Shizuka Uchida

Research output

Research output per year 2005 2015 2016 2018 2019 2020 2022 2023

• 65 Journal article
• 36 Conference abstract in journal
• 19 Review article
• 8 Editorial
• 11 More
  • 4 Comment/debate
  • 2 Letter
  • 1 Book
  • 1 Book chapter
  • 1 Conference abstract for conference
  • 1 Paper without publisher/journal
  • 1 Other contribution

Research output per year

Research output per year

Search results

• 2023

  Knockdown of Circular RNAs Using LNA-Modified Antisense Oligonucleotides

  Løvendorf, M. B., Holm, A., Petri, A., Thrue, C. A., Uchida, S., Venø, M. T. & Kauppinen, S., 1 Jan 2023, In: Nucleic Acid Therapeutics. 33, 1, p. 45-57 13 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Circular RNA 100%
  • Antisense Oligonucleotide 55%
  • Gene 22%
  • Protein 22%
  • Gene Expression 11%

• Potential Usages of A-to-I RNA Editing Patterns as Diagnostic Biomarkers

  Rodriguez-Morales, D., Ilieva, M., Rennie, S. & Uchida, S., 27 Feb 2023, (E-pub ahead of print) In: American Journal of Physiology: Cell Physiology. 1.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • RNA Editing 100%
  • Adenosine 42%
  • Inosine 42%
  • RNA 42%
  • Lysozyme 14%
• 2022

  Circulating MicroRNA-122-5p Is Associated With a Lack of Improvement in Left Ventricular Function After Transcatheter Aortic Valve Replacement and Regulates Viability of Cardiomyocytes Through Extracellular Vesicles

  Hosen, M. R., Goody, P. R., Zietzer, A., Xiang, X., Niepmann, S. T., Sedaghat, A., Tiyerili, V., Chennupati, R., Moore, J. B., Boon, R. A., Uchida, S., Sinning, J-M., Zimmer, S., Latz, E., Werner, N., Nickenig, G. & Jansen, F., 13 Dec 2022, In: Circulation. 146, 24, p. 1836-1854 19 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • microRNA 122 100%
  • Percutaneous Aortic Valve Replacement 56%
  • Aortic Valve 56%
  • Cardiomyocyte 50%
  • microRNA 31%
  4 Citations (Scopus)

• Collagen Type XIX Regulates Cardiac Extracellular Matrix Structure and Ventricular Function

  Sadri, G., Fischer, A. G., Brittian, K. R., Elliott, E., Nystoriak, M. A., Uchida, S., Wysoczynski, M., Leask, A., Jones, S. P. & Moore IV, J. B., May 2022, In: Matrix Biology. 109, p. 49-69 21 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • Collagen 100%
  • Heart 29%
  • Fibroblast 23%
  • Fibrillar Collagen 23%
  • Triple Helix 17%
  1 Citation (Scopus)

  19 Downloads (Pure)

• Emerging roles of long noncoding and circular RNAs in pancreatic ductal adenocarcinoma

  Sato, H., Hara, T., Tatekawa, S., Sasaki, K., Kobayashi, S., Kitagawa, T., Doki, Y., Eguchi, H., Ogawa, K., Uchida, S. & Ishii, H., 14 Nov 2022, In: Frontiers in Physiology. 13

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • Long Noncoding RNA 100%
  • RNA 100%
  • MicroRNA 33%
  • Messenger RNA 33%
  • Biological Functions 33%
  4 Downloads (Pure)

• FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis

  Ilieva, M. S., Miller, H. E., Agarwal, A., Paulus, G. K., Madsen, J. H., Bishop, A. J. R., Kauppinen, S. & Uchida, S., 28 Jan 2022, In: Non-coding RNA. 8, 1, 13.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • Long Untranslated RNA 100%
  • Long Non-Coding RNA 100%
  • Fibrosis 57%
  • Fibroblast 57%
  • Gene 57%
  5 Citations (Scopus)

  28 Downloads (Pure)

• Metabolic Signatures of Pregnancy-Induced Cardiac Growth

  Fulghum, K. L., Smith, J. B., Chariker, J., Garrett, L. F., Brittian, K. R., Lorkiewicz, P., McNally, L. A., Uchida, S., Jones, S. P., Hill, B. G. & Collins, H. E., 27 Jun 2022, In: American Journal of Physiology: Heart and Circulatory Physiology. 323, 1, p. H146-H164 56 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Pregnancy 100%
  • Heart 71%
  • Proteomics 28%
  • Pyruvate Dehydrogenase Kinase 4 28%
  • Childbirth 28%
  1 Citation (Scopus)

• Spaceflight-Associated Changes of snoRNAs in Peripheral Blood Mononuclear Cells and Plasma Exosomes—A Pilot Study

  Rai, A. K., Rajan, K. S., Bisserier, M., Sebastian, A., Brojakowska, A., Coleman, M., Mills, P. J., Arakelyan, A., Uchida, S., Hadri, L., Goukassian, D. & Garikipati, VN. S., 24 Jun 2022, In: Frontiers in Cardiovascular Medicine. 9, 886689.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • Blood 100%
  • RNA 62%
  • Peripheral Blood Mononuclear Cell 62%
  • Small Nucleolar RNA 62%
  • Blood Product 50%
  1 Citation (Scopus)

  9 Downloads (Pure)

• Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease

  Ilieva, M., Dao, J., Miller, H. E., Madsen, J. H., Bishop, A. J. R., Kauppinen, S. & Uchida, S., 22 Jul 2022, In: Non-coding RNA. 8, 4, 16 p., 56.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • Nonalcoholic Fatty Liver 100%
  • Non-Alcoholic Fatty Liver Disease 90%
  • Long Untranslated RNA 72%
  • Liver 72%
  • Long Non-Coding RNA 54%
  1 Citation (Scopus)

  8 Downloads (Pure)

• The current status of gene expression profilings in COVID-19 patients

  Ilieva, M., Tschaikowski, M., Vandin, A. & Uchida, S., Sep 2022, In: Clinical and Translational Discovery. 2, 3, e104.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • COVID-19 100%
  • RNA Sequence 50%
  • Severe Acute Respiratory Syndrome Coronavirus 2 37%
  • Sample 31%
  • Patient 31%
  41 Downloads (Pure)
• 2021

  CAD increases the long noncoding RNA PUNISHER in small extracellular vesicles and regulates endothelial cell function via vesicular shuttling

  Hosen, M. R., Li, Q., Liu, Y., Zietzer, A., Maus, K., Goody, P., Uchida, S., Latz, E., Werner, N., Nickenig, G. & Jansen, F., 3 Sep 2021, In: Molecular Therapy - Nucleic Acids. 25, p. 388-405 18 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • Coronary Artery Disease 100%
  • Coronary Artery 100%
  • Long Untranslated RNA 83%
  • Vasculotropin A 66%
  • Long Noncoding RNA 66%
  16 Citations (Scopus)

  28 Downloads (Pure)

• Cardiac PANK1 Deletion Exacerbates Ventricular Dysfunction During Pressure Overload

  Audam, T. N., Howard, C. M., Garrett, L. F., Zheng, Y. W., Bradley, J. A., Brittian, K. R., Frank, M. W., Fulghum, K. L., Pólos, M., Herczeg, S., Merkely, B., Radovits, T., Uchida, S., Hill, B. G., Dassanayaka, S., Jackowski, S. & Jones, S. P., 1 Oct 2021, In: American Journal of Physiology: Heart and Circulatory Physiology. 321, 4, p. H784-H797

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Coenzyme A 100%
  • Pressure 72%
  • Homeostasis 18%
  • Enzyme 18%
  • Biosynthesis 18%
  4 Citations (Scopus)

• Chronic Benzene Exposure Aggravates Pressure Overload-Induced Cardiac Dysfunction

  Zelko, I. N., Dassanayaka, S., Malovichko, M. V., Howard, C. M., Garrett, L. F., Uchida, S., Brittian, K. R., Conklin, D. J., Jones, S. P. & Srivastava, S., 28 Dec 2021, In: Toxicological Sciences. 185, 1, p. 64-76 13 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • Benzene 100%
  • Neutrophil Granulocyte 38%
  • Neutrophil 38%
  • Adhesion 30%
  • Constriction 30%
  2 Citations (Scopus)

  13 Downloads (Pure)

• Gene Expression Profiling Reveals the Shared and Distinct Transcriptional Signatures in Human Lung Epithelial Cells Infected With SARS-CoV-2, MERS-CoV, or SARS-CoV: Potential Implications in Cardiovascular Complications of COVID-19

  Jha, P. K., Vijay, A., Halu, A., Uchida, S. & Aikawa, M., 15 Jan 2021, In: Frontiers in Cardiovascular Medicine. 7, 15 p., 623012.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File
  18 Citations (Scopus)

  41 Downloads (Pure)

• Long Non-Coding RNAs in Diffuse Large B-Cell Lymphoma

  Karstensen, K. T., Schein, A., Petri, A., Bøgsted, M., Dybkær, K., Uchida, S. & Kauppinen, S., Jan 2021, In: Non-coding RNA. 7, 1, 13 p., 1.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  File

  • Diffuse Large B-Cell Lymphoma 100%
  • Diffuse Large B Cell Lymphoma 100%
  • B Cell 100%
  • Long Untranslated RNA 85%
  • Long Non-Coding RNA 71%
  5 Citations (Scopus)

  31 Downloads (Pure)

• Subclinical markers of cardiovascular toxicity of benzene inhalation in mice

  Malovichko, M. V., Abplanalp, W. T., McFall, S. A., Taylor, B. S., Wickramasinghe, N. S., Sithu, I. D., Zelko, I. N., Uchida, S., Hill, B. G., Sutaria, S. R., Nantz, M. H., Bhatnagar, A., Conklin, D. J., O'Toole, T. E. & Srivastava, S., 15 Nov 2021, In: Toxicology and Applied Pharmacology. 431, p. 115742 115742.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Benzene 100%
  • Cardiovascular Toxicity 66%
  • Endothelial Microparticle 41%
  • Biological Marker 33%
  • Microparticle 33%
  5 Citations (Scopus)
• 2020

  Administration of cardiac mesenchymal cells modulates innate immunity in the acute phase of myocardial infarction in mice

  Kang, Y., Nasr, M., Guo, Y., Uchida, S., Weirick, T., Li, H., Kim, J., Moore, J. B., Muthusamy, S., Bolli, R. & Wysoczynski, M., 8 Sep 2020, In: Scientific Reports. 10, 1, p. 14754 14754.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Cells 100%
  • Myocardial Infarction 50%
  • Immunocompetent Cell 50%
  • Heart Infarction 50%
  • Innate Immunity 33%
  5 Citations (Scopus)

• Cardiac mesenchymal cells from failing and nonfailing hearts limit ventricular dilation when administered late after infarction

  Audam, T. N., Nong, Y., Tomlin, A., Jurkovic, A., Li, H., Zhu, X., Long, B. W., Zheng, Y. W., Weirick, T., Brittian, K. R., Riggs, D. W., Gumpert, A., Uchida, S., Guo, Y., Wysoczynski, M. & Jones, S. P., Jul 2020, In: American Journal of Physiology - Heart and Circulatory Physiology. 319, 1, p. H109-H122

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • Cells 100%
  • Cardiovascular System 43%
  • Heart 34%
  • Heart Failure 30%
  • Cell Therapy 13%
  4 Citations (Scopus)

• Clinical value of non-coding RNAs in cardiovascular, pulmonary, and muscle diseases

  Bonnet, S., Boucherat, O., Paulin, R., Wu, D., Hindmarch, C. C. T., Archer, S. L., Song, R., Moore Iv, J. B., Provencher, S., Zhang, L. & Uchida, S., 2020, In: American Journal of Physiology - Cell Physiology. 318, 1, p. C1-C28

  Research output: Contribution to journal › Journal article › Research › peer-review

  • RNA 100%
  • Protein 66%
  • Cardiovascular Disease 66%
  • Untranslated RNA 66%
  • Protein Function 66%
  20 Citations (Scopus)

• Long Noncoding RNA TYKRIL Plays a Role in Pulmonary Hypertension via the p53-Mediated Regulation of PDGFRβ

  Zehendner, C. M., Valasarajan, C., Werner, A., Boeckel, J-N., Bischoff, F. C., John, D., Weirick, T., Glaser, S. F., Rossbach, O., Jaé, N., Demolli, S., Khassafi, F., Yuan, K., de Jesus Perez, V. A., Michalik, K. M., Chen, W., Seeger, W., Guenther, A., Wasnick, R. M., Uchida, S., & 3 othersZeiher, A. M., Dimmeler, S. & Pullamsetti, S. S., 15 Nov 2020, In: American Journal of Respiratory and Critical Care Medicine. 202, 10, p. 1445-1457 13 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Tyrosine Kinase Receptor 100%
  • Long Untranslated RNA 38%
  • Long Non-Coding RNA 33%
  • Pulmonary Hypertension 25%
  • Hypertension 25%
  28 Citations (Scopus)

• The effect of cardiogenic factors on cardiac mesenchymal cell anti-fibrogenic paracrine signaling and therapeutic performance

  Heidel, J. S., Fischer, A. G., Tang, X. L., Sadri, G., Wu, W. J., Moisa, C. R., Stowers, H., Sandella, N., Wysoczynski, M., Uchida, S. & Moore, J. B., 2020, In: Theranostics. 10, 4, p. 1514-1530 17 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • Fibrogenesis 100%
  • Transcription Factor GATA 4 100%
  • Paracrine Signaling 100%
  • Cells 100%
  • MEF2C 100%
  5 Citations (Scopus)
• 2019

  A novel macrophage subtype directs hematopoietic stem cell homing and retention

  Wysoczynski, M., Moore, J. B. & Uchida, S., Jul 2019, In: Annals of Translational Medicine. 7, Suppl 3, p. S79

  Research output: Contribution to journal › Journal article › Research › peer-review

• Circular RNAs as diagnostic tool for renal transplant patients with acute rejection

  Moore, J. B., Merchant, M. L. & Uchida, S., Dec 2019, In: Annals of Translational Medicine. 7, Suppl 8, p. S302

  Research output: Contribution to journal › Journal article › Research › peer-review

• E2f1 deletion attenuates infarct-induced ventricular remodeling without affecting O-GlcNAcylation

  Dassanayaka, S., Brittian, K. R., Jurkovic, A., Higgins, L. A., Audam, T. N., Long, B. W., Harrison, L. T., Militello, G., Riggs, D. W., Chitre, M. G., Uchida, S., Muthusamy, S., Gumpert, A. M. & Jones, S. P., 1 Jul 2019, In: Basic Research in Cardiology. 114, 4, 28.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • E2F1 100%
  • Myocardial Infarction 54%
  • Heart Infarction 54%
  • Transferase 45%
  • Heart Ventricle Remodeling 36%
  22 Citations (Scopus)

• Epigenetically modified cardiac mesenchymal stromal cells limit myocardial fibrosis and promote functional recovery in a model of chronic ischemic cardiomyopathy

  Moore, J. B., Tang, X. L., Zhao, J., Fischer, A. G., Wu, W. J., Uchida, S., Gumpert, A. M., Stowers, H., Wysoczynski, M. & Bolli, R., 1 Jan 2019, In: Basic Research in Cardiology. 114, 1, 3.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Cells 100%
  • Entinostat 66%
  • HDAC1 50%
  • Myocyte 50%
  • Cardiac Fibrosis 33%
  40 Citations (Scopus)

• Hematopoietic deficiency of the long noncoding RNA malat1 promotes atherosclerosis and plaque inflammation

  Cremer, S., Michalik, K. M., Fischer, A., Pfisterer, L., Jaé, N., Winter, C., Boon, R. A., Muhly-Reinholz, M., John, D., Uchida, S., Weber, C., Poller, W., Günther, S., Braun, T., Li, D. Y., Maegdefessel, L., Perisic Matic, L., Hedin, U., Soehnlein, O., Zeiher, A., & 1 othersDimmeler, S., 5 Mar 2019, In: Circulation. 139, 10, p. 1320-1334 15 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Metastatic Carcinoma 100%
  • Lung Adenocarcinoma 100%
  • Mouse 100%
  • Lung 100%
  • Metastasis 100%
  133 Citations (Scopus)

• Investigation of RNA editing sites within bound regions of RNA-binding proteins

  Weirick, T., Militello, G., Hosen, M. R., John, D., Moore, J. B. & Uchida, S., Dec 2019, In: High-Throughput. 8, 4, 19.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • RNA Editing 100%
  • RNA-Binding Protein 66%
  • RNA 33%
  • RNA-binding Protein 33%
  • Adenosine 25%
  2 Citations (Scopus)
• 2018

  Airn regulates IGF2BP2 translation in cardiomyocytes

  Hosen, M. R., Militello, G., Weirick, T., Ponomareva, Y., Dassanayaka, S., Moore, J. B., Döring, C., Wysoczynski, M., Jones, S. P., Dimmeler, S. & Uchida, S., May 2018, In: Circulation Research. 122, 10, p. 1347-1353 7 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Messenger RNA 100%
  • Protein Binding 100%
  • Somatomedin B 100%
  • Binding Protein 100%
  • Insulin-Like Growth Factor 2 100%
  23 Citations (Scopus)

• A novel long non-coding RNA Myolinc regulates myogenesis through TDP-43 and Filip1

  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. & Uchida, S., 1 Apr 2018, In: Journal of Molecular Cell Biology. 10, 2, p. 102-117 16 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • Muscle 100%
  • Long Untranslated RNA 83%
  • TAR DNA Binding Protein 83%
  • Long Non-Coding RNA 83%
  • Muscle Development 66%
  44 Citations (Scopus)

• A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation

  Kılıç, A., Santolini, M., Nakano, T., Schiller, M., Teranishi, M., Gellert, P., Ponomareva, Y., Braun, T., Uchida, S., Weiss, S. T., Sharma, A. & Renz, H., 7 Jun 2018, In: JCI Insight. 3, 11

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • microRNA 100%
  • MicroRNA 100%
  • T Helper 2 Cell 57%
  • Immune Response 28%
  • CD4 28%
  8 Citations (Scopus)

• DRETools: A tool-suite for differential RNA editing detection [version 2; peer review: 1 approved, 1 approved with reservations, 1 not approved]

  Weirick, T., Trainor, P., Rouchka, E., Defilippis, A. & Uchida, S., 19 Sep 2018, In: F1000Research. 7, 1366.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • RNA Editing 100%
  • Epitranscriptomics 12%
  • Comprehension 12%
  • Sample 12%
  • Diseases 12%

• Increasing workflow development speed and reproducibility with Vectools [version 2; peer review: 2 approved]

  Weirick, T., Müller, R. & Uchida, S., 18 Oct 2018, In: F1000Research. 7, 11 p., 1499.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • Reproducibility 100%
  • Workflows 100%
  • Functions 66%
  • Vectors 66%
  • Velocity 66%

• Logic programming to infer complex RNA expression patterns from RNA-seq data

  Weirick, T., Militello, G., Ponomareva, Y., John, D., Döring, C., Dimmeler, S. & Uchida, S., 1 Mar 2018, In: Briefings in Bioinformatics. 19, 2, p. 199-209 11 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Databases 100%
  • Cells 100%
  • Data Base 100%
  • Logic Programming 100%
  • RNA 66%
  11 Citations (Scopus)

• TAK1 regulates skeletal muscle mass and mitochondrial function

  Hindi, S. M., Sato, S., Xiong, G., Bohnert, K. R., Gibb, A. A., Gallot, Y. S., McMillan, J. D., Hill, B. G., Uchida, S. & Kumar, A., 8 Feb 2018, In: JCI Insight. 3, 3

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • Kinase 100%
  • Phosphotransferase 100%
  • Skeletal Muscle 63%
  • Mouse 27%
  • Adult 27%
  30 Citations (Scopus)
• 2017

  Exercise-Induced Changes in Glucose Metabolism Promote Physiological Cardiac Growth

  Gibb, A. A., Epstein, P. N., Uchida, S., Zheng, Y., McNally, L. A., Obal, D., Katragadda, K., Trainor, P., Conklin, D. J., Brittian, K. R., Tseng, M. T., Wang, J., Jones, S. P., Bhatnagar, A. & Hill, B. G., 28 Nov 2017, In: Circulation. 136, 22, p. 2144-2157 14 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • Exercise 100%
  • Heart 85%
  • Growth 71%
  • Mouse 71%
  • 6 Phosphofructokinase 57%
  73 Citations (Scopus)

• High-Throughput Methods to Detect Long Non-Coding RNAs

  Uchida, S., 31 Aug 2017, In: High-Throughput. 6, 3

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Long Non-Coding RNA 100%
  • Long Untranslated RNA 100%
  • Microarrays 83%
  • RNA Sequence 50%
  • RNA 50%

• Identification and Functional Characterization of Hypoxia-Induced Endoplasmic Reticulum Stress Regulating lncRNA (HypERlnc) in Pericytes

  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. & Zehendner, C. M., 4 Aug 2017, In: Circulation Research. 121, 4, p. 368-375 8 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Endoplasmic Reticulum Stress 100%
  • Long Untranslated RNA 94%
  • Hypoxia 88%
  • Long Non-Coding RNA 76%
  • Pericyte 70%
  40 Citations (Scopus)

• Long Noncoding RNA MANTIS Facilitates Endothelial Angiogenic Function

  Leisegang, M. S., Fork, C., Josipovic, I., Richter, F. M., Preussner, J., Hu, J., Miller, M. J., Epah, J., 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., & 11 othersStellos, K., Schermuly, R. T., Weissmann, N., Devraj, K., Wittig, I., Boon, R. A., Dimmeler, S., Pullamsetti, S. S., Looso, M., Miller, F. J. & Brandes, R. P., 4 Jul 2017, In: Circulation. 136, 1, p. 65-79 15 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • Long Untranslated RNA 100%
  • Long Noncoding RNA 55%
  • Endothelial Cell 33%
  • Cells 33%
  • Immunoprecipitation 22%
  156 Citations (Scopus)

• Resolving the problem of multiple accessions of the same transcript deposited across various public databases

  Weirick, T., John, D. & Uchida, S., 2017, In: Briefings in Bioinformatics. 18, 2, p. 226-235 10 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • Annotation 100%
  • Data Base 71%
  • References 28%
  • Algorithm 28%
  • Algorithms 14%
  6 Citations (Scopus)

• RNAEditor: Easy detection of RNA editing events and the introduction of editing islands

  John, D., Weirick, T., Dimmeler, S. & Uchida, S., 1 Nov 2017, In: Briefings in Bioinformatics. 18, 6, p. 993-1001 9 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Events 100%
  • RNA Editing 71%
  • Detection 28%
  • RNA Sequence 28%
  • Inosine 28%
  46 Citations (Scopus)

• Screening and validation of lncRNAs and circRNAs as miRNA sponges

  Militello, G., Weirick, T., John, D., Döring, C., Dimmeler, S. & Uchida, S., 1 Sep 2017, In: Briefings in Bioinformatics. 18, 5, p. 780-788 9 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • microRNA 100%
  • MicroRNA 100%
  • RNA 55%
  • Long Untranslated RNA 55%
  • Biological Product 33%
  256 Citations (Scopus)
• 2016

  Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation

  Stellos, K., Gatsiou, A., Stamatelopoulos, K., Perisic Matic, L., John, D., Lunella, F. F., 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., & 6 othersSchwalbe, H., Bindereif, A., Eriksson, P., Hedin, U., Zeiher, A. M. & Dimmeler, S., 1 Oct 2016, In: Nature Medicine. 22, 10, p. 1140-1150 11 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Cathepsin S 100%
  • Messenger RNA 77%
  • RNA Editing 77%
  • Vascular Disease 33%
  • Adenosine 33%
  165 Citations (Scopus)

• ANGIOGENES: Knowledge database for protein-coding and noncoding RNA genes in endothelial cells

  Müller, R., Weirick, T., John, D., Militello, G., Chen, W., Dimmeler, S. & Uchida, S., 1 Sep 2016, In: Scientific Reports. 6, 32475.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • Long Untranslated RNA 100%
  • Long Noncoding RNA 100%
  • Protein 83%
  • Coding 83%
  • Cytochromes 83%
  21 Citations (Scopus)

• Computational detection of stage-specific transcription factor clusters during heart development

  Zeidler, S., Meckbach, C., Tacke, R., Raad, F. S., Roa, A., Uchida, S., Zimmermann, W. H., Wingender, E. & Gültas, M., 23 Mar 2016, In: Frontiers in Genetics. 7, MAR, 33.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • Transcription Factor 100%
  • Transcription Factors 100%
  • Binding Site 61%
  • Gene 30%
  • Nested Gene 30%
  11 Citations (Scopus)

• Mesenchymal stem cells attenuate inflammatory processes in the heart and lung via inhibition of TNF signaling

  Martire, A., Bedada, F. B., Uchida, S., Pöling, J., Krüger, M., Warnecke, H., Richter, M., Kubin, T., Herold, S. & Braun, T., 1 Sep 2016, In: Basic Research in Cardiology. 111, 5, 54.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • Mesenchymal Stem Cell 100%
  • Tumor Necrosis Factor 90%
  • Serositis 40%
  • Inflammation 40%
  • Tissues 30%
  37 Citations (Scopus)

• Specific phenotype and function of CD56-expressing innate immune cell subsets in human thymus

  Gerstner, S., Köhler, W., Heidkamp, G., Purbojo, A., Uchida, S., Ekici, A. B., Heger, L., Luetke-Eversloh, M., Schubert, R., Bade, P., Klingebiel, T., Koehl, U., Mackensen, A., Romagnani, C., Cesnjevar, R., Dudziak, D. & Ullrich, E., Dec 2016, In: Journal of Leukocyte Biology. 100, 6, p. 1297-1310 14 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Cells 100%
  • Natural Killer Cell 37%
  • Cytotoxicity 25%
  • Immunocompetent Cell 25%
  • NKG2D 25%
  2 Citations (Scopus)

• The identification and characterization of novel transcripts from RNA-seq data

  Weirick, T., Militello, G., Müller, R., John, D., Dimmeler, S. & Uchida, S., 1 Jul 2016, In: Briefings in Bioinformatics. 17, 4, p. 678-685 8 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Sequencing 100%
  • Next Generation Sequencing 75%
  • RNA Sequence 62%
  • RNA 37%
  • Analysis 37%
  22 Citations (Scopus)
• 2015

  C-It-Loci: A knowledge database for tissue-enriched loci

  Weirick, T., John, D., Dimmeler, S. & Uchida, S., 18 Dec 2015, In: Bioinformatics. 31, 21, p. 3537-3543 7 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  • Tissues 100%
  • Protein 83%
  • Untranslated RNA 83%
  • Non-Coding RNA 83%
  • Gene 50%
  25 Citations (Scopus)

• Doublecortin marks a new population of transiently amplifying muscle progenitor cells and is required for myofiber maturation during skeletal muscle regeneration

  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, SI., Yamamoto, H. & Fukada, S. I., 1 Jan 2015, In: Development (Cambridge). 142, 1, p. 51-61 11 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • Maturation 100%
  • Myoblast 80%
  • Cells 80%
  • MyoD 80%
  • Muscle Regeneration 60%
  24 Citations (Scopus)

• Epigenetic regulation of angiogenesis by JARID1B-induced repression of HOXA5

  Fork, C., Gu, L., Hitzel, J., Josipovic, I., Hu, J., Wong, M. S., Ponomareva, Y., Albert, M., Schmitz, S. U., Uchida, S., Fleming, I., Helin, K., Steinhilber, D., Leisegang, M. S. & Brandes, R. P., 27 Jul 2015, In: Arteriosclerosis, Thrombosis, and Vascular Biology. 35, 7, p. 1645-1652 8 p.

  Research output: Contribution to journal › Journal article › Research › peer-review

  Open Access

  • JARID1B 100%
  • Angiogenesis 30%
  • Human Umbilical Vein Endothelial Cell 30%
  • Chromatin 20%
  • Lysozyme 20%
  27 Citations (Scopus)