, Illinois, November 15-19, 2014. The abstract published in Circulation. 130(Suppl 2): A18576-A18576, 2014. 14. Jae, N., Neumann, P., Knau, A., Uchida, S., Krüger, M., and Dimmeler, S.: Functional characterization of hypoxia-induced long non-coding RNAs in endothelial cells. 81st Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 8-11, 2015. 15. Boon, R. A., Hofmann, P., Michalik, K. M., Knau, A., Ponomareva, Y., Zeiher, A. M., Uchida, S., and Dimmeler, S.: Long non-coding RNA Meg3 controls endothelial cell function: Implications for endothelial aging and senescence. 81st Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 8-11, 2015. 16. Heumüller, A., Boeckel, J. N., Jae, N., Chen, W., Boon, R. A., Fichtlscherer, S., Zeiher, A. M., John, D., Uchida, S., and Dimmeler, S.: Hypoxia regulates endothelial circular RNAs independent on the expression of host genes. 81st Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 8-11, 2015. 17. Stellos, K., Gatsiou, A., Boon, R. A., John, D., Fürtig, B., Manavski, Y., Doddaballapur, A., Lunella, F., Amrhein, C., You, X., Uchida, S., Boeckel, J. N., Chen, W., Schwalbe, H., Zeiher, A. M., and Dimmeler, S.: Adenosine-to-Inosine RNA Editing Controls Angiogenesis. 81st Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 8-11, 2015. 18. Boeckel, J. N., Jae, N., Heumüller, A., Chen, W., Boon, R. A., Fichtlscherer, S., Zeiher, A. M., John, D., Uchida, S., and Dimmeler, S.: Identification and characterization of hypoxia-regulated endothelial circular RNA and their regulation in the plasma of ACS patients. 81st Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 8-11, 2015. 19. Fork, C., Gu, L., Leisegang, M. S., Hu, J., Uchida, S., Ponomareva, Y., and Brandes, R. P.: JARID1B represses HOXA5 and thereby maintains angiogenesis. 81st Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 8-11, 2015. 20. Stellos, K., Gatsiou, A., Boon, R., John, D., Uchida, S., Keller, T., Chen, W., Schwalbe, H., Zeiher, A. M., and Dimmeler, S.: RNA editing is essential for vascular homeostasis in vivo and controls gene expression in patients with cardiovascular disease. ESC Congress, London, U.K., August 29 - September 2, 2015. The abstract published in Eur Heart J. 36(Abstract Supplement):377-377, 2015. 21. Weirick, T., John, D., Dimmeler, S., and Uchida, S.: C-It-Loci: A knowledge database for tissue- enriched loci. GIW / InCoB 2015, Tokyo, Japan, September 9-11, 2015. 22. John, D., Weirick, T., Dimmeler, S., and Uchida, S.: RnaEditor: a bioinforma/c tool to analyze RNA edi/ng events. GIW / InCoB 2015, Tokyo, Japan, September 9-11, 2015. 23. Neumann, P., Jaé, N., John, D., Uchida, S., Krüger, M., and Dimmeler, S.: Characterization of Hypoxia- induced Long Non-coding RNAs in Endothelial Cells. American Heart Association (AHA) Scientific Sessions, Orlando, Florida, November 7-11, 2015. The abstract published in Circulation. 132(Suppl 3):A15235-A15235, 2015. 24. Boon, R., Hofmann, P., Michalik, K., Knau, A., Ponomareva, Y., Zeiher, A. M., Uchida, S., and Dimmeler, S.: Long Non-coding RNA Meg3 Controls Endothelial Cell Function: Implications for Endothelial Aging and Senescence (Best of Basic Science Abstract). American Heart Association (AHA) Scientific Sessions, Orlando, Florida, November 7-11, 2015. The abstract published in Circulation. 132(Suppl 3):A16761-A16761, 2015. 25. Stellos, K., Gatsiou, A., Boon, R., John, D., Fürtig, B., Lunella, F. F., Amrhein, C., Manavski, Y., You, X., Uchida, S., Keller, T., Boeckel, J. N., Chen, W., Schwalbe, H., Zeiher, A. M., and Dimmeler, S.: RNA Editing Controls Gene Expression in Atherosclerotic Heart Disease by Enabling HuR-mediated Posttranscriptional Regulation. American Heart Association (AHA) Scientific Sessions, Orlando, Florida, November 7-11, 2015. The abstract published in Circulation. 132(Suppl 3):A16994-A16994, 2015. 26. Zehendner, C. M., Werner, A., Bischoff, F., Boeckel, J. N., Demolli, S., Michalik, K., Meder, B., Katus, H. A., Haas, H., John, D., Uchida, S., Zeiher, A. M., and Dimmeler, S.: The Pro-angiogenic Long Non- coding Rna Tykril Controls Human Pericyte Function Through Regulation Of P53 Activity and Pdgfrß Shizuka Uchida, 04/17/2018 Page 8 of 18

Expression. American Heart Association (AHA) Scientific Sessions, Orlando, Florida, November 7-11, 2015. The abstract published in Circulation. 132(Suppl 3):A17867-A17867, 2015. 27. Boeckel, J. N., Heumüller, A., Jae, N., Y., Chen, W., Boon, R. A., John, D., Zeiher, A. M., Uchida, S., and Dimmeler, S.: The Circular RNA cZNF292 is Regulated by Hypoxia and Controls Endothelial Cell Functions. 82nd Annual Meeting of the German Cardiac Society, Mannheim, Germany, March 30 - April 2, 2016. 28. Leisegang, M. S., Fork, C., Josipovic, I., Richter, F., Preussner, J., Miller, M. J., Epah, J., Hofmann, P., Ponomareva, Y., Maegdefessel, L., Ulitsky, I., M. J., Uchida, S., Wittig, I., Boon, R. A., Looso, M., Miller, F. J., and Brandes, R. P.: The LncRNA MANTIS maintains the endothelial angiogenic phenotype. 82nd Annual Meeting of the German Cardiac Society, Mannheim, Germany, March 30 - April 2, 2016. 29. Jae, N., Neumann, P., Knau, A., John, D., Uchida, S., Krüger, M., and Dimmeler, S.: Hypoxia-regulated long non-coding RNA Hyp_up_1 interacts with the epigenetic regulator LOXL2 and controls sprouting angiogenesis. 82nd Annual Meeting of the German Cardiac Society, Mannheim, Germany, March 30 - April 2, 2016. 30. Stellos, K., Gatsiou, A., Stamatelopoulos, K., John, D., Perisic, L., Lunella, F. F., Amrhein, C., Sigala, F., Boon, R. A., Fürtig, B., Manavski, Y., You, X., Uchida, S., Keller, T., Boeckel, J. N., Maegdefessel, L., Chen, W., Schwalbe, H., Eriksson, P., Hedin, U., Zeiher, A. M., and Dimmeler, S.: RNA editing controls gene expression in atherosclerotic heart disease by enabling HuR-mediated posttranscriptional regulation. 82nd Annual Meeting of the German Cardiac Society, Mannheim, Germany, March 30 - April 2, 2016. 31. Stellos, K., Gatsiou, A., Stamatelopoulos, K., Hosp, A., Perisci, L., John, D., Lunella, F. F., Jae, N., Rossbach, O., Amrhein, C., Sigala, F., Boon, R. A., Fuertig, B., Manavski, Y., You, X., Uchida, S., Keller, T., Boeckel J. N., Franco-Cereceda, A., Maegdefessel, L., Chen, W., Schawlbe, H., Bindereif, A., Eriksson, P., Hedin, U., Zeiher, A. M., and Dimmeler, S.: Role of Adenosine-to-Inosine RNA Editing 19 of Alu Elements in Human Vascular Inflammatory Diseases. Arteriosclerosis, Thrombosis and Vascular Biology Peripheral Vascular Disease | Scientific Sessions 2016, Nashville, Tennessee, May 5-7, 2016. 32. Zehendner, C. M., Thal, S. C., Werner, A., Boeckel, J. N., Bischoff, F., John, D., Weirick, T., Jaé, N., Demolli, S., Hummel, R., Michalik, K., Meder, B., Katus, H. A., Haas, J., Chen, W., Uchida, S., Zeiher, A. M., and Dimmeler, S.: Long Non-coding RNA TYKRIL Regulates Pericyte Survival in the Cardiovascular and Central Nervous System in vivo in a p53 Dependent Manner. American Heart Association (AHA) Scientific Sessions, New Orleans, Louisiana, November 12-16, 2016. The abstract published in Circulation. 134(Suppl 1):A16105-A16105, 2016. 33. Uchida, S.: Epitranscriptomics: A New Frontier in Cardiovascular Medicine. American Heart Association (AHA) Scientific Sessions: Frontiers in Science: Stem Cells Summit, Anaheim, California, November 14, 2017.

Local/Regional Meetings 1. Uchida, S., Jenniches, K., Gellert, P., and Braun, T.: Tissue-Enriched Biology: 1,000 Genes Project. Forum Bioinformatik, Giessen, Germany, February 11, 2010. 2. Gellert, P., Uchida, S., Jenniches, K., and Braun, T.: Systematically screening for uncharacterized genes and splicing isoforms. Forum Bioinformatik, Giessen, Germany, February 11, 2010. 3. Uchida, S., De Gaspari, P., Kostin, S., grosse Kreymborg, K., Jenniches, K., Izumiya, Y., Walsh, K., and Braun T: Renewal of the myocardium by Sca1-derived cells. Excellence Cluster Cardio-Pulmonary System (ECCPS) Retreat 2010, Bad Nauheim, Germany, May 28, 2010. 4. Uchida, S.*, De Gaspari, P., and Braun, T. (2011) Are we there yet? A story about cardiac stem cells. workshop “The Future of Scientific Publishing” hosted by InTech - Open Access Publisher, Leipzig, Germany, November 3, 2011. *Invited talk. 5. Uchida, S.*: Single-cell OMICS approaches to profile adult stem cells. Fluidigm seminar, Hamburg, Germany, June 13, 2012. *Invited talk. Shizuka Uchida, 04/17/2018 Page 9 of 18

6. Uchida, S.*: Lineage tracing of adult stem cells: Genetics and Bioinformatics. Herzzentrum Göttingen, Abteilung Pharmakologie, Germany, November 26, 2012. *Invited talk. 7. Uchida, S.*: Cardiovascular Bioinformatics: Perspective on long non-coding RNAs. BioNF Seminar, Frankfurt am Main, Germany, December 8, 2014. *Invited talk. 8. Uchida, S.*: Cardiovascular Bioinformatics: Perspective on long non-coding RNAs. Kolloquium für Bioinformatik und Systembiologie, Gießen, Germany, March 3, 2015. *Invited talk. 9. Uchida, S.*: Building of bioinformatics tools and validating their performance with biological experiments. First Bioengineering Department Spring 2017 seminar, University of Louisville, January 11, 2017. *Invited talk. 10. Uchida, S.*: Long Non-Coding RNAs and Circular RNAs. KBRIN Bioinformatics Journal Club, University of Louisville, February 15, 2017. *Invited talk. 11. Uchida, S.*: Bioinformatics and Long Non-Coding RNAs. Biochemistry Seminar, Department of Biochemistry & Molecular Genetics, University of Louisville, February 20, 2017. *Invited talk. 12. Uchida, S.*: From screening to validation: lncRNAs and circRNAs. Seminar, James Black Centre, King's College London, U.K., March 17, 2017. *Invited talk. 13. Uchida, S.*: Long Non-Coding RNAs. Biology Department Seminar Series, Department of Biology, University of Louisville, October 6, 2017. *Invited talk. 14. Uchida, S.*: Epitranscriptomics in the heart and cardiovascular disease. Cardiovascular Medicine Grand Rounds, University of Louisville, February 21, 2018. *Invited talk

POSTERS

National/International Meetings 1. Uchida, S., Fushimi, K., Sabi, M. and Tsukahara, T.: Cell commitment of teratocarcinoma cells during cardiomyocyte differentiation. 27th Annual Meeting of The Molecular Biology Society of Japan, Kobe, Japan, December 8-11, 2004. 2. Uchida, S., Fushimi, K., Sabi, M., Tatsuhama, T. and Tsukahara, T.: Identifying key genes in cardiac commitment of teratocarcinoma cells. 50th NIBB Conference Structure and Dynamics of Complex Biological Networks, Aichi, Japan, February 8-10, 2005. 3. Uchida, S., Tatsuhama, T., and Tsukahara, T.: Transcriptional study of Cardiac Differentiation Mechanism of DMSO. 58th Annual Meeting of Japan Society for Cell Biology, Saitama, Japan, June 14-17, 2005. 4. Uchida, S., Fuke, S., Tatsuhama, T., and Tsukahara, T: Expression profiling of P19CL6 during cardiac commitment. Jaist International Symposium on Nano Technology 2005, Ishikawa, Japan, September 15-17, 2005. 5. Uchida, S., Fuke, S., Tatsuhama, T., and Tsukahara, T.: The dysfunctional oxytocin/oxytocin receptor system in P19CL6 cells during the cardiomyocyte differentiation. 28th Annual Meeting of The Molecular Biology Society of Japan, Fukuoka, Japan, December 7-10, 2005. 6. Uchida, S. and Tsukahara, T: Transcriptomic Approach for Identifying Key Genes During the Cardiac Commitment Time. ESF-EMBO Symposium: Stem Cells in Tissue Engineering - Isolation, Culture, Characterisation and Applications, Sant Feliu de Guixols, Spain, October 28 - November 2, 2006. 7. Jenniches, K., Uchida, S., Schneider, A., Jungblut, B., Zarjitskaya, P., and Braun, T.: The Role of Lrrc39 in the Organisation of Cardiac and Skeletal Myocytes. 18th Meeting of the Society for Developmental Biology, Hannover, Germany, March 25-27, 2009. 8. Uchida, S., Jenniches, K., Zarjitskaya, P., Gellert, P., Schneider, A., and Braun, T.: A systematic identification and characterization of heart-specific genes with unknown functions. German Symposium on Systems Biology 2009, Heidelberg, Germany, May 12-15, 2009. Shizuka Uchida, 04/17/2018 Page 10 of 18

9. Gellert, P., Uchida, S., and Braun, T.: Systematically Screening for Tissue-Specific Alternative Splicing: heart as an example. German Symposium on Systems Biology 2009, Heidelberg, Germany, May 12- 15, 2009. 10. Wolff, J.C., Fuchs, D., Fink, L., Wilhelm, J., Uchida, S., Schneider, A., Braun, T., Seeger, W., and Voswinckel, R.: Identification of putative regulators of alveolarization . American Thoracic Society 2010 International Conference, New Orleans, Louisiana, May 14-19, 2010. The abstract published in Am J Respir Crit Care Med. 181:2010:A4940, 2010. 11. Uchida, S., Gellert, P., Jenniches, K., De Gaspari, P., Teranishi, M., and Braun, T.: Annotating evolutionary-conserved, tissue-enriched genes with unknown functions. EMBO Conference Series: From Functional Genomics to Systems Biology, Heidelberg, Germany, November 13-16, 2010. 12. Uchida, S., Gellert, P., Jenniches, K., De Gaspari, P., Teranishi, M., and Braun, T.: Annotating New Genes: From In Silico Screening to Validations by Experiments. EMBO Myogenesis Conference Series: The Molecular and Cellular Mechanisms, Regulating Skeletal Muscle, Development and Regeneration, Wiesbaden, Germany, May 10-15, 2011. 13. De Gaspari, P., Jenniches, K., Gellert, P., Teranishi, M., John, D., Buettner, C., Kostin, S., Uchida, S., and Braun, T.: Lineage tracing of muscle-derived stem cells based on Sca1 expression. EMBO Myogenesis Conference Series: The Molecular and Cellular Mechanisms, Regulating Skeletal Muscle, Development and Regeneration, Wiesbaden, Germany, May 10-15, 2011. 14. Uchida, S., Gellert, P., Jenniches, K., De Gaspari, P., Teranishi, M., and Braun, T.: Annotating New Genes: From In Silico Screening to Validations by Experiments. 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology, Vienna, Austria, July 17-19, 2011. 15. John, D., Gellert, P., Dominik, A., Braun, T., and Uchida, S.: SNP4Disease: a knowledge database to detect disease associated SNPs. 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology, Vienna, Austria, July 17-19, 2011. 16. Gellert, P., Teranishi, M., Jenniches, K., De Gaspari, P., John, D., grosse Kreymborg, K., Braun, T., and Uchida, S.: Gene Array Analyzer: Alternative usage of gene arrays to study alternative splicing events. 19th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational Biology, Vienna, Austria, July 17-19, 2011. 17. Uchida, S., De Gaspari, P., Kostin, S., Jenniches, K., Izumiya, Y., Shiojima, I., grosse Kreymborg, K., Walsh, K., and Braun, T.: Sca1-derived cells as a source of cardiomyocyte renewal. 2nd International Symposium of the Excellence Cluster Cardio Pulmonary System (ECCPS), Bad Nauheim, Germany, June 16-18, 2011. 18. Martire, A., Bedada, F. B., Uchida, S., Poeling, J., Wietelmann, A., Krueger, M., Kubin, T., Szibor, M., Warnecke, H., and Braun, T.: Mesenchymal Stem Cells Modulate Inflammatory Responses in Murine Heart by Inhibition of the TNF System. American Heart Association (AHA) Scientific Sessions, Orland, Florida, November 12-16, 2011. The abstract published in Circulation. 124:A9673, 2011. 19. Uchida, S., De Gaspari, P., Kilic, A., Schiller, M., Giel, G., Renz, H., and Braun, T.: Single cell analysis of Sca1-positive cells in lung. UGMLC/DZL Symposium 2012: Remodeling, Repair and Regeneration in Lung Disease, Marburg, Germany, June 21-23, 2012. 20. Kılıç, A., Schiller, M., Uchida, S., Teranishi, M., Gellert, P., Braun, T., and Renz, H.: De-regulated expression of microRNAs contributes to augmented T helper (TH) cell activity in experimental asthma. UGMLC/DZL Symposium: Remodeling, Repair and Regeneration in Lung Diseases, Marburg, Germany, June 21–23, 2012. The abstract published in Pneumologie. 66(06): A205, 2012. 21. Uchida, S., De Gaspari, P., Dimmeler, S., and Braun, T.: Uncovering the heterogeneity of adult stem cells at the level of single cells. EMBO Conference Series: From Functional Genomics to Systems Biology, Heidelberg, Germany, November 17-20, 2012. Shizuka Uchida, 04/17/2018 Page 11 of 18

22. Ponomareva, Y., Gellert, P., Dimmeler, S., Braun, T., and Uchida, S.: Screening and elucidating the functions of histone H3-bound lncRNAs. EMBO Conference Series: From Functional Genomics to Systems Biology, Heidelberg, Germany, November 17-20, 2012. 23. John, D., Dimmeler, S., and Uchida, S.: Combined tools to analyze the effects of SNPs at the levels of genes and ncRNAs. EMBO Conference Series: From Functional Genomics to Systems Biology, Heidelberg, Germany, November 17-20, 2012. 24. Stellos, K., Amrhein, C., Boeckel, J. N., Michalik, K. M., Kaluza, D., Wagner, J., John, D., You, X., Uchida, S., Chen, W., Boon, R. A., Zeiher, A. M., and Dimmeler, S.: The RNA Editing Enzymes ADAR1 and ADAR2 Modulate the Angiogenic Properties of Endothelial Cells and Differentially Regulate the Transcriptome: First Evidence of RNA Editing in Human Endothelial Cells. 79th Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 3, 2013. 25. Uchida, S., De Gaspari, P., Dimmeler, S., and Braun, T.: Uncovering the heterogeneity of adult stem cells at the level of single cells. EMBO | EMBL Symposium Cardiac Biology: From Development to Regenerative Medicine, Heidelberg, Germany, June 7-10, 2013 26. Arndt, A. K., Musso, G., Gellert, P., Hoff, K., Uchida, S., Toka, O., Siebert, R., MacRae, C. A., Klaassen, S., and Kramer, H. H.: Transcriptome Sequencing in Hypoplastic Left Heart Syndrome Myocardium Reveals Dysregulated Cell Cycle Genes. 45th Annual Meeting of the German Society for Pediatric Cardiology. Weimar, Germany, November 2-5, 2013. The abstract published in Thorac Cardiovasc Surg. 61 (S02): V16. 27. John, D., Ponomareva, Y., Dimmeler, S., and Uchida, S.: RNAeditor: Bioinformatic tool to analyze RNA editing events. EMBO|EMBL Symposium: Non-Coding Genome, Heidelberg, Germany, October 9-12, 2013. 28. Militello, G., Gellert, P., John, D., Ponomareva, Y., Dimmeler, S., and Uchida, S.: Identification of positionally-conserved lincRNAs between human and mouse. EMBO|EMBL Symposium: Non-Coding Genome, Heidelberg, Germany, October 9-12, 2013. 29. Ponomareva, Y., John, D., Gellert, P., Dimmeler, S., and Uchida, S.: Screening of cell-type-specific histone‐bound lncRNAs. EMBO|EMBL Symposium: Non-Coding Genome, Heidelberg, Germany, October 9-12, 2013. 30. Leisegang, M. S., Fork, C., Ponomareva, Y., Uchida, S., and Brandes, R. P.: The Long non-coding RNA n342419 (Mantis) is an important component for the homeostasis of the vascular system. 93 Annual Meeting of the German Physiological Society, Mainz, Germany, March 13-15, 2014. The abstract published in Acta Physiologica. 210 (s695): 98-99, 2014. 31. Fork, C., Gu, L., Uchida, S., Ponomareva, Y., and Brandes, R. P.: Jarid1b maintains endothelium- dependent relaxation and is essential for angiogenesis. 93 Annual Meeting of the German Physiological Society, Mainz, Germany, March 13-15, 2014. The abstract published in Acta Physiologica. 210 (s695): 121-122, 2014. 32. Cencioni, C., Spallotta, F., Uchida, S., Zeiher, A. M., and Gaetano, C.: Role of long non-coding RNAs and zinc finger E-box binding homeobox factor 1 and 2 (Zeb1, Zeb2) in cardiovascular programming of mouse embryonic stem cells. 80th Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 23-26, 2014. 33. Stellos, K., Boon, R. A., Fürtig, B., John, D., Gatsiou, A., Manavski, Y., Amrhein, C., Boeckel, J. N., You, X., Uchida, S., Chen, W., Schwalbe, H., Zeiher, A. M., and Dimmeler, S.: RNA Editing Controls Angiogenesis By Posttranscriptional Regulation of Cathepsin S. 80th Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 23-26, 2014. 34. Fork, C., Gu, L., Uchida, S., Ponomareva, Y., Brandes, R. P.: Jarid1b maintains endothelium- dependent relaxation and is essential for angiogenesis. 80th Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 23-26, 2014. 35. John, D., Dimmeler, S., and Uchida, S.: RNAeditor: a bioinformatics tool to analyze RNA editing events. EMBO | EMBL Symposia: The Complex Life of mRNA, Heidelberg, Germany, October 5-8, 2014. Shizuka Uchida, 04/17/2018 Page 12 of 18

36. Militello, G., Ponomareva, Y., Gellert, P., John, D., Dimmeler, S., and Uchida, S.: Identification of positionally-conserved lincRNAs between human and mouse. EMBO | EMBL Symposia: The Complex Life of mRNA, Heidelberg, Germany, October 5-8, 2014. 37. Ponomareva, Y., Militello, G., John, D., Gellert, P., Dimmeler, S., and Uchida, S.: Screening of cell- type-specific histone-bound lncRNAs. EMBO | EMBL Symposia: The Complex Life of mRNA, Heidelberg, Germany, October 5-8, 2014. 38. Fork, C., Gu, L., Leisegang, M., Hu, J., Uchida, S., Ponomareva, Y., and Brandes, R. P.: Jarid1b represses Hoxa5 and thereby maintains angiogenesis. 94th Annual Meeting of the German Physiological Society, Magdeburg, German, March 5-7, 2015. The abstract published in Acta Physiologica. 213 (S699):89-90, 2015. 39. Leisegang, M. S., Fork, C., Miller, M. J., Ponomareva, Y., Uchida, S., Miller, F. J., and Brandes, R. P.: The long non-coding Rna Mantis is highly expressed during vascular regeneration and essential for the Vegf-a-induced angiogenic function. 94th Annual Meeting of the German Physiological Society, Magdeburg, German, March 5-7, 2015. The abstract published in Acta Physiologica. 213 (S699):148- 149, 2015. 40. Neumann, P., Jae, N., Uchida, S., and Dimmeler, S.: The Hypoxia reduced lncRNA Hyp_down_1 regulates angiogenic functions of endothelial cells in a let-7-independet manner. 81st Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 8-11, 2015. 41. Michalik, K. M., John, D., Chen, W., Uchida, S., Schober, A., Weber, C., Boon, R. A., and Dimmeler, S.: The lncRNA MALAT1 regulates the inflammatory response of endothelial cells. 81st Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 8-11, 2015. 42. Zehendner, C. M., Demolli, S., Michalik, K. M., John, D., Uchida, S., Zeiher, A. M., and Dimmeler, S.: Hypoxia induced long-noncoding RNAs regulate human pericyte function. 81st Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 8-11, 2015. 43. Leisegang, M. S., Fork, C., Miller, M. J., Ponomareva, Y., Uchida, S., Miller, F. J., Brandes, R. P.: The long non-coding RNA Mantis is highly expressed during vascular regeneration and essential for the VEGF-A-induced angiogenic function. 81st Annual Meeting of the German Cardiac Society, Mannheim, Germany, April 8-11, 2015. 44. Ponomareva, Y., Gellert, P., John, D., Militello, G., Dimmeler, S., and Uchida, S.: Screening of cell- type-specific histone-bound long noncoding RNAs. 3rd International Annual Conference of the Germany Stem Cell Network (GSCN), Frankfurt am Main, Germany, September 9-11, 2015. 45. Hosen, M. R., Militello, G., Ponomarave, Y., Dimmeler, S., and Uchida, S.: Elucidation of the role of Airn in murine cardiomyocytes. 3rd International Annual Conference of the Germany Stem Cell Network (GSCN), Frankfurt am Main, Germany, September 9-11, 2015. 46. Militello, G., Ponomareva, Y., Gellert, P., John, D., Weirick, T., Döring, C., Fukada, S., Dimmeler, S., and Uchida, S.: An evolutionary-conserved novel long non-coding RNA Myolinc regulates muscle differentation. EMBO|EMBL Symposium: Non-Coding Genome, Heidelberg, Germany, October 18- 21, 2015. 47. John, D., Weirick, T., Dimmeler, S., and Uchida, S.: RnaEditor: a bioinforma/c tool to analyze RNA edi/ng events. EMBO|EMBL Symposium: Non-Coding Genome, Heidelberg, Germany, October 18- 21, 2015. 48. Müller, R., Weirick, T., John, D., Militello, G., Dimmeler, S., and Uchida, S.: ANGIOGENES: knowledge database for protein-coding and non-coding RNA genes in endothelial cells. EMBO|EMBL Symposium: Non-Coding Genome, Heidelberg, Germany, October 18-21, 2015. 49. Weirick, T., John, D., Dimmeler, S., and Uchida, S.: C-It-Loci: A knowledge database for tissue- enriched loci. EMBO|EMBL Symposium: Non-Coding Genome, Heidelberg, Germany, October 18-21, 2015. 50. Ponomareva, Y., Gellert, P., Militello, G., John, D., Weirick, T., Döring, C., Dimmeler, S., and Uchida S.: The Non-Coding Genome, Heidelberg, Germany, October 18-21, 2015. Shizuka Uchida, 04/17/2018 Page 13 of 18

51. Heumüller,, A. W., Boeckel, J. N., Jaé, N., Ponomareva, Y., Chen, W., Boon, R. A., John, D., Zeiher, A. M., Uchida, S., and Dimmeler, S.: Hypoxia Regulated Circular RNAs Control Endothelial Cell Functions (Best of Basic Science Abstract). American Heart Association (AHA) Scientific Sessions, Orlando, Florida, November 7-11, 2015. The abstract published in Circulation. 132(Suppl 3):A19222-A19222, 2015. 52. Raad, F., Roa, A., Hudson, J., Tiburcy, M., Uchida, S., and Zimmermann, W. H.: Modelling Human Heart Development and Faulty Cardiogenesis in Bioengineered Heart Muscle. 82nd Annual Meeting of the German Cardiac Society, Mannheim, Germany, March 30 - April 2, 2016. 53. Bischoff, F., Werner, A., Boeckel, J. N., Demolli, S., Michalik, K. M., Meder, B., Katus, H. A., Haas, J., Chen, W., John, D., Uchida, S., Zeiher, A. M., Dimmeler, S., and Zehendner, C. M.: The Long-Non- Coding RNA HypERrlnc Regulates Human Pericyte Function by Modulation of the ER Stress Cell Response. 82nd Annual Meeting of the German Cardiac Society, Mannheim, Germany, March 30 - April 2, 2016. 54. Raad, F. S., Roa, A., Hudson, J. E., Tiburcy, M., Uchida, S., and Zimmermann, W. H.: Modeling Human Heart Development and Faulty Cardiogenesis in Bioengineered Heart Muscle. 82nd Annual Meeting of the German Cardiac Society, Mannheim, Germany, March 30 - April 2, 2016. 55. Boeckel, J. N., Glaser, S. F., Heumüller, A., Becker-Pergola, G., Jae, N., Chen, W., John, D., Uchida, S., and Dimmeler, S.: Regulation of Inflammatory Resolution by the Circular RNA cTRIO in Endothelial Cells 82nd Annual Meeting of the German Cardiac Society, Mannheim, Germany, March 30 - April 2, 2016. 56. Hosen, M. R., Militello, G., John, D., Ponomareva, Y., Claycomb, W. C., Döring, C., Müller-McNicoll, M., Dimmeler, S., and Uchida, S.: Elucidation of the role of Airn in murine cardiomyocytes. 4th Annual GSCN Conference, Hannover, Germany, September 12-14, 2016. 57. Jaé, N., Neumann, P., John, D., Uchida, S., Krüger, M., and Dimmeler, S.: The Antisense Transcript of GATA6 Interacts With the H3K4me3 Deaminase LOXL2 and Epigenetically Regulates Endothelial Gene Expression. American Heart Association (AHA) Scientific Sessions, New Orleans, Louisiana, November 12-16, 2016. The abstract published in Circulation. 134(Suppl 1):A14714-A14714, 2016. 58. Bischoff, F., Werner, A., Boeckel, J. N., Demolli, S., Michalik, K., Meder, B., Katus, H. A., Haas, J., Chen, W., John, D., Uchida, S., Zeiher, A. M., Dimmeler, and S., Christoph M Zehendner, C. M.: Long-Non- Coding RNA HypERrlnc Regulates Human Pericyte Function by Modulation of the Endoplasmic Reticulum-Stress Cell Response. American Heart Association (AHA) Scientific Sessions, New Orleans, Louisiana, November 12-16, 2016. The abstract published in Circulation. 134(Suppl 1):A15078- A15078, 2016. 59. Neumann, P., Fouani, Y., Jaé, N., Knau, A., John, D., Uchida, S., Heidler, J., Wittig, and I., Dimmeler, S.: The Hypoxia-induced Long Non-coding RNA Hyp_up_3 Regulates Alternative Splicing and Controls Angiogenesis of Endothelial Cells. American Heart Association (AHA) Scientific Sessions, New Orleans, Louisiana, November 12-16, 2016. The abstract published in Circulation. 134(Suppl 1):A15654-A15654, 2016. 60. Gibb, A., Epstein, P., Uchida, S., Zheng, Y., Mcnally, L., Trainor, P., Conklin, D., Brittian, K., Tseng, M., Jones, S., Bhatnagar, A., and Hill: B. APS Conference: Physiological Bioenergetics: Mitochondria from Bench to Bedside, San Diego, CA, August 27-30, 2017. 61. Weirick, and Uchida, S.: Maximizing the information extraction of RNA-seq data for achieving personalized medicine. Human Genome Meeting (HGM) 2018, Yokohama, Japan, March 13-15, 2018.

Local/Regional Meetings 1. Uchida, S., Schneider, A., Wiesnet, M., Jungblut, B., Zarjitskaya, P., grosse Kreymborg, K., and Braun, T.: Systematic Categorization of Uncharacterized, Heart-Specific Genes. Leopoldina Symposium on Remodeling and Reverse Remodeling in the Cardiopulmonary System, Bad Nauheim, Germany, June 29 - July 2, 2008. Shizuka Uchida, 04/17/2018 Page 14 of 18

2. Uchida, S., Gellert, P., Jenniches, K., De Gaspari, P, Teranishi, M., and Braun, T.: Annotating evolutionary-conserved, tissue-enriched genes with unknown functions. Internal PhD Symposium: Research in Molecular and Cell Biological Sciences, Frankfurt am Main, Germany, March 24-25, 2011. 3. Uchida, S., Ponomareva, Y., John, D., Gellert, P., Militello, G., Kilic, A., Sadek H., Porello, E., Zimmermann, W. H., and Dimmeler, S.: Systematic screening of chromatin-associated lncRNAs coupled with bioinformatics analysis. Joint Symposium ECCPS/PVRI 2014, Bad Nauheim, Germany, January 27-31, 2014. 4. John, D., Ponomareva, Y., Dimmeler, S., and Uchida, S.: Development of bioinformatics tools to analyze RNA editing events. Joint Symposium ECCPS/PVRI 2014, Bad Nauheim, Germany, January 27-31, 2014. 5. Ponomareva, Y., John, D., Gellert, P., Dimmeler, S., and Uchida, S.: Characterization of histone-bound lncRNAs in murine ES cells. Joint Symposium ECCPS/PVRI 2014, Bad Nauheim, Germany, January 27- 31, 2014. 6. Militello, G., Ponomareva, Y., John, D., Dimmeler, S., and Uchida, S.: Identification of positionally- conserved lincRNAs between human and mouse. Joint Symposium ECCPS/PVRI 2014, Bad Nauheim, Germany, January 27-31, 2014. 7. Michalik, K. M., You, X., Doddaballapur, A., Jaé, N., John, D., Chen, W., Uchida, S., Boon, R. A., and Dimmeler, S.: Identification of laminar flow regulated non-coding RNAs in endothelial cells. Joint Symposium ECCPS/PVRI 2014, Bad Nauheim, Germany, January 27-31, 2014. 8. Cencioni, C., Spallotta, F., Uchida, S., Zeiher, A. M., and Gaetano, C.: Role of long non-coding RNAs and zinc finger E-box binding homeobox factor 1 and 2 (Zeb1, Zeb2) in stemness maintenance of mouse embryonic stem cells. Joint Symposium ECCPS/PVRI 2014, Bad Nauheim, Germany, January 27-31, 2014. 9. Leisegang, M. S., Fork, C., Miller, M. J., Ponomareva, Y., Uchida, S., and Brandes, R. P.: The LncRNA n342419 (Mantis) is involved in the homeostasis of the vascular system. Joint Symposium ECCPS/PVRI 2014, Bad Nauheim, Germany, January 27-31, 2014. 10. Stellos, K., Boon, R. A., Gatsiou, K., Amerhein, C., John, D., Fürtig, B., Boeckel, J. N., Michalik, K., You, X., Uchida, S., Chen, W., Schwalbe, H., Zeiher, A., and Dimmeler, S.: Control of endothelial cell posttranscriptional regulation of gene expression and angiogenesis by RNA editing. Joint Symposium ECCPS/PVRI 2014, Bad Nauheim, Germany, January 27-31, 2014. 11. Fork, C., Gu, L., Uchida, S., Ponomareva, Y., and Brandes, R. P.: Jarid1b maintains endothelium- dependent relaxation and is essential for angiogenesis. Joint Symposium ECCPS/PVRI 2014, Bad Nauheim, Germany, January 27-31, 2014. 12. Gibb, A., Epstein, P., Uchida, S., Zheng, Y., Mcnally, L., Trainor, P., Conklin, D., Brittian, K., Tseng, M., Jones, S., Bhatnagar, A., and Hill, B. Research!Louisville, Louisville, KY, September 11-15, 2017.

PUBLICATIONS

PEER-REVIEWED Journal articles published Original research articles 1. Uchida, S.#, Nishida, Y.#, Satou, K., Muta, S., Tashiro, K., and Kuhara, S.: Detection and normalization of biases present in spotted cDNA microarray data: a composite method addressing dye, intensity-dependent, spatially-dependent, and print-order biases. DNA Res. 12(1):1-7, 2005. #Shared first-author. PMID: 16106748. 2. Fushimi, K., Uchida, S., Matsushita, R., and Tsukahara, T.: Prediction of tertiary structure of NSSRs' RNA recognition motif and the RNA binding activity. Sci. Tech. Adv. Mater. 6:475-483, 2005. Shizuka Uchida, 04/17/2018 Page 15 of 18

3. Uchida, S., Fuke, S., and Tsukahara, T.: Upregulations of Gata4 and oxytocin receptor are important in cardiomyocyte differentiation processes of P19CL6 cells. J Cell Biochem. 100(3):629-41, 2007. PMID: 16960874. 4. Belema-Bedada, F., Uchida, S., Martire, A., Kostin, S., and Braun, T.: Efficient homing of multipotent adult mesenchymal stem cells depends on FROUNT-mediated clustering of CCR2. Cell Stem Cell. 2(6):566-75, 2008. PMID: 18522849. 5. Uchida, S.#, Schneider, A.#, Wiesnet, M., Jungblut, B., Zarjitskaya, P., Jenniches, K., Kreymborg, K.G., Seeger, W., and Braun, T.: An integrated approach for the systematic identification and characterization of heart-enriched genes with unknown functions. BMC Genomics. 10:100, 2009. #Shared first-author. PMID: 19267916. PMCID: PMC2657154. 6. Gellert, P.*, Uchida, S., and Braun, T.: Exon Array Analyzer: a web interface for Affymetrix exon array analysis. Bioinformatics. 25(24):3323-4, 2009. *Student mentored by me. PMID: 19808879. 7. Gellert, P.*, Jenniches, K.*, Braun, T., and Uchida, S.: C-It: a knowledge database for tissue- enriched genes. Bioinformatics. 26(18):2328-33, 2010. *Students mentored by me. PMID: 20628071. 8. Kreymborg, K.g., Uchida, S., Gellert, P.*, Schneider, A., Boettger, T., Voswinckel, R., Wietelmann, A., Szibor, M., Weissmann, N., Ghofrani, A.H., Schermuly, R., Schranz, D., Seeger, W., and Braun, T.: Identification of right heart-enriched genes in a murine model of chronic outflow tract obstruction. J Mol Cell Cardiol. 49(4):598-605, 2010. *Students mentored by me. PMID: 20673770. 9. Gellert, P.*#, Teranishi, M.*#, Jenniches, K.*, De Gaspari, P.*, John, D.*, Kreymborg, K.G., Braun, T., and Uchida, S.: Gene Array Analyzer: alternative usage of gene arrays to study alternative splicing events. Nucleic Acids Res. 40(6):2414-25, 2012. *Students mentored by me. #Joint first-author. PMID: 22123740. PMCID: PMC3315316. 10. Uchida, S.*, De Gaspari, P*, Kostin S, Jenniches, K., Kilic, A., Izumiya, Y., Shiojima, I., Grosse Kreymborg, K., Renz, H., Walsh, K., and Braun, T.: Sca1-derived cells are a source of myocardial renewal in the murine adult heart. Stem Cell Reports. 1(5):397-410, 2013. *Joint first-author. PMID: 24286028. PMCID: PMC3841250. 11. Gellert, P.*, Ponomareva, Y.*, Braun, T., and Uchida, S.: Noncoder: a web interface for exon array-based detection of long non-coding RNAs. Nucleic Acids Res. 41(1):e20, 2013. *Student mentored by me. PMID: 23012263. PMCID: PMC3592461. 12. Heinrich, E.M., Wagner, J., Krüger, M., John, D.*, Uchida, S., Weigand, J.E., Suess, B., and Dimmeler, S.: Regulation of miR-17-92a cluster processing by the microRNA binding protein SND1. FEBS Lett. 587(15):2405-11, 2013. *Student mentored by me. PMID: 23770094. 13. Michalik, K.M., You, X., Manavski, Y., Doddaballapur, A., Zörnig, M., Braun, T., John, D.*, Ponomareva, Y.*, Chen, W., Uchida, S., Boon, R.A., and Dimmeler, S.: Long noncoding RNA MALAT1 regulates endothelial cell function and vessel growth. Circ Res. 114(9):1389-97, 2014. *Student mentored by me. PMID: 24602777. 14. Ogawa, R., Ma, Y., Yamaguchi, M., Ito, T., Watanabe, Y., Ohtani, T., Murakami, S., Uchida, S., De Gaspari, P.*, Uezumi, A., Nakamura, M., Miyagoe-Suzuki, Y., Tsujikawa, K., Hashimoto, N., Braun, T., Tanaka, T., Takeda, S., Yamamoto, H., and Fukada, S.: Doublecortin marks a new population of transiently amplifying muscle progenitor cells and is required for myofiber maturation during skeletal muscle regeneration. Development. 142(1):51-61, 2015. *Student mentored by me. PMID: 25480916. 15. Fork, C., Gu, L., Hitzel, J., Josipovic, I., Hu, J., SzeKa Wong, M., Ponomareva, Y.*, Albert, M., Schmitz, S.U., Uchida, S., Fleming, I., Helin, K., Steinhilber, D., Leisegang, M.S., and Brandes, R.P.: Epigenetic Regulation of Angiogenesis by JARID1B-Induced Repression of HOXA5. Arterioscler Thromb Vasc Biol. 35(7):1645-52, 2015. *Student mentored by me. PMID: 26023081. Shizuka Uchida, 04/17/2018 Page 16 of 18

16. Boeckel, J.N., Jaé, N., Heumüller, A.W., Chen, W., Boon, R.A., Stellos, K., Zeiher, A.M., John, D.*, Uchida, S.#, and Dimmeler, S.#: Identification and Characterization of Hypoxia-Regulated Endothelial Circular RNA. Circ Res. 117(10):884-90, 2015. *Student mentored by me. #Shared senior-author. PMID: 26377962. 17. Weirick, T.*, John, D.*, Dimmeler, S., and Uchida S.: C-It-Loci: a knowledge database for tissue- enriched loci. Bioinformatics. 31(21):3537-43, 2015. *Students mentored by me. PMID: 26163692. 18. Zeidler, S., Meckbach, C., Tacke, R., Raad, F., Roa, A., Uchida, S., Zimmermann, W., Wingender, E. and Gültas, M.: Computational detection of stage-specific transcription factor clusters during heart development. Front Genet. 7:33, 2016. PMID: 27047536. PMCID: PMC4804722. 19. Weirick, T.*#, Militello, G.*#, Müller, R.*#, John, D.*, Dimmeler, S., and Uchida, S.: The identification and characterization of novel transcripts from RNA-seq data. Brief Bioinform. 17(4):678-85, 2016. *Students mentored by me. #Shared first-author. PMID: 26283677. 20. Martire, A., Bedada, F.B., Uchida, S., Pöling, J., Krüger, M., Warnecke, H., Richter, M., Kubin, T., Herold, S., and Braun, T.: Mesenchymal stem cells attenuate inflammatory processes in the heart and lung via inhibition of TNF signaling. Basic Res Cardiol. 111(5):54, 2016. PMID: 27435289; PMCID: PMC4951509. 21. Müller, R.*#, Weirick, T.*#, John, D.*#, Militello, G.*, Chen, W., Dimmeler, S., and Uchida, S.: ANGIOGENES: knowledge database for protein-coding and noncoding RNA genes in endothelial cells. Sci Rep. 6: 32475, 2016. *Students mentored by me. #Shared first-author. PMID: 27582018. PMCID: PMC5007478. 22. Stellos, K., Gatsiou, A., Stamatelopoulos, K., Perisic Matic, L., John, D.*, Lunella, FF., Jaé, N., Rossbach, O., Amrhein, C., Sigala, F., Boon, R.A., Fürtig, B., Manavski, Y., You, X., Uchida, S., Keller, T., Boeckel, J.N., Franco-Cereceda, A., Maegdefessel, L., Chen, W., Schwalbe, H., Bindereif, A., Eriksson, P., Hedin, U., Zeiher, A.M., and Dimmeler, S.: Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated posttranscriptional regulation. Nat Med. 22(10):1140-1150, 2016. *Students mentored by me. PMID: 27595325. 23. Gerstner, S., Köhler, W., Heidkamp, G., Purbojo, A., Uchida, S., Ekici, A.B., Heger, L., Luetke- Eversloh, M., Schubert, R., Bader, P., Klingebiel, T., Koehl, U., Mackensen, A., Romagnani, C., Cesnjevar, R., Dudziak, D., Ullrich, E.: Specific phenotype and function of CD56-expressing innate immune cell subsets in human thymus. J Leukoc Biol. 100(6):1297-1310, 2016. PMID: 27354408. 24. Weirick, T.*, John, D.*, and Uchida, S.: Resolving the problem of multiple accessions of the same transcript deposited across various public databases. Brief Bioinform. 18(2):226-235, 2017. *Students mentored by me. PMID: 26921280. 25. Leisegang, M.S., Fork, C., Josipovic, I., Richter, F., Preussner, J., Hu, J., Miller, M.J., Epah, J.N., Hofmann, P., Günther, S., Moll, F., Valasarajan, C., Heidler, J., Ponomareva, Y.*, Freiman, T.M., Maegdefessel, L., Plate, K.H., Mittelbronn, M., Uchida, S., Künne, C., Stellos, K., Schermuly, R.T., Weissmann, N., Devraj, K., Wittig, I., Boon, R.A., Dimmeler, S., Pullamsetti, S.S., Looso, M., Miller, F.J., and Brandes, R.P.: Long Noncoding RNA MANTIS Facilitates Endothelial Angiogenic Function. Circulation. 136(1):65-79, 2017. *Students mentored by me. PMID: 28351900. 26. Bischoff, F.C., Werner, A., John, D.*, Boeckel, J.N., Melissari, M.T., Grote, P., Glaser, S.F., Demolli, S., Uchida, S., Michalik, K.M., Meder, B,. Katus, H.A., Haas, J., Chen, W., Pullamsetti, S.S., Seeger, W., Zeiher, A.M., Dimmeler, S., and Zehendner, C.M.: Identification and Functional Characterization of Hypoxia-Induced Endoplasmic Reticulum Stress Regulating lncRNA (HypERlnc) in Pericytes. Circ Res. 121(4):368-375, 2017. *Students mentored by me. PMID: 28611075. Shizuka Uchida, 04/17/2018 Page 17 of 18

27. Militello, G.*#, Weirick, T.*#, John, D.*, Döring, C., Dimmeler, S., and Uchida, S.: Screening and validation of lncRNAs and circRNAs as miRNA sponges. Brief Bioinform. 18(5):780-788, 2017. *Students mentored by me. #Shared first-author. PMID: 27373735. 28. John, D.*, Weirick, T.*, Dimmeler, S., and Uchida, S.: RNAEditor: easy detection of RNA editing events and the introduction of editing islands. Brief Bioinform. 18(6):993-1001, 2017. *Students mentored by me. PMID: 27694136. 29. Gibb, A.A., Epstein, P.N., Uchida, S., Zheng, Y., McNally, L.A., Obal, D., Katragadda, K., Trainor, P.J., Conklin, D.J., Brittian, K.R., Tseng, M.T., Wang, J., Jones, S.P., Bhatnagar, A., and Hill, B.G.: Exercise-Induced Changes in Glucose Metabolism Promote Physiologic Cardiac Growth. Circulation. 136(22):2144-2157, 2017. PMID: 28860122. PMCID: PMC5704654. 30. Hindi, S.M., Sato, S., Xiong, G., Bohnert, K.R., Gibb, A.A., Gallot, Y.S., McMillan, J.D., Hill, B.G., Uchida, S., and Kumar, A.: TAK1 regulates skeletal muscle mass and mitochondrial function. JCI Insight. 3(3), 2018. PMID: 29415881. PMCID: PMC5821216. 31. Hosen, M.R.*#, Militello, G.*#, Weirick, T.M.*, Ponomareva, Y.*, Dassanayaka, S., Moore, J.B., Doering, C., Wysoczynski, M., Jones, S.P., Dimmeler, S., and Uchida, S.: Airn Regulates Igf2bp2 Translation in Cardiomyocytes. Circ Res. 2018 Feb 26. pii: CIRCRESAHA.117.312215. doi: 10.1161/CIRCRESAHA.117.312215. [Epub ahead of print] *Students mentored by me. #Shared first-author. PMID: 29483092. 32. Weirick, T.*#, Militello, G.*#, Ponomareva, Y.*, John, D.*, Döring, C., Dimmeler, S., and Uchida, S.: Logic programming to infer complex RNA expression patterns from RNA-seq data. Brief Bioinform. 2016 Dec 22. pii: bbw117. [Epub ahead of print] *Students mentored by me. #Shared first-author. PMID: 28011754. 33. Militello, G.*, Hosen, M.R.*, Ponomareva, Y.*, Gellert, P., Weirick, T.*, John, D.*, Hindi, S.M., Mamchaoui, K., Mouly, V., Döring, C., Zhang, L., Nakamura, M., Kumar, A., Fukada, S.I., Dimmeler, S., and Uchida, S.: A novel long non-coding RNA Myolinc regulates myogenesis through TDP-43 and Filip1. J Mol Cell Biol. 2018 Apr 3. doi: 10.1093/jmcb/mjy025. [Epub ahead of print] *Students mentored by me. Featured as Cover Image. PMID: 29618024.

Review articles 1. Uchida, S., Gellert, P.*, and Braun, T.: Deeply dissecting stemness: making sense to non-coding RNAs in stem cells. Stem Cell Rev. 8(1):78-86, 2012. *Students mentored by me. PMID: 21706141. 2. Uchida, S., and Dimmeler, S.: Long noncoding RNAs in cardiovascular diseases. Circ Res. 116(4):737-50, 2015. PMID: 25677520. 3. Uchida, S., and Dimmeler, S.: Exercise controls non-coding RNAs. Cell Metab. 21(4):511-2, 2015. PMID: 25863242. 4. Uchida, S.: Besides Imprinting Meg3 Regulates Cardiac Remodeling in Cardiac Hypertrophy. Circ Res. 121:486-487, 2017. (Editorial). PMID: 28819035. 5. Uchida, S.: High‐Throughput Methods to Detect Long Non‐Coding RNAs. High-Throughput 6(3): 3, 2017. PMID: 29485610. 6. Uchida, S., and Bolli, R.: Short and long non-coding RNAs regulate the epigenetic status of cells. Antioxid Redox Signal. 2017 Aug 28. doi: 10.1089/ars.2017.7262. [Epub ahead of print]. PMID: 28847161. 7. Uchida, S., and Jones, S.P.: RNA Editing: Unexplored Opportunities in the Cardiovascular System. Circ Res. 22(3):399-401, 2018. PMID: 29420208. PMCID: PMC5808601.

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Books, book chapters, monographs 1. Uchida, S., De Gaspari, P., and Braun, T.: Are We There Yet? a Story about Cardiac Stem Cells. In Stem Cells in Clinic and Research, Ali Gholamrezanezhad (Ed.), ISBN: 978-953-307-797-0, InTech, 2011, Chapter 9.

NON-PEER-REVIEWED Book 1. Author: Uchida, S.: Annotating new genes: From in silico screening to experimental validation (Woodhead Publishing Series in Biomedicine) [Hardcover]. Woodhead Publishing, Cambridge, UK, 2012, 196 pp.

Complete List of Published Work in My Bibliography: http://www.ncbi.nlm.nih.gov/sites/myncbi/1hMCF8NW84t/bibliography/40124675/public/?sort=date&direction=desce nding https://scholar.google.com/citations?user=N-KHfvUAAAAJ&hl=en