Publications

    2023 (21 Publications)
  1. Zhang, K., Cheng, Y., Peng, Y., Jiang, F., Zhang, C., Ng, C. S. H., Rosell, R., Efird, J. T., Lal, A., Nappi, F., Weiskirchen, R., Uchida, S., Chua, M. T. and D’Ambrosi, R.: Scope highlights of Annals of Translational Medicine based on a review of the history, definition, and scope of translational medicine. Annals of Translational Medicine. 11(11):381. (Link)

  2. Sopic, M., Vilne, B., Gerdts, E., Trindade, F., Uchida, S., Khatib, S., Wettinger, S.B., Devaux, Y., Magni, P., and EU-AtheroNET COST Action CA21153: Multiomics tools for improved atherosclerotic cardiovascular disease management. Trends in Molecular Medicine. S1471-4914(23): 00219-8, 2023. (Link)

  3. Velissari, R., Ilieva, M., Dao, J., Miller, H.E., Madsen, J.H., Gorodkin, J., Aikawa, M., Ishii, H., and Uchida, S.: Systematic analysis and characterization of long non-coding RNA genes in inflammatory bowel disease. Briefings in Functional Genomics. elad044, 2023. (Link)

  4. Uchida, S.: Identification and Functional Prediction of lncRNAs using Bioinformatic Techniques. Current Bioinformatics. 2023. (Link)

  5. Morales, D.R., Rennie, S., and Uchida, S.: Benchmarking RNA Editing Detection Tools. BioTech. 12(3):56, 2023. (Link)

  6. Qian, N., Distefano, R., Ilieva, M., Madsen, J.H., Rennie, S., and Uchida, S.: Systematic Analysis of Long Non-Coding RNAs in Inflammasome Activation in Monocytes/Macrophages. Noncoding RNA. 9(5):50, 2023. (Link)

  7. Ilieva, M. and Uchida, S.: Methods and Tools in RNA Biology. Noncoding RNA. 9(4):46, 2023. (Link)

  8. Distefano, R., Ilieva, M., Rennie, S., and Uchida, S.: Recommendations for Bioinformatic Tools in LncRNA Research. Current Bioinformatics. (E-pub Abstract Ahead of Print), 2023. (Link)

  9. Jha, P., Barbeiro, M., Lupieri, A., Aikawa, E., Uchida, S., and Aikawa, M.: Computational methods for functional characterization of lncRNAs in human diseases: A focus on co-expression networks. Current Bioinformatics. (E-pub Abstract Ahead of Print), 2023. (Link)

  10. Tang, X.L., Nasr, M., Zheng, S., Zoubul, T., Stephan, J.K., Uchida, S., Singhal, R., Khan, A., Gumpert, A., Bolli, R., and Wysoczynski, M.: Bone Marrow and Wharton's Jelly Mesenchymal Stromal Cells are Ineffective for Myocardial Repair in an Immunodeficient Rat Model of Chronic Ischemic Cardiomyopathy. Stem Cell Reviews and Reports . 2023 Jul 28. doi: 10.1007/s12015-023-10590-6. Online ahead of print. (Link)

  11. Distefano, R., Ilieva, M., Madsen, J.H., Rennie, S., and Uchida, S.: DoxoDB: A Database for the Expression Analysis of Doxorubicin-Induced lncRNA Genes. Noncoding RNA. 9(4):39, 2023. (Link)

  12. Distefano, R., Ilieva, M., Madsen, J.H., and Uchida, S.: CrohnDB: A Web Database for Expression Profiling of Protein-Coding and Long Non-Coding RNA Genes in Crohn Disease. Computation. 11(6):105, 2023. (Link)

  13. Ilieva, M., Kauppinen, S., and Uchida, S.: Chapter 7 - The emerging roles of epitranscriptomic marks in cancer. Epigenetic Cancer Therapy (Second Edition). 129-141, 2023. (Link)

  14. Distefano, R., Ilieva, M., Madsen, J.H., Ishii, H., Aikawa, M., Rennie, S., and Uchida, S.: T2DB: A Web Database for Long Non-Coding RNA Genes in Type II Diabetes. Noncoding RNA. 9(3):30, 2023. (Link)

  15. Shiu, P.K.T., Ilieva, M., Holm, A., Uchida, S., DiStefano, J.K., Bronisz, A., Yang, L., Asahi, Y., Goel, A., Yang, L., Nuthanakanti, A., Serganov, A., Alahari, S.K., Lin, C., Pardini, B., Naccarati, A., Jin, J., Armanios, B., Zhong, X.B., Sideris, N., Bayraktar, S., Castellano, L., Gerber, A.P., Lin, H., Conn, S.J., Sleem, D.M.M., and Timmons, L.: The Non-Coding RNA Journal Club: Highlights on Recent Papers-12. Noncoding RNA. 9(2):28, 2023. (Link)

  16. Sen, I., Uchida, S., and Garikipati, V.N.S.: Long non-coding RNA lnc-CHAF1B-3 as a new player in fibrosis. Molecular Therapy - Nucleic Acids. 31:566-567, 2023. (Link)

  17. Rodriguez-Morales, D., Ilieva, M., Rennie, S., and Uchida, S.: Potential Usages of A-to-I RNA Editing Patterns as Diagnostic Biomarkers. American Journal of Physiology-Cell Physiology. 2023 Feb 27. doi: 10.1152/ajpcell.00024.2023. Online ahead of print. (Link)

  18. Mathiyalagan, P., Martelotto, L.G., Ounzain, S., El-Osta, A., and Uchida, S.: Editorial: RNA-chromatin interactions: Biology, mechanism, disease and therapeutics. Frontiers in Genetics. 13:1069427, 2023. (Link) Online ahead of print.

  19. Ilieva, M., and Uchida, S.: Potential Involvement of LncRNAs in Cardiometabolic Diseases. Genes (Basel). 14(1):213, 2023. (Link)

  20. Delpire, E., Hawke, T.J., Karthikeyan, M., Kong, W., Nyström, A., Uchida, S., and Schaefer, L.: American Journal of Physiology-Cell Physiology in 2022: at a glance. Am J Physiol Cell Physiol. 2023 Jan 16. doi: 10.1152/ajpcell.00009.2023. (Link) Online ahead of print.

  21. Løvendorf, M.B., Holm, A., Petri, A., Thrue, C.A., Uchida, S., , Venø, M.T., and Kauppinen, S.: Knockdown of Circular RNAs Using LNA-Modified Antisense Oligonucleotides. Nucleic Acid Therapeutics 33(1):45-57, 2023. (Link)



    22. 2022 (22 Publications)
  22. Ilieva, M., and Uchida, S.: Perspectives of LncRNAs for therapy. Cell Biology and Toxicology 38(6):915-917, 2022. (Link)

  23. Sato, H., Hara, T., Tatekawa, S., Sasaki, K., Kobayashi, S., Kitagawa, T., Doki, Y., Eguchi, H., Ogawa, K., Uchida, S., and Ishii, H.: Emerging roles of long noncoding and circular RNAs in pancreatic ductal adenocarcinoma. Frontiers in Physiology. 13:1025923, 2022. (Link)

  24. Ilieva, M., Panella, R.. and Uchida, S.: MicroRNAs in Cancer and Cardiovascular Disease. Cells. 11, 3551, 2022.(Link)

  25. Sato, H., Sasaki, K., Hara, T., Tsuji, Y., Arao, Y., Otsuka, C., Hamano, Y., Ogita, M., Kobayashi, S., di Luccio, E., Hirotsu, T., Doki, Y., Eguchi, H., Satoh, T., Uchida, S., and Ishii, H.: Pancreatic Cancer Research beyond DNA Mutations. Biomolecules. 12: 1503, 2022.(Link)

  26. Uchida, S., Yu, J., Goldman, M., Asmis, R., Yang, X., Aikawa, E., Bourantas, C., Aikawa, M., and Tevaearai Stahel, H.: Editorial: Research reproducibility and preventing fraud. Front. Cardiovasc. Med. 9:979467, 2022.(Link)

  27. Ilieva, M., Dao, J., Miller, H.E., Madsen, J.H., Bishop, A.J.R., Kauppinen, S., and Uchida, S.: Systematic Analysis of Long Non-Coding RNA Genes in Nonalcoholic Fatty Liver Disease. Noncoding RNA. 2022 8(4): 56. (Link)

  28. Ilieva, M., Tschaikowski, M., Vandin, A., and Uchida, S.: The current status of gene expression profilings in COVID-19 patients. Clin Transl Disc. 2022 2:3104. (Link)

  29. Ilieva, M., and Uchida, S.: Long Non-Coding RNAs in Cardiac and Pulmonary Fibroblasts and Fibrosis. Noncoding RNA. 2022 8(4): 53. (Link)

  30. Nakayama, M., Ozato, Y., Tsuji, Y., Arao, Y., Otsuka, C., Hamano, Y., Sumi, G., Ofusa, K., Uchida, S., Vecchione, A., and Ishii, H.: RNA Modification in Inflammatory Bowel Diseases. Biomedicines. 2022 10(7):1695. (Link)

  31. 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., and Jansen, F.: 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. Circulation. 146(24):1836-1854, 2022 (Link)

  32. Ilieva, M., and Uchida, S.: Functional roles of epitranscriptomic marks in the cardiovascular system and disease: a narrative review. Ann Transl Med. 2022 July 4 doi: 10.21037/atm-22-1074. Online ahead of print (Link)

  33. Sansbury, B.E., Nystoriak, M.A., Uchida, S. Wysoczynski, M. and Moore, J.B. IV: Rigor Me This: What Are the Basic Criteria for a Rigorous, Transparent, and Reproducible Scientific Study? Front. Cardiovasc. Med. 9:913612, 2022. (Link)

  34. Rai, A.K., Rajan, K.S., Bisserier, M., Brojakowska, A., Sebastian, A., Evans, A.C., Coleman, M.A., Mills, P.J., Arakelyan, A., Uchida, S. Hadri, L., Goukassian, D.A., and Garikipati, V.N.S.: Spaceflight-Associated Changes of snoRNAs in Peripheral Blood Mononuclear Cells and Plasma Exosomes—A Pilot Study. Front. Cardiovasc. Med. 9:886689, 2022. (Link)

  35. Ilieva, M., and Uchida, S.: Extracellular RNAs as communicators in cardiovascular disease: a narrative review. ExRNA. 2022 June 14 doi: 10.21037/exrna-22-3. Online ahead of print (Link)

  36. 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., and Collins, H.E.: Metabolic Signatures of Pregnancy-Induced Cardiac Growth. Am J Physiol Heart Circ Physiol. 2022 Jul 1;323(1):H146-H164. (Link)

  37. Bonnet, H., Bogard, B., Hubé, F., Ilieva, M., Uchida, S., Ariza-Mateos, M.A., Serganov, A., Pardini, B., Naccarati, A., Santulli, G., Varzideh, F., Xiao, H., and Shiu, P.K.T.: The Non-Coding RNA Journal Club: Highlights on Recent Papers—11. Noncoding RNA. 8(3), 31, 2022 (Link)

  38. Ilieva, M., and Uchida, S.: Epitranscriptomics in fibroblasts and fibrosis. Am J Physiol Cell Physiol. 2022 Jun 1;322(6):C1110-C1116. (Link)

  39. Wysoczynski, M., Stephan, J., and Uchida, S.: Glucosamine regulates macrophage function in heart failure. Clin Transl Med. 12:e819, 2022 (Link)

  40. Miller, H.E., Ilieva, M., Bishop, A.J.R., and Uchida, S.: Current Status of Epitranscriptomic Marks Affecting lncRNA Structures and Functions. Noncoding RNA. 8(2), 23, 2022 (Link)

  41. Sadri, G., Fischer, A.G., Brittian, K.R., Elliott, E., Nystoriak, M.A., Uchida, S., Wysoczynski, M., Leask, A., Jones, S.P., and Moore, J.B. 4th.: Collagen Type XIX Regulates Cardiac Extracellular Matrix Structure and Ventricular Function. Matrix Biol. 2022 May;109:49-69. (Link)

  42. Ilieva, M. and Uchida, S.: Long Non-Coding RNAs in Induced Pluripotent Stem Cells and Their Differentiation. Am J Physiol Cell Physiol. 322(4):C769-C774, 2022. (Link)

  43. Ilieva, M., Miller, H.E., Agarwal, A., Paulus, G.K., Madesn, J.H., Bishop, A.J.R., Kauppinen, S., and Uchida, S.: FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis. Noncoding RNA. 8(1), 13, 2022 (Link)


    44. 2021 (8 Publications)
  44. 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., and Srivastava, S.: Chronic benzene exposure aggravates pressure overload-induced cardiac dysfunction. Toxicol Sci. 185(1):64-76, 2021 (Link)

  45. 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., and Srivastava, S.: Subclinical markers of cardiovascular toxicity of benzene inhalation in mice. Toxicol Appl Pharmacol. 431:115742, 2021. (Link)

  46. 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., and Jones, S.P.: Cardiac PANK1 deletion exacerbates ventricular dysfunction during pressure overload. Am J Physiol Heart Circ Physiol. 321(4):H784-H797, 2021. (Link)

  47. Hosen, M.R., Li, Q., Liu, Y., Zeitzer, A., Maus, K., Goody, P., Uchida, S. Latz, E., Werner, N., Nickenig, G., and Jansen, F.: Coronary artery disease increases the long noncoding RNA PUNISHER in small extracellular vesicles and regulates endothelial cell function via vesicular shuttling. Mol Ther Nucleic Acids. 25:388-405, 2021. (Link)

  48. Rai, A.K., Lee, B., Hebbard, C., Uchida, S. and Garikipati, V.K.S.: Decoding the complexity of circular RNAs in cardiovascular disease. Pharmacol Res. 171:105766, 2021. (Link)

  49. Garikipati, V.K.S. and Uchida, S.: Elucidating the functions of non-coding RNAs from the perspective of RNA modifications. Noncoding RNA. 7(2):31, 2021. (Link)

  50. Jha, P.K., Vijay, A., Halu, A., Uchida, S. , and Aikawa, M.: 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. Front. Cardiovasc. Med. 7:623012, 2021. (Link)

  51. Karstensen, K.T., Schein, A., Petri, A., Bøgsted, M., Dybkær, K., Uchida, S. , and Kauppinen, S.: Long non-coding RNAs in diffuse large B-cell lymphoma. Noncoding RNA. 7(1):E1, 2021. (Link)


    52. 2020 (9 Publications)
  52. Kang, Y., Nasr, M., Guo, Y., Uchida, S. , Weirick, T., Li, H., Kim, J., Moore, J.B. 4th, Muthusamy, S., Bolli, R., and Wysoczynski, M.: Administration of cardiac mesenchymal cells modulates innate immunity in the acute phase of myocardial infarction in mice. Sci Rep. 10(1):14754, 2020. (Link)

  53. Uchida, S. and Kauppinen, S.: Long Non-Coding RNAs in Liver Cancer and Nonalcoholic Steatohepatitis. Noncoding RNA. 6(3):34, 2020. (Link)

  54. Wysoczynski, M., Kim, J., Moore, J.B. 4th., and Uchida, S.: Macrophage Long Non-Coding RNAs in Pathogenesis of Cardiovascular Disease. Non-Coding RNA. 6(3):28, 2020. (Link)

  55. 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., Zeiher, A.M., Dimmeler, S., and Pullamsetti, S.S.: Long Noncoding RNA TYKRIL Plays a Role in Pulmonary Hypertension via the p53-Mediated Regulation of PDGFRβ. Am J Respir Crit Care Med. 202(10):1445-1457, 2020. (Link)

  56. 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.M., Uchida, S., Guo, Y., Wysoczynski, M., and Jones, S.P.: Cardiac Mesenchymal Cells from Failing and Non-Failing Hearts Limit Ventricular Dilation when Administered Late after Infarction. Am J Physiol Heart Circ Physiol. 319(1):H109-H122, 2020. (Link)

  57. Moore, J.B. 4th., Sadri, G., Fischer, A., Weirick, T., Militello, G., Wysoczynski, M., Gumpert, A.M., Braun, T., and Uchida, S.: The A-to-I RNA Editing Enzyme Adar1 Is Essential for Normal Embryonic Cardiac Growth and Development. Circ Res. 127(4):550-552, 2020. (Link)

  58. Moore, J.B. 4th., and Uchida, S.: Functional characterization of long noncoding RNAs. Curr Opin Cardiol. 35(3):199-206, 2020. (Link)

  59. Heidel, J.S., Fischer, A.G., Tang, X-L., Sadri, G., Wu, W-J., Moisa, C.R., Stower, H., Sandella, N., Wysoczynski, M., Uchida, S., and Moore, J.B. 4th.: The Effect of Cardiogenic Factors on Cardiac Mesenchymal Cell Anti-Fibrogenic Paracrine Signaling and Therapeutic Performance. Theranostics. 10(4):1514-1530, 2020. (Link)

  60. Bonnet, S., Boucherat, O., Paulin, R., Wu, D., Hindmarch, C.C.T., Archer, S.L., Song, R., Moore IV, J.B., Provencher, S., Zhang, R., and Uchida, S.: Clinical values of non-coding RNAs in cardiovascular, pulmonary, and muscle diseases. Am J Physiol Cell Physiol. 318(1):C1-C28, 2020. (Link)


    61. 2019 (7 Publications)
  61. Wierick, T., Militello, G., Hosen, M.R., John, D., Moore, J.B. 4th., and Uchida, S.: Investigation of RNA editing sites within bound regions of RNA-binding proteins. High-Throughput. 8(4), 2019. (Link)

  62. Moore, J.B. 4th., Merchant, M.L., and Uchida, S.: Circular RNAs as diagnostic tool for renal transplant patients with acute rejection. Ann Transl Med. 7(Suppl 8):S302, 2019. (Link)

  63. Wysoczynski, M., Moore, J.B. 4th., and Uchida, S.: A novel macrophage subtype directs hematopoietic stem cell homing and retention. Ann Transl Med. 7(Suppl 3):S79, 2019. (Link)

  64. Uchida, S., and Adams, JC.: Roles of Non-coding RNAs in Human Diseases[Introductory Editorial for the Theme: Roles of non-coding RNAs in Human Diseases]. Am J Physiol Cell Physiol. 317(1):C1-C2, 2019. (Link)

  65. 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., and Jones, S.P.: E2f1 deletion attenuates infarct-induced ventricular remodeling without affecting O-GlcNAcylation. Basic Res Cardiol. 114(4):28, 2019. (Link)

  66. 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, L.M., Hedin, U., Soehnlein, O., Zeiher, A., and Dimmeler, S.: Hematopoietic deficiency of the long non-coding RNA MALAT1 promotes atherosclerosis and plaque inflammation. Circulation. 139(10):1320-1334, 2019. (Link)

  67. LeBlanc, A.J. and Uchida, S.: A step closer to improving cardiac homing of adipose-derived mesenchymal stem cells. Am J Physiol Heart Circ Physiol. 316(2):H260-H261, 2019. (Link)


    68. 2018 (11 Publications)
  68. Moore, J.B. 4th, Tang, X.L., Zhao, J., Fischer, A.G., Wu, W.J., Uchida, S., Gumpert, A.M., Stowers, H., Wysoczynski, M., and Bolli, R.: Epigenetically modified cardiac mesenchymal stromal cells limit myocardial fibrosis and promote functional recovery in a model of chronic ischemic cardiomyopathy. Basic Res Cardiol. 114(1):3, 2018. (Link)

  69. Weirick, T., Müller, R., and Uchida, S.: Increasing workflow development speed and reproducibility with Vectools. F1000Research. 7:1499, 2018. (Link)

  70. Weirick, T., Trainor, P., Rouchka, E., DeFilipppis, A., and Uchida, S.: DRETools: A tool-suite for differential RNA editing detection. F1000Research. 7:1366, 2018. (Link)

  71. Kılıç, A., Santolini, M., Nakano, T., Schiller, M., Teranishi, M., Gellert, P., Ponomareva, Y., Braun, T., Uchida, S., Weiss, S.T., Sharma, A, and Renz, H.: A systems immunology approach identifies the collective impact of 5 miRs in Th2 inflammation. JCI Insight. 3(11):e97503, 2018. (Link)

  72. Weirick, T., Militello, G., and Uchida, S.: Long non-coding RNAs in endothelial biology. Front Physiol. 9:522, 2018. (Link)

  73. Militello, G., Hosen, M.R., Ponomareva, Y., Gellert, P., Weirick, T.M., John, D., Hindi, S.M., Mamchaoui, K., Mouly, V., Döring, C., Dassanayaka, S., 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. 10(2):102-117, 2018. (Link)

  74. 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. 122(10):1347-1353, 2018. (Link)

  75. Uchida, S. and Jones, S.P.: RNA Editing: Unexplored Opportunities in the Cardiovascular System. Circ Res. 122(3):399-401, 2018. (Link)

  76. 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. (Link)

  77. Uchida, S., and Bolli, R.: Short and long non-coding RNAs regulate the epigenetic status of cells. Antioxid Redox Signal. 29(9):832-845, 2018. (Link)

  78. 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. 19(2):199-209, 2018. *Shared first-author. (Link)


    79. 2017 (8 Publications)
  79. 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. (Link)

  80. 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. *Shared first-author. (Link)

  81. 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. (Link)

  82. Uchida, S.: High‐Throughput Methods to Detect Long Non‐Coding RNAs. High-Throughput 6(3):3, 2017. (Link)

  83. Uchida, S.: Besides Imprinting: Meg3 Regulates Cardiac Remodeling in Cardiac Hypertrophy. Circ Res. 121(5):486-487, 2017. (Link)

  84. 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. (Link)

  85. 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. (Link)

  86. 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. (Link)


    87. 2016 (6 Publications)
  87. 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 post-transcriptional regulation. Nat Med. 22(10):1140-1150, 2016. (Link)

  88. 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. 2016 6: 32475, 2016. *Shared first-author. (Link)

  89. 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. (Link)

  90. 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. (Link)

  91. 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. (Link)

  92. 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. *Shared first-author. (Link)


    93. 2015 (6 Publications)
  93. 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. (Link)

  94. 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. *Shared first-author. †Shared senior-author. (Link)

  95. 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. (Link)

  96. Uchida, S., and Dimmeler, S.: Exercise controls non-coding RNAs. Cell Metab. 21(4):511-2, 2015. (Link)

  97. Uchida, S., and Dimmeler, S.: Long noncoding RNAs in cardiovascular diseases. Circ Res. 116(4):737-50, 2015. (Link)

  98. 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. (Link)


    99. 2014 (1 Publication)
  99. 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. (Link)


    100. 2013 (3 Publications)
  100. 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. (Link)

  101. 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. (Link)

  102. 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. (Link)


    103. 2012 (3 Publications)
  103. 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. (Link)

  104. 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. (Link)

  105. 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. 2012 Mar;40(6):2414-25, 2012. *Joint first-author. (Link)


    106. 2011 (1 Publication)
  106. 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. (Link)


    107. 2010 (2 Publications)
  107. 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. (Link)

  108. Gellert, P., Jenniches, K.*, Braun, T., and Uchida, S.: C-It: a knowledge database for tissue-enriched genes. Bioinformatics. 26(18):2328-33, 2010. (Link)


    109. 2009 (2 Publications)
  109. Gellert, P., Uchida, S., and Braun, T.: Exon Array Analyzer: a web interface for Affymetrix exon array analysis. Bioinformatics. 25(24):3323-4, 2009. (Link)

  110. 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. (Link)


    111. 2008 (1 Publication)
  111. 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. (Link)


    112. 2007 (1 Publication)
  112. 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. (Link)


    113. 2005 (2 Publications)
  113. 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.

  114. 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. (Link)