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Eric C. Rouchka, D.Sc. - Publications

Affiliations: 
Computer Engineering and Computer Science University of Louisville, Louisville, KY, United States 
Website:
http://bioinformatics.louisville.edu/lab/
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77 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Rouchka E, de Almeida C, House R, Daneshmand J, Chariker J, Saraswat Ohri S, Gomes C, Sharp M, Shum-Siu A, Cesarz G, Petruska J, Magnuson DSK. Construction of a searchable database for gene expression changes in spinal cord injury experiments. Journal of Neurotrauma. PMID 37917105 DOI: 10.1089/neu.2023.0035  0.662
2023 Rouchka EC, de Almeida C, House RB, Daneshmand JC, Chariker JH, Saraswat-Ohri S, Gomes C, Sharp M, Shum-Siu A, Cesarz GM, Petruska JC, Magnuson DSK. Construction of a searchable database for gene expression changes in spinal cord injury experiments. Biorxiv : the Preprint Server For Biology. PMID 36778366 DOI: 10.1101/2023.02.01.526630  0.663
2020 Hwang JY, Jung S, Kook TL, Rouchka EC, Bok J, Park JW. rMAPS2: an update of the RNA map analysis and plotting server for alternative splicing regulation. Nucleic Acids Research. PMID 32286627 DOI: 10.1093/Nar/Gkaa237  0.332
2020 Chariker JH, Sharp M, Ohri SS, Gomes C, Brabazon F, Harman KA, Whittemore SR, Petruska JC, Magnuson DS, Rouchka EC. RNA-seq data of soleus muscle tissue after spinal cord injury under conditions of inactivity and applied exercise. Data in Brief. 28: 105056. PMID 32226812 DOI: 10.1016/J.Dib.2019.105056  0.663
2020 Li X, Cooper NGF, O'Toole TE, Rouchka EC. Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies. Bmc Genomics. 21: 75. PMID 31992223 DOI: 10.1186/S12864-020-6502-7  0.354
2019 Rouchka EC, Flight RM, Fasciotto BH, Estrada R, Eaton JW, Patibandla PK, Waigel SJ, Li D, Kirtley JK, Sethu P, Keynton RS. Dataset for dose and time-dependent transcriptional response to ionizing radiation exposure. Data in Brief. 27: 104624. PMID 31692674 DOI: 10.1016/J.Dib.2019.104624  0.731
2019 Scalf CS, Chariker JH, Rouchka EC, Ashley NT. Transcriptomic analysis of immune response to bacterial lipopolysaccharide in zebra finch (Taeniopygia guttata). Bmc Genomics. 20: 647. PMID 31412766 DOI: 10.1186/S12864-019-6016-3  0.313
2019 Chariker JH, Ohri SS, Gomes C, Brabazon F, Harman KA, DeVeau KM, Magnuson DSK, Hetman M, Petruska JC, Whittemore SR, Rouchka EC. Activity/exercise-induced changes in the liver transcriptome after chronic spinal cord injury. Scientific Data. 6: 88. PMID 31197156 DOI: 10.1038/S41597-019-0087-5  0.673
2019 Chariker JH, Gomes C, Brabazon F, Harman KA, Ohri SS, Magnuson DSK, Whittemore SR, Petruska JC, Rouchka EC. Transcriptome of dorsal root ganglia caudal to a spinal cord injury with modulated behavioral activity. Scientific Data. 6: 83. PMID 31175296 DOI: 10.1038/S41597-019-0088-4  0.644
2019 Harrison BJ, Park JW, Gomes C, Petruska JC, Sapio MR, Iadarola MJ, Chariker JH, Rouchka EC. Detection of Differentially Expressed Cleavage Site Intervals Within 3' Untranslated Regions Using CSI-UTR Reveals Regulated Interaction Motifs. Frontiers in Genetics. 10: 182. PMID 30915105 DOI: 10.3389/Fgene.2019.00182  0.756
2018 Li X, Rouchka EC, Brock GN, Yan J, O'Toole TE, Tieri DA, Cooper NGF. A combined approach with gene-wise normalization improves the analysis of RNA-seq data in human breast cancer subtypes. Plos One. 13: e0201813. PMID 30089167 DOI: 10.1371/Journal.Pone.0201813  0.358
2018 Schultz DJ, Krishna A, Vittitow SL, Alizadeh-Rad N, Muluhngwi P, Rouchka EC, Klinge CM. Transcriptomic response of breast cancer cells to anacardic acid. Scientific Reports. 8: 8063. PMID 29795261 DOI: 10.1038/S41598-018-26429-X  0.306
2017 Melikishvili M, Chariker JH, Rouchka EC, Fondufe-Mittendorf YN. Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis. Cell Discovery. 3: 17043. PMID 29387452 DOI: 10.1038/Celldisc.2017.43  0.31
2017 Saka E, Harrison BJ, West K, Petruska JC, Rouchka EC. Framework for reanalysis of publicly available Affymetrix® GeneChip® data sets based on functional regions of interest. Bmc Genomics. 18: 875. PMID 29244006 DOI: 10.1186/S12864-017-4266-5  0.793
2017 Bamji SF, Rouchka E, Zhang Y, Li X, Kalbfleisch T, Corbitt C. Next generation sequencing analysis of soy glyceollins and 17-β estradiol: Effects on transcript abundance in the female mouse brain. Molecular and Cellular Endocrinology. PMID 28483703 DOI: 10.1016/J.Mce.2017.05.007  0.326
2017 Li X, Brock GN, Rouchka EC, Cooper NGF, Wu D, O'Toole TE, Gill RS, Eteleeb AM, O'Brien L, Rai SN. A comparison of per sample global scaling and per gene normalization methods for differential expression analysis of RNA-seq data. Plos One. 12: e0176185. PMID 28459823 DOI: 10.1371/Journal.Pone.0176185  0.743
2017 Yao S, Flight RM, Rouchka EC, Moseley HN. Perspectives and Expectations in Structural Bioinformatics of Metalloproteins. Proteins. PMID 28168746 DOI: 10.1002/Prot.25263  0.652
2017 Yao S, Flight RM, Rouchka EC, Moseley HN. Aberrant coordination geometries discovered in the most abundant metalloproteins. Proteins. PMID 28142195 DOI: 10.1002/Prot.25257  0.642
2017 Li X, Cooper NG, Shyr Y, Wu D, Rouchka EC, Gill RS, O Toole TE, Brock GN, Rai SN. Inference and Sample Size Calculations Based on Statistical Tests in a Negative Binomial Distribution for Differential Gene Expression in RNAseq Data Journal of Biometrics & Biostatistics. 8. DOI: 10.4172/2155-6180.1000332  0.304
2017 Rouchka EC, Chariker JH, Tieri DA, Park JW, Rajurkar S, Singh V, Verma NK, Cui Y, Farman M, Condon B, Moore N, Jaromczyk J, Jaromczyk J, Harris D, Calie P, et al. Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: bioinformatics Bmc Bioinformatics. 18. DOI: 10.1186/S12859-017-1781-Y  0.636
2016 Rouchka EC, Chariker JH, Harrison BJ, Park JW, Cao X, Pounds S, Raimondi S, Downing J, Ribeiro R, Rubnitz J, Lamba J, Daigle BJ, Burgess D, Gehrlich S, Carmen JC, et al. Proceedings of the 15th Annual UT-KBRIN Bioinformatics Summit 2016 Bmc Bioinformatics. 17: 297. PMID 28166713 DOI: 10.1186/S12859-016-1154-Y  0.556
2016 Rezzoug F, Thomas SD, Rouchka EC, Miller DM. Discovery of a Family of Genomic Sequences Which Interact Specifically with the c-MYC Promoter to Regulate c-MYC Expression. Plos One. 11: e0161588. PMID 27551915 DOI: 10.1371/Journal.Pone.0161588  0.355
2016 Matveeva E, Maiorano J, Zhang Q, Eteleeb AM, Convertini P, Chen J, Infantino V, Stamm S, Wang J, Rouchka EC, Fondufe-Mittendorf YN. Involvement of PARP1 in the regulation of alternative splicing. Cell Discovery. 2: 15046. PMID 27462443 DOI: 10.1038/Celldisc.2015.46  0.738
2016 Park JW, Jung S, Rouchka EC, Tseng YT, Xing Y. rMAPS: RNA map analysis and plotting server for alternative exon regulation. Nucleic Acids Research. PMID 27174931 DOI: 10.1093/Nar/Gkw410  0.341
2016 Rouchka EC, Jeoung M, Jang ER, Liu J, Wang C, Li X, Galperin E. Data set for transcriptional response to depletion of the Shoc2 scaffolding protein. Data in Brief. 7: 770-8. PMID 27077079 DOI: 10.1016/J.Dib.2016.03.012  0.339
2016 Harrison BJ, Venkat G, Lamb JL, Hutson TH, Drury C, Rau KK, Bunge MB, Mendell LM, Gage FH, Johnson RD, Hill CE, Rouchka EC, Moon LD, Petruska JC. The Adaptor Protein CD2AP Is a Coordinator of Neurotrophin Signaling-Mediated Axon Arbor Plasticity. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 36: 4259-75. PMID 27076424 DOI: 10.1523/Jneurosci.2423-15.2016  0.722
2016 Rouchka EC, Flight RM, Fasciotto BH, Estrada R, Eaton JW, Patibandla PK, Waigel SJ, Li D, Kirtley JK, Sethu P, Keynton RS. Transcriptional profile of immediate response to ionizing radiation exposure. Genomics Data. 7: 82-5. PMID 26981369 DOI: 10.1016/J.Gdata.2015.11.027  0.735
2016 Jeoung M, Jang ER, Liu J, Wang C, Rouchka EC, Li X, Galperin E. Shoc2-tranduced ERK1/2 motility signals - novel insights from functional genomics. Cellular Signalling. PMID 26876614 DOI: 10.1016/J.Cellsig.2016.02.005  0.317
2016 Rouchka EC, Flight RM, Fasciotto BH, Estrada R, Eaton JW, Patibandla PK, Waigel SJ, Li D, Kirtley JK, Sethu P, Keynton RS. Transcriptional profile of immediate response to ionizing radiation exposure Genomics Data. 7: 82-85. DOI: 10.1016/j.gdata.2015.11.027  0.622
2015 Harrison BJ, Venkat G, Hutson T, Rau KK, Bunge MB, Mendell LM, Gage FH, Johnson RD, Hill C, Rouchka EC, Moon L, Petruska JC. Transcriptional changes in sensory ganglia associated with primary afferent axon collateral sprouting in spared dermatome model. Genomics Data. 6: 249-52. PMID 26697387 DOI: 10.1016/J.Gdata.2015.10.005  0.735
2015 Rouchka EC, Chariker JH, Harrison BJ. Proceedings of the 14th Annual UT-KBRIN Bioinformatics Summit 2015. Bmc Bioinformatics. I1-P21. PMID 26510995 DOI: 10.1186/1471-2105-16-s15-i1  0.439
2015 Nalabothula N, Al-Jumaily T, Eteleeb AM, Flight RM, Xiaorong S, Moseley H, Rouchka EC, Fondufe-Mittendorf YN. Genome-Wide Profiling of PARP1 Reveals an Interplay with Gene Regulatory Regions and DNA Methylation. Plos One. 10: e0135410. PMID 26305327 DOI: 10.1371/Journal.Pone.0135410  0.779
2015 Yao S, Flight RM, Rouchka EC, Moseley HN. A less-biased analysis of metalloproteins reveals novel zinc coordination geometries. Proteins. 83: 1470-87. PMID 26009987 DOI: 10.1002/Prot.24834  0.66
2015 Riedmann C, Ma Y, Melikishvili M, Godfrey SG, Zhang Z, Chen KC, Rouchka EC, Fondufe-Mittendorf YN. Inorganic Arsenic-induced cellular transformation is coupled with genome wide changes in chromatin structure, transcriptome and splicing patterns. Bmc Genomics. 16: 212. PMID 25879800 DOI: 10.1186/S12864-015-1295-9  0.336
2015 Rouchka EC, Chariker JH, Harrison BJ. Proceedings of the Fourteenth Annual UT- KBRIN Bioinformatics Summit 2015 Bmc Bioinformatics. 16. DOI: 10.1186/1471-2105-16-S15-I1  0.508
2014 Flight RM, Harrison BJ, Mohammad F, Bunge MB, Moon LD, Petruska JC, Rouchka EC. categoryCompare, an analytical tool based on feature annotations. Frontiers in Genetics. 5: 98. PMID 24808906 DOI: 10.3389/Fgene.2014.00098  0.784
2014 Harrison BJ, Flight RM, Gomes C, Venkat G, Ellis SR, Sankar U, Twiss JL, Rouchka EC, Petruska JC. IB4-binding sensory neurons in the adult rat express a novel 3' UTR-extended isoform of CaMK4 that is associated with its localization to axons. The Journal of Comparative Neurology. 522: 308-36. PMID 23817991 DOI: 10.1002/Cne.23398  0.784
2014 Harrison BJ, Flight RM, Eteleeb AM, Rouchka EC, Petruska JC. UTR extension and alternate polyadenylation in neuroplasticity: An emerging paradigm? Bmc Bioinformatics. 15. DOI: 10.1186/1471-2105-15-S10-P11  0.766
2014 Rezzoug F, Thomas SD, Rouchka EC, Miller DM. Abstract 3811: G-quadruplex-forming genomic sequences homologous to Pu27 interact with c-Myc promoter and regulate c-Myc transcription Cancer Research. 74: 3811-3811. DOI: 10.1158/1538-7445.Am2014-3811  0.36
2014 Eteleeb AM, Moseley HN, Rouchka EC. A comparison of combined P-value methods for gene differential expression using RNA-seq data Acm Bcb 2014 - 5th Acm Conference On Bioinformatics, Computational Biology, and Health Informatics. 417-425. DOI: 10.1145/2649387.2649421  0.716
2013 Eteleeb AM, Flight RM, Harrison BJ, Petruska JC, Rouchka EC. An Island-Based Approach for Differential Expression Analysis. 2013 Acm Conference On Bioinformatics, Computational Biology and Biomedical Informatics : Acm - Bcb 2013 : Washington, D.C., U.S.a., September 22 - 25, 2013 / Cathy Wu and Sridhar Hannenhalli, General Co-Chairs. Acm Conference On Bioinf.... 2013: 419-429. PMID 25632406 DOI: 10.1145/2506583.2506589  0.786
2013 Rouchka EC, Flight RM. Proceedings of the 12th Annual UT-ORNL-KBRIN Bioinformatics Summit 2013. Bmc Bioinformatics. 14: A1. PMID 24625056 DOI: 10.1186/1471-2105-14-S17-A1  0.603
2013 Flight RM, Eteleeb AM, Rouchka EC. Affymetrix® mismatch (MM) probes: Useful after all Proceedings of the 2012 Ase International Conference On Biomedical Computing, Biomedcom 2012. 6-13. DOI: 10.1109/BioMedCom.2012.8  0.736
2012 Hougland MT, Harrison BJ, Magnuson DS, Rouchka EC, Petruska JC. The Transcriptional Response of Neurotrophins and Their Tyrosine Kinase Receptors in Lumbar Sensorimotor Circuits to Spinal Cord Contusion is Affected by Injury Severity and Survival Time. Frontiers in Physiology. 3: 478. PMID 23316162 DOI: 10.3389/Fphys.2012.00478  0.717
2012 Mohammad F, Flight RM, Harrison BJ, Petruska JC, Rouchka EC. AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. Bmc Bioinformatics. 13: 229. PMID 22967011 DOI: 10.1186/1471-2105-13-229  0.778
2012 Rouchka EC, Flight RM, Moseley HN. Abstracts of the 11th Annual UT-ORNL-KBRIN Bioinformatics Summit 2012. Louisville, Kentucky, USA. March 30-April 1, 2012. Bmc Bioinformatics. PMID 22873757 DOI: 10.1186/1471-2105-13-S12-A1  0.632
2012 States JC, Singh AV, Knudsen TB, Rouchka EC, Ngalame NO, Arteel GE, Piao Y, Ko MS. Prenatal arsenic exposure alters gene expression in the adult liver to a proinflammatory state contributing to accelerated atherosclerosis. Plos One. 7: e38713. PMID 22719926 DOI: 10.1371/Journal.Pone.0038713  0.321
2012 Mahdi RN, Rouchka EC. Codon usage bias as a function of generation time and life expectancy. Bioinformation. 8: 158-62. PMID 22368389 DOI: 10.6026/97320630008158  0.765
2012 Harrison BJ, Flight RM, Eteleeb A, Rouchka EC, Petruska JC. RNASeq profiling of UTR expression during neuronal plasticity Bmc Bioinformatics. 13: A4. DOI: 10.1186/1471-2105-13-S12-A4  0.762
2012 Saka E, Rouchka E. Poster: Image registration and visualization tool for in-situ gene expression images 2012 Ieee 2nd International Conference On Computational Advances in Bio and Medical Sciences, Iccabs 2012. DOI: 10.1109/ICCABS.2012.6182658  0.527
2011 Rouchka EC, Flight RM, Homayouni R. Proceedings of the Tenth Annual UT-ORNL-KBRIN Bioinformatics Summit 2011. Bmc Bioinformatics. 12: A1. PMID 21999392 DOI: 10.1186/1471-2105-12-S7-A1  0.612
2011 Mahdi RN, Rouchka EC. Reduced HyperBF networks: regularization by explicit complexity reduction and scaled Rprop-based training. Ieee Transactions On Neural Networks / a Publication of the Ieee Neural Networks Council. 22: 673-86. PMID 21421438 DOI: 10.1109/Tnn.2011.2109736  0.751
2011 Li D, Rouchka EC. Integrative biclustering of heterogeneous datasets using a Bayesian nonparametric model with application to chemogenomics Bmc Bioinformatics. 12. DOI: 10.1186/1471-2105-12-S7-A6  0.553
2011 Kirtley J, Rouchka EC, Flight RM, Sethu P, Eaton JW, Keynton RS. Meta-analysis of gene expression changes in response to radiation exposure Bmc Bioinformatics. 12: 1-2. DOI: 10.1186/1471-2105-12-S7-A20  0.668
2011 Flight RM, Petruska JC, Harrison BJ, Rouchka EC. categoryCompare: high-throughput data meta-analysis using gene annotations Bmc Bioinformatics. 12: A16. DOI: 10.1186/1471-2105-12-S7-A16  0.776
2011 Mohammad F, Flight RM, Harrison BJ, Petruska JC, Rouchka EC. A heuristic algorithm for detecting intercellular interactions Proceedings - 2011 11th Ieee International Conference On Bioinformatics and Bioengineering, Bibe 2011. 1-8. DOI: 10.1109/BIBE.2011.9  0.744
2011 Mohammad F, Flight RM, Harrison BJ, Petruska JC, Rouchka EC. Interval trees for detection of overlapping genetic entities Proceedings - 2011 11th Ieee International Conference On Bioinformatics and Bioengineering, Bibe 2011. 278-281. DOI: 10.1109/BIBE.2011.49  0.744
2010 Rouchka E, Montoya-Durango DE, Stribinskis V, Ramos K, Kalbfleisch T. Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data. Bmc Bioinformatics. 11: S12. PMID 21044359 DOI: 10.1186/1471-2105-11-S9-S12  0.327
2010 Rouchka EC. Database of exact tandem repeats in the Zebrafish genome. Bmc Genomics. 11: 347. PMID 20515480 DOI: 10.1186/1471-2164-11-347  0.325
2010 Gearheart CM, Arazi B, Rouchka EC. DNA-based random number generation in security circuitry. Bio Systems. 100: 208-14. PMID 20303385 DOI: 10.1016/J.Biosystems.2010.03.005  0.755
2010 Rouchka EC, Flight RM, Rinehart C. Proceedings of the ninth annual UT-ORNL-KBRIN Bioinformatics Summit 2010 Bmc Bioinformatics. 11. DOI: 10.1186/1471-2105-11-S4-I1  0.64
2010 Gearheart CM, Rouchka EC, Arazi B. DNA-based dynamic logic circuitry Midwest Symposium On Circuits and Systems. 248-251. DOI: 10.1109/MWSCAS.2010.5548656  0.722
2009 Mahdi RN, Rouchka EC. RBF-TSS: identification of transcription start site in human using radial basis functions network and oligonucleotide positional frequencies. Plos One. 4: e4878. PMID 19287502 DOI: 10.1371/Journal.Pone.0004878  0.785
2009 Rouchka EC, Cha IE. Current trends in pseudogene detection and characterization Current Bioinformatics. 4: 112-119. DOI: 10.2174/157489309788184792  0.585
2009 Mahdi RN, Rouchka EC. Feature selection in cancer classification from mRNA data based on localized dimension reduction 8th International Conference On Machine Learning and Applications, Icmla 2009. 443-448. DOI: 10.1109/ICMLA.2009.81  0.755
2008 Mahdi RN, Rouchka EC. Evidence of bias towards buffered codons in human transcripts. Proceedings of the ... Ieee International Symposium On Signal Processing and Information Technology. Ieee International Symposium On Signal Processing and Information Technology. 2008: 29-34. PMID 20622995 DOI: 10.1109/ISSPIT.2008.4775640  0.788
2008 Mahdi RN, Rouchka EC. Model Based Unsupervised Learning Guided by Abundant Background Samples. Proceedings of the ... International Conference On Machine Learning. International Conference On Machine Learning. 7: 203-210. PMID 20436793 DOI: 10.1109/ICMLA.2008.28  0.755
2008 Rouchka EC, Phatak AW, Singh AV. Effect of single nucleotide polymorphisms on Affymetrix match-mismatch probe pairs. Bioinformation. 2: 405-11. PMID 18795114 DOI: 10.6026/97320630002405  0.302
2008 Mahdi R, Rouchka EC. Buffered codons in human transcriptional units Bmc Bioinformatics. 9. DOI: 10.1186/1471-2105-9-S7-P8  0.785
2008 Morris J, Rouchka E, Schultz D. Techniques for the analysis of trichome Pelagonium xhortorum expressed sequence tags Bmc Bioinformatics. 9: P25. DOI: 10.1186/1471-2105-9-S7-P25  0.327
2007 Winchester JS, Rouchka EC, Rowland NS, Rice NA. In Silico characterization of phosphorylase kinase: evidence for an alternate intronic polyadenylation site in PHKG1. Molecular Genetics and Metabolism. 92: 234-42. PMID 17692548 DOI: 10.1016/J.Ymgme.2007.06.015  0.337
2007 Rouchka EC, Hardin CT. rMotifGen: random motif generator for DNA and protein sequences. Bmc Bioinformatics. 8: 292. PMID 17683637 DOI: 10.1186/1471-2105-8-292  0.327
2005 Rouchka EC, Khalyfa A, Cooper NG. MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays. Bmc Bioinformatics. 6: 175. PMID 16014168 DOI: 10.1186/1471-2105-6-175  0.361
2003 Thompson W, Rouchka EC, Lawrence CE. Gibbs Recursive Sampler: finding transcription factor binding sites. Nucleic Acids Research. 31: 3580-5. PMID 12824370 DOI: 10.1093/Nar/Gkg608  0.311
2002 Rouchka EC, Gish W, States DJ. Comparison of whole genome assemblies of the human genome. Nucleic Acids Research. 30: 5004-14. PMID 12434005 DOI: 10.1093/Nar/Gkf633  0.605
2001 Kan Z, Rouchka EC, Gish WR, States DJ. Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. Genome Research. 11: 889-900. PMID 11337482 DOI: 10.1101/Gr.155001  0.724
1998 Rouchka EC, States DJ. Sequence assembly validation by multiple restriction digest fragment coverage analysis. Proceedings / ... International Conference On Intelligent Systems For Molecular Biology ; Ismb. International Conference On Intelligent Systems For Molecular Biology. 6: 140-7. PMID 9783219  0.57
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