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For: Stöckel D, Kehl T, Trampert P, Schneider L, Backes C, Ludwig N, Gerasch A, Kaufmann M, Gessler M, Graf N, Meese E, Keller A, Lenhof HP. Multi-omics enrichment analysis using the GeneTrail2 web service. Bioinformatics 2016;32:1502-8. [PMID: 26787660 DOI: 10.1093/bioinformatics/btv770] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 12/28/2015] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
51
Chen Q, Huang Y, Wang Z, Teng S, Hanif Q, Lei C, Sun J. Whole-genome resequencing reveals diversity and selective signals in Longlin goat. Gene 2020;771:145371. [PMID: 33346103 DOI: 10.1016/j.gene.2020.145371] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/03/2020] [Accepted: 12/11/2020] [Indexed: 11/30/2022]
52
Hiller M, Geissler M, Janssen G, van Veelen P, Aartsma-Rus A, Spitali P. The mRNA Binding Proteome of Proliferating and Differentiated Muscle Cells. GENOMICS PROTEOMICS & BIOINFORMATICS 2020;18:384-396. [PMID: 33338663 PMCID: PMC8242265 DOI: 10.1016/j.gpb.2020.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/29/2020] [Accepted: 06/04/2020] [Indexed: 01/24/2023]
53
Gerstner N, Kehl T, Lenhof K, Müller A, Mayer C, Eckhart L, Grammes NL, Diener C, Hart M, Hahn O, Walter J, Wyss-Coray T, Meese E, Keller A, Lenhof HP. GeneTrail 3: advanced high-throughput enrichment analysis. Nucleic Acids Res 2020;48:W515-W520. [PMID: 32379325 PMCID: PMC7319559 DOI: 10.1093/nar/gkaa306] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/31/2020] [Accepted: 04/20/2020] [Indexed: 12/26/2022]  Open
54
Kern F, Fehlmann T, Solomon J, Schwed L, Grammes N, Backes C, Van Keuren-Jensen K, Craig DW, Meese E, Keller A. miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems. Nucleic Acids Res 2020;48:W521-W528. [PMID: 32374865 PMCID: PMC7319446 DOI: 10.1093/nar/gkaa309] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/06/2020] [Accepted: 04/22/2020] [Indexed: 01/01/2023]  Open
55
Lankes K, Hassan Z, Doffo MJ, Schneeweis C, Lier S, Öllinger R, Rad R, Krämer OH, Keller U, Saur D, Reichert M, Schneider G, Wirth M. Targeting the ubiquitin-proteasome system in a pancreatic cancer subtype with hyperactive MYC. Mol Oncol 2020;14:3048-3064. [PMID: 33099868 PMCID: PMC7718946 DOI: 10.1002/1878-0261.12835] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 09/11/2020] [Accepted: 10/04/2020] [Indexed: 12/12/2022]  Open
56
Nuthikattu S, Milenkovic D, Rutledge JC, Villablanca AC. Sex-Dependent Molecular Mechanisms of Lipotoxic Injury in Brain Microvasculature: Implications for Dementia. Int J Mol Sci 2020;21:E8146. [PMID: 33142695 PMCID: PMC7663125 DOI: 10.3390/ijms21218146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 10/16/2020] [Accepted: 10/28/2020] [Indexed: 12/14/2022]  Open
57
Vavougios GD, Nday C, Pelidou SH, Zarogiannis SG, Gourgoulianis KI, Stamoulis G, Doskas T. Double hit viral parasitism, polymicrobial CNS residency and perturbed proteostasis in Alzheimer's disease: A data driven, in silico analysis of gene expression data. Mol Immunol 2020;127:124-135. [PMID: 32971399 DOI: 10.1016/j.molimm.2020.08.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 07/25/2020] [Accepted: 08/30/2020] [Indexed: 01/04/2023]
58
Vavougios GD, Zarogiannis SG, Krogfelt KA, Stamoulis G, Gourgoulianis KI. Epigenetic regulation of apoptosis via the PARK7 interactome in peripheral blood mononuclear cells donated by tuberculosis patients vs. healthy controls and the response to treatment: A systems biology approach. Tuberculosis (Edinb) 2020;123:101938. [PMID: 32741527 DOI: 10.1016/j.tube.2020.101938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/22/2020] [Accepted: 04/14/2020] [Indexed: 12/22/2022]
59
Biederstädt A, Hassan Z, Schneeweis C, Schick M, Schneider L, Muckenhuber A, Hong Y, Siegers G, Nilsson L, Wirth M, Dantes Z, Steiger K, Schunck K, Langston S, Lenhof HP, Coluccio A, Orben F, Slawska J, Scherger A, Saur D, Müller S, Rad R, Weichert W, Nilsson J, Reichert M, Schneider G, Keller U. SUMO pathway inhibition targets an aggressive pancreatic cancer subtype. Gut 2020;69:1472-1482. [PMID: 32001555 PMCID: PMC7398468 DOI: 10.1136/gutjnl-2018-317856] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 12/13/2022]
60
Bankvall M, Östman S, Jontell M, Torinsson Naluai Å. A family-based genome-wide association study of recurrent aphthous stomatitis. Oral Dis 2020;26:1696-1705. [PMID: 32558109 DOI: 10.1111/odi.13490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 04/29/2020] [Accepted: 06/04/2020] [Indexed: 01/06/2023]
61
Schneider L, Kehl T, Thedinga K, Grammes NL, Backes C, Mohr C, Schubert B, Lenhof K, Gerstner N, Hartkopf AD, Wallwiener M, Kohlbacher O, Keller A, Meese E, Graf N, Lenhof HP. ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification. Bioinformatics 2020;35:5171-5181. [PMID: 31038669 PMCID: PMC6954665 DOI: 10.1093/bioinformatics/btz302] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/02/2019] [Accepted: 04/26/2019] [Indexed: 01/10/2023]  Open
62
Nuthikattu S, Milenkovic D, Rutledge JC, Villablanca AC. Lipotoxic Injury Differentially Regulates Brain Microvascular Gene Expression in Male Mice. Nutrients 2020;12:E1771. [PMID: 32545722 PMCID: PMC7353447 DOI: 10.3390/nu12061771] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/05/2020] [Accepted: 06/12/2020] [Indexed: 12/22/2022]  Open
63
Krammes L, Hart M, Rheinheimer S, Diener C, Menegatti J, Grässer F, Keller A, Meese E. Induction of the Endoplasmic-Reticulum-Stress Response: MicroRNA-34a Targeting of the IRE1α-Branch. Cells 2020;9:cells9061442. [PMID: 32531952 PMCID: PMC7348704 DOI: 10.3390/cells9061442] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/04/2020] [Accepted: 06/08/2020] [Indexed: 12/12/2022]  Open
64
Gi WT, Haas J, Sedaghat-Hamedani F, Kayvanpour E, Tappu R, Lehmann DH, Shirvani Samani O, Wisdom M, Keller A, Katus HA, Meder B. Epigenetic Regulation of Alternative mRNA Splicing in Dilated Cardiomyopathy. J Clin Med 2020;9:jcm9051499. [PMID: 32429430 PMCID: PMC7291244 DOI: 10.3390/jcm9051499] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/04/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022]  Open
65
Oh M, Park S, Kim S, Chae H. Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations. Brief Bioinform 2020;22:66-76. [PMID: 32227074 DOI: 10.1093/bib/bbaa032] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/05/2020] [Accepted: 02/25/2020] [Indexed: 02/06/2023]  Open
66
Lund C, Yellapragada V, Vuoristo S, Balboa D, Trova S, Allet C, Eskici N, Pulli K, Giacobini P, Tuuri T, Raivio T. Characterization of the human GnRH neuron developmental transcriptome using a GNRH1-TdTomato reporter line in human pluripotent stem cells. Dis Model Mech 2020;13:dmm040105. [PMID: 31996360 PMCID: PMC7075073 DOI: 10.1242/dmm.040105] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 01/16/2020] [Indexed: 12/21/2022]  Open
67
Hu Y, Thapa A, Fan H, Ma T, Wu Q, Ma S, Zhang D, Wang B, Li M, Yan L, Wei F. Genomic evidence for two phylogenetic species and long-term population bottlenecks in red pandas. SCIENCE ADVANCES 2020;6:eaax5751. [PMID: 32133395 PMCID: PMC7043915 DOI: 10.1126/sciadv.aax5751] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 12/04/2019] [Indexed: 05/09/2023]
68
Ramzan F, D'Souza RF, Durainayagam BR, Milan AM, Markworth JF, Miranda-Soberanis V, Sequeira IR, Roy NC, Poppitt SD, Mitchell CJ, Cameron-Smith D. Circulatory miRNA biomarkers of metabolic syndrome. Acta Diabetol 2020;57:203-214. [PMID: 31435783 DOI: 10.1007/s00592-019-01406-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/08/2019] [Indexed: 12/19/2022]
69
Rouka E, Hatzoglou C, Gourgoulianis KI, Zarogiannis SG. Interactome networks between the human respiratory syncytial virus (HRSV), the human metapneumovirus (ΗMPV), and their host: In silico investigation and comparative functional enrichment analysis. Microb Pathog 2020;141:104000. [PMID: 31988005 DOI: 10.1016/j.micpath.2020.104000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 11/16/2019] [Accepted: 01/23/2020] [Indexed: 01/21/2023]
70
Kehl T, Kern F, Backes C, Fehlmann T, Stöckel D, Meese E, Lenhof HP, Keller A. miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database. Nucleic Acids Res 2020;48:D142-D147. [PMID: 31691816 PMCID: PMC7145528 DOI: 10.1093/nar/gkz1022] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Revised: 10/17/2019] [Accepted: 10/19/2019] [Indexed: 12/13/2022]  Open
71
Spitali P, Zaharieva I, Bohringer S, Hiller M, Chaouch A, Roos A, Scotton C, Claustres M, Bello L, McDonald CM, Hoffman EP, Koeks Z, Eka Suchiman H, Cirak S, Scoto M, Reza M, 't Hoen PAC, Niks EH, Tuffery-Giraud S, Lochmüller H, Ferlini A, Muntoni F, Aartsma-Rus A. TCTEX1D1 is a genetic modifier of disease progression in Duchenne muscular dystrophy. Eur J Hum Genet 2020;28:815-825. [PMID: 31896777 PMCID: PMC7253478 DOI: 10.1038/s41431-019-0563-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 11/08/2019] [Accepted: 12/03/2019] [Indexed: 11/29/2022]  Open
72
Wang H, Zhao H, Sun K, Huang X, Jin L, Feng J. Evolutionary Basis of High-Frequency Hearing in the Cochleae of Echolocators Revealed by Comparative Genomics. Genome Biol Evol 2020;12:3740-3753. [PMID: 31730196 PMCID: PMC7145703 DOI: 10.1093/gbe/evz250] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2019] [Indexed: 12/25/2022]  Open
73
Nuthikattu S, Milenkovic D, Rutledge J, Villablanca A. The Western Diet Regulates Hippocampal Microvascular Gene Expression: An Integrated Genomic Analyses in Female Mice. Sci Rep 2019;9:19058. [PMID: 31836762 PMCID: PMC6911042 DOI: 10.1038/s41598-019-55533-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 11/22/2019] [Indexed: 01/05/2023]  Open
74
Formica C, Malas T, Balog J, Verburg L, 't Hoen PAC, Peters DJM. Characterisation of transcription factor profiles in polycystic kidney disease (PKD): identification and validation of STAT3 and RUNX1 in the injury/repair response and PKD progression. J Mol Med (Berl) 2019;97:1643-1656. [PMID: 31773180 PMCID: PMC6920240 DOI: 10.1007/s00109-019-01852-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 11/01/2019] [Accepted: 11/07/2019] [Indexed: 01/12/2023]
75
(-)-Epicatechin metabolites promote vascular health through epigenetic reprogramming of endothelial-immune cell signaling and reversing systemic low-grade inflammation. Biochem Pharmacol 2019;173:113699. [PMID: 31756325 DOI: 10.1016/j.bcp.2019.113699] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 11/06/2019] [Indexed: 12/16/2022]
76
Palmblad M, Lamprecht AL, Ison J, Schwämmle V. Automated workflow composition in mass spectrometry-based proteomics. Bioinformatics 2019;35:656-664. [PMID: 30060113 PMCID: PMC6378944 DOI: 10.1093/bioinformatics/bty646] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 07/06/2018] [Accepted: 07/26/2018] [Indexed: 11/28/2022]  Open
77
Kalmbach A, Schröder C, Klein-Hitpass L, Nordström K, Ulz P, Heitzer E, Speicher MR, Rahmann S, Wieczorek D, Horsthemke B, Bramswig NC. Genome-Wide Analysis of the Nucleosome Landscape in Individuals with Coffin-Siris Syndrome. Cytogenet Genome Res 2019;159:1-11. [PMID: 31658463 DOI: 10.1159/000503266] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 01/15/2023]  Open
78
Kehl T, Schneider L, Kattler K, Stöckel D, Wegert J, Gerstner N, Ludwig N, Distler U, Schick M, Keller U, Tenzer S, Gessler M, Walter J, Keller A, Graf N, Meese E, Lenhof HP. REGGAE: a novel approach for the identification of key transcriptional regulators. Bioinformatics 2019;34:3503-3510. [PMID: 29741575 PMCID: PMC6184769 DOI: 10.1093/bioinformatics/bty372] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Accepted: 05/03/2018] [Indexed: 12/13/2022]  Open
79
Caiazza F, Oficjalska K, Tosetto M, Phelan JJ, Noonan S, Martin P, Killick K, Breen L, O'Neill F, Nolan B, Furney S, Power R, Fennelly D, Craik CS, O'Sullivan J, Sheahan K, Doherty GA, Ryan EJ. KH-Type Splicing Regulatory Protein Controls Colorectal Cancer Cell Growth and Modulates the Tumor Microenvironment. THE AMERICAN JOURNAL OF PATHOLOGY 2019;189:1916-1932. [PMID: 31404541 PMCID: PMC6892187 DOI: 10.1016/j.ajpath.2019.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 06/06/2019] [Accepted: 07/03/2019] [Indexed: 01/18/2023]
80
Riessland M, Kolisnyk B, Kim TW, Cheng J, Ni J, Pearson JA, Park EJ, Dam K, Acehan D, Ramos-Espiritu LS, Wang W, Zhang J, Shim JW, Ciceri G, Brichta L, Studer L, Greengard P. Loss of SATB1 Induces p21-Dependent Cellular Senescence in Post-mitotic Dopaminergic Neurons. Cell Stem Cell 2019;25:514-530.e8. [PMID: 31543366 DOI: 10.1016/j.stem.2019.08.013] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 04/09/2019] [Accepted: 08/16/2019] [Indexed: 01/07/2023]
81
Kim JY, Jeong S, Kim KH, Lim WJ, Lee HY, Kim N. Discovery of Genomic Characteristics and Selection Signatures in Korean Indigenous Goats Through Comparison of 10 Goat Breeds. Front Genet 2019;10:699. [PMID: 31440273 PMCID: PMC6694180 DOI: 10.3389/fgene.2019.00699] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Accepted: 07/03/2019] [Indexed: 12/16/2022]  Open
82
Borgmästars E, de Weerd HA, Lubovac-Pilav Z, Sund M. miRFA: an automated pipeline for microRNA functional analysis with correlation support from TCGA and TCPA expression data in pancreatic cancer. BMC Bioinformatics 2019;20:393. [PMID: 31311505 PMCID: PMC6636046 DOI: 10.1186/s12859-019-2974-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 06/28/2019] [Indexed: 12/14/2022]  Open
83
Hart M, Walch-Rückheim B, Krammes L, Kehl T, Rheinheimer S, Tänzer T, Glombitza B, Sester M, Lenhof HP, Keller A, Meese E. miR-34a as hub of T cell regulation networks. J Immunother Cancer 2019;7:187. [PMID: 31311583 PMCID: PMC6636054 DOI: 10.1186/s40425-019-0670-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/08/2019] [Indexed: 12/27/2022]  Open
84
Seeger B, Mentz A, Knebel C, Schmidt F, Bednarz H, Niehaus K, Albaum S, Kalinowski J, Noll T, Steinberg P, Marx-Stoelting P, Heise T. Assessment of mixture toxicity of (tri)azoles and their hepatotoxic effects in vitro by means of omics technologies. Arch Toxicol 2019;93:2321-2333. [PMID: 31254001 DOI: 10.1007/s00204-019-02502-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/17/2019] [Indexed: 01/08/2023]
85
Will T, Helms V. Differential analysis of combinatorial protein complexes with CompleXChange. BMC Bioinformatics 2019;20:300. [PMID: 31159772 PMCID: PMC6547514 DOI: 10.1186/s12859-019-2852-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 04/26/2019] [Indexed: 11/10/2022]  Open
86
Witusik-Perkowska M, Zakrzewska M, Jaskolski DJ, Liberski PP, Szemraj J. Artificial microenvironment of in vitro glioblastoma cell cultures changes profile of miRNAs related to tumor drug resistance. Onco Targets Ther 2019;12:3905-3918. [PMID: 31190889 PMCID: PMC6535444 DOI: 10.2147/ott.s190601] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/09/2019] [Indexed: 12/26/2022]  Open
87
Zhou Y, Zhou B, Pache L, Chang M, Khodabakhshi AH, Tanaseichuk O, Benner C, Chanda SK. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10:1523. [PMID: 30944313 PMCID: PMC6447622 DOI: 10.1038/s41467-019-09234-6] [Citation(s) in RCA: 8471] [Impact Index Per Article: 1411.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 02/22/2019] [Indexed: 02/06/2023]  Open
88
Gu W, Yildirimman R, Van der Stuyft E, Verbeeck D, Herzinger S, Satagopam V, Barbosa-Silva A, Schneider R, Lange B, Lehrach H, Guo Y, Henderson D, Rowe A. Data and knowledge management in translational research: implementation of the eTRIKS platform for the IMI OncoTrack consortium. BMC Bioinformatics 2019;20:164. [PMID: 30935364 PMCID: PMC6444691 DOI: 10.1186/s12859-019-2748-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 03/18/2019] [Indexed: 01/04/2023]  Open
89
Tiong KL, Yeang CH. MGSEA - a multivariate Gene set enrichment analysis. BMC Bioinformatics 2019;20:145. [PMID: 30885118 PMCID: PMC6421703 DOI: 10.1186/s12859-019-2716-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 03/06/2019] [Indexed: 11/10/2022]  Open
90
Grade-specific diagnostic and prognostic biomarkers in breast cancer. Genomics 2019;112:388-396. [PMID: 30851359 DOI: 10.1016/j.ygeno.2019.03.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 02/09/2019] [Accepted: 03/01/2019] [Indexed: 11/21/2022]
91
Rocha S, Carvalho J, Oliveira P, Voglstaetter M, Schvartz D, Thomsen AR, Walter N, Khanduri R, Sanchez J, Keller A, Oliveira C, Nazarenko I. 3D Cellular Architecture Affects MicroRNA and Protein Cargo of Extracellular Vesicles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2019;6:1800948. [PMID: 30828519 PMCID: PMC6382357 DOI: 10.1002/advs.201800948] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/30/2018] [Indexed: 05/05/2023]
92
Beltrán-Anaya FO, Romero-Córdoba S, Rebollar-Vega R, Arrieta O, Bautista-Piña V, Dominguez-Reyes C, Villegas-Carlos F, Tenorio-Torres A, Alfaro-Riuz L, Jiménez-Morales S, Cedro-Tanda A, Ríos-Romero M, Reyes-Grajeda JP, Tagliabue E, Iorio MV, Hidalgo-Miranda A. Expression of long non-coding RNA ENSG00000226738 (LncKLHDC7B) is enriched in the immunomodulatory triple-negative breast cancer subtype and its alteration promotes cell migration, invasion, and resistance to cell death. Mol Oncol 2019;13:909-927. [PMID: 30648789 PMCID: PMC6441920 DOI: 10.1002/1878-0261.12446] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 11/29/2018] [Accepted: 12/30/2018] [Indexed: 12/31/2022]  Open
93
Micro-RNA-Regulated Proangiogenic Signaling in Arteriovenous Loops in Patients with Combined Vascular and Soft-Tissue Reconstructions: Revisiting the Nutrient Flap Concept. Plast Reconstr Surg 2019;142:489e-502e. [PMID: 29979372 DOI: 10.1097/prs.0000000000004750] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
94
Henn D, Abu-Halima M, Wermke D, Falkner F, Thomas B, Köpple C, Ludwig N, Schulte M, Brockmann MA, Kim YJ, Sacks JM, Kneser U, Keller A, Meese E, Schmidt VJ. MicroRNA-regulated pathways of flow-stimulated angiogenesis and vascular remodeling in vivo. J Transl Med 2019;17:22. [PMID: 30635008 PMCID: PMC6330440 DOI: 10.1186/s12967-019-1767-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 01/02/2019] [Indexed: 12/14/2022]  Open
95
Chen Z, Amro EM, Becker F, Hölzer M, Rasa SMM, Njeru SN, Han B, Di Sanzo S, Chen Y, Tang D, Tao S, Haenold R, Groth M, Romanov VS, Kirkpatrick JM, Kraus JM, Kestler HA, Marz M, Ori A, Neri F, Morita Y, Rudolph KL. Cohesin-mediated NF-κB signaling limits hematopoietic stem cell self-renewal in aging and inflammation. J Exp Med 2019;216:152-175. [PMID: 30530755 PMCID: PMC6314529 DOI: 10.1084/jem.20181505] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/06/2018] [Accepted: 11/19/2018] [Indexed: 01/02/2023]  Open
96
Misra BB, Langefeld C, Olivier M, Cox LA. Integrated omics: tools, advances and future approaches. J Mol Endocrinol 2019;62:R21-R45. [PMID: 30006342 DOI: 10.1530/jme-18-0055] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022]
97
Fehlmann T, Laufer T, Backes C, Kahramann M, Alles J, Fischer U, Minet M, Ludwig N, Kern F, Kehl T, Galata V, Düsterloh A, Schrörs H, Kohlhaas J, Bals R, Huwer H, Geffers L, Krüger R, Balling R, Lenhof HP, Meese E, Keller A. Large-scale validation of miRNAs by disease association, evolutionary conservation and pathway activity. RNA Biol 2018;16:93-103. [PMID: 30567465 DOI: 10.1080/15476286.2018.1559689] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
98
Comparative transcriptomics of shear stress treated Pkd1−/− cells and pre-cystic kidneys reveals pathways involved in early polycystic kidney disease. Biomed Pharmacother 2018;108:1123-1134. [DOI: 10.1016/j.biopha.2018.07.178] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/30/2018] [Accepted: 07/31/2018] [Indexed: 02/08/2023]  Open
99
Kehl T, Schneider L, Kattler K, Stöckel D, Wegert J, Gerstner N, Ludwig N, Distler U, Tenzer S, Gessler M, Walter J, Keller A, Graf N, Meese E, Lenhof HP. The role of TCF3 as potential master regulator in blastemal Wilms tumors. Int J Cancer 2018;144:1432-1443. [PMID: 30155889 DOI: 10.1002/ijc.31834] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 07/05/2018] [Accepted: 08/13/2018] [Indexed: 12/11/2022]
100
Lee JH, Lewis KM, Moural TW, Kirilenko B, Borgonovo B, Prange G, Koessl M, Huggenberger S, Kang C, Hiller M. Molecular parallelism in fast-twitch muscle proteins in echolocating mammals. SCIENCE ADVANCES 2018;4:eaat9660. [PMID: 30263960 PMCID: PMC6157964 DOI: 10.1126/sciadv.aat9660] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 08/10/2018] [Indexed: 06/08/2023]
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